PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. Planarian Anatomy Ontology (PLANA) Planarian_Anatomy 1.2 CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 2023-03-13 definition 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 editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note 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 term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by Relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y is indirect 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 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. external_definition Notes on the homology status of this class. homology_notes has_relational_adjective Notes on the how instances of this class vary across species. taxon_notes Notes on how similar or equivalent classes are represented in other ontologies. external_ontology_notes IAO:0100001 synonym typically used in the context of human anatomy IAO:0100001 synonym typically used in the context of vertebrate anatomy http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator creator http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description description http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title title http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license IAO:0100001 namespace-id-rule IAO:0100001 synonym_type_property has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 IAO:0100001 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 IAO:0100001 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 IAO:0100001 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 IAO:0100001 has_obo_format_version IAO:0100001 has_obo_namespace An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 IAO:0100001 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 IAO:0100001 has_scope IAO:0100001 has_synonym_type in_subset IAO:0100001 shorthand Sofia Robb 2017-07-26T18:19:59Z treat-xrefs-as-genus-differentia 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 spatial 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) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 external quality spatial uberon has_part has_part has part has part has_part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. 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 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 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 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 x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000096 rostral_to spatial anterior_to anterior_to anterior to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 spatial dorsal_to dorsal_to dorsal to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000099 caudal to spatial posterior_to posterior_to posterior to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm caudal to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 spatial ventral_to ventral_to ventral to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:0000104 spatial approximately_perpendicular_to approximately_perpendicular_to approximately perpendicular to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 spatial deep_to deep_to deep to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 spatial superficial_to superficial_to superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm Direcly opposite to. i.e. on the opposite side through the axis. BSPO:0000113 spatial opposite_to opposite_to opposite to Direcly opposite to. i.e. on the opposite side through the axis. BSPO:cjm X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 spatial in_left_side_of in_left_side_of in left side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:0000121 spatial in_right_side_of in_right_side_of in right side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:PATO_mtg_2009 X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. spatial parallel_to parallel to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. BSPO:curators x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 spatial immediately_deep_to immediately_deep_to immediately deep to x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators BSPO:0015001 spatial finishes_axis finishes_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p finishes axis crossing at right angles BSPO:0015005 spatial orthogonal_to orthogonal_to orthogonal to crossing at right angles BSPO:cjm Intersects at two points. BSPO:0015006 spatial passes_through passes_through passes through Intersects at two points. BSPO:cjm BSPO:0015007 spatial starts_axis starts_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p starts axis BSPO:0015008 spatial surface_of surface_of placeholder. used for relation between anatomical surface and an anatomical side. surface of x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 spatial immediately_superficial_to immediately_superficial_to immediately superficial to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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. 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 has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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 has characteristic 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 catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality 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 has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains 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 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 David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes RO:0002092 external happens_during happens_during happens during RO:0002093 external ends_during ends_during ends during x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 spatial overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm 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 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. 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 This is the transitive form of the develops from relation develops from inverse of develops from develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) 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)". 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 capable of part of true A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 spatial 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. 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 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to 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 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 has developmental contribution from inverse of has developmental contribution from developmentally contributes to 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 In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. 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 Inverse of developmentally preceded by developmentally succeeded by p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Chris Mungall inheres in part of characteristic of part of true 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) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. 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 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 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 inverse of has input Chris Mungall input of 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). 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 has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y 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 has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) 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. 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 A relationship that holds between two entities in which the processes executed by the two entities are causally connected. 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. Considering relabeling as 'pairwise interacts with' 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/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 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 The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 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. has part that occurs in true Chris Mungall is kinase activity 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 physical entity and a process or stage 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)) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x 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). 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. 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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. 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 entities Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ Chris Mungall molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences 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. GOC:cjm lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity luminal space of p directly regulates q iff p is immediately causally upstream of q and p regulates q. 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 p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) 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. 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 a produced_by b iff some process that occurs_in b has_output a. produced by 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 The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. https://orcid.org/0000-0001-9625-1899 https://orcid.org/0000-0003-2620-0345 A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic 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] 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] 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. 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] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] material MaterialEntity 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 entity A 2D surface of an anatomical continuant. FMA:24137 surface spatial BSPO:0000005 to be merged into CARO anatomical surface A 2D surface of an anatomical continuant. BSPO:cjm A straight line through space, intersecting an anatomical entity. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG spatial BSPO:0000010 Axis directions are defined in terms of axes. anatomical axis A straight line through space, intersecting an anatomical entity. BSPO:cjm An axis that extends through an organism from head end to opposite end of body or tail. A-P axis AP axis anteroposterior axis cephalocaudal axis craniocaudal axis rostral/caudal rostrocaudal axis spatial longitudinal axis BSPO:0000013 In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM] anterior-posterior axis An axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm cephalocaudal axis http://en.wikipedia.org/wiki/Anatomical_terms_of_location craniocaudal axis rostral/caudal rostrocaudal axis An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. apical/basal spatial longitudinal axis BSPO:0000014 apical-basal axis relative to substrate An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. BSPO:mah An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). proximal/distal proximodistal spatial BSPO:0000015 In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate. proximal-distal axis An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). BSPO:curators http://en.wikipedia.org/wiki/Anatomical_terms_of_location An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. D-V axis DV axis dorsoventral axis anterior-posterior axis spatial BSPO:0000016 dorsal-ventral axis An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. BSPO:curators anterior-posterior axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. L-R axis LR axis R-L axis RL axis dextro-sinister axis left to right axis right to left axis right-left axis spatial BSPO:0000017 left-right axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. BSPO:cjm Anatomical plane that divides body into anterior and posterior parts. FMA:12247 axial plane axial section transverse section spatial cross-section BSPO:0000018 transverse plane Anatomical plane that divides body into anterior and posterior parts. BSPO:mah Anatomical plane that divides bilateral body into dorsal and ventral parts. FMA:52810 frontal plane horizontal anatomical plane horizontal section spatial coronal section frontal section BSPO:0000019 horizontal plane Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:mah horizontal anatomical plane FMA:52810 Anatomical region that overlaps the anterior and dorsal regions of a body or body part. Melissa Haendel 2009-06-15T01:01:38Z anterodorsal region spatial BSPO:0000026 antero-dorsal region Anatomical region that overlaps the anterior and dorsal regions of a body or body part. BSPO:wd Anatomical region that overlaps the anterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:04:59Z anteroventral region spatial BSPO:0000027 antero-ventral region Anatomical region that overlaps the anterior and ventral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and lateral regions of the body or body part. Melissa Haendel 2009-06-15T01:06:01Z posterolateral region spatial BSPO:0000028 postero-lateral region Anatomical region that overlaps the posterior and lateral regions of the body or body part. BSPO:wd Anatomical region that overlaps the anterior and lateral regions of a body or body part. Melissa Haendel 2009-06-15T01:07:18Z anterolateral region spatial BSPO:0000029 antero-lateral region Anatomical region that overlaps the anterior and lateral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and dorsal regions of the body or body part. Melissa Haendel 2009-06-15T01:08:13Z posterodorsal region spatial BSPO:0000030 postero-dorsal region Anatomical region that overlaps the posterior and dorsal regions of the body or body part. BSPO:wd Anatomical region that overlaps the posterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:08:38Z posteroventral region spatial BSPO:0000035 postero-ventral region Anatomical region that overlaps the posterior and ventral regions of a body or body part. BSPO:wd An anatomical region bounded by a plane perpendicular to an axis through the middle. FBql:00005841 spatial BSPO:0000054 anatomical side An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:cjm An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000053 FBql:00005848 anterior rostral spatial BSPO:0000055 anterior side An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000065 FBql:00005849 posterior caudal spatial BSPO:0000056 posterior side An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:wd caudal Anatomical side that is located on the apical end of an organism or structure. FBcv:0000054 FBql:00005854 apical spatial BSPO:0000057 apical side Anatomical side that is located on the apical end of an organism or structure. BSPO:wd Anatomical side that is located on the basal end of an organism or structure. FBcv:0000055 FBql:00005855 basal spatial BSPO:0000058 The part of the organism attached to a substrate. Axis of symmetry. basal side Anatomical side that is located on the basal end of an organism or structure. BSPO:wd An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. FBcv:0000059 FBql:00005842 dorsal spatial BSPO:0000063 dorsal side An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:wd FBcv:0000063 FBql:00005844 lateral spatial BSPO:0000066 lateral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. FBcv:0000070 FBql:00005843 ventral spatial BSPO:0000068 ventral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:RW BSPO:wd A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. FBql:00005841 spatial BSPO:0000070 to be merged into CARO anatomical region A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:cjm Anatomical region anteriorly located on the body or body part. FBql:00005848 spatial BSPO:0000071 anterior region Anatomical region anteriorly located on the body or body part. BSPO:wd Anatomical region posteriorly located on the body or body part. FBql:00005849 spatial BSPO:0000072 posterior region Anatomical region posteriorly located on the body or body part. BSPO:wd Anatomical region located on the apical end on the body or body part. FBql:00005854 spatial BSPO:0000073 apical region Anatomical region located on the apical end on the body or body part. BSPO:wd Anatomical region located basally on the body or body part. FBql:00005855 spatial BSPO:0000074 basal region Anatomical region located basally on the body or body part. BSPO:wd Anatomical region dorsally located on the body or body part. FBql:00005842 spatial BSPO:0000079 dorsal region Anatomical region dorsally located on the body or body part. BSPO:wd Anatomical region that overlaps the dorsal and lateral regions of a body or body part. FBql:00005845 dorsolateral region spatial BSPO:0000080 dorso-lateral region Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:wd Anatomical region laterally located on the body or body part. FBql:00005844 spatial BSPO:0000082 lateral region Anatomical region laterally located on the body or body part. BSPO:wd Anatomical region ventrally located on the body or body part. FBql:00005843 spatial BSPO:0000084 ventral region Anatomical region ventrally located on the body or body part. BSPO:wd Anatomical region that overlaps the ventral and lateral regions of a body or body part. FBql:00005846 ventrolateral region spatial BSPO:0000085 This is an example of a composition of two axis positions. ventro-lateral region Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:wd FBql:00005873 FMA:9647 spatial BSPO:0000086 to be merged into CARO anatomical compartment FBql:00005881 spatial BSPO:0000092 to be merged into CARO anatomical compartment boundary FBcv:0000034 FBql:00005879 spatial BSPO:0000094 dorsal/ventral compartment boundary An anatomical axis that extends from the center of the body outwards or externally. wasila.dahdul 2013-07-02T11:21:42Z spatial proximal-distal axis BSPO:0000196 The medial-external axis could apply to a sphere-shaped body. medial-external axis An anatomical axis that extends from the center of the body outwards or externally. BSPO:curators An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. wasila.dahdul 2013-07-02T11:29:33Z spatial BSPO:0000198 oral-aboral axis An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. BSPO:PM Anatomical surface that is located on the anterior side of the body or body part. FBql:00005848 spatial BSPO:0000371 anterior surface Anatomical surface that is located on the anterior side of the body or body part. BSPO:wd Anatomical surface that is located on the posterior side of the body or body part. FBql:00005849 spatial BSPO:0000372 posterior surface Anatomical surface that is located on the posterior side of the body or body part. BSPO:wd Anatomical surface that is located on the apical side of the body or body part. FBql:00005854 spatial BSPO:0000373 apical surface Anatomical surface that is located on the apical side of the body or body part. BSPO:wd Anatomical surface that is located on the basal side of the body or body part. FBql:00005855 spatial BSPO:0000374 basal surface Anatomical surface that is located on the basal side of the body or body part. BSPO:wd Anatomical surface that located on the dorsal side of the body or body part. FBql:00005842 spatial BSPO:0000379 dorsal surface Anatomical surface that located on the dorsal side of the body or body part. BSPO:wd Anatomical surface that located on the lateral side of the body or body part. FBql:00005844 spatial BSPO:0000382 lateral surface Anatomical surface that located on the lateral side of the body or body part. BSPO:wd Anatomical surface that is located on the ventral side of the body or body part. FBql:00005843 spatial BSPO:0000384 ventral surface Anatomical surface that is located on the ventral side of the body or body part. BSPO:wd A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. FMA:242982 anatomical cross-section anatomical section plane section spatial cross-section BSPO:0000400 These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical. anatomical plane A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. BSPO:cjm Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. FMA:11361 left/right plane median plane sagittal section spatial BSPO:0000417 sagittal plane Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. BSPO:DOS BSPO:cjm BSPO:mah An axis that extends from the center of organism to one or other side. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG M-L axis ML axis medio-lateral axis mediolateral axis spatial proximal-distal axis BSPO:0001001 Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart. medial-lateral axis An axis that extends from the center of organism to one or other side. BSPO:cjm 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. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. 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. spatial CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. anatomical entity 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. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CAROC:Brownsville2014 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:MAH Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. spatial CARO:0000003 anatomical structure connected 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. CC:DOS An anatomical entity that has mass. spatial CARO:0000006 material anatomical entity material anatomical entity An anatomical entity that has mass. CC:DOS An anatomical entity that has no mass. spatial CARO:0000007 immaterial anatomical entity An anatomical entity that has no mass. CC:DOS A one dimensional, immaterial anatomical entity. spatial CARO:0000008 anatomical line A one dimensional, immaterial anatomical entity. CC:DOS A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. spatial CARO:0000010 anatomical boundary A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CC:DOS biological entity The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. G1 phase of mitotic cell cycle biological_process GO:0000080 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. S phase of mitotic cell cycle S-phase of mitotic cell cycle biological_process GO:0000084 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. G2 phase of mitotic cell cycle biological_process GO:0000085 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. GOC:mtg_cell_cycle A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. M phase of mitotic cell cycle M-phase of mitotic cell cycle biological_process GO:0000087 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. biological_process GO:0000088 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic prophase The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. biological_process GO:0000089 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic metaphase The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle. biological_process GO:0000090 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic anaphase The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0000093 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic telophase The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible. Wikipedia:Leptotene Wikipedia:Meiosis#Leptotene biological_process GO:0000237 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). leptotene The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible. GOC:mtg_cell_cycle The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur. Wikipedia:Meiosis#Zygotene Wikipedia:Zygotene biological_process GO:0000238 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). zygotene The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur. GOC:mtg_cell_cycle The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome. Wikipedia:Meiosis#Pachytene Wikipedia:Pachytene biological_process GO:0000239 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). pachytene The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome. GOC:mtg_cell_cycle The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves. Wikipedia:Diplotene Wikipedia:Meiosis#Diplotene biological_process GO:0000240 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). diplotene The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves. GOC:mtg_cell_cycle The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred. Wikipedia:Diakinesis Wikipedia:Meiosis#Diakinesis biological_process GO:0000241 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). diakinesis The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred. GOC:mtg_cell_cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. Wikipedia:M_phase M-phase biological_process GO:0000279 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. GOC:mtg_cell_cycle The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb 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 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 catalytic activity 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 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. biological_process GO:0007128 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic prophase I The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I. biological_process GO:0007132 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic metaphase I The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I. GOC:mtg_cell_cycle The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I. biological_process GO:0007133 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic anaphase I The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0007134 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic telophase I The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. biological_process GO:0007136 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic prophase II The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II. biological_process GO:0007137 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic metaphase II The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II. GOC:mtg_cell_cycle The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II. biological_process GO:0007138 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic anaphase II The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0007139 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic telophase II The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 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 is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt 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 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah 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 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 transferase activity transferase activity, transferring phosphorus-containing groups A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). Wikipedia:Sexual_reproduction The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0022403 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). cell cycle phase One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:mtg_cell_cycle A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. jl 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. biological_process GO:0043473 pigmentation The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. GOC:jl A distinct period or stage in a biological process or cycle. jl 2014-07-16T13:12:40Z biological_process GO:0044848 Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. biological phase A distinct period or stage in a biological process or cycle. GOC:jl The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. Wikipedia:G1_phase biological_process GO:0051318 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). Wikipedia:G2_phase biological_process GO:0051319 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place. Wikipedia:S_phase S-phase biological_process GO:0051320 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). S phase The cell cycle phase, following G1, during which DNA synthesis takes place. GOC:mtg_cell_cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. https://github.com/geneontology/go-ontology/issues/24599 GO:0007126 Wikipedia:Meiosis biological_process meiosis GO:0051321 Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. meiotic cell cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. GOC:ai The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. Wikipedia:Anaphase biological_process GO:0051322 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). anaphase The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. GOC:mtg_cell_cycle The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. Wikipedia:Metaphase biological_process GO:0051323 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). metaphase The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. Wikipedia:Prophase biological_process GO:0051324 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). prophase The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. resting phase Wikipedia:Interphase karyostasis biological_process GO:0051325 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. Wikipedia:Telophase biological_process GO:0051326 note that this term should not be used for direct annotation. if you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic s-phase). to capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). telophase The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle. M phase of meiotic cell cycle biological_process GO:0051327 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA. interphase of meiotic cell cycle biological_process GO:0051328 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic interphase The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. interphase of mitotic cell cycle biological_process GO:0051329 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis. G1 phase of meiotic cell cycle biological_process GO:0051330 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis. G2 phase of meiotic cell cycle biological_process GO:0051331 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis. GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle. S phase of meiotic cell cycle S-phase of meiotic cell cycle premeiotic S-phase biological_process GO:0051332 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle. GOC:mtg_cell_cycle A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0098762 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic cell cycle phase One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:dos One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0098763 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic cell cycle phase One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:dos A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs. biological_process GO:0098764 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiosis I cell cycle phase A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs. GOC:dos A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division). biological_process GO:0098765 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiosis II cell cycle phase A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division). GOC:dos One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division One of the two nuclear divisions that occur as part of the meiotic cell cycle. PMID:9334324 A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T14:44:23Z mitosis biological_process GO:0140014 mitotic nuclear division A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. ISBN:0198547684 A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process A process that is part of the meiotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 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 about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part 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 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type 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 code set of PubMed identifiers associated with journal articles. A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Justin Whorton PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 centrally registered identifier registry identifier An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Justin Whorton Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen dubbing process naming https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen identifier creating process An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton Mathias Brochhausen code map code system codeset coding system controlled vocabulary https://github.com/information-artifact-ontology/IAO/issues/237 Alan Ruttenberg Clint Dowland Matt Diller Sarah Bost William R. Hogan Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. The information content entities do not denote each other. code set planned process A process that realizes a plan which is the concretization of a plan specification. planned process A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A 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 A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. PATO:0000137 angular placement quality amount of rotation angle angular magnitude plane angle PATO:0000133 orientation A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. PATOC:JE A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A 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 shape quality inhering in a bearer by virtue of the bearer's having three angles. deltoid quality delta shaped triangle triangle-shaped PATO:0001875 triangular A shape quality inhering in a bearer by virtue of the bearer's having three angles. wordreference:wordreference A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. wedge-shaped quality PATO:0001955 cuneate A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. wordreference:wordreference A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. 2014-10-17T14:24:19Z quality PATO:0005024 longitudinal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. PATOC:WD A shape that is in the form of a plug, being tube-like and expanded on one end. 2018-11-12T18:24:41Z plug like quality PATO:0040012 plug shaped A shape that is in the form of a plug, being tube-like and expanded on one end. https://orcid.org/0000-0003-3162-7490 A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 1 A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium. PMID:28072387 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 protosphere Schmidtea_mediterranea_Developmental_Stages Stage 2 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 3 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 4 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 5 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 6 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 PMID:28812561 Schmidtea_mediterranea_Developmental_Stages Stage 7 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 hatchling newborn hatchling Schmidtea_mediterranea_Developmental_Stages Stage 8 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:15972844 PMID:25017721 PMID:25956527 PMID:26457503 PMID:26651295 PMID:27013241 PMID:27150006 PMID:27542689 PMID:28287248 PMID:28686611 PMID:28757112 PMID:29557542 PMID:29674432 PMID:29906446 sigma class neoblast sigma-class neoblast Planarian_Anatomy sigma neoblast A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. PMID:25017721 Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr,required for maintenance and regeneration of protonephridial cell types. Planarian_Anatomy PLANA:0000011 protonephridial progenitor cell Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr,required for maintenance and regeneration of protonephridial cell types. PMID:24523458 PMID:28072387 Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. neural committed stem cell neural precursor cell neural progenitor cell neuronal progenitor Planarian_Anatomy PLANA:0000012 neural progenitor cell Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. PMID:21282632 PMID:24173799 PMID:25356635 PMID:26057828 PMID:26525673 PMID:28072387 PMID:29674432 Musculature surrounding internal organs of the body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00005070 PMID:26904543 PMID:30471994 visceral muscle Planarian_Anatomy visceral musculature Musculature surrounding internal organs of the body. PMID:26904543 PMID:30471994 Image is an electron micrograph depicting the visceral musculature (arrowheads) that lies beneath the gut. The gut is identifiable by the collection of darkly stained lipid droplets in the top right corner and the white of the lumen at the top of the image. Scale bar is 10um An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25017721 PMID:25956527 PMID:26457503 PMID:26651295 PMID:27013241 PMID:27150006 PMID:27542689 PMID:28292427 PMID:28757112 PMID:28807897 PMID:29158443 PMID:29557542 PMID:29674431 PMID:29674432 PMID:29906446 zeta zeta class zeta class neoblast zeta-class neoblast zeta-neoblast Planarian_Anatomy zeta neoblast An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). PMID:25017721 An epithelial cell lacking cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 XAO:0004225 Planarian_Anatomy non ciliated epithelial cell Image is an electron micrograph of the dorsal side of the animal where there is a transition from nonciliated epidermal cells to ciliated ones. On the left side of the image are the ciliated cells and on the right are the nonciliated. A few nonciliated have been marked with arrowheads. Scale bar is 10um. A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:15866156 PMID:16033796 PMID:16311336 PMID:16890156 PMID:17251262 PMID:17376870 PMID:17390146 PMID:17670787 PMID:17905225 PMID:17942485 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:18456843 PMID:18786419 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:19852954 PMID:19933103 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20511647 PMID:20599901 PMID:20707997 PMID:20865784 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21295483 PMID:21356107 PMID:21458439 PMID:21664348 PMID:21747960 PMID:21806978 PMID:21828097 PMID:21852957 PMID:21894189 PMID:21937596 PMID:22125640 PMID:22339734 PMID:22371573 PMID:22385657 PMID:22411224 PMID:22439894 PMID:22451003 PMID:22543868 PMID:22884275 PMID:23079596 PMID:23123964 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23405188 PMID:23629965 PMID:23652002 PMID:23954785 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24704339 PMID:24737865 PMID:24922054 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25558068 PMID:25725068 PMID:25956527 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26459857 PMID:26525673 PMID:26711341 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27122174 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27441386 PMID:27501047 PMID:27551436 PMID:27612382 PMID:27612384 PMID:27654173 PMID:28072387 PMID:28126842 PMID:28171748 PMID:28245923 PMID:28287248 PMID:28292427 PMID:28434803 PMID:28461239 PMID:28495872 PMID:28686611 PMID:28807897 PMID:28893948 PMID:29291981 PMID:29674431 PMID:29906446 PMID:30194301 PMID:30237141 PMID:30282036 PMID:30383829 PMID:30399335 PMID:30471994 PMID:30485821 PMID:30729158 PMID:30962434 https://doi.org/10.1101/279364 definitive pharynx Planarian_Anatomy pharynx A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. OCLC:16809160 Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16033796 PMID:17251262 PMID:17390146 PMID:17553481 PMID:17905225 PMID:17942485 PMID:18202849 PMID:19048075 PMID:20967238 PMID:21282632 PMID:21852957 PMID:22339734 PMID:22411224 PMID:22427692 PMID:22445864 PMID:22549959 PMID:22884275 PMID:23250205 PMID:23318641 PMID:24063805 PMID:24922054 PMID:25254346 PMID:25356635 PMID:25493551 PMID:25772472 PMID:26017970 PMID:26618653 PMID:27068018 PMID:27606067 PMID:27612384 PMID:27800171 PMID:28137894 PMID:28216315 PMID:28245923 PMID:28495872 PMID:28976975 PMID:29547123 PMID:29674431 PMID:29674432 PMID:30143032 PMID:30399335 PMID:30471994 PMID:30485821 UBERON:0006562 PRN neuronal photoreceptive cell optical neuron photoreceptive neuron photoreceptor cell photosensitive cell visual neuron Planarian_Anatomy photoreceptor neuron Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. PMID:21852957 PMID:22884275 Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:22439894 PMID:25017721 PMID:26457503 PMID:28072387 Planarian_Anatomy Category 4 cell Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. PMID:25017721 PMID:26457503 Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29674431 PMID:29674432 PMID:30471994 Planarian_Anatomy muscle progenitor cell Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. PMID:25017721 Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:19852954 PMID:19933103 PMID:21828097 PMID:21937596 PMID:22479207 PMID:23318635 PMID:23318641 PMID:23954785 PMID:24063805 PMID:24523458 PMID:24737865 PMID:24992682 PMID:25017721 PMID:25254346 PMID:26057828 PMID:26457503 PMID:26651295 PMID:26711341 PMID:27068018 PMID:27150006 PMID:27501047 PMID:27551436 PMID:27612384 PMID:28245923 PMID:28292427 PMID:28807897 PMID:29100657 PMID:29158443 PMID:29674431 PMID:29674432 UBERON:0006973 excretory organ nephridia osmoregulatory duct protonephridial tubule Planarian_Anatomy protonephridia Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. OCLC:16809160 PMID:21828097 PMID:26057828 http://purl.obolibrary.org/obo/Depicted by field contains a whole-mount acetylated tubulin (AcTub) staining. Scale bars_ 500 um. Inset to right shows depth-coded projection of AcTub staining. Superficial structures are in blue and deeper structures are in red. Scale bars: 50 um Organisms sharing a specified genotype or karyotype. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy biotype Post-mitotic, ciliated epidermal cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25017721 PMID:28072387 Planarian_Anatomy Category 5 cell Post-mitotic, ciliated epidermal cells. PMID:25017721 An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00001866 ISBN:9780070316607 PMID:28072387 temporary embryonic pharynx Planarian_Anatomy embryonic pharynx An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms in on the embryonic pharynx. Asexual animal strains that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:11972158 PMID:28812561 asexual asexual adult asexual biotype Planarian_Anatomy Smed asexual biotype Asexual animal strains that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. PMID:11972158 PMID:17376870 Image is an scanning electron micrograph of the dorsal side of an entire animal. This is an adult asexual Schmidtea mediterranea. Anterior is to the right and posterior is to the left. Scale bar is 500um. The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, 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]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16033796 PMID:16311336 PMID:17251262 PMID:18202849 PMID:19048075 PMID:19211673 PMID:19247960 PMID:20223763 PMID:20707997 PMID:20967238 PMID:21806978 PMID:22339734 PMID:22427692 PMID:22445864 PMID:22549959 PMID:22696458 PMID:23079596 PMID:23250205 PMID:23297191 PMID:23318641 PMID:23903188 PMID:24131630 PMID:24173799 PMID:24737865 PMID:24950970 PMID:25254346 PMID:25278423 PMID:25725068 PMID:26062938 PMID:26114597 PMID:26556349 PMID:27013241 PMID:27068018 PMID:27163480 PMID:27501047 PMID:27523733 PMID:27551436 PMID:27612384 PMID:27864883 PMID:28292427 PMID:29357350 PMID:29557542 PMID:29674431 PMID:30399335 UBERON:0001016 nerve system Planarian_Anatomy nervous system The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, 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]. UBERON:0001016 The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the gut through the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:17553481 PMID:17942485 PMID:18063757 PMID:18287199 PMID:19174194 PMID:19247960 PMID:19933103 PMID:20707997 PMID:20865784 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21356107 PMID:21458439 PMID:21566185 PMID:21566195 PMID:21664348 PMID:21806978 PMID:21828097 PMID:22411224 PMID:22439894 PMID:22451003 PMID:22899852 PMID:23079596 PMID:23235145 PMID:23250205 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23903188 PMID:23954785 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24173799 PMID:24238224 PMID:24415944 PMID:24737865 PMID:24950970 PMID:24992682 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25558068 PMID:25956527 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26556349 PMID:26651295 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27122174 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27441386 PMID:27501047 PMID:27542689 PMID:27551436 PMID:27612382 PMID:27612384 PMID:27864883 PMID:28072387 PMID:28216315 PMID:28245923 PMID:28287248 PMID:28292427 PMID:28461239 PMID:28686611 PMID:28807897 PMID:29100657 PMID:29158443 PMID:29547123 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30143032 PMID:30194301 PMID:30282036 PMID:30297872 PMID:30383829 PMID:30471994 PMID:30962434 UBERON:0000160 https://doi.org/10.1101/279364 adult gut blind gut definitive gut digestive tract gastrovascular digestive tract gastrovascular tract intestinal tract intestine three-branched gut triclad gut Planarian_Anatomy gut The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the gut through the pharynx. PMID:3490491 Strains of cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:11972158 PMID:19022767 PMID:28812561 hermaphroditic biotype sexual sexual hermaphrodite Planarian_Anatomy Smed sexual biotype Strains of cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. PMID:11972158 PMID:19022767 Depicted by field contains light micrscope image of asexual and sexual biotypes of Schmidtea meditteranea with their respective karyotypes. Note that the asexual bioptype has a chromosome inversion compared to the sexual. Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:20040488 PMID:21894189 PMID:22385657 PMID:22427692 PMID:22439894 PMID:22899852 PMID:23318635 PMID:23629965 PMID:24063805 PMID:24173799 PMID:24367277 PMID:25017721 PMID:26114597 PMID:26651295 PMID:27013241 PMID:27068018 PMID:27542689 PMID:28072387 PMID:29674431 Category 2 gene expressing cell NB.21.11e expressing cell Smed-NB.21.11e+ cell early division progeny early epidermal progenitor early neoblast progeny early post-mitotic progeny early progeny prog-1+ epidermal progenitor cell Planarian_Anatomy Category 2 cell Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Planarian_Anatomy primitive ectoderm A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The median line/ plane of bilateral symmetry along the anteroposterior axis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C81170 Planarian_Anatomy midline Illustration of the midline (in green). Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17251262 PMID:17390146 PMID:17553481 PMID:17905225 PMID:20967238 PMID:21282632 PMID:21458439 PMID:21852957 PMID:22339734 PMID:22445864 PMID:22884275 PMID:23250205 PMID:23318641 PMID:24063805 PMID:25254346 PMID:25493551 PMID:26017970 PMID:27122174 PMID:27551436 PMID:27606067 PMID:28137894 PMID:28245923 PMID:28287248 PMID:28495872 PMID:28976975 PMID:29158443 PMID:29674431 PMID:29674432 PMID:30471994 eye pigment cell eye pigment cup cell eye pigment producing cell eye pigmented cell melanin pigment cell optic cup cell photoceptor pigmented cell Planarian_Anatomy pigment cup cell Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. PMID:21852957 PMID:22884275 The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal. dorsal region of midline Planarian_Anatomy PLANA:0000032 dorsal midline Illustration of the dorsal midline (in green). Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. epithelial progenitor Planarian_Anatomy PLANA:0000033 epidermal progenitor cell Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. PMID:27150006 PMID:27606067 PMID:29674432 PMID:30282036 A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:15866156 PMID:16311336 PMID:18786419 PMID:19048075 PMID:19247960 PMID:19852954 PMID:20215344 PMID:20511647 PMID:20599901 PMID:20865784 PMID:21179478 PMID:21282632 PMID:21295483 PMID:22252539 PMID:22549959 PMID:23235145 PMID:23297191 PMID:23954785 PMID:24120894 PMID:24173799 PMID:24922054 PMID:24950970 PMID:25558068 PMID:25772472 PMID:26114597 PMID:26457503 PMID:26651295 PMID:26711341 PMID:27034770 PMID:27074666 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27501047 PMID:27612384 PMID:28137894 PMID:28216315 PMID:28245923 PMID:28292427 PMID:28686611 PMID:28757112 PMID:28976975 PMID:29100657 PMID:29158443 PMID:29273738 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30194301 PMID:30282036 PMID:30962434 UBERON:0001003 definitive epidermis epidermal layer epidermis epithelium mature epidermis tegument Planarian_Anatomy At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium). epidermis A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. OCLC:16809160 Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:20040488 PMID:21894189 PMID:22252539 PMID:22427692 PMID:22439894 PMID:22899852 PMID:23297191 PMID:23318635 PMID:23629965 PMID:23954785 PMID:24063805 PMID:24173799 PMID:24367277 PMID:26114597 PMID:26457503 PMID:26651295 PMID:27013241 PMID:27068018 PMID:28072387 AGAT-1 expressing cell AGAT1 expressing cell Category 3 gene expressing cell Smed-AGAT-1+ cell late division progeny late epidermal progenitor late neoblast progeny late postmitotic progeny late progeny Planarian_Anatomy Category 3 cell Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. PMID:18786419 PMID:20040488 PMID:26114597 PMID:26457503 An organ that detects light. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:15972844 PMID:16311336 PMID:16890156 PMID:17251262 PMID:17553481 PMID:17905225 PMID:17942485 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:18456843 PMID:18786419 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:19805089 PMID:19852954 PMID:20040488 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20599901 PMID:20707997 PMID:20865784 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21295481 PMID:21295483 PMID:21356107 PMID:21458439 PMID:21566185 PMID:21566195 PMID:21747960 PMID:21806978 PMID:21828097 PMID:21852957 PMID:21894189 PMID:21937596 PMID:22125640 PMID:22318224 PMID:22339734 PMID:22385657 PMID:22411224 PMID:22439894 PMID:22445864 PMID:22479207 PMID:22549959 PMID:22884275 PMID:22899852 PMID:23235145 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23629965 PMID:23903188 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24415944 PMID:24704339 PMID:24737865 PMID:24922054 PMID:24950970 PMID:24992682 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25493551 PMID:25558068 PMID:25725068 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26525673 PMID:26556349 PMID:26618653 PMID:26711341 PMID:26884331 PMID:27034770 PMID:27063937 PMID:27150006 PMID:27240733 PMID:27542689 PMID:27551436 PMID:27606067 PMID:27654173 PMID:27800171 PMID:28171748 PMID:28216315 PMID:28287248 PMID:28292427 PMID:28495872 PMID:28686611 PMID:28893948 PMID:28976975 PMID:29100657 PMID:29158443 PMID:29273738 PMID:29291974 PMID:29291981 PMID:29357350 PMID:29547123 PMID:29674431 PMID:30237141 PMID:30282036 PMID:30297872 PMID:30383829 PMID:30485821 PMID:30962434 UBERON:0000970 https://doi.org/10.1101/279364 cerebral eye eye spot eye-spot eyespot ocelli photoreceptor Planarian_Anatomy Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um eye An organ that detects light. UBERON:0000970 we will move forward using "tissue" instead. We have not listed anything as a regenerating or developing tissue, so this seems unnecessary obsolete definitive tissue true The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal. ventral region of midline Planarian_Anatomy PLANA:0000038 ventral midline Illustration of the ventral midline (in green). An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25017721 PMID:26651295 PMID:27013241 PMID:27150006 PMID:27542689 PMID:28287248 PMID:28757112 PMID:28807897 PMID:29674431 PMID:29674432 PMID:29906446 gamma gamma class neoblast gamma-neoblast gut progenitor cell Planarian_Anatomy gamma neoblast An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. PMID:25017721 this term is not needed. All previous children of this term (Stage 1, Sage 2, etc) are now children of GO life cycle stage or zygote stage obsolete Schmidtea mediterranea developmental stage true Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 UBERON:0008259 Planarian_Anatomy aboral hemisphere Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx. PMID:28072387 The single, central gut branch of the triclad gut anterior to the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:3490491 Planarian_Anatomy anterior primary gut branch The single, central gut branch of the triclad gut anterior to the pharynx. PMID:3490491 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um Region along the edge of the animal where the dorsal and ventral surfaces meet. D/V boundary DV border DV boundary DV domain DV margin body edge body margin body periphery dorsal ventral boundary dorsal-ventral boundary dorsal/ventral compartment boundary of whole organism dorsoventral margin edge Planarian_Anatomy PLANA:0000043 dorsal ventral margin of the whole animal Region along the edge of the animal where the dorsal and ventral surfaces meet. ISBN:9780070316607 PMID:17905225 PMID:19174194 PMID:20865784 PMID:21295481 PMID:21295483 PMID:21458439 PMID:22549959 PMID:22696458 PMID:24415944 PMID:26457503 PMID:28216315 PMID:29357350 PMID:29674431 PMID:29674432 PMID:30399335 PMID:30485821 The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:15866156 PMID:16033796 PMID:16344473 PMID:16890156 PMID:17251262 PMID:17376870 PMID:17553481 PMID:17670787 PMID:17905225 PMID:17942485 PMID:17999079 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:20215344 PMID:20422023 PMID:20844018 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21295481 PMID:21458439 PMID:21566195 PMID:21806978 PMID:22074376 PMID:22125640 PMID:22339734 PMID:22411224 PMID:22445864 PMID:22451003 PMID:22549959 PMID:23235145 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23652002 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24415944 PMID:24950970 PMID:25254346 PMID:25278423 PMID:25356635 PMID:25404302 PMID:25725068 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26884331 PMID:27013241 PMID:27074666 PMID:27163480 PMID:27612382 PMID:27612384 PMID:27800171 PMID:28072387 PMID:28126842 PMID:28216315 PMID:28287248 PMID:29291974 PMID:29291981 PMID:29547123 PMID:29674431 PMID:30194301 PMID:30237141 UBERON:0000955 https://doi.org/10.1101/279364 bi-lobed brain bi-lobed cephalic ganglia brain cerebral ganglia Planarian_Anatomy cephalic ganglia Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md circular muscle fiber Planarian_Anatomy circular muscle cell Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The first layer of muscle cells beneath the basal lamina (BL), circular muscle, have been colored and labeled with arrowheads. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16344473 PMID:19247960 PMID:20215344 PMID:21566185 PMID:21852957 PMID:21937596 PMID:22318224 PMID:22385657 PMID:22411224 PMID:22543868 PMID:22549959 PMID:22884275 PMID:22899852 PMID:23079596 PMID:23297191 PMID:23318641 PMID:23652002 PMID:23954785 PMID:24040508 PMID:24120894 PMID:24173799 PMID:25017721 PMID:25254346 PMID:25356635 PMID:26711341 PMID:27063937 PMID:27074666 PMID:27149082 PMID:27150006 PMID:27502555 PMID:27523733 PMID:27551436 PMID:28434803 PMID:29357350 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30962434 adult pluripotent stem cell cNeoblast clonogenic stem cell pluripotent stem cell Planarian_Anatomy clonogenic neoblast Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. PMID:21566185 Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26057828 PMID:27068018 PMID:29674431 UBERON:0001232 collection duct Planarian_Anatomy collecting duct Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. PMID:26057828 Image is an electron micrograph depicting a collecting duct (arrowheads) passing through the basal lamina (BL). Dorsal is up and the scale bar is 5 um. Body wall muscle fibers arrayed diagonally along the anteroposterior axis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:23903188 PMID:26904543 PMID:27068018 PMID:28461239 PMID:28807897 PMID:30471994 diagonal fiber diagonal muscle diagonal muscle fiber Planarian_Anatomy diagonal muscle cell Body wall muscle fibers arrayed diagonally along the anteroposterior axis. PMID:26904543 Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The third layer of cells beneath the basement membrane, diagonal muscle cells, have been colored and labeled with arrowheads. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:16311336 PMID:16344473 PMID:17390146 PMID:17553481 PMID:17905225 PMID:18063757 PMID:18287199 PMID:19048075 PMID:19247960 PMID:19766622 PMID:19933103 PMID:20040488 PMID:20215344 PMID:20707997 PMID:21356107 PMID:21664348 PMID:21806978 PMID:22451003 PMID:22479207 PMID:23079596 PMID:24737865 PMID:24922054 PMID:25254346 PMID:25558068 PMID:26556349 PMID:27068018 PMID:27501047 PMID:29357350 UBERON:0001007 gastrointestinal system gastrovascular system Planarian_Anatomy 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. UBERON:0001007 removing all processes. may bring back if PLANA expanded to cover processes. obsolete direct development true removing all processes. may bring back if PLANA expanded to cover processes. obsolete dispersed cleavage true Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:27068018 UBERON:0004135 Planarian_Anatomy distal tubule Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. PMID:21828097 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while thecollecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. dorsal epithelium dorsal region of epidermis Planarian_Anatomy PLANA:0000054 dorsal region of the epidermis Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. ISBN:9780070316607 PMID:17942485 PMID:19048075 PMID:19852954 PMID:20599901 PMID:20844018 PMID:22385657 PMID:22479207 PMID:26457503 PMID:27612382 PMID:28292427 Image is an electron micrograph depicting the dorsal epidermis (arrowheads). Also visible in this micrograph, immediately deep to the epidermis is the basal lamina and beneath that is a photoreceptor. Scale bar is 10 um. Ciliated epithelial cells along the dorsal midline. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17553481 racing stripe Planarian_Anatomy dorsal stripe Ciliated epithelial cells along the dorsal midline. PMID:17553481 Image is an electron micrograph showing the dorsal side of the head of an adult worm. Arrowheads mark where the ciliated cells of the dorsal stripe can be seen. Anterior is up and scale bar is 100um. Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22074376 PMID:27149082 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md Planarian_Anatomy ectolecithal embryo Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. PMID:22074376 PMID:27149082 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md removing all processes. may bring back if PLANA expanded to cover processes. obsolete embryonic cleavage true A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 UBERON:6001842 Planarian_Anatomy embryonic digestive system A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. PMID:28072387 Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic gut cell Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. PMID:28072387 The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:12888018 PMID:28072387 Planarian_Anatomy embryonic wall The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. OCLC:16809160 PMID:12888018 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. Visceral muscle surrounding the gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:22411224 PMID:23079596 PMID:26904543 PMID:30471994 PMID:30962434 UBERON:2001324 enteric muscle intestinal muscle Planarian_Anatomy enteric musculature Image is an electron micrograph depicting the enteric musculature (arrowheads) surrounding the gut, which extends across the top of the image. These cells are very small compared to the layer of medial muscle underneath them. Scale bar is 1um. Attachment between the triclad gut and the proximal end of the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:18063757 PMID:20707997 PMID:21806978 PMID:24737865 PMID:27063937 PMID:29674431 PMID:30485821 UBERON:0001043 gut pharynx intersection pharynx root root of pharynx Planarian_Anatomy esophagus 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000478 Planarian_Anatomy 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. UBERON:0000478 Terminal structure of protonephridia unit; consists of flame cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:26057828 Planarian_Anatomy flame bulb Image is an electron micrograph depicting a flame cell (outlined), which is a part of the flame bulb. "N" marks this cell's nucleus and the cilia are noted by an arrowhead. Scale bar is 1um. Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:17670787 PMID:19247960 PMID:19852954 PMID:21828097 PMID:21937596 PMID:24523458 PMID:26057828 PMID:26711341 PMID:27068018 PMID:27542689 PMID:29674431 PMID:29674432 Planarian_Anatomy flame cell Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. OCLC:16809160 PMID:21828097 PMID:26057828 Image is an electron micrograph depicting a flame cell (outlined), which is a part of the flame bulb. "N" marks this cell's nucleus and the cilia are noted by an arrowhead. Scale bar is 1um. The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000509 ISBN:9780070316607 PMID:21282632 PMID:21664348 PMID:24120894 PMID:25558068 PMID:27441386 PMID:27501047 PMID:28287248 PMID:30608231 gut epithelia gut epithelium intestinal epithelium Planarian_Anatomy gastrodermis The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. PMID:3490491 Secretory cells that release digestive enzymes into the lumen of the intestine. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0001540 PMID:20865784 PMID:21664348 PMID:23079596 PMID:27501047 PMID:28137894 PMID:28287248 PMID:29674431 PMID:29674432 Planarian_Anatomy goblet cell Secretory cells that release digestive enzymes into the lumen of the intestine. PMID:3490491 Image is an electron micrograph showing part of the gastrodermis. A goblet cell, a type of gastrodermal cell is labeled with arrowheads. Note the large, dark mucus granules contained in the cell body. The lumen of the gut can be seen on the right side of the image and has been labeled with "L." Scale bar is 1 um. Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic gut cavity Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut. PMID:28072387 Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:26904543 PMID:30962434 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md inner longitudinal muscle fiber inner longitudinal muscle layer Planarian_Anatomy inner longitudinal muscle cell Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Absorptive digestive cells that engulf food particles for intracellular digestion. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19933103 PMID:21664348 PMID:23079596 PMID:27542689 PMID:28072387 PMID:29674431 PMID:29674432 enterocyte gut enterocyte gut phagocyte intestinal epithelial cell Planarian_Anatomy intestinal phagocyte Absorptive digestive cells that engulf food particles for intracellular digestion. PMID:3490491 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:23903188 PMID:26904543 PMID:27551436 PMID:28461239 PMID:28807897 PMID:30471994 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md BW longitudinal fiber body wall longitudinal fiber longitudinal fiber longitudinal muscle longitudinal muscle cell longitudinal muscle fiber Planarian_Anatomy longitudinal muscle cell Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The longitudinal muscle cells (arrowheads) sit behind both the circular muscle and the diagonal muscle. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:17251262 PMID:17905225 PMID:18287199 PMID:19174194 PMID:19211673 PMID:20707997 PMID:21295481 PMID:21458439 PMID:21806978 PMID:23954785 PMID:26457503 PMID:26556349 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27122174 PMID:28807897 PMID:29674431 PMID:30399335 PMID:30471994 PMID:30485821 UBERON:0000165 anus manus Planarian_Anatomy mouth The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. OCLC:16809160 Image is an electron micrograph of the mouth (arrowheads), which is located on the ventral side of the animal. Note the heavily ciliated pharynx that is peeking out. Scale bar is 10um. A female germ cell that has entered meiosis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000023 PMID:25278423 PMID:27149082 PMID:27163480 PMID:27304889 PMID:27330085 PMID:27501047 PMID:28072387 PMID:28434803 PMID:28812561 egg female gamete ovum Planarian_Anatomy oocyte A female germ cell that has entered meiosis. CL:0000023 A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:20707997 PMID:20865784 PMID:21458439 PMID:21828097 PMID:21852957 PMID:22411224 PMID:22427692 PMID:22445864 PMID:22549959 PMID:22884275 PMID:25493551 PMID:26017970 PMID:26618653 PMID:27068018 PMID:27240733 PMID:27542689 PMID:27606067 PMID:27800171 PMID:28495872 PMID:29547123 PMID:30143032 PMID:30194301 UBERON:0003072 eye cup photoreceptor pigment cup photoreceptor pigmentation pigment cup pigmented cell cup pigmented optic cup Planarian_Anatomy optic cup A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. PMID:21852957 PMID:22884275 Stage 3-5 embryo hemisphere centered around the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy oral hemisphere Stage 3-5 embryo hemisphere centered around the embryonic pharynx. PMID:28072387 Illustration of the oral hemispshere (in green). Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md outer longitudinal muscle layer Planarian_Anatomy outer longitudinal muscle cell Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:30962434 dorsoventral muscle fibers parenchymal muscle Planarian_Anatomy parenchymal musculature Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles. OCLC:16809160 Image is an electron micrograph of the parenchyma. Three muscle cells have been notated with an arrowhead. Scale bar is 2 um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20967238 PMID:22339734 PMID:23903188 PMID:26017970 PMID:26884331 PMID:27150006 PMID:27612382 PMID:29674431 UBERON:0000010 Planarian_Anatomy peripheral nervous system 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. UBERON:0000010 An epithelial structure housing the pharynx, connected to the esophagus and mouth. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 pharyngeal pocket pharyngeal pouch Planarian_Anatomy pharynx pouch An epithelial structure housing the pharynx, connected to the esophagus and mouth. OCLC:16809160 racing stripe is now a synonym of PLANA:0000055 dorsal stripe obsolete racing stripe true The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:23318641 PMID:24063805 major posterior gut branch primary posterior intestinal branch Planarian_Anatomy posterior primary gut branch The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. PMID:3490491 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The posterior primary gut branch is indicated by arrows. Scale bar = 250um A phagocytic cell closely associated with the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy primitive gut cell A phagocytic cell closely associated with the embryonic pharynx. PMID:28072387 removing all processes. may bring back if PLANA expanded to cover processes. obsolete protosphere true Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:21937596 PMID:26057828 PMID:27068018 UBERON:0004134 Planarian_Anatomy proximal tubule Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. PMID:21828097 Image is an electron micrograph depicting a proximal tubule (arrowheads) of the protonephridia structure. Note the cilia and the characteristic way the cell membrane connects with other proximal tubule epithelial cells. Scale bar is 2um. The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:17670787 PMID:19048075 PMID:19247960 PMID:19852954 PMID:20707997 PMID:21828097 PMID:21937596 PMID:22427692 PMID:23079596 PMID:23235145 PMID:23903188 PMID:24173799 PMID:24523458 PMID:24737865 PMID:25254346 PMID:26057828 PMID:26711341 PMID:27068018 PMID:27542689 PMID:28461239 PMID:29674431 PMID:30297872 UBERON:0001008 excretory system protonephridial system Planarian_Anatomy renal system The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. UBERON:0001008 Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:27122174 PMID:28287248 PMID:30471994 Planarian_Anatomy secondary gut branch Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. PMID:3490491 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The secondary gut branch is indicated by arrows. Scale bar = 250um A mature male germ cell that develops from a spermatid. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000019 PMID:17390146 PMID:20844018 PMID:22074376 PMID:25278423 PMID:27149082 PMID:27163480 PMID:27304889 PMID:28072387 PMID:29095551 https://doi.org/10.1101/279364 mature sperm spermatozoa Planarian_Anatomy sperm A mature male germ cell that develops from a spermatid. CL:0000019 removing all processes. may bring back if PLANA expanded to cover processes. obsolete sphere formation true Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:15599763 syncytial yolk cell Planarian_Anatomy yolk syncytium Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. PMID:15599763 Gut branches originating from and connected to the secondary gut branches. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:23250205 PMID:27122174 PMID:28137894 PMID:28287248 PMID:30194301 PMID:30471994 tertiary branch tertiary intestinal branch Planarian_Anatomy tertiary gut branch Gut branches originating from and connected to the secondary gut branches. PMID:3490491 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The tertiary gut branch indicated is by arrows. Scale bar = 250um removing all processes. may bring back if PLANA expanded to cover processes. obsolete tissue morphogenesis true Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21852957 PMID:22884275 PMID:23250205 PMID:24040508 PMID:27606067 PMID:28072387 PMID:28245923 PMID:29674431 PMID:30485821 eye progenitor eye progenitor cell ovo+ eye progenitor Planarian_Anatomy trail cell Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. PMID:22884275 Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells cilated ventral epidermis ciliated ventral epithelium ventral epidermin ventral epithelia ventral epithelium ventral region of epidermis Planarian_Anatomy PLANA:0000096 ventral epidermis Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells ISBN:9780070316607 PMID:15866156 PMID:17942485 PMID:19852954 PMID:20599901 PMID:21282632 PMID:23144623 PMID:23903188 PMID:24523458 PMID:25017721 PMID:26457503 PMID:26912790 PMID:27068018 PMID:28292427 PMID:29100657 PMID:30383829 PMID:30962434 The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0002328 EFO:0000896 FBbt:00001102 ISBN:9780070316607 MAT:0000339 MIAA:0000339 PMID:16033796 PMID:16890156 PMID:17251262 PMID:17390146 PMID:17553481 PMID:17905225 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19174194 PMID:19211673 PMID:19247960 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20599901 PMID:20707997 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21566185 PMID:21806978 PMID:21828097 PMID:22074376 PMID:22125640 PMID:22339734 PMID:22479207 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23954785 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24950970 PMID:25254346 PMID:25356635 PMID:25558068 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26062938 PMID:26457503 PMID:26556349 PMID:27013241 PMID:27034770 PMID:27150006 PMID:27163480 PMID:27612382 PMID:28072387 PMID:28126842 PMID:28245923 PMID:28807897 PMID:29291974 PMID:29674431 PMID:30143032 PMID:30471994 UBERON:0000934 WBbt:0005829 http://en.wikipedia.org/wiki/Ventral:nerve:cord nlx:146329 VNC nerve cord ventral cord Planarian_Anatomy ventral nerve cord The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]. UBERON:0000934 Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000854 CL:0000365 PMID:28812561 UBERON:0000106 Planarian_Anatomy zygote Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]. CL:0000365 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000938 CL:0000540 NCIT:C12623 PMID:16033796 PMID:16890156 PMID:17553481 PMID:17905225 PMID:18202849 PMID:18287199 PMID:19048075 PMID:19174194 PMID:19211673 PMID:20215344 PMID:21566185 PMID:22411224 PMID:22439894 PMID:22479207 PMID:22549959 PMID:23297191 PMID:23903188 PMID:23954785 PMID:24040508 PMID:24131630 PMID:24173799 PMID:24737865 PMID:24922054 PMID:24950970 PMID:25254346 PMID:25356635 PMID:25558068 PMID:26457503 PMID:26525673 PMID:27013241 PMID:27063937 PMID:27150006 PMID:27163480 PMID:27542689 PMID:27612382 PMID:27612384 PMID:27864883 PMID:28072387 PMID:28126842 PMID:28137894 PMID:28245923 PMID:28292427 PMID:28461239 PMID:28807897 PMID:29100657 PMID:29184198 PMID:29291974 PMID:29291981 PMID:29357350 PMID:29674432 PMID:30143032 PMID:30399335 WBbt:0003679 differentiated neuron nerve cell neural cell neuronal cell Planarian_Anatomy neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. CL:0000540 A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000066 PMID:18202849 PMID:19048075 PMID:20865784 PMID:22479207 PMID:24737865 PMID:26114597 PMID:28072387 PMID:28461239 epidermis cell Planarian_Anatomy epithelial cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina. CL:0000066 A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000187 PMID:15972844 PMID:18202849 PMID:19174194 PMID:20422023 PMID:20511647 PMID:21458439 PMID:21828097 PMID:22252539 PMID:22479207 PMID:23318641 PMID:23405188 PMID:23954785 PMID:24415944 PMID:24737865 PMID:25254346 PMID:25558068 PMID:26062938 PMID:27063937 PMID:27523733 PMID:28216315 PMID:28287248 PMID:28292427 PMID:28461239 PMID:28686611 PMID:28807897 PMID:28893948 PMID:30471994 PMID:30962434 muscle fiber myocyte Planarian_Anatomy muscle cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 Image is an electron micrograph depicting a muscle cell (arrowheads) cut in a transverse orientation with respect to the fiber length. Note the texture of the cytoplasm that comes from the organization of myofibrils. Scale bar is 1um. A subdivision of an anatomical compartment. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BSPO:0000070 PMID:28292427 PMID:29547123 body region Planarian_Anatomy anatomical region 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16033796 PMID:16344473 PMID:16890156 PMID:17251262 PMID:17553481 PMID:17670787 PMID:17905225 PMID:17942485 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19174194 PMID:19247960 PMID:19933103 PMID:20865784 PMID:20967238 PMID:21282632 PMID:21295481 PMID:21458439 PMID:21664348 PMID:21806978 PMID:21828097 PMID:22125640 PMID:22252539 PMID:22339734 PMID:22385657 PMID:22411224 PMID:22427692 PMID:22439894 PMID:22445864 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23903188 PMID:24063805 PMID:24173799 PMID:24367277 PMID:24704339 PMID:24737865 PMID:24922054 PMID:24950970 PMID:25356635 PMID:25493551 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26459857 PMID:26711341 PMID:26884331 PMID:27013241 PMID:27063937 PMID:27068018 PMID:27074666 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27523733 PMID:27542689 PMID:27612382 PMID:27612384 PMID:27800171 PMID:27864883 PMID:28126842 PMID:28434803 PMID:28461239 PMID:28807897 PMID:28976975 PMID:29273738 PMID:29291981 PMID:30399335 PMID:30471994 PMID:30729158 PMID:30962434 UBERON:0001017 https://doi.org/10.1101/279364 CNS head-restricted nervous system Planarian_Anatomy central nervous system The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. UBERON:0001017 Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 Planarian_Anatomy rhabdite Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. OCLC:16809160 Image is an electron micrograph depicting the epidermis. Inside of the epidermal cells, rhabdites (arrowheads) can be seen in various stages of expansion. Scale bar is 5 um. A cell that specializes in controlled release of one or more substances. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000151 NCIT:C13055 Planarian_Anatomy secretory cell A cell that specializes in controlled release of one or more substances. CL:0000151 Image is an electron micrograph of a viscid gland cell (arrowheads) passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct transports mucus to the outside of the animal, through the secretory pore. Ventral is down and scale bar is 5um. An epithelial cell that has cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000067 PMID:24737865 PMID:28461239 PMID:28807897 ciliated epidermal cell Planarian_Anatomy ciliated epithelial cell An epithelial cell that has cilia. CL:0000067 An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000428 ISBN:9780070316607 PMID:22074376 PMID:27149082 PMID:28072387 PMID:28434803 PMID:29674431 vitellocyte Planarian_Anatomy yolk cell An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. PMID:27149082 extra layer of complexity not needed upon further examination obsolete anatomical compartment subdivision feature true foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx. Planarian_Anatomy PLANA:0000110 pharynx progenitor cell foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx. PMID:24737865 PMID:25254346 Ciliated epithelial cells that assemble into proximal tubules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0006154 PMID:21828097 PMID:29674431 proximal tubule cell Planarian_Anatomy proximal tubule epithelial cell Ciliated epithelial cells that assemble into proximal tubules. PMID:21828097 Image is an electron micrograph of a proximal tubule epithelial cell (arrowheads). N = nucleus. Note the way the cell is wrapped around the cilia, creating the lumen in the middle. Scale bar is 2um. removing all processes. may bring back if PLANA expanded to cover processes. obsolete Schmidtea mediterranea developmental term true 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000479 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Planarian_Anatomy tissue 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. UBERON:0000479 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000467 Planarian_Anatomy anatomical system Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. UBERON:0000467 Nonciliated epithelial cells that assemble into protonephridial distal tubules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:29674431 distal tubule cell Planarian_Anatomy distal tubule epithelial cell Nonciliated epithelial cells that assemble into protonephridial distal tubules. PMID:21828097 Image is an electron micrograph showing a cell (outlined) that is part of the collecting duct. Note how much more stained this cell is, compared to the surrounding ones. Also note the visible lumen of the collecting duct inside the cell where it is white and wrinkled. Scale bar is 1um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000922 Planarian_Anatomy 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. UBERON:0000922 Anatomical structure that is part of an embryo. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000174 UBERON:0002050 Planarian_Anatomy embryonic structure Anatomical structure that is part of an embryo. UBERON:0002050 Nonciliated epithelial cells that assemble into collecting ducts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26057828 Planarian_Anatomy collecting duct epithelial cell Nonciliated epithelial cells that assemble into collecting ducts. PMID:26057828 Image is an electron micrograph showing a cell (outlined) that is part of the collecting duct. Note how much more stained this cell is, compared to the surrounding ones. Also note the visible lumen of the collecting duct inside the cell where it is white and wrinkled. Scale bar is 1um. A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29674432 Planarian_Anatomy terminally differentiated cell A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21852957 PMID:29674432 https://doi.org/10.1101/279364 precursor cell Planarian_Anatomy progenitor cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000034 PMID:17376870 PMID:19805089 PMID:20422023 PMID:20707997 PMID:21937596 PMID:22385657 PMID:23123964 PMID:23318635 PMID:24063805 PMID:24173799 PMID:26062938 PMID:26651295 PMID:26711341 PMID:27013241 PMID:27034770 PMID:27501047 PMID:29124009 https://doi.org/10.1101/279364 Planarian_Anatomy stem cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CL:0000034 A mature sexual reproductive cell having a single set of unpaired chromosomes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000300 PMID:20844018 PMID:23652002 PMID:27149082 PMID:27163480 PMID:27304889 PMID:28434803 Planarian_Anatomy gamete A mature sexual reproductive cell having a single set of unpaired chromosomes. CL:0000300 A cell of the embryo. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0002321 Planarian_Anatomy embryonic cell A cell of the embryo. CL:0002321 The sensory system subserving the sense of vision. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0002104 Planarian_Anatomy visual system The sensory system subserving the sense of vision. UBERON:0002104 Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0001032 Planarian_Anatomy sensory system Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Anatomical system that has as its parts the organs concerned with reproduction. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000990 Planarian_Anatomy reproductive system Anatomical system that has as its parts the organs concerned with reproduction. UBERON:0000990 Ciliated epithelial cells that assemble into the oviduct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22074376 Planarian_Anatomy oviduct epithelial cell Ciliated epithelial cells that assemble into the oviduct. PMID:22074376 Ciliated epithelial cells comprising the sperm ducts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:22074376 Planarian_Anatomy sperm duct epithelial cell Ciliated epithelial cells comprising the sperm ducts. PMID:19022767 PMID:22074376 replacing with UBERON term obsolete anatomical structure true piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29168507 Planarian_Anatomy circular muscle progenitor cell piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. PMID:29168507 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0001048 Planarian_Anatomy primordium Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. UBERON:0001048 removing all processes. may bring back if PLANA expanded to cover processes. obsolete gametogenesis true A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18202849 PMID:7466176 mechanoreceptor Planarian_Anatomy mechanoreceptor cell A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. PMID:18202849 PMID:7466176 piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29168507 Planarian_Anatomy longitudinal muscle progenitor cell piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. PMID:29168507 Cells expressing nanos that are located ventrally in the location that the ovaries form. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with oogonial stem cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17390146 Planarian_Anatomy female primordial germ cell Cells expressing nanos that are located ventrally in the location that the ovaries form. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with oogonial stem cell. PMID:17390146 Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17251262 PMID:26711341 PMID:27502555 PMID:28976975 PMID:29906446 UBERON:0000468 WW intact animal intact planarian whole animal whole body whole worm Planarian_Anatomy whole organism Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria. UBERON:0000468 The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0031099 GOC:mah GOC:pr Wikipedia:Regeneration:(biology) regernative development Planarian_Anatomy regeneration The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). GO:0031099 PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29100657 Planarian_Anatomy Hyman vesicle PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites. PMID:29100657 Image is an immunoelectron micrograph depicting hyman vesicles in the apical side of an epidermal cell. Scale bar is 1um. Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. anterior region of whole organism Planarian_Anatomy PLANA:0000140 anterior region of the whole animal Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. ISBN:9780070316607 OCLC:16809160 PMID:16033796 PMID:16311336 PMID:17251262 PMID:17376870 PMID:17390146 PMID:18063757 PMID:18456843 PMID:18786419 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:19805089 PMID:19852954 PMID:19933103 PMID:20215344 PMID:20422023 PMID:21282632 PMID:21295481 PMID:21356107 PMID:21566185 PMID:21806978 PMID:21828097 PMID:21852957 PMID:21894189 PMID:21937596 PMID:22339734 PMID:22385657 PMID:22439894 PMID:22479207 PMID:22696458 PMID:22899852 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23405188 PMID:23629965 PMID:23903188 PMID:24040508 PMID:24063805 PMID:24367277 PMID:24415944 PMID:24523458 PMID:24950970 PMID:25017721 PMID:25278423 PMID:25356635 PMID:25493551 PMID:25558068 PMID:26062938 PMID:26114597 PMID:26556349 PMID:26651295 PMID:26884331 PMID:27013241 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27150006 PMID:27240733 PMID:27612382 PMID:27612384 PMID:27800171 PMID:28072387 PMID:28287248 PMID:28893948 PMID:29273738 PMID:29547123 PMID:29557542 PMID:29906446 PMID:30143032 PMID:30471994 PMID:30485821 PMID:30962434 Illustration of the anterior region of the whole animal (in green). Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes. dorsal region of whole organism Planarian_Anatomy PLANA:0000141 dorsal region of the whole animal Illustration of the dorsal region of the whole animal (in green). Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail. posterior compartment of the whole animal posterior region of whole organism Planarian_Anatomy PLANA:0000142 posterior region of the whole animal Illustration of the posterior compartement of the whole animal (in green). Compartment along the dorsoventral axis that is below the anteroposterior axis. ventral region of whole organism Planarian_Anatomy PLANA:0000143 ventral region of the whole animal Illustration of the ventral region of the whole animal (in green). The passageway connecting the genital atrium to the copulatory bursa. Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the copulatory bursa before travelling up the oviducts to the tuba. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20967238 PMID:22074376 PMID:25278423 PMID:27149082 Planarian_Anatomy bursal canal The passageway connecting the genital atrium to the copulatory bursa. Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the copulatory bursa before travelling up the oviducts to the tuba. PMID:22074376 The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:19247960 PMID:20967238 PMID:21566185 PMID:22074376 PMID:22899852 PMID:25278423 PMID:27149082 PMID:28072387 PMID:28434803 https://doi.org/10.1101/279364 common gonopore genital pore Planarian_Anatomy gonopore The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. PMID:22074376 A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 NCIT:C12404 PMID:16344473 PMID:17376870 PMID:17390146 PMID:18456843 PMID:19247960 PMID:20844018 PMID:20967238 PMID:22074376 PMID:22318224 PMID:22371573 PMID:23652002 PMID:25278423 PMID:25404302 PMID:27149082 PMID:27163480 PMID:27330085 PMID:28072387 PMID:28434803 PMID:28812561 https://doi.org/10.1101/279364 female gonad Planarian_Anatomy ovary A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. PMID:17376870 Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:17376870 PMID:19247960 PMID:20844018 PMID:20967238 PMID:22074376 PMID:23652002 PMID:25278423 PMID:27149082 PMID:27163480 PMID:28072387 https://doi.org/10.1101/279364 ovovitilline duct Planarian_Anatomy oviduct Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. PMID:22074376 A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20967238 PMID:22074376 PMID:23652002 PMID:25278423 PMID:27074666 PMID:28072387 PMID:28434803 https://doi.org/10.1101/279364 penis penis bulb Planarian_Anatomy penis papilla A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. PMID:22074376 A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:17390146 PMID:19022767 PMID:19247960 PMID:20844018 PMID:20967238 PMID:22074376 PMID:23652002 PMID:25278423 PMID:27149082 PMID:27304889 PMID:28072387 PMID:28434803 ZFA:0001268 https://doi.org/10.1101/279364 seminal duct sperm ductule Planarian_Anatomy sperm duct A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. PMID:19022767 PMID:22074376 A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:17376870 PMID:18456843 PMID:19022767 PMID:19247960 PMID:20844018 PMID:20967238 PMID:22074376 PMID:22318224 PMID:22371573 PMID:23629965 PMID:23652002 PMID:25278423 PMID:25404302 PMID:27149082 PMID:27163480 PMID:27304889 PMID:27330085 PMID:28072387 PMID:28434803 PMID:28812561 PMID:29095551 UBERON:0000473 https://doi.org/10.1101/279364 male gonad testis lobe testis lobule Planarian_Anatomy testis A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. PMID:19022767 replacing with UBERON term obsolete developing anatomical structure true Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Planarian_Anatomy primitive ectoderm cell Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md replace with blastomere only obsolete blastomere compartment true A postnatal stage of Smed development that initiates with hatching and proceeds until sexual maturity is reached. Reproductive structures develop during the juvenile stage. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0034919 Planarian_Anatomy juvenile stage Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy reproductive system product A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:17376870 PMID:18942102 PMID:20967238 PMID:22074376 PMID:22371573 PMID:25278423 PMID:27149082 PMID:28072387 PMID:28434803 PMID:28812561 https://doi.org/10.1101/279364 capsule cocoon Planarian_Anatomy egg capsule A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk. PMID:18942102 Reproductive organ that produces and releases eggs (ovary) or sperm (testis). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:17376870 PMID:17390146 PMID:20844018 PMID:22074376 PMID:22252538 PMID:22371573 PMID:23652002 PMID:27149082 PMID:27163480 PMID:28434803 PMID:28976975 UBERON:0000991 https://doi.org/10.1101/279364 Planarian_Anatomy gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). UBERON:0000991 Cells coexpressing piwi-1 and nanos that are required for male gonad formation. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with spermatogonial stem cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17376870 PMID:17390146 Planarian_Anatomy male primordial germ cell Cells coexpressing piwi-1 and nanos that are required for male gonad formation. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with spermatogonial stem cell. PMID:17376870 PMID:17390146 gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:20844018 PMID:27163480 PMID:27330085 SSC male germline stem cell Planarian_Anatomy spermatogonial stem cell gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. PMID:19022767 PMID:20844018 PMID:27163480 PMID:27330085 An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000020 PMID:23629965 PMID:27163480 PMID:27330085 https://doi.org/10.1101/279364 spermatogonial cell Planarian_Anatomy spermatogonium An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. PMID:27163480 PMID:27330085 A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000017 PMID:17376870 PMID:20844018 PMID:22074376 PMID:25278423 PMID:25404302 PMID:27163480 PMID:27304889 PMID:27330085 PMID:29095551 primary spermatocyte Planarian_Anatomy spermatocyte A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. PMID:27330085 A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000018 PMID:17376870 PMID:20844018 PMID:22074376 PMID:25278423 PMID:25404302 PMID:27163480 PMID:27304889 PMID:27330085 Planarian_Anatomy spermatid A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. CL:0000018 A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:23652002 PMID:25278423 PMID:27149082 PMID:27163480 PMID:27330085 female germ cell female germline cell female germline stem cell oogonial stem cell ovarian germline stem cell Planarian_Anatomy oogonial stem cell A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. PMID:19022767 PMID:20844018 Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M ISBN:9780070316607 PMID:18942102 PMID:20967238 PMID:22074376 PMID:23652002 PMID:25278423 PMID:27149082 shell gland Planarian_Anatomy cement gland Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk. ASIN:B000M4NK9M PMID:18942102 PMID:22074376 PMID:27149082 removing all processes. may bring back if PLANA expanded to cover processes. obsolete oviparity true removing all processes. may bring back if PLANA expanded to cover processes. obsolete cross-fertilization true 1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000535 Planarian_Anatomy germ cell 1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex. BTO:0000535 A male germ cell is a germ cell that supports male gamete production. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000015 PMID:23652002 PMID:27304889 PMID:27330085 Planarian_Anatomy male germ cell A male germ cell is a germ cell that supports male gamete production. CL:0000015 Female germ cell is a germ cell that supports female gamete production. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000021 Planarian_Anatomy female germ cell Female germ cell is a germ cell that supports female gamete production. CL:0000021 A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:20844018 PMID:22074376 PMID:25278423 PMID:27149082 PMID:27163480 PMID:28434803 Planarian_Anatomy tuba A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:16932928 PMID:17390146 PMID:18942102 PMID:19247960 PMID:22074376 PMID:23652002 PMID:27149082 PMID:27163480 PMID:27501047 PMID:28072387 PMID:28434803 https://doi.org/10.1101/279364 vitellaria vitellarium yolk gland Planarian_Anatomy vitelline gland Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. PMID:16932928 PMID:18942102 PMID:27149082 Accessory reproductive structures involved in copulation, egg capsule development and laying. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16344473 PMID:17376870 PMID:17390146 PMID:19247960 PMID:20967238 PMID:22074376 PMID:23652002 PMID:27149082 PMID:27163480 PMID:28434803 copulatory complex Planarian_Anatomy copulatory apparatus Accessory reproductive structures involved in copulation, egg capsule development and laying. PMID:22074376 An organ that receives and stores sperm from mating partners. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20967238 PMID:22074376 PMID:25278423 https://doi.org/10.1101/279364 bursa male antrum Planarian_Anatomy copulatory bursa An organ that receives and stores sperm from mating partners. PMID:22074376 Glandular pouches adjoining the sperm ducts which produce seminal fluid. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C12787 PMID:19022767 PMID:22074376 UBERON:0000998 Planarian_Anatomy seminal vesicle Glandular pouches adjoining the sperm ducts which produce seminal fluid. PMID:19022767 PMID:22074376 A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, andundergo morphogenesis to produce mature sperm. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20844018 PMID:27163480 PMID:27304889 PMID:27330085 PMID:29095551 https://doi.org/10.1101/279364 Planarian_Anatomy round spermatid A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, andundergo morphogenesis to produce mature sperm. PMID:27163480 PMID:27330085 Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20844018 PMID:27163480 PMID:27304889 PMID:27330085 PMID:29095551 elongating spermatid Planarian_Anatomy elongate spermatid Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. PMID:27163480 PMID:27330085 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FMA:83673 Planarian_Anatomy oogonial cell An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 Any collection of muscles that is part of a body wall [Automatically generated definition]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BSA:0000058 BTO:0001863 FMA:86931 PMID:19048075 PMID:19174194 PMID:21828097 PMID:22385657 PMID:24992682 PMID:27063937 PMID:27074666 PMID:28171748 PMID:29100657 PMID:29547123 PMID:29674431 PMID:29674432 PMID:30471994 PMID:30962434 UBERON:0004462 WBbt:0005813 BWM body muscle body wall muscle body wall muscles body-wall muscle body-wall musculature muscle layer surrounding the body wall Planarian_Anatomy body wall musculature Any collection of muscles that is part of a body wall [Automatically generated definition]. UBERON:0004462 http://purl.obolibrary.org/obo/Image is an electron micrograph of the dorsal epidermis, basal lamina (BL), and underlying body wall musculature. Three types of muscle cells have been color coded form superficial to deep_ Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. Pharynx muscle fibers running anteroposterior (proximal to distal). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M pharyngeal longitudinal muscle cell pharyngeal longitudinal muscle fiber pharynx longitudinal muscle fiber Planarian_Anatomy pharynx longitudinal muscle cell Pharynx muscle fibers running anteroposterior (proximal to distal). ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. The inner longitudinal muscle (arrowheads) is immediately deep to the inner circular muscle of the pharynx. Magenta = circular; green = longitudinal; red = radial. Scale bar is 2 um. replacing with UBERON term obsolete anatomical cavity true replacing with UBERON term obsolete anatomical entity true replacing with UBERON term obsolete immaterial anatomical entity true replacing with UBERON term obsolete anatomical point true replacing with UBERON term obsolete anatomical space true Anatomical space enclosed by the pharynx inner epithelium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17251262 PMID:26711341 PMID:27502555 PMID:28976975 PMID:29906446 UBERON:0000468 cavity of pharynx pharyngeal lumen pharynx cavity Planarian_Anatomy pharynx lumen Anatomical space enclosed by the pharynx inner epithelium. UBERON:0000468 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Cavity of pharynx is indicated by arrows. Scale bar = 250um An anatomical space that is surrounded by a digestive tract. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17553481 PMID:21664348 PMID:21828097 PMID:28072387 UBERON:0006909 digestive system lumen gut cavity lumen of digestive tract Planarian_Anatomy digestive tract lumen An anatomical space that is surrounded by a digestive tract. PMID:21664348 Depicted by field contains hematoxylin and eosin staining on a coronal section of a asexual adult animal. The lumen of the digestive tract is indicated by arrows. Scale bar = 250um The orifice that connects the mouth to the exterior of the body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17670787 PMID:29674431 PMID:30399335 UBERON:0000166 pharyngeal mouth opening pharynx opening Planarian_Anatomy oral opening The orifice that connects the mouth to the exterior of the body. UBERON:0000166 Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 pharnygeal cavity pharyngeal pouch cavity Planarian_Anatomy pharynx pouch cavity Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch. OCLC:16809160 Depicted by field contains hematoxylin and eosin stainingcoronal section section of a asexual adult animal. Parapharyngeal pouch cavity is indicated by arrows. Scale bar = 250um The apical surface of the single layered epidermis that is in contact with the environment. apical surface of epidermis Planarian_Anatomy PLANA:0000409 apical surface of the epidermis Electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The apical epidermis surface is noted with magenta arrows. Scale bar is 5um. The basal surface of the epidermis in direct contact with the basal lamina. basal surface of epidermis Planarian_Anatomy PLANA:0000410 basal surface of the epidermis Electron micrograph of the dorsal epidermis in a transverse plane. The basal epidermis surface is noted with magenta arrows. Scale bar is 5um. The surface of the gastrodermis in contact with the gut lumen. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 lumen gut surface Planarian_Anatomy gastrodermis surface The surface of the gastrodermis in contact with the gut lumen. PMID:21664348 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the anterior primary gut branch. The lumen gut surface is marked by black arrows. Scale bar is 200um. The epithelial surface lining the interior of the pharynx, facing the lumen. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0001731 pharyngeal inner epidermis surface pharyngeal inner epithelial surface pharyngeal lumen epithelial surface pharynx inner epidermis surface pharynx lumen epithelial surface Planarian_Anatomy pharynx inner epithelium surface Image is an electron micrograph of a transverse section through the pharynx. An epidermal cell, a part of the inner epithelial layer, has been marked with arrowheads. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um. Epithelial surface covering the outside of the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:24120894 PMID:29865769 doi:10.1002/jmor.1052060308 pharyngeal outer epidermis surface pharyngeal outer epithelial surface pharynx outer epidermis surface pharynx outer side Planarian_Anatomy pharynx outer epithelium surface Epithelial surface covering the outside of the pharynx. PMID:29865769 doi:10.1002/jmor.1052060308 Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. The outer epithelium has been labeled with arrowheads. Immediately deep to the outer epithelial layer of the pharynx is musculature that has been colored. Red = circular; blue = longitudinal. Scale bar is 2 um. The surface of the parapharyngeal pouch facing the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 pharyngeal pouch surface pharynx pouch surface Planarian_Anatomy pharynx pouch epithelial surface The surface of the parapharyngeal pouch facing the pharynx. OCLC:16809160 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. Anterior is up. The parapharyngeal pouch surface is marked by black arrows. Scale bar is 200um. replacing with UBERON term obsolete organism subdivision true Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy definitive organism subdivision The head is the anterior-most division of the body [GO]. A three dimensional compartment bounded by the anterior margin or the head and the posterior boundary of the cephalic ganglia (brain). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000033 head Planarian_Anatomy head region Depicted by field contains diagram representation of body region. Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:17251262 PMID:18202849 PMID:18287199 PMID:21295481 PMID:21852957 PMID:22339734 PMID:23318641 PMID:24120894 PMID:24922054 PMID:26556349 PMID:27063937 PMID:27150006 PMID:28216315 PMID:28245923 PMID:28287248 PMID:28893948 PMID:29547123 PMID:29674431 https://doi.org/10.1101/279364 neck pre-pharyngeal region pre-pharynx region Planarian_Anatomy prepharyngeal region Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx. OCLC:16809160 Depicted by field contains diagram representation of body region. Region of the animal lateral to and surrounding the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22125640 PMID:25956527 PMID:26651295 PMID:28807897 PMID:29674431 PMID:30143032 para-pharyngeal parapharyngeal peri-pharyngeal peripharyngeal region trunk Planarian_Anatomy Trunk is a synonym here because the parapharyngeal region is always contained in a trunk fragment. However, a trunk fragment may also contain some neck and some tail. parapharyngeal region Depicted by field contains diagram representation of body region. Caudal region, beginning at the mouth and ending at posterior pole. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0002415 tail Planarian_Anatomy tail region Depicted by field contains diagram representation of body region. Medial region of the tail; the parenchymal space between the posterior primary gut branches. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy tail stripe Medial region of the tail; the parenchymal space between the posterior primary gut branches. PMID:29906446 Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy embryonic subdivision replacing with UBERON term obsolete material anatomical entity true extra layer of complexity not needed upon further examination obsolete definitive anatomical structure true replacing with UBERON term obsolete acellular anatomical structure true An anatomical structure that has more than one cell as a part. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0010000 Planarian_Anatomy multicellular anatomical structure An anatomical structure that has more than one cell as a part. UBERON:0010000 Total musculature of the planarian body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:17942485 PMID:20707997 PMID:24950970 PMID:27068018 PMID:28137894 UBERON:0001015 muscular system musculature Planarian_Anatomy musculature system Total musculature of the planarian body. UBERON:0001015 A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0006347 PMID:15866156 PMID:15972844 PMID:16033796 PMID:16311336 PMID:16344473 PMID:16890156 PMID:17251262 PMID:17376870 PMID:17390146 PMID:17553481 PMID:17670787 PMID:17905225 PMID:18063755 PMID:18202849 PMID:18287199 PMID:18456843 PMID:18786419 PMID:19048075 PMID:19174194 PMID:19247960 PMID:19564616 PMID:19766622 PMID:19805089 PMID:20040488 PMID:20215344 PMID:20223763 PMID:20599901 PMID:20844018 PMID:21179477 PMID:21179478 PMID:21282632 PMID:21356107 PMID:21458439 PMID:21566185 PMID:21664348 PMID:21747960 PMID:21806978 PMID:21852957 PMID:21894189 PMID:21937596 PMID:22125640 PMID:22223737 PMID:22252538 PMID:22252539 PMID:22318224 PMID:22339734 PMID:22371573 PMID:22385657 PMID:22411224 PMID:22427692 PMID:22439894 PMID:22445864 PMID:22451003 PMID:22479207 PMID:22543868 PMID:22549959 PMID:22696458 PMID:22884275 PMID:22899852 PMID:23079596 PMID:23235145 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23629965 PMID:23903188 PMID:23954785 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24367277 PMID:24415944 PMID:24523458 PMID:24704339 PMID:24737865 PMID:24903754 PMID:24922054 PMID:24992682 PMID:25017721 PMID:25254346 PMID:25278423 PMID:25356635 PMID:25956527 PMID:26057828 PMID:26114597 PMID:26457503 PMID:26459857 PMID:26516985 PMID:26525673 PMID:26556349 PMID:26618653 PMID:26651295 PMID:26884331 PMID:27013241 PMID:27063937 PMID:27068018 PMID:27122174 PMID:27149082 PMID:27150006 PMID:27163480 PMID:27304889 PMID:27441386 PMID:27501047 PMID:27502555 PMID:27523733 PMID:27542689 PMID:27551436 PMID:27606067 PMID:27612384 PMID:27654173 PMID:27864883 PMID:28072387 PMID:28137894 PMID:28171748 PMID:28216315 PMID:28287248 PMID:28292427 PMID:28461239 PMID:28686611 PMID:28757112 PMID:28893948 PMID:29095551 PMID:29100657 PMID:29124009 PMID:29273738 PMID:29291974 PMID:29364871 PMID:29547123 PMID:29557542 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30143032 PMID:30194301 PMID:30237141 PMID:30282036 PMID:30297872 PMID:30471994 PMID:30485821 PMID:30729158 PMID:30962434 https://doi.org/10.1101/279364 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md ASC adult somatic stem cell adult stem cell cycling cell irradiation-sensitive cell neoblast compartment pASC planarian adult stem cell planarian stem cell somatic stem cell Planarian_Anatomy neoblast A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. PMID:16311336 PMID:21566185 PMID:22899852 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md Image is an electron micrograph showing a neoblast undergoing mitotic telophase (outlined). The condensed chromatin is visible toward the left side of the cell and has been outlined by the nuclear envelope. Scale bar is 1um. A part of an epithelial cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy epithelial cell component Anatomical structure that performs a specific function or group of functions. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29547123 UBERON:0000062 Planarian_Anatomy organ Anatomical structure that performs a specific function or group of functions. UBERON:0000062 replacing with UBERON term obsolete regenerating anatomical structure true replacing with GO term obsolete cellular component true A decussation of the diencephalon where the fibers of the optic nerve cross https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 AAO:0010622 BAMS:DC BAMS:OC BAMS:och BAMS:ox BM:Tel-OCX C90609 DHBA:10644 DMBA:17783 EHDAA2:0001302 EHDAA:10227 EMAPA:17603 FMA:62045 GAID:832 HBA:9310 MA:0001098 MBA:117 MESH:D009897 NCIT:C90609 Optic:chiasm PMID:15866156 PMID:16033796 PMID:17553481 PMID:17905225 PMID:18202849 PMID:18466009 PMID:19048075 PMID:19211673 PMID:21282632 PMID:22339734 PMID:22445864 PMID:25356635 PMID:25493551 PMID:26618653 PMID:27800171 PMID:28495872 PMID:30194301 PMID:30962434 TAO:0000556 UBERON:0000959 UMLS:C0029126 VHOG:0000190 XAO:0004071 ZFA:0000556 birnlex:1416 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 http://linkedlifedata.com/resource/umls/id/C0029126 http://www.snomedbrowser.com/Codes/Details/244453006 chiasm chiasma chiasma nervorum opticorum chiasma opticum decussation of optic nerve fibers optic chiasm (Rufus of Ephesus) optic chiasma optic chiasmata Planarian_Anatomy optic chiasm A decussation of the diencephalon where the fibers of the optic nerve cross PMID:18466009 A bundle of nerve fibers connecting the two cephalic ganglia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000935 anterior brain commissure Planarian_Anatomy anterior commissure A bundle of nerve fibers connecting the two cephalic ganglia. UBERON:0000935 Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:12128224 PMID:18287199 PMID:18466009 PMID:20422023 PMID:21282632 PMID:21806978 PMID:24922054 PMID:25254346 PMID:27612384 PMID:29674431 PMID:30399335 PMID:4452894 PMID:9493832 bilateral cephalic ganglia branch brain branch cephalic brain branch cephalic branch lateral brain branch Planarian_Anatomy lateral branch Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. PMID:12128224 PMID:18466009 PMID:27612384 PMID:4452894 PMID:9493832 A cell that performs a sensory function. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0001037 ISBN:9780070316607 NCIT:C12628 PMID:17251262 PMID:17942485 Planarian_Anatomy sensory cell Neurons that express choline acetyltransferase. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20338223 PMID:21566185 PMID:23652002 PMID:23903188 PMID:24131630 PMID:24173799 PMID:24950970 PMID:25356635 PMID:26525673 PMID:27163480 PMID:27612382 PMID:27864883 PMID:28126842 PMID:28137894 PMID:29291981 PMID:30143032 PMID:30194301 acetylcholinergic neuron Planarian_Anatomy cholinergic neuron Neurons that express choline acetyltransferase. PMID:20338223 Neurons that express glutamine decarboxylase. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000617 FBbt:00007228 PMID:18440152 PMID:23903188 PMID:24131630 PMID:24173799 PMID:24922054 PMID:24950970 PMID:25356635 PMID:26525673 PMID:27864883 PMID:28216315 PMID:29291981 PMID:30194301 PMID:30485821 WBbt:0005190 ZFA:0009276 GABA neuron GABAergic cell gabanergic neuron inhibitory neuron Planarian_Anatomy GABAergic neuron Neurons that express glutamine decarboxylase. PMID:18440152 Plexus of nerves located in the pharynx comprised of inner and outer wall rings. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16033796 PMID:17905225 PMID:20967238 PMID:23250205 PMID:23297191 nerve ganglia of pharynx neural plexus of the pharynx pharyngeal nerve plexus pharyngeal nerve ring pharyngeal nervous system pharyngeal neural plexus pharynx nerve ring Planarian_Anatomy pharynx nerve plexus Plexus of nerves located just between the epidermis and the body wall musculature. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27612384 doi:10.1002/jmor.1051550208 Planarian_Anatomy subepidermal nerve plexus Plexus of nerves that innervate the body wall musculature. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy submuscular nerve plexus A thin net of single nerve fibers located around the gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17999079 doi.org/10.1002/jmor.1051550208 Planarian_Anatomy gastrodermal plexus A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0005268 C12617 CALOHA:TS-2403 FBbt:00005139 FMA:261269 GAID:740 MESH:D019581 NIF:Subcellular:sao205380252 PMID:16033796 PMID:17553481 PMID:24173799 PMID:24950970 PMID:25356635 PMID:27612382 PMID:27612384 PMID:29291974 PMID:29291981 UBERON:0002606 UMLS:C0228081 birnlex:1142 http://en.wikipedia.org/wiki/Neuropil http://linkedlifedata.com/resource/umls/id/C0228081 http://www.snomedbrowser.com/Codes/Details/67146008 central neuropil cephalic ganglia neuropil neuropilus Planarian_Anatomy neuropil A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. PMID:27612384 Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M PMID:29674431 epithelial pharynx lining outer pharyngeal epidermis outer pharyngeal epithelium outer pharynx epidermis outer pharynx epithelium Planarian_Anatomy pharynx outer epithelium Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. ASIN:B000M4NK9M Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M ISBN:9780070316607 outer circular muscle layer pharyneal outer circular muscle fiber pharyngeal outer circular muscle cell pharynx outer circular muscle fiber Planarian_Anatomy pharynx outer circular muscle cell Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. The outer circular muscle (arrowheads) is immediately deep to the outer longitudinal muscle of the pharynx. Red = circular; blue = longitudinal. Scale bar is 2 um. Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M inner circular muscle layer pharyngeal inner circular muscle cell pharyngeal inner circular muscle fiber pharynx inner circular muscle fiber Planarian_Anatomy pharynx inner circular muscle cell Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. The pharynx lumen it to the left. The inner circular muscle (arrowheads) is immediately deep to the inner epithelial layer of the pharynx. Magenta = circular; green = longitudinal; red = radial. Scale bar is 2 um. Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M ISBN:9780070316607 inner longitudinal muscle layer pharyngeal inner longitudinal muscle cell pharyngeal inner longitudinal muscle fiber pharynx inner longitudinal muscle fiber Planarian_Anatomy pharynx inner longitudinal muscle cell Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. The inner longitudinal muscle (arrowheads) is immediately deep to the inner circular muscle of the pharynx. Magenta = circular; green = longitudinal; red = radial. Scale bar is 2 um. Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M pharyngeal outer longitudinal muscle cell pharyngeal outer longitudinal muscle fiber pharynx outer longitudinal muscle fiber Planarian_Anatomy pharynx outer longitudinal muscle cell Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. The outer longitudinal muscle (arrowheads) is immediately deep to the outer epithelium of the pharynx. Red = circular; blue = longitudinal. Scale bar is 2 um. Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M PMID:28072387 pharyngeal radial muscle cell pharyngeal radial muscle fiber pharynx radial muscle fiber radial muscle cell radial muscle fiber Planarian_Anatomy pharynx radial muscle cell Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um. The total musculature within the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:26904543 PMID:29674432 UBERON:0004467 pharyngeal musculature pharynx muscle pharynx musculature Planarian_Anatomy pharynx musculature The total musculature within the pharynx. PMID:26904543 Ring of the pharynx nerve plexus that is proximal to the lumen. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 inner pharyngeal nerve ring inner pharynx nerve ring pharynx inner nerve plexus Planarian_Anatomy pharynx inner nerve plexus Ring of the pharynx nerve plexus that is proximal to the lumen. ISBN:9780070316607 Image is an electron micrograph of a transverse section through the pharynx. Neuronal cells/tissue are marked with arrowheads. The inner nerve plexus is immediately deep to the inner longitudinal musculature. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um. Ring of the pharynx nerve plexus that is proximal to the exterior surface. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:27612384 doi:10.1002/jmor.1051550208 outer pharyngeal nerve ring outer pharynx nerve plexus outer pharynx nerve ring Planarian_Anatomy pharynx outer nerve plexus Ring of the pharynx nerve plexus that is proximal to the exterior surface. ISBN:9780070316607 Image is an electron micrograph of a transverse section through the pharynx.The pharynx pouch cavity is at the top. The outer nerve plexus (arrowheads) is immediately deep to the outer circular muscle of the pharynx. Red = circular; blue = longitudinal. Scale bar is 2 um. Neurons that express the neurotransmitter serotonin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000850 FBbt:00005133 PMID:23903188 PMID:24131630 PMID:24173799 PMID:24922054 PMID:24950970 PMID:25356635 PMID:26525673 PMID:27864883 PMID:28137894 PMID:29357350 PMID:30194301 WBbt:0006837 ZFA:0009361 serotonergic cell Planarian_Anatomy serotonergic neuron Neurons that express the neurotransmitter serotonin. PMID:17624455 A neuron that expresses the neurotransmitter dopamine. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000700 FBbt:00005131 PMID:17565705 PMID:21458439 PMID:23250205 PMID:23903188 PMID:24131630 PMID:24173799 PMID:24950970 PMID:25356635 PMID:27864883 PMID:30194301 WBbt:0006746 ZFA:0009301 Planarian_Anatomy dopaminergic neuron A neuron that expresses the neurotransmitter dopamine. PMID:17565705 Neurons that express the biogenic amine octopamine. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00007364 PMID:18926867 Planarian_Anatomy octopaminergic neuron Neurons that express the biogenic amine octopamine. PMID:18926867 Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20865784 WBbt:0006850 Planarian_Anatomy secretory system Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. PMID:20865784 Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly throughepithelial cells and form a secretory pore at the surface. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CLYH:1000090 ISBN:9780070316607 PMID:19247960 PMID:20865784 PMID:23318635 PMID:24737865 PMID:28807897 PMID:29674431 PMID:30962434 WBbt:0003670 secretory gland cell Planarian_Anatomy gland cell Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly throughepithelial cells and form a secretory pore at the surface. PMID:20865784 Image is an electron micrograph depicting a portion of a gland cell (arrowheads). Note the nucleus surrounded by endoplasmic reticulum and the dark mucus granules that fill the long cytoplasmic projection. Scale bar is 2 um. The opening by which the gland cells secrete mucus to the exterior of the animal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20865784 pore Planarian_Anatomy secretory pore The opening by which the gland cells secrete mucus to the exterior of the animal. PMID:20865784 Image is an electron micrograph of a viscid gland cell passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct transports mucus to the outside of the animal, through the secretory pore (arrowhead). Ventral is down and scale bar is 5um. One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsoventral border of the animal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20865784 eosinophilic gland cell erythrophilous gland cell Planarian_Anatomy acidophilic gland cell One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsoventral border of the animal. PMID:20865784 One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20865784 PMID:23405188 cyanophilic gland cell cyanophilic secretory cell cyanophilous gland Planarian_Anatomy basophilic gland cell One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. PMID:20865784 replacing with CARO term obsolete anatomical line true replacing with BSPO term obsolete anatomical plane true let odk import from BSPO if needed replacing with UBERON term obsolete plane of autonomy obsolete plane of autotomy true Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 AEO:0000138 BTO:0000205 C12929 EHDAA2:0003138 EHDAA:3780 FMA:5901 ISBN:9780070316607 MA:0002407 PMID:16311336 PMID:21566185 PMID:22899852 UBERON:0001810 UMLS:C0501403 http://en.wikipedia.org/wiki/Nervous:system:plexus http://linkedlifedata.com/resource/umls/id/C0501403 http://www.snomedbrowser.com/Codes/Details/122455009 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md neural network neural plexus plexus Planarian_Anatomy nerve plexus Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. UBERON:0001810 we will just use commissural neuron moving forward obsolete nervous system commissure true any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0005970 Planarian_Anatomy brain commissure any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain UBERON:0005970 A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 AEO:0000192 BTO:0001638 CARO:0000010 EFO:0003658 FMA:50705 PMID:15866156 PMID:15972844 PMID:16033796 PMID:16890156 PMID:17251262 PMID:17553481 PMID:17670787 PMID:17905225 PMID:17942485 PMID:18063755 PMID:18202849 PMID:18456843 PMID:19048075 PMID:19174194 PMID:19247960 PMID:19766622 PMID:19852954 PMID:20040488 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20599901 PMID:21179478 PMID:21295481 PMID:21295483 PMID:21356107 PMID:21458439 PMID:21566195 PMID:21664348 PMID:21806978 PMID:21937596 PMID:22125640 PMID:22252539 PMID:22318224 PMID:22411224 PMID:22439894 PMID:22451003 PMID:22479207 PMID:22549959 PMID:22884275 PMID:22899852 PMID:23235145 PMID:23250205 PMID:23318641 PMID:23405188 PMID:23629965 PMID:23652002 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24173799 PMID:24415944 PMID:24523458 PMID:24704339 PMID:24922054 PMID:25254346 PMID:25558068 PMID:25725068 PMID:25772472 PMID:25956527 PMID:26062938 PMID:26459857 PMID:26525673 PMID:26711341 PMID:26884331 PMID:27013241 PMID:27068018 PMID:27240733 PMID:27542689 PMID:27551436 PMID:27606067 PMID:27612382 PMID:27612384 PMID:28126842 PMID:28137894 PMID:28171748 PMID:28216315 PMID:28461239 PMID:28757112 PMID:28807897 PMID:28893948 PMID:29158443 PMID:29273738 PMID:29291974 PMID:29291981 PMID:29357350 PMID:30194301 PMID:30237141 PMID:30282036 PMID:30297872 PMID:30471994 PMID:30485821 PMID:30729158 TAO:0001270 UBERON:0005306 XAO:0004060 https://doi.org/10.1101/279364 ncithesaurus:Blastemal_Cell regeneration blastema regenerative blastema Planarian_Anatomy blastema A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise. UBERON:0005306 replacing with UBERON term obsolete anatomical boundary true replacing with UBERON term obsolete anatomical junction true replacing duplicate PLANA term obsolete main body axis true A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CALOHA:TS-2035 CL:0000000 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 Planarian_Anatomy The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CL:0000000 PLANA:0000500 child terms moved to cellular component (GO:0005575) term and we think better serves interoperability and searchability obsolete cell part true A prolongation or process extending from a cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0042995 Planarian_Anatomy cell projection A prolongation or process extending from a cell. GO:0042995 A cell projection supported by an assembly of actin filaments. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0098858 Planarian_Anatomy actin-based cell projection A cell projection supported by an assembly of actin filaments. GO:0098858 inadvertently duplicated, going with ID that is best annotated obsolete cilium true Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005902 Planarian_Anatomy microvillus Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. GO:0005902 Image is an electron micrograph depicting a portion of the outer epithelium of the pharynx. Microvilli on the left hand of the image have been labeled with arrowheads. To the right of the microvilli are larger cilia. Note the difference in width and length. Scale bar is 2 um. Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044291 Planarian_Anatomy cell-cell contact zone Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions. GO:0044291 A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0030054 PMID:20511647 PMID:21458439 Planarian_Anatomy cell junction A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. GO:0030054 Image is an electron micrograph of two outer epidermal cells of the pharynx. There is an adherens junction (arrowheads) between two cells. Scale bar is 0.5 um. A cell junction that forms a connection between two or more cells in a multicellular organism; this excludes direct cytoplasmic junctions such as ring canals. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005911 Planarian_Anatomy cell-cell junction A cell junction that forms a connection between two or more cells in a multicellular organism; this excludes direct cytoplasmic junctions such as ring canals. GO:0005911 Image is an electron micrograph of two outer epidermal cells of the pharynx. There is an adherens junction (arrowheads) between two cells. Scale bar is 0.5 um. The attachment of one cell to another cell via adhesion molecules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0098609 Planarian_Anatomy cell-cell adhesion The attachment of one cell to another cell via adhesion molecules. GO:0098609 Image is an electron micrograph of two outer epidermal cells of the pharynx. There is an adherens junction (arrowheads) between two cells. Scale bar is 0.5 um. Any constituent part of 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044424 Planarian_Anatomy intracellular part Any constituent part of 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. GO:0044424 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005737 PMID:16890156 PMID:28976975 Planarian_Anatomy cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures GO:0005737 Image is an electron micrograph depicting a portion of a cell. Outside of the nucleus (N), the arrowheads mark areas of cytoplasm, which appears as a mottled gray filling. Scale bar is 0.5um. term is not needed. obsolete acidophilic cytoplasm true term is not needed. obsolete basophilic cytoplasm true Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044444 Planarian_Anatomy cytoplasmic part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0044444 Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044433 Planarian_Anatomy cytoplasmic vesicle part Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. GO:0044433 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005773 Planarian_Anatomy vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GO:0005773 term is not needed. obsolete cytoskeleton organization true 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043229 Planarian_Anatomy 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. GO:0043229 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043232 Planarian_Anatomy intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes GO:0043232 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0016020 Planarian_Anatomy membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GO:0016020 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0098588 Planarian_Anatomy bounding membrane of organelle Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. GO:0098588 Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044425 Planarian_Anatomy membrane part Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO:0044425 Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044459 Planarian_Anatomy plasma membrane part Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0044459 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0031090 Planarian_Anatomy organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GO:0031090 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043226 Planarian_Anatomy 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. GO:0043226 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043227 Planarian_Anatomy 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. GO:0043227 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043231 Planarian_Anatomy 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. GO:0043231 A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005794 Planarian_Anatomy Golgi apparatus A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. GO:0005794 Image is an electron micrograph showing golgi bodies (arrowheads). Many secretory vesicles can be seen, as well as rough endoplasmic reticulum on the right side of the micrograph. Scale bar is 0.2 um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005634 ISBN:9780070316607 PMID:23405188 PMID:25404302 PMID:26457503 PMID:28976975 PMID:29100657 PMID:29357350 Planarian_Anatomy 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. GO:0005634 Image is an electron micrograph of several nuclei (N) close to and a part of the dorsal epidermis. Note how the epidermal cell nuclei appear more wrinkled and have stained differently than the cells lying beneath the basal lamina (BL). Scale bar is 2 um. A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0099503 Planarian_Anatomy secretory vesicle A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GO:0099503 Image is an electron micrograph depicting two golgi bodies and accompanying secratory vesicles. A few have been labeled with arrowheads. Scale bar is 200 nm. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043228 Planarian_Anatomy non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GO:0043228 Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044428 Planarian_Anatomy nuclear part Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GO:0044428 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044428 Planarian_Anatomy nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. GO:0044428 Image is an electron micrograph depicting a nucleus. Inside, the nucleolus has been labeled with arrowheads. Scale bar is 1 um. The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0000785 Planarian_Anatomy chromatin The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome. GO:0000785 Image is an electron micrograph showing a mitotic cell with condensed chromatin (arrowhead). Scale bar is 1um. A compact and highly condensed form of chromatin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0000792 Planarian_Anatomy heterochromatin A compact and highly condensed form of chromatin. GO:0000792 A dispersed and relatively uncompacted form of chromatin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0000791 Planarian_Anatomy euchromatin A dispersed and relatively uncompacted form of chromatin. GO:0000791 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ https://www.worldcat.org/search?q=bn%3A0198506732 ] https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005840 Planarian_Anatomy ribosome An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ https://www.worldcat.org/search?q=bn%3A0198506732 ] GO:0005840 Image is an electron micrograph depicting ribosomes (arrowheads) in two separate cells. They can be seen as small dots in the cytoplasm and associating with the rough endoplasmic reticulum in the cell in the bottom of the micrograph. Scale bar is 200 nm. A group of axons linking two or more neuropils and having a common origin, termination https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22884275 PMID:24950970 PMID:28137894 UBERON:0001018 axon bundle axon bundles axon tracts Planarian_Anatomy axon tract A group of axons linking two or more neuropils and having a common origin, termination UBERON:0001018 A cell whose function is determined by its response to an electric signal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000393 Planarian_Anatomy electrically responsive cell A cell whose function is determined by its response to an electric signal. CL:0000393 A cell that initiates an electrical signal and passes that signal to another cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000404 Planarian_Anatomy electrically signaling cell A cell that initiates an electrical signal and passes that signal to another cell. CL:0000404 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27612382 PMID:27800171 UBERON:0001021 nerve bundle nerves neural subtree peripheral nerve Planarian_Anatomy nerve 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. UBERON:0001021 A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CARO:0001001 UBERON:0000122 Planarian_Anatomy neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 A neuron which conveys sensory information centrally from the periphery. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000526 FMA:87653 input neuron Planarian_Anatomy afferent neuron A neuron which conveys sensory information centrally from the periphery. CL:0000526 A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000103 FMA:67282 ISBN:9780070316607 PMID:16033796 PMID:18202849 PMID:21458439 PMID:22445864 PMID:24173799 PMID:25493551 bipolar nerve cell Planarian_Anatomy bipolar neuron A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. CL:0000103 A neuron that has an axon which crosses the midline. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000678 PMID:22339734 Planarian_Anatomy commissural neuron A neuron that has an axon which crosses the midline. CL:0000678 A neuron which sends impulses peripherally to activate muscles or secretory cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000527 output neuron Planarian_Anatomy efferent neuron A neuron which sends impulses peripherally to activate muscles or secretory cells. CL:0000527 A motor neuron that is capable of directly inducing muscle contraction. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0008014 PMID:25356635 excitatory neuron Planarian_Anatomy In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. excitatory motor neuron A motor neuron that is capable of directly inducing muscle contraction. CL:0008014 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0003811 CL:0000099 FBbt:00005125 FMA:67313 WBbt:0005113 Planarian_Anatomy interneuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. CL:0000099 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0001037 CL:0000101 FBbt:00005124 FMA:84649 WBbt:0005759 Planarian_Anatomy sensory neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. CL:0000101 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000312 CL:0000100 FMA:83617 WBbt:0005409 motoneuron Planarian_Anatomy motor neuron An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. CL:0000100 Neuronal cells which synthesize, store and release neurohormones. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000381 FBbt:00005130 PMID:24173799 neurosecretory cell Planarian_Anatomy neurosecretory neuron Neuronal cells which synthesize, store and release neurohormones. CL:0000381 Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0011103 Planarian_Anatomy sympathetic neuron Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. CL:0011103 Neuron with one neurite that extends from the cell body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000106 FMA:67278 ISBN:9780070316607 PMID:18499291 PMID:24173799 unipolar nerve cell Planarian_Anatomy unipolar neuron Neuron with one neurite that extends from the cell body. CL:0000106 Neuron with an axon and two or more dendrites. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000104 FMA:67287 ISBN:9780070316607 PMID:18499291 multipolar nerve cell Planarian_Anatomy multipolar neuron Neuron with an axon and two or more dendrites. CL:0000104 Cells that are in close proximity to neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000130 Planarian_Anatomy neuron associated cell (sensu Nematoda and Protostomia) Cells that are in close proximity to neurons. CL:0000130 Any neuron that is part of a central nervous system. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:2000029 Planarian_Anatomy central nervous system neuron Any neuron that is part of a central nervous system. CL:2000029 Any neuron that is part of a peripheral nervous system. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:2000032 PMID:23123964 PMID:23954785 PMID:25254346 PMID:26711341 PMID:29184198 peripheral neuron Planarian_Anatomy peripheral nervous system neuron Any neuron that is part of a peripheral nervous system. CL:2000032 A neruon whose cell body is within an autonomic ganglion. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000107 FMA:80121 Planarian_Anatomy autonomic neuron A neruon whose cell body is within an autonomic ganglion. CL:0000107 A neruon contained within with the enteric nervous system (gastrodermal plexus). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0007011 Planarian_Anatomy enteric neuron A neruon contained within with the enteric nervous system (gastrodermal plexus). CL:0007011 Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 AAO:0010269 AEO:0000065 BILA:0000065 C32186 CARO:0000065 EHDAA2:0003065 FMA:62918 HAO:0000065 ISBN:9780070316607 MESH:D001485 NIF_Subcellular:sao1397492660 PMID:18786419 PMID:19048075 PMID:21664348 PMID:21828097 PMID:22479207 PMID:23079596 PMID:23405188 PMID:23903188 PMID:25017721 PMID:26057828 PMID:26457503 PMID:27551436 PMID:29100657 PMID:30383829 PMID:30962434 TAO:0001485 TGMA:0001850 UMLS:C0085872 VHOG:0001592 WBbt:0005756 XAO:0003163 ZFA:0001485 basal lamina basal lamina of epithelium basement membrane Planarian_Anatomy this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell. basal lamina of epidermis Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue. CARO:0000065 Image is an electron micrograph showing the dorsal epidermis. Epidermal cells can be seen above (superfical to) the basal lamina (BL) and the body wall musculature can be seen below. Scale bar is 2um. Rhabdites that are located basally to the epidermis, in the mesenchyme. In Smed these are present in cells likely on their way to becoming part of the mature epidermis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 Planarian_Anatomy http://purl.obolibrary.org/obo/part_of 'dorsal epidermis progenitor cell' (PLANA_0003501), 'ventral epidermis progenitor cell' (PLANA:0003503)because EM data we can see immature adenal rhbadites in cells just underneath the basal lamina dorsally and ventrally. adenal rhabdite Rhabdites that are located basally to the epidermis, in the mesenchyme. In Smed these are present in cells likely on their way to becoming part of the mature epidermis. ISBN:9780070316607 Image is an electron micrograph showing the dorsal epidermis and underlying basal lamina at the top. Adenal rhabdites are marked with "Rh" and can be seen in cells underneath or medial to the basal lamina. Scale bar is 2um. A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005912 PMID:26556349 Planarian_Anatomy adherens junction A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments. GO:0005912 Image is an electron micrograph of two outer epidermal cells of the pharynx. There is an adherens junction (arrowheads) between two cells. Scale bar is 0.5 um. Finger-like processes at the terminal pore of adhesive gland cells around the marginal adhesive zone. They protrude past the epidermis and are longer microvilli, and shorter than cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 adhesive papillae Planarian_Anatomy adhesive papilla Finger-like processes at the terminal pore of adhesive gland cells around the marginal adhesive zone. They protrude past the epidermis and are longer microvilli, and shorter than cilia. ISBN:9780070316607 Image is an electron micrograph of the outside of an animal at the marginal adhesive zone. The adhesive papilla (arrowheads) are colored in blue and surround each secretory pore (yellow). Mucus and cilia are both green. Scale bar is 2um. A wound resulting in two or more separate tissue fragments. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy amputation A branch of the triclad gut located anterior to the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18063757 PMID:18287199 PMID:19174194 PMID:20707997 PMID:21458439 PMID:21664348 PMID:21806978 PMID:22451003 PMID:22479207 PMID:23318635 PMID:24063805 PMID:28287248 PMID:30194301 anterior branch anterior intestinal branch Planarian_Anatomy anterior gut branch A branch of the triclad gut located anterior to the pharynx. PMID:21664348 The anterior-medial region of the head margin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:15866156 PMID:18063755 PMID:22479207 PMID:24415944 PMID:24992682 PMID:27063937 PMID:28126842 PMID:28216315 PMID:29547123 PMID:30962434 head tip Planarian_Anatomy anterior tip The anterior-medial region of the head margin. PMID:22479207 Illustration of the anterior tip in green. A chamber formation in an organ. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 NCIT:C97102 Planarian_Anatomy antrum A chamber formation in an organ. ISBN:9780070316607 A sense organ located along the dorsolateral head margin. The auricular groove is highly innervtated by ciliated sensory neurons, and has an altered epidermis devoid of rhabdites and gland cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:27800171 PMID:28495872 PMID:30399335 PMID:30485821 Planarian_Anatomy auricle A sense organ located along the dorsolateral head margin. The auricular groove is highly innervtated by ciliated sensory neurons, and has an altered epidermis devoid of rhabdites and gland cells. ISBN:9780070316607 Image is a scanning electron micrograph of the dorsal side of the head of an adult worm. The auricles (arrowheads) appear as a short groove on each side of the head. Anteror is down and scale bar is 100um. The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0030424 PMID:16033796 PMID:17251262 PMID:17553481 PMID:18202849 PMID:20707997 PMID:21566185 PMID:22445864 PMID:23318641 PMID:23903188 PMID:25254346 PMID:25356635 PMID:25493551 PMID:25772472 PMID:27800171 PMID:28495872 nerve fiber Planarian_Anatomy axon The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. GO:0030424 Image is an electron micrograph showing a cross section of an axon (arrowheads), right underneath or medial to the dorsal body wall musculature. Dorsal is up and the scale bar is 2um. The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005930 PMID:23144623 PMID:26057828 PMID:26912790 Planarian_Anatomy axoneme The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GO:0005930 Image is an electron micrograph of several cilia where a cross-section reveals the axoneme with a 9+2 arrangement of microtubles. Arrowheads denote microtubules. Scale bar is 100nm. A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0036064 ISBN:9780070316607 PMID:21282632 PMID:21828097 PMID:21937596 Planarian_Anatomy basal body A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. GO:0036064 Image is an electron micrograph showing a cross-section of a cilium, revealing the basal body (arrowhead). Scale bar is 0.5um. Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16033796 PMID:26618653 visual center Planarian_Anatomy brain visual center Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons). PMID:16033796 An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 https://doi.org/10.1101/279364 bulbar lumen Planarian_Anatomy bulbar cavity An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla. ISBN:9780070316607 Irradiation-sensitive, mesenchymal cells that are absent from the head region anterior to the eyes and the pharynx. The Category 1 designation encompasses the neoblast population. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:21894189 PMID:22439894 Category 1 gene expressing cell Planarian_Anatomy Category 1 cell Irradiation-sensitive, mesenchymal cells that are absent from the head region anterior to the eyes and the pharynx. The Category 1 designation encompasses the neoblast population. PMID:18786419 The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0044297 PMID:15866156 PMID:16033796 PMID:20865784 PMID:27612384 PMID:28495872 Planarian_Anatomy cell body The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. GO:0044297 One of two bilaterally symmetric structures comprising the planarian brain. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:16033796 PMID:16890156 PMID:17251262 PMID:17553481 PMID:17670787 PMID:17905225 PMID:17999079 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19211673 PMID:19247960 PMID:19766622 PMID:19852954 PMID:20223763 PMID:20422023 PMID:20707997 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21566185 PMID:21806978 PMID:21828097 PMID:21852957 PMID:22074376 PMID:22125640 PMID:22318224 PMID:22371573 PMID:22427692 PMID:22439894 PMID:22445864 PMID:22451003 PMID:22479207 PMID:22884275 PMID:23123964 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23652002 PMID:23903188 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24523458 PMID:24704339 PMID:24950970 PMID:24992682 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25493551 PMID:25558068 PMID:25772472 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26525673 PMID:26556349 PMID:26618653 PMID:27013241 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27149082 PMID:27150006 PMID:27163480 PMID:27523733 PMID:27606067 PMID:27612382 PMID:27612384 PMID:27800171 PMID:27864883 PMID:28126842 PMID:28137894 PMID:28171748 PMID:28245923 PMID:28287248 PMID:28434803 PMID:28686611 PMID:28807897 PMID:28893948 PMID:29100657 PMID:29158443 PMID:29291974 PMID:29291981 PMID:29357350 PMID:29547123 PMID:29557542 PMID:29674431 PMID:29674432 PMID:30143032 PMID:30194301 PMID:30282036 PMID:30383829 PMID:30399335 PMID:30485821 PMID:30729158 bi-lobed brain bi-lobed cephalic ganglia brain ganglia brain lobe Planarian_Anatomy cephalic ganglia lobe One of two bilaterally symmetric structures comprising the planarian brain. PMID:17999079 A central nervous system neuron located within the planarian brain. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17999079 PMID:24173799 PMID:27612382 brain neuron Planarian_Anatomy cephalic ganglia neuron A central nervous system neuron located within the planarian brain. PMID:17999079 Amputation carried out by application of chemicals. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:24737865 Planarian_Anatomy chemical amputation Amputation carried out by application of chemicals. PMID:24737865 Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:24737865 chemical pharyngeal amputation Planarian_Anatomy chemical pharynx amputation Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide. PMID:24737865 Any neuron that capable of some detection of chemical stimulus involved in sensory perception. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00005922 PMID:18202849 PMID:26525673 PMID:27612382 PMID:28126842 PMID:28686611 PMID:29547123 chemoreceptive neuron chemoreceptor neuron Planarian_Anatomy chemosensory neuron Any neuron that capable of some detection of chemical stimulus involved in sensory perception. FBbt:00005922 A membrane-less, cytoplasmic ribonucleoprotein granule present in neoblasts and germ cells implicated in post-transcriptional regulation. The RNA helicase DHH1/RCK, Tudor, SmB, methylated substrates of PRMT5, PIWI-3 and Germinal Histone H4 localize to chromatoid bodies in neoblasts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0033391 PMID:19247960 PMID:20215344 PMID:21356107 PMID:22318224 PMID:22385657 PMID:22439894 PMID:22543868 PMID:24120894 PMID:24367277 PMID:24903754 PMID:25017721 PMID:27523733 nuage Planarian_Anatomy chromatoid body A membrane-less, cytoplasmic ribonucleoprotein granule present in neoblasts and germ cells implicated in post-transcriptional regulation. The RNA helicase DHH1/RCK, Tudor, SmB, methylated substrates of PRMT5, PIWI-3 and Germinal Histone H4 localize to chromatoid bodies in neoblasts. PMID:22318224 PMID:24903754 Image is an electron micrograph showing a chromatoid body (arrowhead) next to the cell's nucleus (N) which takes up the bottom left corner. Scale bar is 200nm. A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005694 PMID:25404302 PMID:28757112 PMID:28812561 PMID:29364871 PMID:30143032 Planarian_Anatomy chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. GO:0005694 Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um. Under the microscope chromosomes appear as thin, thread-like structures. They all have a short arm and long arm separated by a primary constriction called the centromere. The short arm is designated as p and the long arm as q. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C13355 PMID:25404302 SO:0000105 Planarian_Anatomy chromosome arm Under the microscope chromosomes appear as thin, thread-like structures. They all have a short arm and long arm separated by a primary constriction called the centromere. The short arm is designated as p and the long arm as q. NCIT:C13355 Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um. Epithelium bearing vibratile cilia on the free surface. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26457503 PMID:26711341 PMID:28216315 PMID:28292427 UBERON:0007601 Planarian_Anatomy ciliated epithelium Epithelium bearing vibratile cilia on the free surface. UBERON:0007601 Image is an electron micrograph of an outer epidermal cell of the pharynx. These cells are heavily ciliated. Scale bar is 2um. A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. The longitudinal array of microtubules are almost always in a 9+2 array with 2 microtubles in the central cilia bundle and 9 sets of doublet microtubules around the perimeter. The exception to this arrangement is spermatazoa flagella, which have a 9+1 array in planarians. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005929 Planarian_Anatomy cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. The longitudinal array of microtubules are almost always in a 9+2 array with 2 microtubles in the central cilia bundle and 9 sets of doublet microtubules around the perimeter. The exception to this arrangement is spermatazoa flagella, which have a 9+1 array in planarians. GO:0005929 Image is an electron micrograph depicting several cilia (arrowheads) emerging from a ventral epidermis cell. Scale bar is 0.5um. A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C32349 Planarian_Anatomy commissure A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord. NCIT:C32349 A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C50518 Planarian_Anatomy cut A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument. NCIT:C50518 A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0030425 PMID:16033796 PMID:17553481 PMID:22445864 PMID:25493551 PMID:28495872 cell dendrite dendritic process dendritic projection Planarian_Anatomy dendrite A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. GO:0030425 A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:30471994 PMID:30962434 DVM dorsal-ventral muscle dorsal-ventral muscle fibers dorsoventral muscle dorsoventralmuscle fibers Planarian_Anatomy dorsal-ventral muscle cell A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal. PMID:30962434 Image is an electron micrograph depicting multiple dorsal-ventral muscle cells (arrowheads). The ventral epidermis is at the bottom of this image. Scale bar is 10um. A premeiotic female germ cell (i.e., a diploid female germline stem cell or transit amplifying oogonial cell). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy early female germ cell A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27330085 Planarian_Anatomy early male germ cell A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell). PMID:27330085 A cryptic digestive cavity comprised of phagocytic embryonic gut cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic gut A cryptic digestive cavity comprised of phagocytic embryonic gut cells. PMID:28072387 An epithelial cell of the integument (the outer layer of an organism). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000362 PMID:21458439 PMID:24922054 PMID:25017721 PMID:26457503 PMID:28292427 PMID:28686611 PMID:28807897 PMID:29100657 PMID:29357350 PMID:30399335 Planarian_Anatomy epidermal cell An epithelial cell of the integument (the outer layer of an organism). CL:0000362 Image is an electron micrograph depicting the dorsal epidermis. A single cell has been labeled with arrowheads. Immediately deep to the epidermis is the basal lamina, labeled with "BL." Scale bar is 2um. Rhabdites located within epidermal cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 Planarian_Anatomy http://purl.obolibrary.org/obo/part of 'dorsal epidermal cell' (PLANA_0003105) and 'ventral epidermal cell' (PLANA:0003101) added because we see rhabdites in both in EM data epidermal rhabdite Rhabdites located within epidermal cells. ISBN:9780070316607 Image is an electron micrograph depicting the epidermis. Rhabdites (arrowheads) can be seen in various stages of expansion inside of the epidermal cells. Scale bar is 5 um. The lipid bilayer surrounding the endoplasmic reticulum. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005789 Planarian_Anatomy ER membrane The lipid bilayer surrounding the endoplasmic reticulum. GO:0005789 Image is an electron micrograph depicting (rough) endoplasmic reticulum adjacent tp the nucleus (N). The arrowheads mark the ER membrane. Note the ribosomes (small dots) that can be seen both in the cytoplasm and lining the ER membrane. Scale bar is 0.2um. The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CHEBI:24009 PMID:25356635 PMID:26017970 PMID:27240733 eye cell pigment eye pigment Planarian_Anatomy eumelanin The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color. PMID:15760337 PMID:26017970 PMID:8812261 A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000424 PMID:21566185 PMID:24173799 Planarian_Anatomy excretory cell A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids. CL:0000424 Image is an electron micrograph showing a cell that is part of the collecting duct. An arrowhead marks the nucleus of this cell. Note the visible lumen of the collecting duct extending out and passing through the basal lamina. This cell is involved in excretion. Scale bar is 2 um. A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0031012 PMID:19048075 PMID:28126842 PMID:28137894 PMID:28807897 PMID:30962434 ECM Planarian_Anatomy extracellular matrix A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. GO:0031012 Image is an electron micrograph showing the extracellular matrix (arrowheads) between two cells. Scale bar is 0.2um. That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005615 PMID:21828097 Planarian_Anatomy extracellular space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. GO:0005615 A form of asexual reproduction resulting in self-amputation of posterior tissue, generating an anterior fragment and a fission fragment. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy fission Planarian undulipodia consisting of spermatazoa cell posterior protrusions. Planarian spermatozoa contain two flagella and are composed of 9 + 1 axonemal microtubule arrangements in their flagella (markedly different from the 9 + 2 structures generally observed in sperm of other animals). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29095551 PMID:4190073 Planarian_Anatomy flagellum Planarian undulipodia consisting of spermatazoa cell posterior protrusions. Planarian spermatozoa contain two flagella and are composed of 9 + 1 axonemal microtubule arrangements in their flagella (markedly different from the 9 + 2 structures generally observed in sperm of other animals). PMID:4190073 A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005921 PMID:17670787 PMID:22125640 Planarian_Anatomy gap junction A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins. GO:0005921 A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the genital atrium; glands surrounding the genital atrium produce the egg capsule shell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID: 22074376 atrium female antrum Planarian_Anatomy genital atrium A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the genital atrium; glands surrounding the genital atrium produce the egg capsule shell. PMID:22074376 A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17376870 PMID:22318224 germ cell cluster Planarian_Anatomy germ cell cyst A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells. PMID:17376870 Stem cell that is the precursor of gametes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000014 FBbt:00004861 PMID:16344473 PMID:17376870 PMID:17390146 PMID:18456843 PMID:19247960 PMID:20215344 PMID:20844018 PMID:22074376 PMID:22252538 PMID:22318224 PMID:22385657 PMID:22543868 PMID:23652002 PMID:24173799 PMID:24367277 PMID:25278423 PMID:27013241 PMID:28434803 PMID:28812561 https://doi.org/10.1101/279364 germ cell germ stem cell germline cell Planarian_Anatomy germline stem cell Stem cell that is the precursor of gametes. FBbt:00004861 Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0042587 PMID:30608231 Planarian_Anatomy glycogen granule Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface. GO:0042587 Image is an electron micrograph depicting glycogen granules (arrowheads) within the cytoplasm of a cell. Scale bar is 200 nm. A surgical cut that breaches the epidermis, made with a defined edge. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy incision Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20511647 inner pharynx epidermal cell Planarian_Anatomy pharynx inner epidermal cell Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated. ISBN:9780070316607 Image is an electron micrograph of a transverse section through the pharynx. The phayrnx lumen is to the bottom left. An epidermal cell, a part of the inner epithelial layer, has been marked with arrowheads. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um. Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 Planarian_Anatomy inner zone of gland cells Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx. ISBN:9780070316607 Image is an electron micrograph depicting a transverse section through the pharynx. Arrowheads label the inner zone of gland cells. They can be identified by the mucus granules the cell body is filled with. Scale bar is 5um. A cell junction that forms a connection between two or more cells in a multicellular organism. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005911 Planarian_Anatomy intercellular junction A cell junction that forms a connection between two or more cells in a multicellular organism. GO:0005911 An amputation performed with a transverse, oblique or longitudinal cut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy linear amputation A breach of the epidermis and optionally down into other structures though an insult with a knife or other instrument, such that the movement includes the z direction and one or more of the x y direction. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 scratch Planarian_Anatomy linear incision An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005811 PMID:30608231 https://doi.org/10.1101/279364 Planarian_Anatomy lipid droplet An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. GO:0005811 Image is an electron micrograph depicting two lipid droplets (arrowheads) within two different cells. Note the mostly round shape of the droplets. Often, mitochondria can be seen clumped around lipids. Scale bar is 1um. The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C94478 Planarian_Anatomy lumen The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine. NCIT:C94478 Zone present along the lateral dorsoventral boundary that sits just underneath the animal, in contact with substrates. It is comprised of bunches of adhesion gland cells whose terminal pores form pore rosettes through the dorsal ventral boundary epidermis.This region of is devoid of rhabdites. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20865784 Planarian_Anatomy marginal adhesive zone Zone present along the lateral dorsoventral boundary that sits just underneath the animal, in contact with substrates. It is comprised of bunches of adhesion gland cells whose terminal pores form pore rosettes through the dorsal ventral boundary epidermis.This region of is devoid of rhabdites. ISBN:9780070316607 Image is an electron micrograph depicting the lateral dorsoventral boundary. Several adhesion gland cells have been labeled with arrowheads to visualize the line of the marginal adhesive zone. Scale bar is 10um. Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00005919 PMID:25725068 PMID:28216315 WBbt:0008431 mechanosensory cell Planarian_Anatomy mechanosensory neuron Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception. FBbt:00005919 Subset of dorsal-ventral muscle cells located in the medial body region. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29674431 PMID:30962434 Planarian_Anatomy medial muscle cell Subset of dorsal-ventral muscle cells located in the medial body region. PMID:30962434 Image is an electron micrograph depicting multiple medial dorsal-ventral muscle cells (arrowheads). At the bottom of this image is the ventral epidermi, to the left is the dark staining of the gut tissue. Scale bar is 10um. A germ cell undergoing meiosis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27330085 Planarian_Anatomy meiotic germ cell A germ cell undergoing meiosis. PMID:27330085 A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0042470 Planarian_Anatomy melanosome A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. GO:0042470 A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21282632 PMID:22653920 UBERON:0000912 Planarian_Anatomy mucus A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance. PMID:22653920 Image is an electron micrograph of the outside of an animal at the marginal adhesive zone. The adhesive papilla are colored in blue and surround each secretory pore (yellow). Mucus (arrowheads) and cilia are both green. Scale bar is 2um. The external opening and terminus of a protonephridium made by a terminal cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:21828097 UBERON:0006972 Planarian_Anatomy nephridiopore The external opening and terminus of a protonephridium made by a terminal cell. ISBN:9780070316607 Image is an electron micrograph depicting a collecting duct (arrowheads) passing through the basal lamina (BL). Dorsal is up and the scale bar is 5 um. Cell appendage of the neuron which includes the axon and the dendrite. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00005113 FMA:61814 ISBN:9780070316607 PMID:27612382 PMID:29547123 neuronal process Planarian_Anatomy neurite Cell appendage of the neuron which includes the axon and the dendrite. FMA:61814 A neuron that produces and releases neuropeptides at chemical synapses. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:24173799 PMID:25356635 PMID:27163480 cns peptidergic cell peptidergic neuron Planarian_Anatomy neuropeptidergic neuron A neuron that produces and releases neuropeptides at chemical synapses. PMID:24173799 Differentiating, immature epidermal cells lacking cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26457503 PMID:28292427 Planarian_Anatomy non-ciliated epidermis Differentiating, immature epidermal cells lacking cilia. PMID:26457503 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005635 https://doi.org/10.1101/279364 Planarian_Anatomy nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005635 Image is an electron micrograph depicting the nuclear envelope (arrowheads). The nucleus takes up the top left corner of the image and the nuclear envelope encloses it. Scale bar is 200 nm. The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005637 inner leaflet Planarian_Anatomy nuclear inner membrane The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope. GO:0005637 Image is an electron micrograph depicting the nuclear envelope. The nucleus takes up the top left corner of the image and the inner nuclear membrane has been labeled with arrowheads. Scale bar is 200 nm. The volume enclosed by the nuclear inner membrane. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0031981 Planarian_Anatomy nuclear lumen The volume enclosed by the nuclear inner membrane. GO:0031981 The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005640 outer leaflet Planarian_Anatomy nuclear outer membrane The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes. GO:0005640 Image is an electron micrograph depicting the nuclear envelope. The nucleus takes up the top left corner of the image and the outer nuclear membrane has been labeled with arrowheads. Scale bar is 200 nm. The portion of the nuclear lumen proximal to the inner nuclear membrane. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0034399 PMID:25404302 Planarian_Anatomy nuclear periphery The portion of the nuclear lumen proximal to the inner nuclear membrane. GO:0034399 Parenchymal cells that synthesize and contain brown ommonchrome pigment. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27240733 non-melanin pigment cell Planarian_Anatomy ommochrome pigment cell Parenchymal cells that synthesize and contain brown ommonchrome pigment. PMID:27240733 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27800171 UBERON:0004904 Planarian_Anatomy optic nerve 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. UBERON:0004904 Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:20511647 outer pharynx epidermal cell Planarian_Anatomy pharynx outer epidermal cell Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature. ISBN:9780070316607 Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. An epidermal cell, a part of the outer epithelium, has been labeled with arrowheads. Immediately deep to the outer epithelial layer of the pharynx is musculature that has been colored. Red = circular; blue = longitudinal. Scale bar is 2 um. A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000234 ISBN:9780070316607 PMID:25956527 PMID:27501047 PMID:30471994 phagocyte Planarian_Anatomy phagocytic cell A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome. ISBN:9780070316607 PMID:30471994 The distal-most end of the pharnyx containing an opening to the pharynx lumen. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy pharynx tip Image is an electron micrograph of the tip of the pharynx. Many gland cells can be seen inside, filled with mucus. Scale bar is 5um. A pigment cell is a cell that contains pigment granules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000147 PMID:26618653 pigment producing cell pigmented cell Planarian_Anatomy pigment cell A pigment cell is a cell that contains pigment granules. CL:0000147 A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0048770 ISBN:9780070316607 PMID:27551436 Planarian_Anatomy pigment granule A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. GO:0048770 A wound resulting from an amputation of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy plug amputation Illustration of an example of a plug amputation showing resultant fragment and donor wound. A breach of the epidermis made with a sharp pointed object, like a needle or an insect pin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 poke Planarian_Anatomy point incision An anatomical space that is an opening, usually at the end of a canal or duct, on the surface of the integument or the lining of an internal anatomical space. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0008915 Planarian_Anatomy pore An anatomical space that is an opening, usually at the end of a canal or duct, on the surface of the integument or the lining of an internal anatomical space. UBERON:0008915 A haploid gamete undergoing terminal differentiation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy post-meiotic germ cell A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0045211 PMID:24950970 post-synaptic cell Planarian_Anatomy postsynaptic cell A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. GO:0045211 A diploid germline stem cell or transit amplifying germ cell that has not committed to undergoing meiotic DNA replication, reductive divisions or terminal differentiation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy premeiotic germ cell The part of a synapse that is part of the presynaptic cell. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0098793 PMID:24950970 pre-synaptic cell Planarian_Anatomy presynaptic cell The part of a synapse that is part of the presynaptic cell. GO:0098793 Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043195 PMID:23903188 pre-synaptic terminal Planarian_Anatomy presynaptic terminal Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it. GO:0043195 A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0008021 PMID:23903188 pre-synaptic vesicle Planarian_Anatomy presynaptic vesicle A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. GO:0008021 The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17553481 PMID:20865784 PMID:21664348 PMID:27122174 PMID:28137894 PMID:29674431 main gut branch primary intestine branch Planarian_Anatomy primary gut branch The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature. PMID:21664348 Four large phagocytic cells associated with the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 primitive endoderm Planarian_Anatomy primitive gut Four large phagocytic cells associated with the embryonic pharynx. PMID:28072387 Gut branches originating from and connected to the tertiary gut branches. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 Planarian_Anatomy quarternary gut branch Gut branches originating from and connected to the tertiary gut branches. PMID:21664348 An organ involved in reproduction https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16344473 PMID:17376870 PMID:20844018 PMID:22074376 PMID:25278423 PMID:27074666 UBERON:0003133 https://doi.org/10.1101/279364 Planarian_Anatomy reproductive organ An organ involved in reproduction UBERON:0003133 Any anatomical structure that is part of the reproductive system. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17376870 UBERON:0005156 Planarian_Anatomy reproductive structure Any anatomical structure that is part of the reproductive system. UBERON:0005156 The light sensing structure consisting of photoreceptor neuron dendrites that project into the optic lumen and show close associations with eumelanin-containing pigment cup cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:15760337 PMID:16033796 PMID:21852957 PMID:26017970 Planarian_Anatomy rhabdome The light sensing structure consisting of photoreceptor neuron dendrites that project into the optic lumen and show close associations with eumelanin-containing pigment cup cells. PMID:15760337 PMID:16033796 PMID:21852957 The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0016028 PMID:15760337 PMID:16033796 PMID:18202849 PMID:20865784 PMID:21282632 PMID:21852957 PMID:22445864 PMID:25772472 PMID:26618653 PMID:27800171 Planarian_Anatomy rhabdomere The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light. PMID:15760337 PMID:16033796 PMID:21852957 A tubular structure that transports secreted or excreted substances. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:30383829 UBERON:0000058 secretory canal Planarian_Anatomy secretory duct A tubular structure that transports secreted or excreted substances. UBERON:0000058 Image is an electron micrograph of a viscid gland cell passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct (arrowhead) transports mucus to the outside of the animal, through the secretory pore. Ventral is down and scale bar is 5um. A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0030141 PMID:29100657 Planarian_Anatomy secretory granule A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. GO:0030141 One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0001268 CL:0002371 PMID:20599901 PMID:21852957 PMID:22074376 PMID:22371573 PMID:22385657 PMID:25404302 PMID:27606067 PMID:28757112 Planarian_Anatomy somatic cell One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells. BTO:0001268 A non-germline cell within the ovary or testis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27163480 PMID:27330085 WBbt:0007815 gonadal niche cell somatic gonadal niche cell somatic gonadal support cell Planarian_Anatomy somatic gonadal cell A non-germline cell within the ovary or testis. PMID:27163480 PMID:27330085 A presumptive progenitor cell that expresses both pan-neoblast markers and pro-differentiation gene(s), frequently developmental transcription factors, implicated in lineage commitment and tissue-specific differentiation programs. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25254346 PMID:26651295 PMID:27542689 PMID:29674432 PMID:30962434 Planarian_Anatomy specialized neoblast A presumptive progenitor cell that expresses both pan-neoblast markers and pro-differentiation gene(s), frequently developmental transcription factors, implicated in lineage commitment and tissue-specific differentiation programs. PMID:23404104 A thin, flexible rod that anchors an egg capsule to a solid substrate. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 Planarian_Anatomy stalk A thin, flexible rod that anchors an egg capsule to a solid substrate. ISBN:9780070316607 A wound produced by non-autonomous physical means. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy surgical wound The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0045202 PMID:18202849 PMID:18287199 PMID:21282632 neural synapse neuronal synapse Planarian_Anatomy synapse The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. GO:0045202 The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043083 PMID:23903188 Planarian_Anatomy synaptic cleft The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released. GO:0043083 Vesicles that store various neurotransmitters that are released at the synapse. The release is regulated by a voltage-dependent calcium channel. Vesicles are essential for propagating nerve impulses between neurons and are constantly recreated by the cell. [Wikipedia] https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0008021 PMID:24950970 Planarian_Anatomy synaptic vesicle Vesicles that store various neurotransmitters that are released at the synapse. The release is regulated by a voltage-dependent calcium channel. Vesicles are essential for propagating nerve impulses between neurons and are constantly recreated by the cell. [Wikipedia] GO:0008021 A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0000795 PMID:25404302 Planarian_Anatomy synaptonemal complex The posterior-medial region of the tail margin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy tail tip Illustration of the tail tip (in green). The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0000781 PMID:22371573 PMID:25404302 https://doi.org/10.1101/279364 Planarian_Anatomy telomere The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. GO:0000781 A cell-cell junction in invertebrates that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0070160 Planarian_Anatomy septate junction A cell-cell junction in invertebrates that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other. GO:0070160 Image is an electron micrograph depicting the inner epithelium of the pharynx. Septate junctions (arrowheads) can be clearly seen between cells. Scale bar is 200 nm. A wound resulting from a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy wedge amputation Illustration of a wedge amputation depicting the resultant donor wound and wedge fragment. An injury that breaches the epidermis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 injury Planarian_Anatomy wound A sorted cell population enriched for irradiation-sensitive, cycling cells (4n cells, with high levels of Hoescht 33342 staining) with scant cytoplasm (low levels of calcein-AM staining). X1 cells are enriched for cycling neoblasts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16872450 PMID:17670787 PMID:18456843 PMID:18786419 PMID:19048075 PMID:20215344 PMID:20223763 PMID:21937596 PMID:22385657 PMID:22427692 PMID:22543868 PMID:22549959 PMID:23235145 PMID:23629965 PMID:24120894 PMID:24367277 PMID:24992682 PMID:25254346 PMID:25558068 PMID:25956527 PMID:26114597 PMID:26457503 PMID:26711341 PMID:27013241 PMID:27068018 PMID:27150006 PMID:27502555 PMID:27523733 PMID:27551436 PMID:28137894 PMID:29100657 PMID:29557542 PMID:29674432 PMID:29906446 PMID:30194301 X1 X1 cell population X1 neoblast X1 population Planarian_Anatomy X1 cell A sorted cell population enriched for irradiation-sensitive, cycling cells (4n cells, with high levels of Hoescht 33342 staining) with scant cytoplasm (low levels of calcein-AM staining). X1 cells are enriched for cycling neoblasts. PMID:16872450 A heterogeneous sorted cell population of unstained planarian cells with similar size and complexity to irradiation-sensitive, cycling cells contained in the X1 gate. Unlike X1 cells, X1(FS) cells are amenable to cell transplantation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21566185 Planarian_Anatomy X1(FS) cell A heterogeneous sorted cell population of unstained planarian cells with similar size and complexity to irradiation-sensitive, cycling cells contained in the X1 gate. Unlike X1 cells, X1(FS) cells are amenable to cell transplantation. PMID:21566185 A sorted cell population containing irradiation-sensitive and irradiation-insensitive cells, characterized by weak Hoescht 33342 and calcein-AM staining. X2 cell populations contain neoblasts as well as a variety of lineage-dedicated post-mitotic progenitor cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16872450 PMID:18786419 PMID:19048075 PMID:20215344 PMID:20223763 PMID:22427692 PMID:22543868 PMID:23629965 PMID:24367277 PMID:25017721 PMID:27013241 PMID:27150006 PMID:27502555 PMID:27606067 PMID:27864883 PMID:28137894 PMID:29674432 Planarian_Anatomy X2 cell A sorted cell population containing irradiation-sensitive and irradiation-insensitive cells, characterized by weak Hoescht 33342 and calcein-AM staining. X2 cell populations contain neoblasts as well as a variety of lineage-dedicated post-mitotic progenitor cells. PMID:16872450 A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16872450 PMID:17670787 PMID:18456843 PMID:18786419 PMID:19048075 PMID:20215344 PMID:20223763 PMID:22427692 PMID:22479207 PMID:22543868 PMID:23629965 PMID:24367277 PMID:24992682 PMID:25558068 PMID:25956527 PMID:26114597 PMID:26457503 PMID:26711341 PMID:27013241 PMID:27502555 PMID:29100657 PMID:29674432 PMID:29906446 PMID:30194301 Xins Xins cell population Xins cells Planarian_Anatomy Xins cell A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types. PMID:16872450 Posterior to the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 post pharyngeal post-pharyngeal post-pharyngeal region postpharyngeal region Planarian_Anatomy postpharyngeal region Adjacent to blastema, or proximal to blastema. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 post-blastema postblastema postblastema region Planarian_Anatomy post-blastema region Illustration of the post-blastema region(in green) in the anterior region of a regenerating tail fragment. A fragment derived from a spontaneous or induced fission event. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy fission fragment term is not needed. obsolete oblique true The avascular cellular layers that cover body surfaces and cavities and may form glands. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C12710 UBERON:0000483 Planarian_Anatomy epithelium The avascular cellular layers that cover body surfaces and cavities and may form glands. NCIT:C12710 Image is an electron micrograph of a transverse section of a planarian through the pharyngeal region depicting 3 different epithelial layers (arrowheads). At the top is the dorsal epidermis, in the middle is the epithelium of the pharyngeal pouch, and at the bottom of the image, the outer epithelium of the pharynx. Scale bar is 5um. The triclad planarian gut is serially bifrucated into connected lumens where each bifrucation is a branch. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy gut branch Organ 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy extraembryonic organ This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 SO:0000830 Planarian_Anatomy chromosome part This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. SO:0000830 An event or occurrence that causes damage to a tissue or organ. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 insult Planarian_Anatomy perturbation structural element of a chromosome, for example, a telomere and a centromere https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 SO:0000628 chromosomal structural element Planarian_Anatomy chromosomal_structural_element structural element of a chromosome, for example, a telomere and a centromere SO:0000628 A longitudinal fragment containing the preexisting midline and medial structures. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy thick fragment Illustration of a thick fragment (in green). A longitudinal fragment lacking a midline and medial structures. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy thin fragment Illustration of a thin fragment (in green). A piece of tissue isolated from the body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 piece Planarian_Anatomy fragment A region bounded by any sagittal plane though the animal and the left or right side of the animal. NOTE: sagittal plane is an anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy longitudinal region Illustration of a longitudinal region (green). An intentional wound produced by non-autonomous chemical means. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy chemical wound A wound resulting from the removal of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy plug wound Illustration of a wound left in a donor animal resulting from a plug amputation. A wound resulting from the removal of a piece of tissue from the lateral margin at any given point that extends interiorly to more medial structures. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy wedge wound Illustration of a wedge wound. A fragment that has undergone wound healing and is undergoing tissue replacement and morphallaxis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy regenerating fragment An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the sagittal plane. This plane runs longitudinally and is not necessarily medial. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 longitudinal orientation Planarian_Anatomy sagittal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane, which runs longitudinally, and is never medial. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PATO:0005023 Planarian_Anatomy parasagittal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane, which runs longitudinally, and is never medial. PATO:0005023 An anatomical entity consisting of a single or a few multinucleated structures https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 AEO:0000203 BTO:0005784 PMID:27330085 Planarian_Anatomy syncytium An anatomical entity consisting of a single or a few multinucleated structures AEO:0000203 Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 MICRO:0000215 Planarian_Anatomy intracellular granule Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy. MICRO:0000215 Image is an electron micrograph depicting a cell with many intracellular granules (arrowheads) visible in the cytoplasm. The scale bar is 1um. Any number of cells from dissociated planarian tissue sorted via a FACS sorter for any parameter. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy FACS sorted cell population Cells isolated from dissociated planarian tissue. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy derived cell population An epithelial monolayer lining the pharynx pouch cavity. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 Planarian_Anatomy pharynx pouch epithelium An epithelial monolayer lining the pharynx pouch cavity. OCLC:16809160 Image is an electron micrograph of a transverse slice through the parapharyngeal region. It includes the dorsal epidermis, pharynx pouch epithelium (arrowheads), and a portion of the pharynx. Dorsal is up and the lumen of the pouch is visible as the white stripe in the middle of the micrograph. Scale bar is 5um. Epithelial surface lining the sperm duct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:22074376 Planarian_Anatomy sperm duct epithelial surface Epithelial surface lining the sperm duct. PMID:19022767 PMID:22074376 A loosely organized collection of connective tissue and cells, including neoblasts and their immediate progeny, located in the space outside of the organs between the body wall musculature and the gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 mesenchyme Planarian_Anatomy parenchyma A loosely organized collection of connective tissue and cells, including neoblasts and their immediate progeny, located in the space outside of the organs between the body wall musculature and the gut. OCLC:16809160 The dorsal region of the tail. dorsal region of tail region Planarian_Anatomy PLANA:0003000 dorsal region of tail Illustration of the dorsal region of the tail (in green). The lateral region of the medio-lateral axis of the whole animal. lateral region of whole organism Planarian_Anatomy PLANA:0003001 lateral region of the whole animal The anterior region of the eye. anterior region of eye Planarian_Anatomy PLANA:0003002 anterior region of the eye The posterior region of the eye. posterior region of eye Planarian_Anatomy PLANA:0003003 posterior region of the eye The center-most region just anterior to the pharynx prepharyngeal region of midline Planarian_Anatomy PLANA:0003004 prepharyngeal midline cell which is part of the testis Planarian_Anatomy PLANA:0003100 testis cell cell which is part of the testis PMID:29674431 cell which is part of the ventral epidermis ventral ciliated cell ventral epithelial cell ventral motile ciliated cell ventral multiciliated cell Planarian_Anatomy PLANA:0003101 ventral epidermis cell cell which is part of the ventral epidermis PMID:22479207 PMID:23144623 cell which is part of the visual system visual cell Planarian_Anatomy PLANA:0003102 visual system cell cell which is part of the visual system PMID:17905225 PMID:24922054 cell which is part of the eye photoreceptor cell photosensitive cell Planarian_Anatomy PLANA:0003103 eye cell cell which is part of the eye PMID:29357350 cell which is part of the enteric musculature gut muscle cell intestinal muscle cell Planarian_Anatomy PLANA:0003104 enteric muscle cell cell which is part of the enteric musculature PMID:23954785 PMID:25558068 cell which is part of the dorsal region of the epidermis dorsal epithelial cell Planarian_Anatomy PLANA:0003105 dorsal epidermis cell cell which is part of the dorsal region of the epidermis PMID:22479207 cell which is part of the adhesion gland Planarian_Anatomy PLANA:0003106 adhesion gland cell cell which is part of the adhesion gland PMID:16890156 PMID:28976975 cell which is part of the body wall musculature body wall muscle fiber body-wall muscle cell Planarian_Anatomy PLANA:0003107 body wall muscle cell cell which is part of the body wall musculature PMID:23954785 PMID:24992682 PMID:25254346 PMID:25725068 PMID:26525673 cell which is part of the gastrodermis gut cell intestinal cell Planarian_Anatomy PLANA:0003108 gastrodermal cell cell which is part of the gastrodermis PMID:19174194 PMID:22479207 PMID:27122174 cell which is part of the anterior pole Planarian_Anatomy PLANA:0003109 anterior pole cell cell which is part of the anterior pole PMID:24992682 PMID:29674431 PMID:30471994 neuron which is part of the pharynx pharyngeal neuron Planarian_Anatomy PLANA:0003110 pharynx neuron neuron which is part of the pharynx PMID:18202849 PMID:29674431 PMID:30485821 epithelial cell which is part of the pharynx pharynx epithelial cell Planarian_Anatomy PLANA:0003111 pharynx epithelial cell epithelial cell which is part of the pharynx PMID:20511647 muscle cell which is part of the pharynx pharynx muscle fiber Planarian_Anatomy PLANA:0003112 pharynx muscle cell muscle cell which is part of the pharynx PMID:27068018 epithelial cell which is part of the pharynx pouch pharyngeal cavity epithelial cell pharynx cavity epithelial cell Planarian_Anatomy PLANA:0003113 pharynx pouch epithelial cell pigment granule which is part of the eumelanin melanin melanosome photoreceptor pigment Planarian_Anatomy PLANA:0003114 melanin pigment granule pigment granule which is part of the eumelanin PMID:25356635 PMID:26017970 PMID:27551436 pigment granule which is part of the ommochrome pigment cell Planarian_Anatomy PLANA:0003115 ommochrome pigment granule cell which is part of the parenchyma Planarian_Anatomy PLANA:0003116 parenchymal cell cell which is part of the parenchyma PMID:19247960 PMID:29674431 cell which is part of the parapharyngeal region Planarian_Anatomy PLANA:0003117 parapharyngeal cell cell which is part of the prepharyngeal region Planarian_Anatomy PLANA:0003118 prepharyngeal cell neoblast undergoing mitotic G1 phase Planarian_Anatomy PLANA:0003200 G1 phase neoblast neoblast undergoing mitotic S phase Planarian_Anatomy PLANA:0003201 S phase neoblast neoblast undergoing mitotic G2 phase Planarian_Anatomy PLANA:0003202 G2 phase neoblast neoblast undergoing mitotic prophase Planarian_Anatomy PLANA:0003203 prophase neoblast Image is an electron micrograph showing a neoblast undergoing mitotic prophase (outlined). Note the difference in appearance compared to neighboring cells, nuclei labeled "N." Scale bar is 2 um. neoblast undergoing mitotic metaphase M phase neoblast Planarian_Anatomy PLANA:0003204 metaphase neoblast Image is an electron micrograph depicting cells in the mesenchyme, near the regeneration blastema. In the middle of the image, outlined, a cell is undergoing mitotic metaphase. This cell's chromosomes can be seen in a vertical arrangement. Scale bar is 2um. neoblast undergoing mitotic anaphase Planarian_Anatomy PLANA:0003205 anaphase neoblast Image is an electron micrograph showing a neoblast undergoing mitotic anaphase. The entire cell has been outlined and the condensed chromatin is visible inside. Scale bar is 2um. neoblast undergoing mitotic telophase Planarian_Anatomy PLANA:0003206 telophase neoblast Image is an electron micrograph showing a neoblast undergoing mitotic telophase (outlined). The condensed chromatin is visible inside and has been partially outlined by the nuclear envelope. Scale bar is 1um. spermatogonial stem cell undergoing mitotic G1 phase Planarian_Anatomy PLANA:0003207 G1 phase spermatogonial stem cell spermatogonial stem cell undergoing mitotic S phase Planarian_Anatomy PLANA:0003208 S phase spermatogonial stem cell spermatogonial stem cell undergoing mitotic G2 phase Planarian_Anatomy PLANA:0003209 G2 phase spermatogonial stem cell spermatogonial stem cell undergoing mitotic prophase Planarian_Anatomy PLANA:0003210 prophase spermatogonial stem cell spermatogonial stem cell undergoing mitotic metaphase Planarian_Anatomy PLANA:0003211 metaphase spermatogonial stem cell spermatogonial stem cell undergoing mitotic anaphase Planarian_Anatomy PLANA:0003212 anaphase spermatogonial stem cell spermatogonial stem cell undergoing mitotic telophase Planarian_Anatomy PLANA:0003213 telophase spermatogonial stem cell oogonial stem cell undergoing mitotic G1 phase Planarian_Anatomy PLANA:0003214 G1 phase oogonial stem cell oogonial stem cell undergoing mitotic S phase Planarian_Anatomy PLANA:0003215 S phase oogonial stem cell oogonial stem cell undergoing mitotic G2 phase Planarian_Anatomy PLANA:0003216 G2 phase oogonial stem cell oogonial stem cell undergoing mitotic prophase Planarian_Anatomy PLANA:0003217 prophase oogonial stem cell oogonial stem cell undergoing mitotic metaphase Planarian_Anatomy PLANA:0003218 metaphase oogonial stem cell oogonial stem cell undergoing mitotic anaphase Planarian_Anatomy PLANA:0003219 anaphase oogonial stem cell oogonial stem cell undergoing mitotic telophase Planarian_Anatomy PLANA:0003220 telophase oogonial stem cell spermatogonium undergoing mitotic G1 phase Planarian_Anatomy PLANA:0003221 G1 phase spermatogonium spermatogonium undergoing mitotic S phase Planarian_Anatomy PLANA:0003222 S phase spermatogonium spermatogonium undergoing mitotic G2 phase Planarian_Anatomy PLANA:0003223 G2 phase spermatogonium spermatogonium undergoing mitotic prophase Planarian_Anatomy PLANA:0003224 prophase spermatogonium spermatogonium undergoing mitotic metaphase Planarian_Anatomy PLANA:0003225 metaphase spermatogonia spermatogonium undergoing mitotic anaphase Planarian_Anatomy PLANA:0003226 anaphase spermatogonia spermatogonium undergoing mitotic telophase Planarian_Anatomy PLANA:0003227 telophase spermatogonium oogonial cell undergoing mitotic G1 phase Planarian_Anatomy PLANA:0003228 G1 phase oogonial cell oogonial cell undergoing mitotic S phase Planarian_Anatomy PLANA:0003229 S phase oogonial cell oogonial cell undergoing mitotic G2 phase Planarian_Anatomy PLANA:0003230 G2 phase oogonial cell oogonial cell undergoing mitotic prophase Planarian_Anatomy PLANA:0003231 prophase oogonial cell oogonial cell undergoing mitotic metaphase Planarian_Anatomy PLANA:0003232 metaphase oogonial cell oogonial cell undergoing mitotic anaphase Planarian_Anatomy PLANA:0003233 anaphase oogonial cell oogonial cell undergoing mitotic telophase Planarian_Anatomy PLANA:0003234 telophase oogonial cell germ cell cyst undergoing mitotic G1 phase Planarian_Anatomy PLANA:0003235 G1 phase germ cell cyst germ cell cyst undergoing mitotic S phase Planarian_Anatomy PLANA:0003236 S phase germ cell cyst germ cell cyst undergoing mitotic G2 phase Planarian_Anatomy PLANA:0003237 G2 phase germ cell cyst germ cell cyst undergoing mitotic prophase Planarian_Anatomy PLANA:0003238 prophase germ cell cyst germ cell cyst undergoing mitotic metaphase Planarian_Anatomy PLANA:0003239 metaphase germ cell cyst germ cell cyst undergoing mitotic anaphase Planarian_Anatomy PLANA:0003240 anaphase germ cell cyst germ cell cyst undergoing mitotic telophase Planarian_Anatomy PLANA:0003241 telophase germ cell cyst spermatocyte undergoing meiotic S phase Planarian_Anatomy PLANA:0003242 meiotic S phase spermatocyte spermatocyte undergoing meiotic G1 phase Planarian_Anatomy PLANA:0003243 meiotic G1 phase spermatocyte spermatocyte undergoing meiotic G2 phase Planarian_Anatomy PLANA:0003244 meiotic G2 phase spermatocyte spermatocyte undergoing meiotic prophase I Planarian_Anatomy PLANA:0003245 meiotic prophase I spermatocyte spermatocyte undergoing leptotene Planarian_Anatomy PLANA:0003246 leptotene stage spermatocyte spermatocyte undergoing zygotene Planarian_Anatomy PLANA:0003247 zygotene stage spermatocyte spermatocyte undergoing zygotene https://doi.org/10.1101/279364 spermatocyte undergoing pachytene Planarian_Anatomy PLANA:0003248 pachytene stage spermatocyte spermatocyte undergoing pachytene https://doi.org/10.1101/279364 spermatocyte undergoing diplotene Planarian_Anatomy PLANA:0003249 diplotene stage spermatocyte spermatocyte undergoing diakinesis Planarian_Anatomy PLANA:0003250 diakinesis stage spermatocyte spermatocyte undergoing meiotic metaphase I Planarian_Anatomy PLANA:0003251 meiotic metaphase 1 stage spermatocyte spermatocyte undergoing meiotic anaphase I Planarian_Anatomy PLANA:0003252 meiotic anaphase I stage spermatocyte spermatocyte undergoing meiotic telophase I Planarian_Anatomy PLANA:0003253 meiotic telophase I spermatocyte spermatocyte undergoing meiosis II cell cycle phase Planarian_Anatomy PLANA:0003254 meiosis II stage spermatocyte spermatocyte undergoing meiotic prophase II Planarian_Anatomy PLANA:0003255 meiotic prophase II spermatocyte spermatocyte undergoing meiotic metaphase II Planarian_Anatomy PLANA:0003256 meiotic metaphase 2 spermatocyte spermatocyte undergoing meiotic anaphase II Planarian_Anatomy PLANA:0003257 meiotic anaphase II spermatocyte spermatocyte undergoing meiotic telophase II Planarian_Anatomy PLANA:0003258 meiotic telophase II spermatocyte This primordium develops into cephalic ganglia PMID:16033796 PMID:17553481 PMID:17905225 PMID:19174194 PMID:21806978 PMID:22339734 PMID:23318635 PMID:25772472 PMID:26525673 brain primordia brain primordium brain primoridia brain rudiment cephalic ganglia primordia cephalic ganglia primordium Planarian_Anatomy PLANA:0003300 cephalic ganglia primordium This primordium develops into eye PMID:22884275 eye aggregate Planarian_Anatomy PLANA:0003301 eye primordium This primordium develops into pharynx PMID:18202849 PMID:21282632 PMID:25254346 PMID:26556349 PMID:27074666 Planarian_Anatomy PLANA:0003302 pharynx primordium This primordium develops into optic cup PMID:21852957 optic cup primordium Planarian_Anatomy PLANA:0003303 pigment cup primordium This primordium develops into testis PMID:23652002 Planarian_Anatomy PLANA:0003304 testis primordium This primordium develops into gonad Planarian_Anatomy PLANA:0003305 gonad primoridium This primordium develops into ovary Planarian_Anatomy PLANA:0003306 ovary primordium lumen which is part of the protonephridia Planarian_Anatomy PLANA:0003400 protonephridial lumen lumen which is part of the protonephridia PMID:26057828 lumen which is part of the testis Planarian_Anatomy PLANA:0003401 testis lumen lumen which is part of the testis PMID:17390146 lumen which is part of the ovary Planarian_Anatomy PLANA:0003402 ovary lumen lumen which is part of the ovary PMID:19247960 lumen which is part of the flame cell flame cell barrel lumen Planarian_Anatomy PLANA:0003403 flame cell lumen lumen which is part of the flame cell PMID:21828097 A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system. brain progenitor brain progentitor cell Planarian_Anatomy cephalic ganglia progenitor cell A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system. PMID:26525673 A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis. Planarian_Anatomy dorsal epidermis progenitor cell A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis. PMID:28292427 A progenitor cell that gives rise to optic cup cells of the eye. optic cup trail cell Planarian_Anatomy optic cup progenitor cell A progenitor cell that gives rise to optic cup cells of the eye. PMID:21852957 A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis. Planarian_Anatomy PLANA:0003503 ventral epidermis progenitor cell A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis. PMID:28292427 This progenitor cell develops into testis somatic gonadal cell Planarian_Anatomy PLANA:0003504 testis somatic gonadal cell progenitor cell This progenitor cell develops into testis somatic gonadal cell PMID: 23652002 A fragment derived from a prepharyngeal amputation encompassing the head. head piece Planarian_Anatomy PLANA:0003600 head fragment A fragment derived from a prepharyngeal amputation encompassing the head. A fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. trunk piece Planarian_Anatomy PLANA:0003601 trunk fragment Illustration of a trunk fragment (in green). A fragment derived from a postpharyngeal amputation encompassing the tail. tail piece Planarian_Anatomy PLANA:0003602 tail fragment A fragment derived from a postpharyngeal amputation encompassing the tail. A fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. neck fragment neck piece Planarian_Anatomy PLANA:0003603 prepharyngeal fragment Illustration of a prepharyngeal fragment (in green). A fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. post-pharyngeal fragment post-pharyngeal piece postpharyngeal piece Planarian_Anatomy PLANA:0003604 postpharyngeal fragment Illustration of a postpharyngeal fragment (in green). A fragment encompassing all or part of the anterior region of the animal. Planarian_Anatomy PLANA:0003605 anterior fragment A fragment encompassing all or part of the anterior region of the animal. A fragment encompassing all or part of the posterior region of the animal. Planarian_Anatomy PLANA:0003606 posterior fragment Illustration of an example of a posterior fragment (in green). A fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. [SMR: a fragment that encompasses the side of the animal, not necessarily longituduinal, or parallel to the midline] edge fragment longitudinal fragment sagittal fragment side fragment Planarian_Anatomy PLANA:0003607 lateral fragment http://purl.obolibrary.org/obo/A fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. [SMR_ a fragment that encompasses the side of the animal, not necessarily longituduinal, or parallel to the midline] a fragment derived from an amputation parallel to the midline. Planarian_Anatomy PLANA:0003608 longitudinal fragment a fragment derived from an amputation parallel to the midline. A 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. Planarian_Anatomy PLANA:0003609 plug fragment Illustration of an example plug fragment in green. A piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. Planarian_Anatomy PLANA:0003610 wedge fragment Illustration of an example wedge fragment in green. The dorsal region of a fragment derived from a prepharyngeal amputation encompassing the head. dorsal region of head fragment Planarian_Anatomy dorsal region of head fragment Illustration of the dorsal region of a head fragment (green). The ventral region of a fragment derived from a prepharyngeal amputation encompassing the head. ventral region of head fragment Planarian_Anatomy ventral region of head fragment Illustration of the ventral region of a head fragment (green). The anterior region of a fragment derived from a prepharyngeal amputation encompassing the head. anterior region of head fragment Planarian_Anatomy anterior region of head fragment Illustration of the anterior region of a head fragment (green). The posterior region of a fragment derived from a prepharyngeal amputation encompassing the head. posterior region of head fragment Planarian_Anatomy posterior region of head fragment Illustration of the posterior region of a head fragment (green). The dorsal region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. dorsal region of trunk fragment Planarian_Anatomy dorsal region of trunk fragment Illustration of the dorsal region of a trunk fragment (green). The ventral region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. ventral region of trunk fragment Planarian_Anatomy ventral region of trunk fragment Illustration of the ventral region of a trunk fragment (green). The anterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. anterior region of trunk fragment Planarian_Anatomy anterior region of trunk fragment Illustration of the anterior region of a trunk fragment (green). The posterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region. posterior region of trunk fragment Planarian_Anatomy posterior region of trunk fragment Illustration of the posterior region of a trunk fragment (green). The dorsal region of a fragment derived from a postpharyngeal amputation encompassing the tail. dorsal region of tail fragment Planarian_Anatomy dorsal region of tail fragment Illustration of the dorsal region of a tail fragment (green). The ventral region of a fragment derived from a postpharyngeal amputation encompassing the tail. ventral region of tail fragment Planarian_Anatomy ventral region of tail fragment Illustration of the ventral region of a tail fragment (green). The anterior region of a fragment derived from a postpharyngeal amputation encompassing the tail. anterior region of tail fragment Planarian_Anatomy anterior region of tail fragment Illustration of the anterior region of a tail fragment (green). The posterior region of a fragment derived from a postpharyngeal amputation encompassing the tail. posterior region of tail fragment Planarian_Anatomy posterior region of tail fragment Illustration of the posterior region of a tail fragment (green). The dorsal region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. dorsal region of prepharyngeal fragment Planarian_Anatomy dorsal region of prepharyngeal fragment Illustration of the dorsal region of a prepharyngeal fragment (green). The ventral region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. ventral region of prepharyngeal fragment Planarian_Anatomy ventral region of prepharyngeal fragment Illustration of the ventral region of a prepharyngeal fragment (green). The anterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. anterior region of prepharyngeal fragment Planarian_Anatomy anterior region of prepharyngeal fragment Illustration of the anterior region of a prepharyngeal fragment (green). The posterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal. posterior region of prepharyngeal fragment Planarian_Anatomy posterior region of prepharyngeal fragment Illustration of the posterior region of a prepharyngeal fragment (green). The dorsal region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. dorsal region of postpharyngeal fragment Planarian_Anatomy dorsal region of postpharyngeal fragment Illustration of the dorsal region of a postpharyngeal fragment (green). The ventral region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. ventral region of postpharyngeal fragment Planarian_Anatomy ventral region of postpharyngeal fragment Illustration of the ventral region of a postpharyngeal fragment (green). The anterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. anterior region of postpharyngeal fragment Planarian_Anatomy anterior region of postpharyngeal fragment Illustration of the anterior region of a postpharyngeal fragment (green). The posterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip. posterior region of postpharyngeal fragment Planarian_Anatomy posterior region of postpharyngeal fragment Illustration of the posterior region of a postpharyngeal fragment (green). The dorsal region of a fragment encompassing all or part of the anterior region of the animal. dorsal region of anterior fragment Planarian_Anatomy dorsal region of anterior fragment Illustration of the dorsal region of an anterior fragment (green). The ventral region of a fragment encompassing all or part of the anterior region of the animal. ventral region of anterior fragment Planarian_Anatomy ventral region of anterior fragment Illustration of the ventral region of an anterior fragment (green). The anterior region of a fragment encompassing all or part of the anterior region of the animal. anterior region of anterior fragment Planarian_Anatomy anterior region of anterior fragment Illustration of the anterior region of an anterior fragment (green). The posterior region of a fragment encompassing all or part of the anterior region of the animal. posterior region of anterior fragment Planarian_Anatomy posterior region of anterior fragment Illustration of the posterior region of an anterior fragment (green). The dorsal region of a fragment encompassing all or part of the posterior region of the animal. dorsal region of posterior fragment Planarian_Anatomy dorsal region of posterior fragment Illustration of the dorsal region of a posterior fragment (green). The ventral region of a fragment encompassing all or part of the posterior region of the animal. ventral region of posterior fragment Planarian_Anatomy ventral region of posterior fragment Illustration of the ventral region of a posterior fragment (green). The anterior region of a fragment encompassing all or part of the posterior region of the animal. anterior region of posterior fragment Planarian_Anatomy anterior region of posterior fragment Illustration of the anterior region of a posterior fragment (green). The posterior region of a fragment encompassing all or part of the posterior region of the animal. posterior region of posterior fragment Planarian_Anatomy posterior region of posterior fragment Illustration of the posterior region of a posterior fragment (green). The dorsal region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. dorsal region of lateral fragment Planarian_Anatomy dorsal region of lateral fragment Illustration of the dorsal region of a lateral fragment (green). The ventral region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. ventral region of lateral fragment Planarian_Anatomy ventral region of lateral fragment Illustration of the ventral region of a lateral fragment (green). The anterior region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. anterior region of lateral fragment Planarian_Anatomy anterior region of lateral fragment Illustration of the anterior region of a lateral fragment (green). The posterior region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. posterior region of lateral fragment Planarian_Anatomy posterior region of lateral fragment Illustration of the posterior region of a lateral fragment (green). The dorsal region of a fragment derived from an amputation parallel to the midline. dorsal region of longitudinal fragment Planarian_Anatomy dorsal region of longitudinal fragment Illustration of the dorsal region of a longitudinal fragment (green). The ventral region of a fragment derived from an amputation parallel to the midline. ventral region of longitudinal fragment Planarian_Anatomy ventral region of longitudinal fragment Illustration of the ventral region of a longitudinal fragment (green). The anterior region of a fragment derived from an amputation parallel to the midline. anterior region of longitudinal fragment Planarian_Anatomy anterior region of longitudinal fragment Illustration of the anterior region of a longitudinal fragment (green). The posterior region of a fragment derived from an amputation parallel to the midline. posterior region of longitudinal fragment Planarian_Anatomy posterior region of longitudinal fragment Illustration of the posterior region of a longitudinal fragment (green). The dorsal region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. dorsal region of plug fragment Planarian_Anatomy dorsal region of plug fragment Illustration of the dorsal region of a plug fragment (green). The ventral region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. ventral region of plug fragment Planarian_Anatomy ventral region of plug fragment Illustration of the ventral region of a plug fragment (green). The anterior region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. anterior region of plug fragment Planarian_Anatomy anterior region of plug fragment Illustration of the anterior region of a plug fragment (green). The posterior region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch. posterior region of plug fragment Planarian_Anatomy posterior region of plug fragment Illustration of the posterior region of a plug fragment (green). The dorsal region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. dorsal region of wedge fragment Planarian_Anatomy dorsal region of wedge fragment Illustration of the dorsal region of a plug fragment (green). The ventral region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. ventral region of wedge fragment Planarian_Anatomy ventral region of wedge fragment Illustration of the ventral region of a plug fragment (green). The anterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. anterior region of wedge fragment Planarian_Anatomy anterior region of wedge fragment Illustration of the anterior region of a wedge fragment (green). The posterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures. posterior region of wedge fragment Planarian_Anatomy posterior region of wedge fragment Illustration of the posterior region of a wedge fragment (green). photoreceptor neuron is contained in the anterior region of the eye photoreceptor neuron contained in anterior region of the eye Planarian_Anatomy anterior photoreceptor neuron photoreceptor neuron is contained in the anterior region of the eye PMID: 20967238 photoreceptor neuron is contained in the posterior region of the eye photoreceptor neuron contained in posterior region of the eye Planarian_Anatomy posterior photoreceptor neuron photoreceptor neuron is contained in the posterior region of the eye PMID: 20967238 muscle cell is contained in the lateral region muscle cell contained in lateral region Planarian_Anatomy lateral muscle cell muscle cell is contained in the lateral region PMID: 29674431 muscle cell is contained in the anterior region muscle cell contained in anterior region Planarian_Anatomy anterior muscle cell muscle cell is contained in the anterior region PMID: 29674432 muscle cell is contained in the posterior region muscle cell contained in posterior region Planarian_Anatomy posterior muscle cell muscle cell is contained in the posterior region PMID: 29674433 blastema which develops into head region Planarian_Anatomy PLANA:0003900 head blastema blastema which develops into tail region Planarian_Anatomy PLANA:0003901 tail blastema a head fragment that is regenerating Planarian_Anatomy regenerating head fragment a trunk fragment that is regenerating Planarian_Anatomy regenerating trunk fragment a tail fragment that is regenerating Planarian_Anatomy regenerating tail fragment a prepharyngeal fragment that is regenerating Planarian_Anatomy regenerating prepharyngeal fragment a postpharyngeal fragment that is regenerating Planarian_Anatomy regenerating postpharyngeal fragment a anterior fragment that is regenerating Planarian_Anatomy regenerating anterior fragment a posterior fragment that is regenerating Planarian_Anatomy regenerating posterior fragment a lateral fragment that is regenerating Planarian_Anatomy regenerating lateral fragment a longitudinal fragment that is regenerating Planarian_Anatomy regenerating longitudinal fragment a plug fragment that is regenerating Planarian_Anatomy regenerating plug fragment a wedge fragment that is regenerating Planarian_Anatomy regenerating wedge fragment A fully formed, sexually mature organism that reproduces through cross-fertilization. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:11972158 PMID:19022767 sexual adult sexually mature adult Planarian_Anatomy adult hermaphrodite A fully formed, sexually mature organism that reproduces through cross-fertilization. PMID:11972158 PMID:19022767 Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm. Asexually reproducing Schmidtea mediterranea exist as constitutive adults, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:11972158 PMID:17376870 Planarian_Anatomy asexual adult Asexually reproducing Schmidtea mediterranea exist as constitutive adults, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. PMID:11972158 PMID:17376870 Depicted by field shows an asexual adult with a scale bar of 500um dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:23652002 PMID:27163480 somatic gonadal cell of the testis somatic niche cell of the testis somatic testis cell Planarian_Anatomy testis somatic gonadal cell dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. PMID:23652002 PMID:27163480 ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27163480 somatic follicular cell of the ovary somatic ovarian cell Planarian_Anatomy ovarian somatic gonadal cell ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. PMID:27163480 Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the embryonic pharynx; the aboral pole is located opposite the embryonic pharynx. oral-aboral axis of embryo Planarian_Anatomy PLANA:0004511 oral-aboral axis of the embryo Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the embryonic pharynx; the aboral pole is located opposite the embryonic pharynx. PMID:28072387 Illustration noting the oral-aboral axis in cyan double headed arrow. It starts at the embryonic pharynx and extends to opposite pole. The apical surface of the single layered primitive ectoderm that is in contact with the environment. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Planarian_Anatomy primitive ectoderm surface The apical surface of the single layered primitive ectoderm that is in contact with the environment. OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The surface of the primitive gut cells in contact with the embryonic wall. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy primtive gut cell surface The surface of the primitive gut cells in contact with the embryonic wall. PMID:28072387 The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic gut cell surface The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. PMID:28072387 The epithelial cell surface lining the embryonic pharynx lumen. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20100474 PMID:28072387 Planarian_Anatomy embryonic pharynx lumen epithelial surface The epithelial cell surface lining the embryonic pharynx lumen. PMID:28072387 An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Blastomeres give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000353 PMID:28072387 Planarian_Anatomy blastomere An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Blastomeres give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. PMID:28072387 Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000349 PMID:28072387 Planarian_Anatomy extraembryonic cell Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. PMID:28072387 A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic pharynx neuron A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. PMID:28072387 Differentiated radial muscle cell present in the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16932928 embryonic pharynx radial muscle fiber Planarian_Anatomy embryonic pharynx radial muscle cell Differentiated radial muscle cell present in the embryonic pharynx. PMID:16932928 foxA1+ epithelial cell contained in the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20100474 PMID:28072387 Planarian_Anatomy embryonic pharynx epithelial cell foxA1+ epithelial cell contained in the embryonic pharynx. PMID:28072387 Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16932928 embryonic pharynx circular muscle fiber Planarian_Anatomy embryonic pharynx circular muscle cell Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx. PMID:16932928 Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22074376 Planarian_Anatomy copulatory region Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. PMID:22074376 Depicted by field contains diagram representation of body region. Epithelia associated with the pharynx organ. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0003351 pharnyx epidermis pharyngeal epidermis pharyngeal epithelium Planarian_Anatomy pharynx epithelium Image is an electron micrograph of a transverse section through the pharynx. Outlined, is the outer epithium, which is an "insunk" epithelium where the nuclei are set back medially away from the epithelium surface. Here, just the surface is outlined.. Scale bar is 2um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0002416 Planarian_Anatomy 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. UBERON:0002416 Anatomical space enclosed by the oviduct epithelium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22074376 TADS:0000435 Planarian_Anatomy oviduct lumen Anatomical space enclosed by the oviduct epithelium. PMID:22074376 Anatomical space enclosed by the sperm duct epithelium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:22074376 Planarian_Anatomy sperm duct lumen Anatomical space enclosed by the sperm duct epithelium. PMID:19022767 PMID:22074376 Ciliated epithelium lining the oviduct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:2000064 PMID:22074376 UBERON:0004804 Planarian_Anatomy oviduct epithelium Ciliated epithelium lining the oviduct. PMID:22074376 Ciliated epithelium lining the sperm duct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:22074376 Planarian_Anatomy sperm duct epithelium Ciliated epithelium lining the sperm duct. PMID:19022767 PMID:22074376 Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 Planarian_Anatomy tuba lumen Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 let odk import from BSPO if needed obsolete coronal plane true Anatomical plane which divides the body into right and left parts. This plane passes through the midline at the midline but does not always the midline. sagittal plane of whole organism Planarian_Anatomy PLANA:0007503 sagittal plane of the whole animal Illustration of a sagittal plane of the whole animal (in green). replaced by dorsal region PLANA:0000141 obsolete dorsal compartment true now using patterned term ventral region PLANA:0000143 obsolete ventral compartment true now using patterned term anterior region obsolete anterior compartment true replaced replacing duplicate PLANA term obsolete posterior compartment true choosing to use UBERON:0000476, acellular anatomical structure instead obsolete extracellular component true The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005886 PMID:20511647 PMID:27523733 cell membrane cytoplasmic membrane Planarian_Anatomy plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005886 Image is an electron micrograph showing several cells. Arrowheads label the plasma membrane, the boundary between cells. Scale bar is 1um. Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0043230 Planarian_Anatomy extracellular organelle Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. GO:0043230 A spherical to rod shaped organelle that generates the majority of a cell's supply of ATP via cellular respiration. Mitochondria have their own genome and consist of outer and inner membranes, the latter folds inward to form cristae. This folding increases the surface area of the membrane and thus increases the space available to produce ATP. The inner and outer membranes are separated by an intermembrane space, and the inner membrane encloses the matrix. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005739 PMID:21828097 PMID:22318224 PMID:26516985 PMID:29100657 mitochondria Planarian_Anatomy mitochondrion Image is an electron micrograph depicting a couple different cells. A few mitochondria have been labeled with arrowheads. Note the variation in shape from spherical to rod-like. This is dependent on cutting orientation at fission/fusion state of the mitochondria. Scale bar is 1 um. Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005783 PMID:30143032 Planarian_Anatomy endoplasmic reticulum Image is an electron micrograph depicting endoplasmic reticulum (magenta) in multiple cells. Scale bar is 0.5um. Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. The outer surface is studded with protein-synthesizing particles known as ribosomes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005791 PMID:30143032 Planarian_Anatomy rough endoplasmic reticulum Image is an electron micrograph depicting the rough endoplasmic reticulum (arrowheads) of a cell. Ribosomes can be seen associating with the ER membrane creating a rough ER, as well as free within the cytoplasm of the cell. Scale bar is 200 nm. Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005790 Planarian_Anatomy smooth endoplasmic reticulum Image is an electron micrograph depicting smooth ER (arrowheads) in a cell, next to the nucleus (N). Ribosomes can be seen within the cytoplasm, but not associating with the ER membrane. Scale bar is 200 nm. Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005643 Planarian_Anatomy nuclear pore Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. GO:0005643 Image is an electron micrograph depicting the nuclear envelope. The nucleus takes up the top left corner of the image and two nuclear pores have been labeled with arrowheads. Scale bar is 200 nm. The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 GO:0005764 ISBN:0-71677033-4 PMID:4853064 Planarian_Anatomy lysosome Image is an electron micrograph depicting two lysosomes (arrowheads) within a cell. The nucleus sits in the bottom left corner. Lysosomes can sometimes be identified by the swirling material they are breaking down inside. Scale bar is 0.5um. Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side. anterior-posterior axis anterior-posterior axis of whole organism body axis longitudinal axis main body axis Planarian_Anatomy PLANA:0007519 anterior-posterior axis of the whole animal Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side. D/V axis DV axis dorsal-ventral axis dorsal-ventral axis of whole organism Planarian_Anatomy PLANA:0007520 dorsal-ventral axis of the whole animal Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side. PMID:18287199 PMID:18786419 PMID:19174194 PMID:21295481 PMID:21295483 PMID:21664348 PMID:21806978 PMID:22445864 PMID:23318641 PMID:23954785 PMID:24415944 PMID:24523458 PMID:25017721 PMID:27063937 PMID:27523733 PMID:27612382 PMID:28137894 PMID:28292427 PMID:28686611 PMID:29100657 PMID:29547123 PMID:29674431 PMID:30471994 Axis perpendicular to both the anteroposterior and dorsoventral axis that runs from the left side of the animal, through the medial region (center) and out to the right side. dextro-sinister axis left-right axis left-right axis of whole organism Planarian_Anatomy PLANA:0007521 left-right axis of the whole animal Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal. medial-lateral axis medial-lateral axis of whole organism mediolateral mediolateral axis Planarian_Anatomy PLANA:0007522 medial-lateral axis of the whole animal Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal. PMID:20707997 PMID:21282632 PMID:21295483 PMID:21664348 PMID:21806978 PMID:23250205 PMID:23318641 PMID:23903188 PMID:23954785 PMID:25017721 PMID:26062938 PMID:26525673 PMID:27523733 PMID:28287248 PMID:29291981 PMID:29547123 PMID:30471994 PMID:30962434 Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body. proximal-distal axis proximal-distal axis of whole organism Planarian_Anatomy PLANA:0007523 proximal-distal axis of the whole animal Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body. PMID:21828097 Pharynx of an asexual adult exposed by tricaine treatment. The proximodistal axis is denoted with the double headed magenta arrow. Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18063755 PMID:21566195 PMID:23297191 PMID:23318641 PMID:23903188 PMID:23954785 PMID:24040508 PMID:24415944 PMID:24523458 PMID:24704339 PMID:24992682 PMID:25254346 PMID:25725068 PMID:26062938 PMID:26525673 PMID:27074666 PMID:27800171 PMID:28216315 PMID:28292427 PMID:28893948 PMID:29547123 PMID:29906446 PMID:30485821 anterior signaling center Planarian_Anatomy anterior pole Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. PMID:21566195 PMID:23297191 PMID:24040508 PMID:24415944 PMID:24704339 PMID:24992682 Illustration of the anterior pole (green). Distinct posterior cluster of muscle cells located at the midline which express wnt1. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18063755 PMID:19805089 PMID:21566195 PMID:23318641 PMID:23903188 PMID:24415944 PMID:25725068 PMID:26062938 PMID:27074666 PMID:30485821 posterior regeneration pole Planarian_Anatomy posterior pole Distinct posterior cluster of muscle cells located at the midline which express wnt1. PMID:18063755 PMID:21680047 Illustration of the posterior pole (in green). A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000125 PMID:27612382 PMID:27612384 PMID:28137894 PMID:29674431 PMID:29674432 PMID:30471994 glia glia cell Planarian_Anatomy glial cell A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. PMID:27612384 Image is an electron micrograph depicting a section of the ventral nerve cord. The arrowheads point at a likely glial cell. Note the difference in darkness of cytoplasm in the cell body of the glial cell compared to the surrounding axons. Scale bar is 2um. A biological tissue mass of nerve cell bodies. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000045 ganglia Planarian_Anatomy ganglion A biological tissue mass of nerve cell bodies. UBERON:0000045 Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:24120894 doi:10.1002/jmor.1051550208 epithelial pharynx lining epithelium lining the lumen of the pharynx inner epithelium inner pharyngeal epidermis inner pharyngeal epithelium inner pharynx epidermis inner pharynx epithelium Planarian_Anatomy pharynx inner epithelium Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. OCLC:16809160 doi:10.1002/jmor.1051550208 Image is an electron micrograph of a transverse section through the pharynx. An epidermal cell, a part of the inner epithelial layer, has been marked with arrowheads. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um. Pharynx muscle fibers running circumferentially about the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ASIN:B000M4NK9M pharyngeal circular muscle cell pharynx circular muscle cell pharynx circular muscle fiber Planarian_Anatomy pharynx circular muscle cell Pharynx muscle fibers running circumferentially about the pharynx. ASIN:B000M4NK9M Image is an electron micrograph of a transverse section through the pharynx. The pharynx lumen it to the left. The inner circular muscle (arrowheads) is immediately deep to the inner epithelial layer of the pharynx. Magenta = circular; green = longitudinal; red = radial. Scale bar is 2 um. using part of instead obsolete specific_to true replacing duplicate PLANA term obsolete brain true Groupings of specialized epithelial cells located along the dorsal ventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epidermal surface. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:20865784 marginal adhesive gland Planarian_Anatomy adhesion gland Groupings of specialized epithelial cells located along the dorsal ventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epidermal surface. OCLC:16809160 PMID:20865784 Image is an electron micrograph showing the multicellular total adhesion gland structure (outlined) embedded in the epidermis. Note that the gland cells cross the basal lamina into the epithelium. Ventral is up and scale bar is 2um. Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:20865784 Planarian_Anatomy anchor cell Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. OCLC:16809160 PMID:20865784 Image is an electron micrograph showing the total multicellualr adhesion gland structure. The anchor cell has been outlined, though mucus-filled projections of gland cells can be seen densely packed inside. Nucleus is that of the anchor cell. Ventral is up and scale bar is 2um. A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:20865784 Planarian_Anatomy viscid gland cell A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. OCLC:16809160 PMID:20865784 Image is an electron micrograph showing the whole adhesion gland structure, specifically outlining a single cell (viscid gland cell) associated with this multicelluar structure. Ventral is up and scale bar is 2um. Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:20865784 Planarian_Anatomy releasing gland cell Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. OCLC:16809160 PMID:20865784 Image is an electron micrograph showing the whole adhesion gland structure. Arrowheads mark releasing gland cells which are associated with this multicelluar structure. The releasing gland cells have very small excretory particles compared to the neighboring viscid gland. Ventral is up and scale bar is 1um. A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25254346 TrpA+ neuron Planarian_Anatomy TrpA+ central nervous system neuron A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. PMID:25254346 A subset of sensory neurons located along the dorsal head margin. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:12557210 PMID:25254346 PMID:29674431 cintillo+ neuron Planarian_Anatomy cintillo+ sensory neuron A subset of sensory neurons located along the dorsal head margin. PMID:12557210 PMID:25254346 PMID:29674431 no longer designating mediolateral regions using the contained_in object property obsolete epidermal compartment true piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25254346 Planarian_Anatomy TrpA+ neural progenitor cell piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. PMID:25254346 piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:24415944 Planarian_Anatomy anterior pole progenitor cell piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. PMID:24415944 Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17999079 Planarian_Anatomy transverse commissure Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. PMID:17999079 no longer designating mediolateral regions using the contained_in object property obsolete body wall musculature compartment true piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:23903188 PMID:24131630 PMID:25254346 Planarian_Anatomy serotonergic neural progenitor cell piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. PMID:23903188 PMID:24131630 PMID:25254346 piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25254346 Planarian_Anatomy klf+ sensory neuron progenitor cell piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. PMID:25254346 A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:27150006 vNeoblast Planarian_Anatomy nu neoblast A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. PMID:27150006 A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17999079 Planarian_Anatomy lateral nerve A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. PMID:17999079 no longer designating mediolateral regions using the contained_in object property obsolete parenchymal compartment true piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25254346 Planarian_Anatomy pax3/7+ neural progenitor cell piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. PMID:25254346 A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic pharynx lumen A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity. PMID:28072387 Nerve plexus surrounding the testis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17999079 PMID:7833618 Planarian_Anatomy testis nerve plexus Nerve plexus surrounding the testis. PMID:17999079 PMID:7833618 Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:11972158 Planarian_Anatomy fission plane Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. OCLC:16809160 PMID:11972158 Nerve plexus surrounding the ovary. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17999079 PMID:7833618 Planarian_Anatomy ovary nerve plexus Nerve plexus surrounding the ovary. PMID:17999079 PMID:7833618 no longer designating mediolateral regions using the contained_in object property obsolete gastrovascular compartment true Peripheral region of the head. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy head margin Neurons that express the biogenic amine glutamate. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000679 PMID:24131630 Planarian_Anatomy glutamatergic neuron Neurons that express the biogenic amine glutamate. PMID:24131630 An individual member of the sexual biotype of Schmidtea mediterranea. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy sexual organism An individual member of the asexual biotype of Schmidtea mediterranea. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CARO:0000030 Planarian_Anatomy asexual organism A neuron cell that does not have cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 non cilated neuron uncilated neuon Planarian_Anatomy non-ciliated neuron A neuron cell that does not have cilia. PMID:29674431 A neuron that has cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 WBbt:0006816 Planarian_Anatomy cilated neuron A neuron that has cilia. PMID:29674431 A cell present near the brain and eye where photoreceptor axons form a bundle projecting out from the eye that are near axon choice points. Guidepost cells are positive for Arrestin, notum, fz5/8-4+, 6G10, and low levels of troponin, tropomyosin, colF-2 and mp-1. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy guidepost cell A cell present near the brain and eye where photoreceptor axons form a bundle projecting out from the eye that are near axon choice points. Guidepost cells are positive for Arrestin, notum, fz5/8-4+, 6G10, and low levels of troponin, tropomyosin, colF-2 and mp-1. PMID:32586989 Guidepost cell associated with the visual circuit that are present near the eye, located along axons just anterior and ventral to the eye. Name acronym stands for notum+ muscle cell near eye. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy NME cell Guidepost cell associated with the visual circuit that are present near the eye, located along axons just anterior and ventral to the eye. Name acronym stands for notum+ muscle cell near eye. PMID:32586989 Guidepost cell assocaited with the visual circuit, present at the axon choice point ventral, posterior to and slightly medial to the eye. Name acronym stands for notum+ muscle cells at the choice point. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy NMC cell Guidepost cell assocaited with the visual circuit, present at the axon choice point ventral, posterior to and slightly medial to the eye. Name acronym stands for notum+ muscle cells at the choice point. PMID:32586989 Guidepost cell present at the medial brain, ventral to the optic chiasm. Closely associated with photoreceptor axons during regneration. Name acronym stands for notum+ brain cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy NBC cell Guidepost cell present at the medial brain, ventral to the optic chiasm. Closely associated with photoreceptor axons during regneration. Name acronym stands for notum+ brain cells. PMID:32586989 A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 juvenile Planarian_Anatomy juvenile organism Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 SCTID:296280003 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. http://orcid.org/0000-0002-6601-2165 A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MESH:D008018 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. https://orcid.org/0000-0002-6601-2165 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 TAO:0001308 TGMA:0001840 VHOG:0001758 Wikipedia:Body_part XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS http://orcid.org/0000-0001-9114-8737 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 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 acellular anatomical structures ZFA:0000382 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 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 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 http://orcid.org/0000-0001-9114-8737 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 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 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 An anatomical structure that is undergoing regeneration. we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure. AEO:0000200 EHDAA2:0003233 TAO:0005147 XAO:0004059 ZFA:0005147 uberon regenerating tissue regenerating tissues regenerative tissue UBERON:0007567 regenerating anatomical structure An anatomical structure that is undergoing regeneration. http://orcid.org/0000-0002-6601-2165 regenerating tissue ZFA:0005147 regenerating tissues ZFA:0005147 example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X