Planarian Anatomy Ontology (PLANA)
type: Ontology
version IRI: http://purl.obolibrary.org/obo/plana/releases/2023-03-13
description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
license: https://creativecommons.org/licenses/by/3.0/
default-namespace: Planarian_Anatomy
has_obo_format_version: 1.2
treat-xrefs-as-genus-differentia: CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327
version info: 2023-03-13

definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
IAO_0000111: editor note
IAO_0000114: ready for release
definition: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

curator note
type: AnnotationProperty
IAO_0000111: curator note
IAO_0000114: ready for release
definition: An administrative note of use for a curator but of no use for a user
IAO_0000117: PERSON:Alan Ruttenberg

imported from
type: AnnotationProperty
IAO_0000111: imported from
IAO_0000114: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

term replaced by
type: AnnotationProperty
IAO_0000111: term replaced by
IAO_0000114: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

is indirect form of
type: AnnotationProperty
definition: 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
definition: 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
creator: https://orcid.org/0000-0002-6601-2165

is a defining property chain axiom
type: AnnotationProperty
definition: 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 where second argument is reflexive
type: AnnotationProperty
definition: 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.

external_definition
type: AnnotationProperty
definition: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.

homology_notes
type: AnnotationProperty
definition: Notes on the homology status of this class.

has_relational_adjective
type: AnnotationProperty

taxon_notes
type: AnnotationProperty
definition: Notes on the how instances of this class vary across species.

external_ontology_notes
type: AnnotationProperty
definition: Notes on how similar or equivalent classes are represented in other ontologies.

synonym typically used in the context of human anatomy
type: AnnotationProperty
database_cross_reference: IAO:0100001
has_scope: has_narrow_synonym
sub property of: synonym_type_property

synonym typically used in the context of vertebrate anatomy
type: AnnotationProperty
database_cross_reference: IAO:0100001
has_scope: has_narrow_synonym
sub property of: synonym_type_property

creator
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-creator
is metadata tag: true
shorthand: dc-creator

description
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-description
is metadata tag: true
shorthand: dc-description

title
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-title
is metadata tag: true
shorthand: dc-title

license
type: AnnotationProperty
has_obo_namespace: uberon
id: dcterms-license
is metadata tag: true
shorthand: dcterms-license

namespace-id-rule
type: AnnotationProperty
database_cross_reference: IAO:0100001

synonym_type_property
type: AnnotationProperty
database_cross_reference: IAO:0100001

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
label: has broad synonym

database_cross_reference
type: AnnotationProperty
database_cross_reference: IAO:0100001

has_exact_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
database_cross_reference: IAO:0100001
label: has exact synonym

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
database_cross_reference: IAO:0100001
label: has narrow synonym

has_obo_format_version
type: AnnotationProperty
database_cross_reference: IAO:0100001

has_obo_namespace
type: AnnotationProperty
database_cross_reference: IAO:0100001

has_related_synonym
type: AnnotationProperty
definition: 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.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
database_cross_reference: IAO:0100001
label: has related synonym

has_scope
type: AnnotationProperty
database_cross_reference: IAO:0100001

has_synonym_type
type: AnnotationProperty
database_cross_reference: IAO:0100001

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty
database_cross_reference: IAO:0100001

treat-xrefs-as-genus-differentia
type: AnnotationProperty
created by: Sofia Robb
creation date: 2017-07-26T18:19:59Z

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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/
editor note: 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'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable entity
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: generically dependent continuant
database_cross_reference: BFO:0000050
has_obo_namespace: external
has_obo_namespace: quality
has_obo_namespace: spatial
has_obo_namespace: uberon
id: part_of
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: part_of
label: part_of

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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/
editor note: 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'.
IAO_0000118: has_part
RO_0001900: RO_0001901
database_cross_reference: BFO:0000051
has_obo_namespace: external
has_obo_namespace: quality
has_obo_namespace: spatial
has_obo_namespace: uberon
id: has_part
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: has_part
label: has_part

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: preceded by
definition: 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.
editor note: 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.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: precedes
definition: 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.
in_subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
IAO_0000111: occurs in
definition: 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
IAO_0000118: occurs_in
IAO_0000118: unfolds in
IAO_0000118: unfolds_in
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
IAO_0000111: site of
definition: [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
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

anterior to
type: ObjectProperty
inverse of: posterior to
type: TransitiveProperty
definition: 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.
database_cross_reference: BSPO:0000096
has_exact_synonym: rostral_to
has_obo_namespace: spatial
id: anterior_to
shorthand: anterior_to

Axiom
annotated source: anterior to
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:cjm

dorsal to
type: ObjectProperty
inverse of: ventral to
type: TransitiveProperty
definition: 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).
database_cross_reference: BSPO:0000098
has_obo_namespace: spatial
id: dorsal_to
shorthand: dorsal_to

Axiom
annotated source: dorsal to
annotated property: definition
annotated target: 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).
database_cross_reference: BSPO:cjm

posterior to
type: ObjectProperty
type: TransitiveProperty
definition: 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.
database_cross_reference: BSPO:0000099
has_narrow_synonym: caudal to
has_obo_namespace: spatial
id: posterior_to
shorthand: posterior_to

Axiom
annotated source: posterior to
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:cjm

Axiom
annotated source: posterior to
annotated property: has_narrow_synonym
annotated target: caudal to
has_synonym_type: synonym typically used in the context of vertebrate anatomy

ventral to
type: ObjectProperty
type: TransitiveProperty
definition: 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).
database_cross_reference: BSPO:0000102
has_obo_namespace: spatial
id: ventral_to
shorthand: ventral_to

Axiom
annotated source: ventral to
annotated property: definition
annotated target: 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).
database_cross_reference: BSPO:cjm

approximately perpendicular to
type: ObjectProperty
domain: anatomical axis
range: anatomical axis
definition: 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.
database_cross_reference: BSPO:0000104
has_obo_namespace: spatial
id: approximately_perpendicular_to
shorthand: approximately_perpendicular_to

Axiom
annotated source: approximately perpendicular to
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:cjm

deep to
type: ObjectProperty
inverse of: superficial to
type: TransitiveProperty
definition: Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
database_cross_reference: BSPO:0000107
has_obo_namespace: spatial
id: deep_to
shorthand: deep_to

Axiom
annotated source: deep to
annotated property: definition
annotated target: Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
database_cross_reference: BSPO:cjm

superficial to
type: ObjectProperty
type: TransitiveProperty
definition: Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
database_cross_reference: BSPO:0000108
has_obo_namespace: spatial
id: superficial_to
shorthand: superficial_to

Axiom
annotated source: superficial to
annotated property: definition
annotated target: Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
database_cross_reference: BSPO:cjm

opposite to
type: ObjectProperty
definition: Direcly opposite to. i.e. on the opposite side through the axis.
database_cross_reference: BSPO:0000113
has_obo_namespace: spatial
id: opposite_to
shorthand: opposite_to

Axiom
annotated source: opposite to
annotated property: definition
annotated target: Direcly opposite to. i.e. on the opposite side through the axis.
database_cross_reference: BSPO:cjm

in left side of
type: ObjectProperty
sub property of: in lateral side of
property disjoint with: in right side of
definition: X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
database_cross_reference: BSPO:0000120
has_obo_namespace: spatial
id: in_left_side_of
shorthand: in_left_side_of

Axiom
annotated source: in left side of
annotated property: definition
annotated target: X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
database_cross_reference: BSPO:PATO_mtg_2009

in right side of
type: ObjectProperty
sub property of: in lateral side of
definition: X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
database_cross_reference: BSPO:0000121
has_obo_namespace: spatial
id: in_right_side_of
shorthand: in_right_side_of

Axiom
annotated source: in right side of
annotated property: definition
annotated target: X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
database_cross_reference: BSPO:PATO_mtg_2009

in lateral side of
type: ObjectProperty
sub property of: part of
definition: 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
database_cross_reference: BSPO:0000126
has_obo_namespace: spatial
id: in_lateral_side_of
shorthand: in_lateral_side_of

Axiom
annotated source: in lateral side of
annotated property: definition
annotated target: 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
database_cross_reference: UBERON:cjm

parallel to
type: ObjectProperty
definition: x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
has_obo_namespace: spatial
id: parallel_to

Axiom
annotated source: parallel to
annotated property: definition
annotated target: x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
database_cross_reference: BSPO:curators

immediately deep to
type: ObjectProperty
sub property of: deep to
inverse of: immediately superficial to
definition: x immediately deep to y iff x deep_to y and x is contiguous with y.
database_cross_reference: BSPO:0001107
has_obo_namespace: spatial
id: immediately_deep_to
shorthand: immediately_deep_to

Axiom
annotated source: immediately deep to
annotated property: definition
annotated target: x immediately deep to y iff x deep_to y and x is contiguous with y.
database_cross_reference: BSPO:curators

finishes axis
type: ObjectProperty
domain: anatomical side
range: anatomical axis
database_cross_reference: BSPO:0015001
has_obo_namespace: spatial
id: finishes_axis
shorthand: finishes_axis
comment: 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

orthogonal to
type: ObjectProperty
domain: anatomical axis
range: anatomical plane
definition: crossing at right angles
database_cross_reference: BSPO:0015005
has_obo_namespace: spatial
id: orthogonal_to
shorthand: orthogonal_to

Axiom
annotated source: orthogonal to
annotated property: definition
annotated target: crossing at right angles
database_cross_reference: BSPO:cjm

passes through
type: ObjectProperty
domain: anatomical axis
definition: Intersects at two points.
database_cross_reference: BSPO:0015006
has_obo_namespace: spatial
id: passes_through
shorthand: passes_through

Axiom
annotated source: passes through
annotated property: definition
annotated target: Intersects at two points.
database_cross_reference: BSPO:cjm

starts axis
type: ObjectProperty
domain: anatomical side
range: anatomical axis
database_cross_reference: BSPO:0015007
has_obo_namespace: spatial
id: starts_axis
shorthand: starts_axis
comment: 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

surface of
type: ObjectProperty
domain: anatomical surface
database_cross_reference: BSPO:0015008
has_obo_namespace: spatial
id: surface_of
shorthand: surface_of
comment: placeholder. used for relation between anatomical surface and an anatomical side.

immediately superficial to
type: ObjectProperty
sub property of: superficial to
sub property of: adjacent to
definition: x immediately superficial to y iff x superficial to y and x is contiguous with y.
database_cross_reference: BSPO:0015014
has_obo_namespace: spatial
id: immediately_superficial_to
shorthand: immediately_superficial_to

Axiom
annotated source: immediately superficial to
annotated property: definition
annotated target: x immediately superficial to y iff x superficial to y and x is contiguous with y.
database_cross_reference: BSPO:curators

is about
type: ObjectProperty
domain: information content entity
IAO_0000112: This document is about information artifacts and their representations
IAO_0000114: pending final vetting
definition: A (currently) primitive relation that relates an information artifact to an entity.
editor note: 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.
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
IAO_0000112: 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.
definition: 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
editor note: 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
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

denoted by
type: ObjectProperty
domain: entity
range: information content entity
definition: inverse of the relation 'denotes'
IAO_0000117: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/206

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
domain: planned process
IAO_0000111: has_specified_output
IAO_0000114: ready for release
definition: The inverse property of is_specified_output_of
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
IAO_0000111: is_specified_output_of
IAO_0000114: ready for release
definition: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters
imported from: obi.owl

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
definition: 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.
IAO_0000118: inheres_in
RO_0001900: RO_0001901
comment: 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.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
editor note: 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.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: 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.
IAO_0000118: function_of
IAO_0000118: is function of
comment: 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
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000112: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
comment: 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
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: 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.
IAO_0000118: is role of
IAO_0000118: role_of
comment: 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.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: 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.
IAO_0000118: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000112: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: 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.
IAO_0000118: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: 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.
IAO_0000118: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in_subset: RO_0002259
comment: 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.

derives from
type: ObjectProperty
inverse of: derives into
IAO_0000112: this cell derives from this parent cell (cell division)
IAO_0000112: this nucleus derives from this parent nucleus (nuclear division)
IAO_0000114: pending final vetting
definition: 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
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
IAO_0000118: derives_from
curator note: 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.
in_subset: ro-eco

derives into
type: ObjectProperty
IAO_0000112: this parent cell derives into this cell (cell division)
IAO_0000112: this parent nucleus derives into this nucleus (nuclear division)
IAO_0000114: pending final vetting
definition: 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
editor note: 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'.
IAO_0000118: derives_into
in_subset: ro-eco

contained in
type: ObjectProperty
inverse of: contains
domain: material entity
range: independent continuant
IAO_0000111: contained in
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
editor note: 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):
editor note: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
IAO_0000118: contained_in
RO_0001900: RO_0001901
in_subset: ro-eco

contains
type: ObjectProperty
IAO_0000111: contains
RO_0001900: RO_0001901
in_subset: ro-eco

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: 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.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: 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.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: 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 positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: 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.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: 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 component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: 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.
created by: dos
creation date: 2017-05-24T09:49:21Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: 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.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: 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.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: 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.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: 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.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: 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.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dos

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
database_cross_reference: RO:0002092
has_obo_namespace: external
id: happens_during
shorthand: happens_during

ends during
type: ObjectProperty
database_cross_reference: RO:0002093
has_obo_namespace: external
id: ends_during
shorthand: ends_during

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
definition: x overlaps y iff they have some part in common.
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
database_cross_reference: RO:0002131
has_obo_namespace: spatial
id: overlaps
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco
shorthand: overlaps
comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

Axiom
annotated source: overlaps
annotated property: definition
annotated target: x overlaps y iff they have some part in common.
database_cross_reference: BSPO:cjm

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: 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
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: ro-eco

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: pending final vetting
definition: 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.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
in_subset: ro-eco

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
IAO_0000114: pending final vetting
definition: 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
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: inverse of develops from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
in_subset: RO_0002259

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
definition: 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.
IAO_0000117: https://orcid.org/0000-0001-7476-6306
IAO_0000117: https://orcid.org/0000-0002-3837-8864
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000117: David Hill
IAO_0000117: Tanya Berardini
IAO_0000119: causal-relations
IAO_0000119: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: 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)".
in_subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
type: SymmetricProperty
domain: independent continuant
range: independent continuant
IAO_0000112: 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.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: 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.
IAO_0000114: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
database_cross_reference: RO:0002220
has_obo_namespace: spatial
id: adjacent_to
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: adjacent_to

Axiom
annotated source: adjacent to
annotated property: IAO_0000112
annotated target: 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.

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: Allen's interval algebra
curator note: 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.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
IAO_0000114: pending final vetting
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: consumes
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: pending final vetting
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
IAO_0000114: pending final vetting
definition: inverse of has developmental contribution from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
IAO_0000114: pending final vetting
definition: 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
editor note: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
curator note: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: 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.
definition: 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.
in_subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: 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.
has_related_synonym: affects
in_subset: valid for go gp2term

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: pending final vetting
definition: Inverse of developmentally preceded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: 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.
RO_0004049: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: 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, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: 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.
RO_0004050: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: 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.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
curator note: 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.
in_subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: actively involved in
IAO_0000118: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
in_subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000589: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
in_subset: RO_0002259

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
in_subset: RO_0002259
in_subset: ro-eco

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
IAO_0000114: requires discussion
definition: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: requires discussion
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: requires discussion
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: requires discussion
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: requires discussion
definition: inverse of upstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: requires discussion
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: indirectly activates
is indirect form of: positively regulates

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: indirectly inhibits
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
definition: 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.
editor note: 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 yie…
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: 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.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
in_subset: valid for go annotation extension
in_subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: 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.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: influences (processual)
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
in_subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: 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
editor note: OWL does not allow defining object properties via a Union
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: executes activity in
has_exact_synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dos

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: 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.
editor note: Considering relabeling as 'pairwise interacts with'
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
curator note: 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.
has_exact_synonym: in pairwise interaction with
in_subset: ro-eco

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: binds
IAO_0000118: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
has_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly inhibits
has_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly activates
has_exact_synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
curator note: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: ro-eco

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has part
annotated target: occurs in
is a defining property chain axiom: true

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

relation between physical entity and a process or stage
type: ObjectProperty
domain: independent continuant
range: occurrent
IAO_0000117: https://orcid.org/0000-0002-6601-2165
curator note: 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.

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
definition: 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))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: 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
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: preceded by
definition: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: 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
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally succeeded by
property chain axiom: precedes
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: 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.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
editor note: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

lumen of
type: ObjectProperty
sub property of: part of
range: material entity
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:cjm
in_subset: ro-eco

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: immaterial entity
definition: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: ro-eco

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: 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.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

produces
type: ObjectProperty
inverse of: produced by
domain: material entity
range: material entity
IAO_0000114: pending final vetting
definition: 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.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in_subset: ro-eco
comment: 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.

produced by
type: ObjectProperty
domain: material entity
range: material entity
IAO_0000114: pending final vetting
definition: a produced_by b iff some process that occurs_in b has_output a.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in_subset: ro-eco

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: 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
RO_0004049: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: 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
RO_0004050: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
created by: cjm
creation date: 2018-03-13T23:55:19Z

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: 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.
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000117: Vasundra Touré

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
definition: 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.
created by: pg
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: pg
creation date: 2022-09-26T06:08:01Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000112: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
IAO_0000117: https://orcid.org/0000-0001-9625-1899
IAO_0000117: https://orcid.org/0000-0003-2620-0345
curator note: 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.
curator note: See github ticket https://github.com/oborel/obo-relations/issues/497
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: 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.
contributor: https://orcid.org/0000-0002-8688-6599

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: 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.
contributor: https://orcid.org/0000-0002-8688-6599

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: 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.
contributor: https://orcid.org/0000-0002-8688-6599

entity
type: Class
BFO_0000179: entity
BFO_0000180: Entity
IAO_0000112: Julius Caesar
IAO_0000112: Verdi’s Requiem
IAO_0000112: the Second World War
IAO_0000112: your body mass index
editor note: 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
editor note: 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
IAO_0000600: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: IAO_0000600
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
definition: 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.
editor note: 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
editor note: 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
IAO_0000600: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0000602: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0000602: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO_0000179: occurrent
BFO_0000180: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
IAO_0000600: 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])
IAO_0000601: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0000601: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0000602: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0000602: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: ic
BFO_0000180: IndependentContinuant
IAO_0000112: a chair
IAO_0000112: a heart
IAO_0000112: a leg
IAO_0000112: a molecule
IAO_0000112: a spatial region
IAO_0000112: an atom
IAO_0000112: an orchestra.
IAO_0000112: an organism
IAO_0000112: the bottom right portion of a human torso
IAO_0000112: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0000602: (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]
IAO_0000602: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

process
type: Class
subclass of: occurrent
BFO_0000179: process
BFO_0000180: Process
IAO_0000112: a process of cell-division, \ a beating of the heart
IAO_0000112: a process of meiosis
IAO_0000112: a process of sleeping
IAO_0000112: the course of a disease
IAO_0000112: the flight of a bird
IAO_0000112: the life of an organism
IAO_0000112: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
IAO_0000602: (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]

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO_0000179: disposition
BFO_0000180: Disposition
IAO_0000112: an atom of element X has the disposition to decay to an atom of element Y
IAO_0000112: certain people have a predisposition to colon cancer
IAO_0000112: children are innately disposed to categorize objects in certain ways.
IAO_0000112: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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.
IAO_0000600: 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])
IAO_0000601: 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])
IAO_0000602: (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]
IAO_0000602: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: IAO_0000602
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: realizable entity
disjoint with: quality
BFO_0000179: realizable
BFO_0000180: RealizableEntity
IAO_0000112: the disposition of this piece of metal to conduct electricity.
IAO_0000112: the disposition of your blood to coagulate
IAO_0000112: the function of your reproductive organs
IAO_0000112: the role of being a doctor
IAO_0000112: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
IAO_0000600: 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])
IAO_0000601: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0000602: (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]
IAO_0000602: (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]

Axiom
annotated source: realizable entity
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: IAO_0000601
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: quality
BFO_0000179: quality
BFO_0000180: Quality
IAO_0000112: the ambient temperature of this portion of air
IAO_0000112: the color of a tomato
IAO_0000112: the length of the circumference of your waist
IAO_0000112: the mass of this piece of gold.
IAO_0000112: the shape of your nose
IAO_0000112: the shape of your nostril
IAO_0000600: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0000602: (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]

Axiom
annotated source: quality
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
IAO_0000112: 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
IAO_0000112: of one-sided specifically dependent continuants: the mass of this tomato
IAO_0000112: 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.
IAO_0000112: the disposition of this fish to decay
IAO_0000112: the function of this heart: to pump blood
IAO_0000112: the mutual dependence of proton donors and acceptors in chemical reactions [79
IAO_0000112: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
IAO_0000112: the pink color of a medium rare piece of grilled filet mignon at its center
IAO_0000112: the role of being a doctor
IAO_0000112: the shape of this hole.
IAO_0000112: the smell of this portion of mozzarella
definition: 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.
definition: 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])
editor note: 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.
IAO_0000602: (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]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: 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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO_0000179: role
BFO_0000180: Role
IAO_0000112: 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.
IAO_0000112: the priest role
IAO_0000112: the role of a boundary to demarcate two neighboring administrative territories
IAO_0000112: the role of a building in serving as a military target
IAO_0000112: the role of a stone in marking a property boundary
IAO_0000112: the role of subject in a clinical trial
IAO_0000112: the student role
definition: 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.
editor note: 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.
IAO_0000600: 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])
IAO_0000602: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: IAO_0000602
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

generically dependent continuant
type: Class
subclass of: continuant
BFO_0000179: gdc
BFO_0000180: GenericallyDependentContinuant
IAO_0000112: 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.
IAO_0000112: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
IAO_0000112: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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])
IAO_0000602: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: IAO_0000602
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO_0000179: function
BFO_0000180: Function
IAO_0000112: the function of a hammer to drive in nails
IAO_0000112: the function of a heart pacemaker to regulate the beating of a heart through electricity
IAO_0000112: the function of amylase in saliva to break down starch into sugar
editor note: 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.
IAO_0000600: 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])
IAO_0000602: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: IAO_0000602
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
BFO_0000179: material
BFO_0000180: MaterialEntity
IAO_0000112: a flame
IAO_0000112: a forest fire
IAO_0000112: a human being
IAO_0000112: a hurricane
IAO_0000112: a photon
IAO_0000112: a puff of smoke
IAO_0000112: a sea wave
IAO_0000112: a tornado
IAO_0000112: an aggregate of human beings.
IAO_0000112: an energy wave
IAO_0000112: an epidemic
IAO_0000112: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
IAO_0000600: 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])
IAO_0000601: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0000601: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0000602: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0000602: (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]
IAO_0000602: (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]

Axiom
annotated source: material entity
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity

anatomical surface
type: Class
subclass of: anatomical boundary
definition: A 2D surface of an anatomical continuant.
database_cross_reference: FMA:24137
has_exact_synonym: surface
has_obo_namespace: spatial
id: BSPO:0000005
comment: to be merged into CARO

Axiom
annotated source: anatomical surface
annotated property: definition
annotated target: A 2D surface of an anatomical continuant.
database_cross_reference: BSPO:cjm

anatomical axis
type: Class
subclass of: anatomical line
subclass of: Restriction
  on property: passes through
  some values from: anatomical entity
definition: A straight line through space, intersecting an anatomical entity.
has_obo_namespace: spatial
id: BSPO:0000010
comment: Axis directions are defined in terms of axes.

Axiom
annotated source: anatomical axis
annotated property: definition
annotated target: A straight line through space, intersecting an anatomical entity.
database_cross_reference: BSPO:cjm

anterior-posterior axis
type: Class
equivalent class: Class
  intersection of: anatomical axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: transverse plane
subclass of: anatomical axis
subclass of: Restriction
  on property: approximately perpendicular to
  some values from: dorsal-ventral axis
subclass of: Restriction
  on property: orthogonal to
  some values from: transverse plane
definition: An axis that extends through an organism from head end to opposite end of body or tail.
has_exact_synonym: A-P axis
has_exact_synonym: AP axis
has_exact_synonym: anteroposterior axis
has_narrow_synonym: cephalocaudal axis
has_narrow_synonym: craniocaudal axis
has_narrow_synonym: rostral/caudal
has_narrow_synonym: rostrocaudal axis
has_obo_namespace: spatial
has_related_synonym: longitudinal axis
id: BSPO:0000013
comment: 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]

Axiom
annotated source: anterior-posterior axis
annotated property: definition
annotated target: An axis that extends through an organism from head end to opposite end of body or tail.
database_cross_reference: BSPO:cjm

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: cephalocaudal axis
database_cross_reference: http://en.wikipedia.org/wiki/Anatomical_terms_of_location

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: craniocaudal axis
has_synonym_type: synonym typically used in the context of vertebrate anatomy

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: rostral/caudal
has_synonym_type: synonym typically used in the context of vertebrate anatomy

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: rostrocaudal axis
has_synonym_type: synonym typically used in the context of vertebrate anatomy

apical-basal axis relative to substrate
type: Class
subclass of: anatomical axis
definition: 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.
has_exact_synonym: apical/basal
has_obo_namespace: spatial
has_related_synonym: longitudinal axis
id: BSPO:0000014

Axiom
annotated source: apical-basal axis relative to substrate
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:mah

proximal-distal axis
type: Class
subclass of: anatomical axis
definition: An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
has_exact_synonym: proximal/distal
has_exact_synonym: proximodistal
has_obo_namespace: spatial
id: BSPO:0000015
comment: 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.

Axiom
annotated source: proximal-distal axis
annotated property: definition
annotated target: An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
database_cross_reference: BSPO:curators
database_cross_reference: http://en.wikipedia.org/wiki/Anatomical_terms_of_location

dorsal-ventral axis
type: Class
equivalent class: Class
  intersection of: anatomical axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: horizontal plane
subclass of: anatomical axis
subclass of: Restriction
  on property: orthogonal to
  some values from: horizontal plane
definition: An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
has_exact_synonym: D-V axis
has_exact_synonym: DV axis
has_exact_synonym: dorsoventral axis
has_narrow_synonym: anterior-posterior axis
has_obo_namespace: spatial
id: BSPO:0000016

Axiom
annotated source: dorsal-ventral axis
annotated property: definition
annotated target: An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
database_cross_reference: BSPO:curators

Axiom
annotated source: dorsal-ventral axis
annotated property: has_narrow_synonym
annotated target: anterior-posterior axis
has_synonym_type: synonym typically used in the context of human anatomy

left-right axis
type: Class
equivalent class: Class
  intersection of: anatomical axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: sagittal plane
subclass of: anatomical axis
subclass of: Restriction
  on property: orthogonal to
  some values from: sagittal plane
definition: An axis that bisects an organism from left to right sides of body, through a sagittal plane.
has_exact_synonym: L-R axis
has_exact_synonym: LR axis
has_exact_synonym: R-L axis
has_exact_synonym: RL axis
has_exact_synonym: dextro-sinister axis
has_exact_synonym: left to right axis
has_exact_synonym: right to left axis
has_exact_synonym: right-left axis
has_obo_namespace: spatial
id: BSPO:0000017

Axiom
annotated source: left-right axis
annotated property: definition
annotated target: An axis that bisects an organism from left to right sides of body, through a sagittal plane.
database_cross_reference: BSPO:cjm

transverse plane
type: Class
subclass of: anatomical plane
definition: Anatomical plane that divides body into anterior and posterior parts.
database_cross_reference: FMA:12247
has_exact_synonym: axial plane
has_exact_synonym: axial section
has_exact_synonym: transverse section
has_obo_namespace: spatial
has_related_synonym: cross-section
id: BSPO:0000018

Axiom
annotated source: transverse plane
annotated property: definition
annotated target: Anatomical plane that divides body into anterior and posterior parts.
database_cross_reference: BSPO:mah

horizontal plane
type: Class
subclass of: anatomical plane
definition: Anatomical plane that divides bilateral body into dorsal and ventral parts.
database_cross_reference: FMA:52810
has_exact_synonym: frontal plane
has_exact_synonym: horizontal anatomical plane
has_exact_synonym: horizontal section
has_obo_namespace: spatial
has_related_synonym: coronal section
has_related_synonym: frontal section
id: BSPO:0000019

Axiom
annotated source: horizontal plane
annotated property: definition
annotated target: Anatomical plane that divides bilateral body into dorsal and ventral parts.
database_cross_reference: BSPO:mah

Axiom
annotated source: horizontal plane
annotated property: has_exact_synonym
annotated target: horizontal anatomical plane
database_cross_reference: FMA:52810

antero-dorsal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: anterior region
subclass of: dorsal region
definition: Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:01:38Z
has_exact_synonym: anterodorsal region
has_obo_namespace: spatial
id: BSPO:0000026

Axiom
annotated source: antero-dorsal region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
database_cross_reference: BSPO:wd

antero-ventral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: anterior region
subclass of: ventral region
definition: Anatomical region that overlaps the anterior and ventral regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:04:59Z
has_exact_synonym: anteroventral region
has_obo_namespace: spatial
id: BSPO:0000027

Axiom
annotated source: antero-ventral region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and ventral regions of a body or body part.
database_cross_reference: BSPO:wd

postero-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: posterior region
subclass of: lateral region
definition: Anatomical region that overlaps the posterior and lateral regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:06:01Z
has_exact_synonym: posterolateral region
has_obo_namespace: spatial
id: BSPO:0000028

Axiom
annotated source: postero-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and lateral regions of the body or body part.
database_cross_reference: BSPO:wd

antero-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: anterior region
subclass of: lateral region
definition: Anatomical region that overlaps the anterior and lateral regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:07:18Z
has_exact_synonym: anterolateral region
has_obo_namespace: spatial
id: BSPO:0000029

Axiom
annotated source: antero-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and lateral regions of a body or body part.
database_cross_reference: BSPO:wd

postero-dorsal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: posterior region
subclass of: dorsal region
definition: Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:08:13Z
has_exact_synonym: posterodorsal region
has_obo_namespace: spatial
id: BSPO:0000030

Axiom
annotated source: postero-dorsal region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
database_cross_reference: BSPO:wd

postero-ventral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: posterior region
subclass of: ventral region
definition: Anatomical region that overlaps the posterior and ventral regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:08:38Z
has_exact_synonym: posteroventral region
has_obo_namespace: spatial
id: BSPO:0000035

Axiom
annotated source: postero-ventral region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and ventral regions of a body or body part.
database_cross_reference: BSPO:wd

anatomical side
type: Class
subclass of: anatomical region
definition: An anatomical region bounded by a plane perpendicular to an axis through the middle.
database_cross_reference: FBql:00005841
has_obo_namespace: spatial
id: BSPO:0000054

Axiom
annotated source: anatomical side
annotated property: definition
annotated target: An anatomical region bounded by a plane perpendicular to an axis through the middle.
database_cross_reference: BSPO:cjm

anterior side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: anterior to
  some values from: posterior side
subclass of: Restriction
  on property: opposite to
  some values from: posterior side
subclass of: Restriction
  on property: starts axis
  some values from: anterior-posterior axis
definition: 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.
database_cross_reference: FBcv:0000053
database_cross_reference: FBql:00005848
has_exact_synonym: anterior
has_exact_synonym: rostral
has_obo_namespace: spatial
id: BSPO:0000055

Axiom
annotated source: anterior side
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:RW

posterior side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: posterior to
  some values from: anterior side
subclass of: Restriction
  on property: finishes axis
  some values from: anterior-posterior axis
definition: 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.
database_cross_reference: FBcv:0000065
database_cross_reference: FBql:00005849
has_exact_synonym: posterior
has_narrow_synonym: caudal
has_obo_namespace: spatial
id: BSPO:0000056

Axiom
annotated source: posterior side
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:RW
database_cross_reference: BSPO:wd

Axiom
annotated source: posterior side
annotated property: has_narrow_synonym
annotated target: caudal
has_synonym_type: synonym typically used in the context of vertebrate anatomy

apical side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: opposite to
  some values from: basal side
subclass of: Restriction
  on property: starts axis
  some values from: apical-basal axis relative to substrate
definition: Anatomical side that is located on the apical end of an organism or structure.
database_cross_reference: FBcv:0000054
database_cross_reference: FBql:00005854
has_exact_synonym: apical
has_obo_namespace: spatial
id: BSPO:0000057

Axiom
annotated source: apical side
annotated property: definition
annotated target: Anatomical side that is located on the apical end of an organism or structure.
database_cross_reference: BSPO:wd

basal side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: apical-basal axis relative to substrate
definition: Anatomical side that is located on the basal end of an organism or structure.
database_cross_reference: FBcv:0000055
database_cross_reference: FBql:00005855
has_exact_synonym: basal
has_obo_namespace: spatial
id: BSPO:0000058
comment: The part of the organism attached to a substrate. Axis of symmetry.

Axiom
annotated source: basal side
annotated property: definition
annotated target: Anatomical side that is located on the basal end of an organism or structure.
database_cross_reference: BSPO:wd

dorsal side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: dorsal to
  some values from: lateral side
subclass of: Restriction
  on property: opposite to
  some values from: ventral side
subclass of: Restriction
  on property: starts axis
  some values from: dorsal-ventral axis
definition: 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.
database_cross_reference: FBcv:0000059
database_cross_reference: FBql:00005842
has_exact_synonym: dorsal
has_obo_namespace: spatial
id: BSPO:0000063

Axiom
annotated source: dorsal side
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:wd

lateral side
type: Class
subclass of: anatomical side
database_cross_reference: FBcv:0000063
database_cross_reference: FBql:00005844
has_exact_synonym: lateral
has_obo_namespace: spatial
id: BSPO:0000066

ventral side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: dorsal-ventral axis
definition: 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.
database_cross_reference: FBcv:0000070
database_cross_reference: FBql:00005843
has_exact_synonym: ventral
has_obo_namespace: spatial
id: BSPO:0000068

Axiom
annotated source: ventral side
annotated property: definition
annotated target: 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.
database_cross_reference: BSPO:RW
database_cross_reference: BSPO:wd

anatomical region
type: Class
subclass of: anatomical structure
definition: A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
database_cross_reference: FBql:00005841
has_obo_namespace: spatial
id: BSPO:0000070
comment: to be merged into CARO

Axiom
annotated source: anatomical region
annotated property: definition
annotated target: A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
database_cross_reference: BSPO:cjm

anterior region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: anterior side
definition: Anatomical region anteriorly located on the body or body part.
database_cross_reference: FBql:00005848
has_obo_namespace: spatial
id: BSPO:0000071

Axiom
annotated source: anterior region
annotated property: definition
annotated target: Anatomical region anteriorly located on the body or body part.
database_cross_reference: BSPO:wd

posterior region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: posterior side
definition: Anatomical region posteriorly located on the body or body part.
database_cross_reference: FBql:00005849
has_obo_namespace: spatial
id: BSPO:0000072

Axiom
annotated source: posterior region
annotated property: definition
annotated target: Anatomical region posteriorly located on the body or body part.
database_cross_reference: BSPO:wd

apical region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: apical side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: apical side
definition: Anatomical region located on the apical end on the body or body part.
database_cross_reference: FBql:00005854
has_obo_namespace: spatial
id: BSPO:0000073

Axiom
annotated source: apical region
annotated property: definition
annotated target: Anatomical region located on the apical end on the body or body part.
database_cross_reference: BSPO:wd

basal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: basal side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: basal side
definition: Anatomical region located basally on the body or body part.
database_cross_reference: FBql:00005855
has_obo_namespace: spatial
id: BSPO:0000074

Axiom
annotated source: basal region
annotated property: definition
annotated target: Anatomical region located basally on the body or body part.
database_cross_reference: BSPO:wd

dorsal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: dorsal side
definition: Anatomical region dorsally located on the body or body part.
database_cross_reference: FBql:00005842
has_obo_namespace: spatial
id: BSPO:0000079

Axiom
annotated source: dorsal region
annotated property: definition
annotated target: Anatomical region dorsally located on the body or body part.
database_cross_reference: BSPO:wd

dorso-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: dorsal region
subclass of: lateral region
definition: Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
database_cross_reference: FBql:00005845
has_exact_synonym: dorsolateral region
has_obo_namespace: spatial
id: BSPO:0000080

Axiom
annotated source: dorso-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
database_cross_reference: BSPO:wd

lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: lateral side
definition: Anatomical region laterally located on the body or body part.
database_cross_reference: FBql:00005844
has_obo_namespace: spatial
id: BSPO:0000082

Axiom
annotated source: lateral region
annotated property: definition
annotated target: Anatomical region laterally located on the body or body part.
database_cross_reference: BSPO:wd

ventral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: ventral side
definition: Anatomical region ventrally located on the body or body part.
database_cross_reference: FBql:00005843
has_obo_namespace: spatial
id: BSPO:0000084

Axiom
annotated source: ventral region
annotated property: definition
annotated target: Anatomical region ventrally located on the body or body part.
database_cross_reference: BSPO:wd

ventro-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: lateral region
subclass of: ventral region
definition: Anatomical region that overlaps the ventral and lateral regions of a body or body part.
database_cross_reference: FBql:00005846
has_exact_synonym: ventrolateral region
has_obo_namespace: spatial
id: BSPO:0000085
comment: This is an example of a composition of two axis positions.

Axiom
annotated source: ventro-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the ventral and lateral regions of a body or body part.
database_cross_reference: BSPO:wd

anatomical compartment
type: Class
subclass of: anatomical structure
database_cross_reference: FBql:00005873
database_cross_reference: FMA:9647
has_obo_namespace: spatial
id: BSPO:0000086
comment: to be merged into CARO

anatomical compartment boundary
type: Class
subclass of: anatomical boundary
database_cross_reference: FBql:00005881
has_obo_namespace: spatial
id: BSPO:0000092
comment: to be merged into CARO

dorsal/ventral compartment boundary
type: Class
subclass of: anatomical compartment boundary
database_cross_reference: FBcv:0000034
database_cross_reference: FBql:00005879
has_obo_namespace: spatial
id: BSPO:0000094

medial-external axis
type: Class
subclass of: anatomical axis
definition: An anatomical axis that extends from the center of the body outwards or externally.
created by: wasila.dahdul
creation date: 2013-07-02T11:21:42Z
has_obo_namespace: spatial
has_related_synonym: proximal-distal axis
id: BSPO:0000196
comment: The medial-external axis could apply to a sphere-shaped body.

Axiom
annotated source: medial-external axis
annotated property: definition
annotated target: An anatomical axis that extends from the center of the body outwards or externally.
database_cross_reference: BSPO:curators

oral-aboral axis
type: Class
subclass of: anatomical axis
definition: An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
created by: wasila.dahdul
creation date: 2013-07-02T11:29:33Z
has_obo_namespace: spatial
id: BSPO:0000198

Axiom
annotated source: oral-aboral axis
annotated property: definition
annotated target: An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
database_cross_reference: BSPO:PM

anterior surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: anterior side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: anterior side
definition: Anatomical surface that is located on the anterior side of the body or body part.
database_cross_reference: FBql:00005848
has_obo_namespace: spatial
id: BSPO:0000371

Axiom
annotated source: anterior surface
annotated property: definition
annotated target: Anatomical surface that is located on the anterior side of the body or body part.
database_cross_reference: BSPO:wd

posterior surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: posterior side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: posterior side
definition: Anatomical surface that is located on the posterior side of the body or body part.
database_cross_reference: FBql:00005849
has_obo_namespace: spatial
id: BSPO:0000372

Axiom
annotated source: posterior surface
annotated property: definition
annotated target: Anatomical surface that is located on the posterior side of the body or body part.
database_cross_reference: BSPO:wd

apical surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: apical side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: apical side
definition: Anatomical surface that is located on the apical side of the body or body part.
database_cross_reference: FBql:00005854
has_obo_namespace: spatial
id: BSPO:0000373

Axiom
annotated source: apical surface
annotated property: definition
annotated target: Anatomical surface that is located on the apical side of the body or body part.
database_cross_reference: BSPO:wd

basal surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: basal side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: basal side
definition: Anatomical surface that is located on the basal side of the body or body part.
database_cross_reference: FBql:00005855
has_obo_namespace: spatial
id: BSPO:0000374

Axiom
annotated source: basal surface
annotated property: definition
annotated target: Anatomical surface that is located on the basal side of the body or body part.
database_cross_reference: BSPO:wd

dorsal surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: dorsal side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: dorsal side
definition: Anatomical surface that located on the dorsal side of the body or body part.
database_cross_reference: FBql:00005842
has_obo_namespace: spatial
id: BSPO:0000379

Axiom
annotated source: dorsal surface
annotated property: definition
annotated target: Anatomical surface that located on the dorsal side of the body or body part.
database_cross_reference: BSPO:wd

lateral surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: lateral side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: lateral side
definition: Anatomical surface that located on the lateral side of the body or body part.
database_cross_reference: FBql:00005844
has_obo_namespace: spatial
id: BSPO:0000382

Axiom
annotated source: lateral surface
annotated property: definition
annotated target: Anatomical surface that located on the lateral side of the body or body part.
database_cross_reference: BSPO:wd

ventral surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: ventral side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: ventral side
definition: Anatomical surface that is located on the ventral side of the body or body part.
database_cross_reference: FBql:00005843
has_obo_namespace: spatial
id: BSPO:0000384

Axiom
annotated source: ventral surface
annotated property: definition
annotated target: Anatomical surface that is located on the ventral side of the body or body part.
database_cross_reference: BSPO:wd

anatomical plane
type: Class
subclass of: anatomical boundary
definition: A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
database_cross_reference: FMA:242982
has_exact_synonym: anatomical cross-section
has_exact_synonym: anatomical section
has_exact_synonym: plane
has_exact_synonym: section
has_obo_namespace: spatial
has_related_synonym: cross-section
id: BSPO:0000400
comment: 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.

Axiom
annotated source: anatomical plane
annotated property: definition
annotated target: A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
database_cross_reference: BSPO:cjm

sagittal plane
type: Class
equivalent class: Class
  intersection of: anatomical plane
  intersection of: Restriction
    on property: parallel to
    some values from: anterior-posterior axis
  intersection of: Restriction
    on property: parallel to
    some values from: dorsal-ventral axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: left-right axis
subclass of: anatomical axis
subclass of: anatomical plane
subclass of: Restriction
  on property: parallel to
  some values from: anterior-posterior axis
subclass of: Restriction
  on property: parallel to
  some values from: dorsal-ventral axis
subclass of: Restriction
  on property: orthogonal to
  some values from: left-right axis
definition: Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
database_cross_reference: FMA:11361
has_exact_synonym: left/right plane
has_exact_synonym: median plane
has_exact_synonym: sagittal section
has_obo_namespace: spatial
id: BSPO:0000417

Axiom
annotated source: sagittal plane
annotated property: definition
annotated target: Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
database_cross_reference: BSPO:DOS
database_cross_reference: BSPO:cjm
database_cross_reference: BSPO:mah

medial-lateral axis
type: Class
subclass of: medial-external axis
definition: An axis that extends from the center of organism to one or other side.
has_exact_synonym: M-L axis
has_exact_synonym: ML axis
has_exact_synonym: medio-lateral axis
has_exact_synonym: mediolateral axis
has_obo_namespace: spatial
has_related_synonym: proximal-distal axis
id: BSPO:0001001
comment: 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.

Axiom
annotated source: medial-lateral axis
annotated property: definition
annotated target: An axis that extends from the center of organism to one or other side.
database_cross_reference: BSPO:cjm

anatomical entity
type: Class
subclass of: biological entity
definition: 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.
definition: 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.
imported from: caro.owl
has_obo_namespace: spatial
id: CARO:0000000
comment: 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.

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: 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.
database_cross_reference: CAROC:Brownsville2014

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: 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.
database_cross_reference: CARO:MAH

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: caro.owl
has_obo_namespace: spatial
id: CARO:0000003
label: connected anatomical structure

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: CC:DOS

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
definition: An anatomical entity that has mass.
imported from: caro.owl
has_obo_namespace: spatial
id: CARO:0000006

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: An anatomical entity that has mass.
database_cross_reference: CC:DOS

immaterial anatomical entity
type: Class
subclass of: immaterial entity
subclass of: anatomical entity
definition: An anatomical entity that has no mass.
has_obo_namespace: spatial
id: CARO:0000007

Axiom
annotated source: immaterial anatomical entity
annotated property: definition
annotated target: An anatomical entity that has no mass.
database_cross_reference: CC:DOS

anatomical line
type: Class
subclass of: immaterial anatomical entity
definition: A one dimensional, immaterial anatomical entity.
has_obo_namespace: spatial
id: CARO:0000008

Axiom
annotated source: anatomical line
annotated property: definition
annotated target: A one dimensional, immaterial anatomical entity.
database_cross_reference: CC:DOS

anatomical boundary
type: Class
subclass of: immaterial anatomical entity
definition: A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
has_obo_namespace: spatial
id: CARO:0000010

Axiom
annotated source: anatomical boundary
annotated property: definition
annotated target: A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
database_cross_reference: CC:DOS

biological entity
type: Class
subclass of: independent continuant

reproduction
type: Class
subclass of: biological_process
disjoint with: biological phase
definition: The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
has_alternative_id: GO:0019952
has_alternative_id: GO:0050876
database_cross_reference: Wikipedia:Reproduction
has_exact_synonym: reproductive physiological process
has_obo_namespace: biological_process
id: GO:0000003
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: reproduction
annotated property: definition
annotated target: The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

mitotic G1 phase
type: Class
subclass of: G1 phase
subclass of: Restriction
  on property: part of
  some values from: mitotic interphase
definition: The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
has_exact_synonym: G1 phase of mitotic cell cycle
has_obo_namespace: biological_process
id: GO:0000080
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic G1 phase
annotated property: definition
annotated target: The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
database_cross_reference: GOC:mtg_cell_cycle

mitotic S phase
type: Class
subclass of: S phase
subclass of: Restriction
  on property: part of
  some values from: mitotic interphase
definition: The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle.
has_exact_synonym: S phase of mitotic cell cycle
has_exact_synonym: S-phase of mitotic cell cycle
has_obo_namespace: biological_process
id: GO:0000084
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic S phase
annotated property: definition
annotated target: The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle.
database_cross_reference: GOC:mtg_cell_cycle

mitotic G2 phase
type: Class
subclass of: G2 phase
subclass of: Restriction
  on property: part of
  some values from: mitotic interphase
definition: The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis.
has_exact_synonym: G2 phase of mitotic cell cycle
has_obo_namespace: biological_process
id: GO:0000085
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic G2 phase
annotated property: definition
annotated target: The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis.
database_cross_reference: GOC:mtg_cell_cycle

mitotic M phase
type: Class
equivalent class: Class
  intersection of: M phase
  intersection of: Restriction
    on property: happens during
    some values from: mitotic cell cycle
subclass of: M phase
subclass of: mitotic cell cycle phase
definition: 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.
has_exact_synonym: M phase of mitotic cell cycle
has_exact_synonym: M-phase of mitotic cell cycle
has_obo_namespace: biological_process
id: GO:0000087
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic M phase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

mitotic prophase
type: Class
subclass of: prophase
subclass of: Restriction
  on property: part of
  some values from: mitotic M phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0000088
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic prophase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

mitotic metaphase
type: Class
subclass of: metaphase
subclass of: Restriction
  on property: part of
  some values from: mitotic M phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0000089
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic metaphase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

mitotic anaphase
type: Class
subclass of: anaphase
subclass of: Restriction
  on property: part of
  some values from: mitotic M phase
definition: The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle.
has_obo_namespace: biological_process
id: GO:0000090
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic anaphase
annotated property: definition
annotated target: The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle.
database_cross_reference: GOC:mtg_cell_cycle

mitotic telophase
type: Class
subclass of: telophase
subclass of: Restriction
  on property: part of
  some values from: mitotic M phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0000093
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic telophase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

leptotene
type: Class
subclass of: meiosis I cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: meiotic prophase I
definition: The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible.
database_cross_reference: Wikipedia:Leptotene
database_cross_reference: Wikipedia:Meiosis#Leptotene
has_obo_namespace: biological_process
id: GO:0000237
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: leptotene
annotated property: definition
annotated target: The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible.
database_cross_reference: GOC:mtg_cell_cycle

zygotene
type: Class
subclass of: meiosis I cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: meiotic prophase I
definition: 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.
database_cross_reference: Wikipedia:Meiosis#Zygotene
database_cross_reference: Wikipedia:Zygotene
has_obo_namespace: biological_process
id: GO:0000238
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: zygotene
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

pachytene
type: Class
subclass of: meiosis I cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: meiotic prophase I
definition: 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.
database_cross_reference: Wikipedia:Meiosis#Pachytene
database_cross_reference: Wikipedia:Pachytene
has_obo_namespace: biological_process
id: GO:0000239
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: pachytene
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

diplotene
type: Class
subclass of: meiosis I cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: meiotic prophase I
definition: 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.
database_cross_reference: Wikipedia:Diplotene
database_cross_reference: Wikipedia:Meiosis#Diplotene
has_obo_namespace: biological_process
id: GO:0000240
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: diplotene
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

diakinesis
type: Class
subclass of: meiosis I cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: meiotic prophase I
definition: The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred.
database_cross_reference: Wikipedia:Diakinesis
database_cross_reference: Wikipedia:Meiosis#Diakinesis
has_obo_namespace: biological_process
id: GO:0000241
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: diakinesis
annotated property: definition
annotated target: The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred.
database_cross_reference: GOC:mtg_cell_cycle

mitotic cell cycle
type: Class
equivalent class: Class
  intersection of: cell cycle
  intersection of: Restriction
    on property: has part
    some values from: mitotic nuclear division
subclass of: cell cycle
subclass of: Restriction
  on property: has part
  some values from: mitotic nuclear division
definition: 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.
has_alternative_id: GO:0007067
database_cross_reference: Wikipedia:Mitosis
has_obo_namespace: biological_process
has_related_synonym: mitosis
id: GO:0000278
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim yeast
comment: 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.

Axiom
annotated source: mitotic cell cycle
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0815316194
database_cross_reference: Reactome:69278

M phase
type: Class
subclass of: cell cycle phase
definition: A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
database_cross_reference: Wikipedia:M_phase
has_exact_synonym: M-phase
has_obo_namespace: biological_process
id: GO:0000279
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: M phase
annotated property: definition
annotated target: A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
database_cross_reference: GOC:mtg_cell_cycle

nuclear division
type: Class
subclass of: organelle fission
definition: The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
has_obo_namespace: biological_process
has_related_synonym: karyokinesis
id: GO:0000280
in_subset: goslim pir

Axiom
annotated source: nuclear division
annotated property: definition
annotated target: The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
database_cross_reference: GOC:mah

developmental process involved in reproduction
type: Class
equivalent class: Class
  intersection of: developmental process
  intersection of: Restriction
    on property: part of
    some values from: reproduction
subclass of: reproductive process
subclass of: developmental process
definition: 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.
has_narrow_synonym: puberty
has_obo_namespace: biological_process
has_related_synonym: reproductive developmental process
id: GO:0003006

Axiom
annotated source: developmental process involved in reproduction
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete

Axiom
annotated source: developmental process involved in reproduction
annotated property: has_narrow_synonym
annotated target: puberty
database_cross_reference: GOC:dph

Axiom
annotated source: developmental process involved in reproduction
annotated property: has_related_synonym
annotated target: reproductive developmental process
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

molecular_function
type: Class
subclass of: process
definition: 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.
IAO_0000589: molecular process
has_exact_synonym: molecular function
id: GO:0003674
comment: 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.

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:pdt

catalytic activity
type: Class
subclass of: molecular_function

cellular_component
type: Class
definition: 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).
has_alternative_id: GO:0008372
database_cross_reference: NIF_Subcellular:sao1337158144
has_exact_synonym: cell or subcellular entity
has_exact_synonym: cellular component
has_obo_namespace: cellular_component
has_related_synonym: subcellular entity
id: GO:0005575
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
comment: 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.

Axiom
annotated source: cellular_component
annotated property: definition
annotated target: 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).
database_cross_reference: GOC:pdt
database_cross_reference: NIF_Subcellular:sao1337158144

Axiom
annotated source: cellular_component
annotated property: has_related_synonym
annotated target: subcellular entity
database_cross_reference: NIF_Subcellular:nlx_subcell_100315

organelle organization
type: Class
subclass of: cellular component organization
definition: 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.
created by: jl
creation date: 2013-12-19T15:25:51Z
has_alternative_id: GO:1902589
has_exact_synonym: organelle organisation
has_exact_synonym: single organism organelle organization
has_obo_namespace: biological_process
has_related_synonym: organelle organization and biogenesis
has_related_synonym: single-organism organelle organization
id: GO:0006996
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: organelle organization
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mah

Axiom
annotated source: organelle organization
annotated property: has_exact_synonym
annotated target: single organism organelle organization
database_cross_reference: GOC:TermGenie

Axiom
annotated source: organelle organization
annotated property: has_related_synonym
annotated target: organelle organization and biogenesis
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

cell cycle
type: Class
subclass of: cellular process
definition: 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.
database_cross_reference: Wikipedia:Cell_cycle
has_exact_synonym: cell-division cycle
has_obo_namespace: biological_process
id: GO:0007049
in_subset: gocheck do not manually annotate
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: cell cycle
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:mtg_cell_cycle

meiotic prophase I
type: Class
subclass of: prophase
subclass of: meiosis I cell cycle phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0007128
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic prophase I
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

meiotic metaphase I
type: Class
subclass of: metaphase
subclass of: meiosis I cell cycle phase
definition: The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I.
has_obo_namespace: biological_process
id: GO:0007132
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic metaphase I
annotated property: definition
annotated target: The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I.
database_cross_reference: GOC:mtg_cell_cycle

meiotic anaphase I
type: Class
subclass of: anaphase
subclass of: meiosis I cell cycle phase
definition: The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I.
has_obo_namespace: biological_process
id: GO:0007133
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic anaphase I
annotated property: definition
annotated target: The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I.
database_cross_reference: GOC:mtg_cell_cycle

meiotic telophase I
type: Class
subclass of: telophase
subclass of: meiosis I cell cycle phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0007134
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic telophase I
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

meiotic prophase II
type: Class
subclass of: prophase
subclass of: meiosis II cell cycle phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0007136
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic prophase II
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

meiotic metaphase II
type: Class
subclass of: metaphase
subclass of: meiosis II cell cycle phase
definition: The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II.
has_obo_namespace: biological_process
id: GO:0007137
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic metaphase II
annotated property: definition
annotated target: The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II.
database_cross_reference: GOC:mtg_cell_cycle

meiotic anaphase II
type: Class
subclass of: anaphase
subclass of: meiosis II cell cycle phase
definition: The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II.
has_obo_namespace: biological_process
id: GO:0007138
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic anaphase II
annotated property: definition
annotated target: The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II.
database_cross_reference: GOC:mtg_cell_cycle

meiotic telophase II
type: Class
subclass of: telophase
subclass of: meiosis II cell cycle phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0007139
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic telophase II
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

biological_process
type: Class
subclass of: process
definition: 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.
definition: 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.
IAO_0000233: https://github.com/geneontology/go-ontology/issues/24968
created by: jl
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
comment: 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.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:pdt

Axiom
annotated source: biological_process
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:pdt

cellular process
type: Class
subclass of: biological_process
disjoint with: biological phase
definition: 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.
created by: jl
creation date: 2012-12-11T16:56:55Z
has_alternative_id: GO:0008151
has_alternative_id: GO:0044763
has_alternative_id: GO:0050875
has_exact_synonym: cell physiology
has_exact_synonym: cellular physiological process
has_narrow_synonym: cell growth and/or maintenance
has_obo_namespace: biological_process
has_related_synonym: single-organism cellular process
id: GO:0009987
in_subset: gocheck do not annotate
in_subset: goslim plant
comment: 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.

Axiom
annotated source: cellular process
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:isa_complete

cellular component organization
type: Class
subclass of: cellular component organization or biogenesis
definition: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
has_alternative_id: GO:0044235
has_alternative_id: GO:0071842
has_exact_synonym: cell organisation
has_exact_synonym: cellular component organisation at cellular level
has_exact_synonym: cellular component organisation in other organism
has_exact_synonym: cellular component organization at cellular level
has_exact_synonym: cellular component organization in other organism
has_obo_namespace: biological_process
has_related_synonym: cell organization and biogenesis
id: GO:0016043
in_subset: goslim agr
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: cellular component organization
annotated property: definition
annotated target: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
database_cross_reference: GOC:ai
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_exact_synonym
annotated target: cellular component organisation at cellular level
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_exact_synonym
annotated target: cellular component organisation in other organism
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_related_synonym
annotated target: cell organization and biogenesis
database_cross_reference: GOC:mah

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: Reactome:R-HSA-6788855
database_cross_reference: Reactome:R-HSA-6788867
has_exact_synonym: phosphokinase activity
id: GO:0016301
comment: 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.

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788867

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity

sexual reproduction
type: Class
subclass of: reproduction
definition: 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).
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22929
database_cross_reference: Wikipedia:Sexual_reproduction
has_obo_namespace: biological_process
id: GO:0019953
comment: 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.

Axiom
annotated source: sexual reproduction
annotated property: definition
annotated target: 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).
database_cross_reference: Wikipedia:Sexual_reproduction

cell cycle process
type: Class
equivalent class: Class
  intersection of: cellular process
  intersection of: Restriction
    on property: part of
    some values from: cell cycle
subclass of: cellular process
subclass of: Restriction
  on property: part of
  some values from: cell cycle
definition: The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
has_obo_namespace: biological_process
id: GO:0022402
in_subset: gocheck do not annotate

Axiom
annotated source: cell cycle process
annotated property: definition
annotated target: The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:mtg_cell_cycle

cell cycle phase
type: Class
subclass of: biological phase
definition: 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.
has_obo_namespace: biological_process
id: GO:0022403
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: cell cycle phase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

reproductive process
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: part of
    some values from: reproduction
subclass of: biological_process
subclass of: Restriction
  on property: part of
  some values from: reproduction
disjoint with: biological phase
definition: 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.
created by: jl
creation date: 2012-09-19T15:56:06Z
has_alternative_id: GO:0044702
has_obo_namespace: biological_process
has_related_synonym: single organism reproductive process
id: GO:0022414
in_subset: goslim generic

Axiom
annotated source: reproductive process
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete

developmental process
type: Class
subclass of: biological_process
disjoint with: biological phase
definition: 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.
created by: jl
creation date: 2012-12-19T12:21:31Z
has_alternative_id: GO:0044767
has_narrow_synonym: development
has_obo_namespace: biological_process
has_related_synonym: single-organism developmental process
id: GO:0032502
in_subset: goslim agr
in_subset: goslim flybase ribbon
in_subset: goslim pir

Axiom
annotated source: developmental process
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:isa_complete

pigmentation
type: Class
subclass of: biological_process
definition: The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
has_obo_namespace: biological_process
id: GO:0043473
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: pigmentation
annotated property: definition
annotated target: The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
database_cross_reference: GOC:jl

biological phase
type: Class
subclass of: biological_process
disjoint with: cellular component organization or biogenesis
definition: A distinct period or stage in a biological process or cycle.
created by: jl
creation date: 2014-07-16T13:12:40Z
has_obo_namespace: biological_process
id: GO:0044848
in_subset: gocheck do not manually annotate
comment: 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.

Axiom
annotated source: biological phase
annotated property: definition
annotated target: A distinct period or stage in a biological process or cycle.
database_cross_reference: GOC:jl

organelle fission
type: Class
subclass of: organelle organization
definition: The creation of two or more organelles by division of one organelle.
has_obo_namespace: biological_process
id: GO:0048285
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: organelle fission
annotated property: definition
annotated target: The creation of two or more organelles by division of one organelle.
database_cross_reference: GOC:jid

anatomical structure development
type: Class
subclass of: developmental process
definition: 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.
has_exact_synonym: development of an anatomical structure
has_obo_namespace: biological_process
id: GO:0048856
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim plant

Axiom
annotated source: anatomical structure development
annotated property: definition
annotated target: 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.
database_cross_reference: GO_REF:0000021

cell division
type: Class
subclass of: cellular process
definition: 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.
database_cross_reference: Wikipedia:Cell_division
has_obo_namespace: biological_process
id: GO:0051301
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim pir
comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.

Axiom
annotated source: cell division
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:di
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:pr

G1 phase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: interphase
definition: 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.
database_cross_reference: Wikipedia:G1_phase
has_obo_namespace: biological_process
id: GO:0051318
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: G1 phase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

G2 phase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: interphase
definition: 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).
database_cross_reference: Wikipedia:G2_phase
has_obo_namespace: biological_process
id: GO:0051319
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: G2 phase
annotated property: definition
annotated target: 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).
database_cross_reference: GOC:mtg_cell_cycle

S phase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: interphase
definition: The cell cycle phase, following G1, during which DNA synthesis takes place.
database_cross_reference: Wikipedia:S_phase
has_exact_synonym: S-phase
has_obo_namespace: biological_process
id: GO:0051320
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: S phase
annotated property: definition
annotated target: The cell cycle phase, following G1, during which DNA synthesis takes place.
database_cross_reference: GOC:mtg_cell_cycle

meiotic cell cycle
type: Class
equivalent class: Class
  intersection of: cell cycle
  intersection of: Restriction
    on property: has part
    some values from: meiotic nuclear division
subclass of: cell cycle
subclass of: reproductive process
subclass of: Restriction
  on property: part of
  some values from: sexual reproduction
subclass of: Restriction
  on property: has part
  some values from: meiotic nuclear division
definition: 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.
IAO_0000233: https://github.com/geneontology/go-ontology/issues/24599
has_alternative_id: GO:0007126
database_cross_reference: Wikipedia:Meiosis
has_obo_namespace: biological_process
has_related_synonym: meiosis
id: GO:0051321
in_subset: goslim drosophila
in_subset: goslim yeast
comment: 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.

Axiom
annotated source: meiotic cell cycle
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:ai

anaphase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: M phase
definition: The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle.
database_cross_reference: Wikipedia:Anaphase
has_obo_namespace: biological_process
id: GO:0051322
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: anaphase
annotated property: definition
annotated target: The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle.
database_cross_reference: GOC:mtg_cell_cycle

metaphase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: M phase
definition: The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell.
database_cross_reference: Wikipedia:Metaphase
has_obo_namespace: biological_process
id: GO:0051323
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: metaphase
annotated property: definition
annotated target: The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell.
database_cross_reference: GOC:mtg_cell_cycle

prophase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: M phase
definition: 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.
database_cross_reference: Wikipedia:Prophase
has_obo_namespace: biological_process
id: GO:0051324
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: prophase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

interphase
type: Class
subclass of: cell cycle phase
definition: 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.
has_broad_synonym: resting phase
database_cross_reference: Wikipedia:Interphase
has_exact_synonym: karyostasis
has_obo_namespace: biological_process
id: GO:0051325
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: interphase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

telophase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: part of
  some values from: M phase
definition: 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.
database_cross_reference: Wikipedia:Telophase
has_obo_namespace: biological_process
id: GO:0051326
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: telophase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

meiotic M phase
type: Class
equivalent class: Class
  intersection of: M phase
  intersection of: Restriction
    on property: happens during
    some values from: meiotic cell cycle
subclass of: M phase
subclass of: meiotic cell cycle phase
definition: 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.
has_exact_synonym: M phase of meiotic cell cycle
has_obo_namespace: biological_process
id: GO:0051327
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic M phase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

meiotic interphase
type: Class
equivalent class: Class
  intersection of: interphase
  intersection of: Restriction
    on property: happens during
    some values from: meiotic cell cycle
subclass of: interphase
subclass of: meiotic cell cycle phase
definition: 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.
has_exact_synonym: interphase of meiotic cell cycle
has_obo_namespace: biological_process
id: GO:0051328
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic interphase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

mitotic interphase
type: Class
equivalent class: Class
  intersection of: interphase
  intersection of: Restriction
    on property: happens during
    some values from: mitotic cell cycle
subclass of: interphase
subclass of: mitotic cell cycle phase
definition: 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.
has_exact_synonym: interphase of mitotic cell cycle
has_obo_namespace: biological_process
id: GO:0051329
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic interphase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:mtg_cell_cycle

meiotic G1 phase
type: Class
subclass of: G1 phase
subclass of: Restriction
  on property: part of
  some values from: meiotic interphase
definition: The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis.
has_exact_synonym: G1 phase of meiotic cell cycle
has_obo_namespace: biological_process
id: GO:0051330
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic G1 phase
annotated property: definition
annotated target: The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis.
database_cross_reference: GOC:mtg_cell_cycle

meiotic G2 phase
type: Class
subclass of: G2 phase
subclass of: Restriction
  on property: part of
  some values from: meiotic interphase
definition: The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis.
has_exact_synonym: G2 phase of meiotic cell cycle
has_obo_namespace: biological_process
id: GO:0051331
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic G2 phase
annotated property: definition
annotated target: The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis.
database_cross_reference: GOC:mtg_cell_cycle

meiotic S phase
type: Class
subclass of: S phase
subclass of: Restriction
  on property: part of
  some values from: meiotic interphase
definition: The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle.
has_exact_synonym: S phase of meiotic cell cycle
has_exact_synonym: S-phase of meiotic cell cycle
has_exact_synonym: premeiotic S-phase
has_obo_namespace: biological_process
id: GO:0051332
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic S phase
annotated property: definition
annotated target: The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle.
database_cross_reference: GOC:mtg_cell_cycle

cellular component organization or biogenesis
type: Class
subclass of: cellular process
definition: A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
created by: mah
creation date: 2010-09-10T01:39:16Z
has_alternative_id: GO:0071841
has_exact_synonym: cellular component organisation or biogenesis
has_exact_synonym: cellular component organisation or biogenesis at cellular level
has_exact_synonym: cellular component organization or biogenesis at cellular level
has_obo_namespace: biological_process
id: GO:0071840
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics

Axiom
annotated source: cellular component organization or biogenesis
annotated property: definition
annotated target: A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization or biogenesis
annotated property: has_exact_synonym
annotated target: cellular component organisation or biogenesis
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization or biogenesis
annotated property: has_exact_synonym
annotated target: cellular component organisation or biogenesis at cellular level
database_cross_reference: GOC:mah

meiotic cell cycle phase
type: Class
equivalent class: Class
  intersection of: cell cycle phase
  intersection of: Restriction
    on property: happens during
    some values from: meiotic cell cycle
subclass of: cell cycle phase
subclass of: Restriction
  on property: happens during
  some values from: meiotic cell cycle
definition: 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.
has_obo_namespace: biological_process
id: GO:0098762
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiotic cell cycle phase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dos

mitotic cell cycle phase
type: Class
equivalent class: Class
  intersection of: cell cycle phase
  intersection of: Restriction
    on property: happens during
    some values from: mitotic cell cycle
subclass of: cell cycle phase
subclass of: Restriction
  on property: happens during
  some values from: mitotic cell cycle
definition: 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.
has_obo_namespace: biological_process
id: GO:0098763
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: mitotic cell cycle phase
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dos

meiosis I cell cycle phase
type: Class
subclass of: meiotic cell cycle phase
definition: A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs.
has_obo_namespace: biological_process
id: GO:0098764
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiosis I cell cycle phase
annotated property: definition
annotated target: A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs.
database_cross_reference: GOC:dos

meiosis II cell cycle phase
type: Class
subclass of: meiotic cell cycle phase
definition: A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division).
has_obo_namespace: biological_process
id: GO:0098765
in_subset: gocheck do not annotate
comment: 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).

Axiom
annotated source: meiosis II cell cycle phase
annotated property: definition
annotated target: A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division).
database_cross_reference: GOC:dos

meiotic nuclear division
type: Class
equivalent class: Class
  intersection of: nuclear division
  intersection of: Restriction
    on property: part of
    some values from: meiotic cell cycle
subclass of: nuclear division
subclass of: meiotic cell cycle process
definition: One of the two nuclear divisions that occur as part of the meiotic cell cycle.
IAO_0000233: https://github.com/geneontology/go-ontology/issues/19910
created by: pg
creation date: 2017-03-23T09:40:00Z
has_exact_synonym: meiosis
has_obo_namespace: biological_process
id: GO:0140013
in_subset: goslim generic

Axiom
annotated source: meiotic nuclear division
annotated property: definition
annotated target: One of the two nuclear divisions that occur as part of the meiotic cell cycle.
database_cross_reference: PMID:9334324

mitotic nuclear division
type: Class
equivalent class: Class
  intersection of: nuclear division
  intersection of: Restriction
    on property: part of
    some values from: mitotic cell cycle
subclass of: nuclear division
subclass of: mitotic cell cycle process
definition: 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.
IAO_0000233: https://github.com/geneontology/go-ontology/issues/19910
created by: pg
creation date: 2017-03-23T14:44:23Z
has_exact_synonym: mitosis
has_obo_namespace: biological_process
id: GO:0140014
in_subset: goslim chembl
in_subset: goslim generic

Axiom
annotated source: mitotic nuclear division
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:0198547684

meiotic cell cycle process
type: Class
equivalent class: Class
  intersection of: cellular process
  intersection of: Restriction
    on property: part of
    some values from: meiotic cell cycle
subclass of: cell cycle process
subclass of: reproductive process
subclass of: Restriction
  on property: part of
  some values from: meiotic cell cycle
disjoint with: mitotic cell cycle process
definition: A process that is part of the meiotic cell cycle.
created by: jl
creation date: 2014-05-22T14:22:28Z
has_obo_namespace: biological_process
id: GO:1903046
in_subset: gocheck do not annotate
in_subset: goslim pombe

Axiom
annotated source: meiotic cell cycle process
annotated property: definition
annotated target: A process that is part of the meiotic cell cycle.
database_cross_reference: GOC:TermGenie
database_cross_reference: GOC:mtg_cell_cycle
database_cross_reference: GO_REF:0000060

mitotic cell cycle process
type: Class
equivalent class: Class
  intersection of: cellular process
  intersection of: Restriction
    on property: part of
    some values from: mitotic cell cycle
subclass of: cell cycle process
subclass of: Restriction
  on property: part of
  some values from: mitotic cell cycle
definition: A process that is part of the mitotic cell cycle.
created by: jl
creation date: 2014-05-22T14:22:34Z
has_obo_namespace: biological_process
id: GO:1903047
in_subset: gocheck do not annotate

Axiom
annotated source: mitotic cell cycle process
annotated property: definition
annotated target: A process that is part of the mitotic cell cycle.
database_cross_reference: GOC:TermGenie
database_cross_reference: GOC:mtg_cell_cycle
database_cross_reference: GO_REF:0000060

data item
type: Class
subclass of: information content entity
IAO_0000111: data item
IAO_0000112: Data items include counts of things, analyte concentrations, and statistical summaries.
IAO_0000114: pending final vetting
definition: 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.
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jonathan Rees
IAO_0000118: data

symbol
type: Class
subclass of: information content entity
IAO_0000111: symbol
IAO_0000112: a serial number such as "12324X"
IAO_0000112: a stop sign
IAO_0000112: a written proper name such as "OBI"
IAO_0000114: pending final vetting
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 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).
IAO_0000117: PERSON: James A. Overton
IAO_0000117: PERSON: Jonathan Rees
IAO_0000119: based on Oxford English Dictionary

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
IAO_0000111: information content entity
IAO_0000112: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000114: ready for release
definition: A generically dependent continuant that is about some thing.
editor note: 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).
editor note: 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.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: OBI_0000142

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
IAO_0000111: curation status specification
IAO_0000114: pending final vetting
definition: 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.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
IAO_0000117: PERSON:Bill Bug
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO_0000119: OBI_0000266

data about an ontology part
type: Class
subclass of: data item
IAO_0000111: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
IAO_0000117: Person:Alan Ruttenberg

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
  one of: out of scope
subclass of: data about an ontology part
IAO_0000111: obsolescence reason specification
IAO_0000114: pending final vetting
definition: 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.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
IAO_0000111: denotator type
IAO_0000112: 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.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
IAO_0000117: Alan Ruttenberg
IAO_0000119: Barry Smith, Werner Ceusters

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: centrally registered identifier
IAO_0000112: 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.
IAO_0000114: metadata complete
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000118: CRID symbol
IAO_0000119: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
IAO_0000112: 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.
IAO_0000114: metadata complete
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 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').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000118: CRID
IAO_0000119: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: code set
IAO_0000112: PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
IAO_0000114: metadata complete
definition: 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.
IAO_0000117: Justin Whorton
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000118: CRID registry
IAO_0000119: Original proposal from Bjoern, discussions at IAO calls
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237

identifier
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: denotes
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: identifier creating process
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: identifier creating process
IAO_0000111: identifier
definition: 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.
IAO_0000117: Justin Whorton
IAO_0000117: Mathias Brochhausen
IAO_0000118: proper name
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen
comment: 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 creating process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: identifier
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: identifier
definition: A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
IAO_0000117: Justin Whorton
IAO_0000117: Mathias Brochhausen
IAO_0000118: dubbing process
IAO_0000118: naming
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen

code set
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: identifier
definition: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: Justin Whorton
IAO_0000117: Mathias Brochhausen
IAO_0000118: code map
IAO_0000118: code system
IAO_0000118: codeset
IAO_0000118: coding system
IAO_0000118: controlled vocabulary
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
contributor: Alan Ruttenberg
contributor: Clint Dowland
contributor: Matt Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: Code sets might include non-entities/things (e.g. missing thumbs).
comment: Does not imply absence vs. presence of any taxonomy.
comment: 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.
comment: 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).
comment: 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).
comment: 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.
comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
comment: The information content entities do not denote each other.

planned process
type: Class
subclass of: process
IAO_0000111: planned process
definition: A process that realizes a plan which is the concretization of a plan specification.
imported from: obi.owl

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
IAO_0000589: quality (PATO)
has_alternative_id: PATO:0000072
has_obo_namespace: quality
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
database_cross_reference: PATOC:GVG

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has_obo_namespace: quality
id: PATO:0000051
in_subset: attribute slim

Axiom
annotated source: morphology
annotated property: definition
annotated target: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
database_cross_reference: PATOC:GVG

shape
type: Class
subclass of: morphology
definition: 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).
has_alternative_id: PATO:0001647
has_exact_synonym: relational shape quality
has_obo_namespace: quality
id: PATO:0000052
in_subset: attribute slim
comment: 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.

Axiom
annotated source: shape
annotated property: definition
annotated target: 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).
database_cross_reference: PATOC:GVG

orientation
type: Class
subclass of: position
definition: 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.
has_alternative_id: PATO:0000137
has_exact_synonym: angular placement
has_obo_namespace: quality
has_related_synonym: amount of rotation
has_related_synonym: angle
has_related_synonym: angular magnitude
has_related_synonym: plane angle
id: PATO:0000133
in_subset: attribute slim
in_subset: relational slim

Axiom
annotated source: orientation
annotated property: definition
annotated target: 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.
database_cross_reference: PATOC:JE

position
type: Class
subclass of: physical quality
definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
has_alternative_id: PATO:0001032
has_alternative_id: PATO:0001631
has_exact_synonym: location
has_exact_synonym: placement
has_exact_synonym: relational spatial quality
has_obo_namespace: quality
id: PATO:0000140
in_subset: attribute slim

Axiom
annotated source: position
annotated property: definition
annotated target: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
database_cross_reference: PATOC:GVG

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has_alternative_id: PATO:0002079
database_cross_reference: Wikipedia:Physical_property
has_exact_synonym: relational physical quality
has_obo_namespace: quality
id: PATO:0001018
in_subset: attribute slim

Axiom
annotated source: physical quality
annotated property: definition
annotated target: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
database_cross_reference: PATOC:GVG

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
database_cross_reference: snap:Quality
has_exact_synonym: monadic quality of a continuant
has_exact_synonym: multiply inhering quality of a physical entity
has_exact_synonym: quality of a continuant
has_exact_synonym: quality of a single physical entity
has_exact_synonym: quality of an object
has_exact_synonym: quality of continuant
has_narrow_synonym: monadic quality of an object
has_narrow_synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: 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.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
database_cross_reference: PATOC:GVG

triangular
type: Class
subclass of: 2-D shape
definition: A shape quality inhering in a bearer by virtue of the bearer's having three angles.
has_exact_synonym: deltoid
has_obo_namespace: quality
has_related_synonym: delta shaped
has_related_synonym: triangle
has_related_synonym: triangle-shaped
id: PATO:0001875
in_subset: cell quality
in_subset: value slim

Axiom
annotated source: triangular
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's having three angles.
database_cross_reference: wordreference:wordreference

cuneate
type: Class
subclass of: triangular
definition: 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.
has_exact_synonym: wedge-shaped
has_obo_namespace: quality
id: PATO:0001955
in_subset: value slim

Axiom
annotated source: cuneate
annotated property: definition
annotated target: 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.
database_cross_reference: wordreference:wordreference

2-D shape
type: Class
subclass of: shape
definition: A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
has_obo_namespace: quality
has_related_synonym: 2-D projection
has_related_synonym: cross-sectional
id: PATO:0002006
in_subset: attribute slim

Axiom
annotated source: 2-D shape
annotated property: definition
annotated target: A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
database_cross_reference: PATOC:CJM

longitudinal orientation
type: Class
subclass of: orientation
definition: 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.
contributor: https://orcid.org/0000-0003-3162-7490
creation date: 2014-10-17T14:24:19Z
has_obo_namespace: quality
id: PATO:0005024
in_subset: value slim

Axiom
annotated source: longitudinal orientation
annotated property: definition
annotated target: 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.
database_cross_reference: PATOC:WD

plug shaped
type: Class
subclass of: shape
definition: A shape that is in the form of a plug, being tube-like and expanded on one end.
date: 2018-11-12T18:24:41Z
contributor: https://orcid.org/0000-0001-5208-3432
has_exact_synonym: plug like
has_obo_namespace: quality
id: PATO:0040012

Axiom
annotated source: plug shaped
annotated property: definition
annotated target: A shape that is in the form of a plug, being tube-like and expanded on one end.
database_cross_reference: https://orcid.org/0000-0003-3162-7490

Stage 1
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 1
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Stage 2
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_exact_synonym: protosphere
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 2
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 2
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um

Stage 3
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 3
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 3
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um

Stage 4
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 4
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 4
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um

Stage 5
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 5
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 5
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um

Stage 6
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 6
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 6
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um

Stage 7
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28812561
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 7
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 7
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um

Stage 8
type: Class
subclass of: embryo stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_exact_synonym: hatchling
has_exact_synonym: newborn hatchling
has_obo_namespace: Schmidtea_mediterranea_Developmental_Stages

Axiom
annotated source: Stage 8
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: Stage 8
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um

sigma neoblast
type: Class
subclass of: neoblast
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:15972844
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27542689
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28686611
database_cross_reference: PMID:28757112
database_cross_reference: PMID:29557542
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
has_exact_synonym: sigma class neoblast
has_exact_synonym: sigma-class neoblast
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sigma neoblast
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:25017721

protonephridial progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: protonephridia
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: protonephridia
definition: 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.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000011

Axiom
annotated source: protonephridial progenitor cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:24523458
database_cross_reference: PMID:28072387

neural progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: nervous system
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: nervous system
definition: Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system.
has_exact_synonym: neural committed stem cell
has_exact_synonym: neural precursor cell
has_exact_synonym: neural progenitor cell
has_exact_synonym: neuronal progenitor
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000012

Axiom
annotated source: neural progenitor cell
annotated property: definition
annotated target: Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system.
database_cross_reference: PMID:21282632
database_cross_reference: PMID:24173799
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26057828
database_cross_reference: PMID:26525673
database_cross_reference: PMID:28072387
database_cross_reference: PMID:29674432

visceral musculature
type: Class
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: musculature system
definition: Musculature surrounding internal organs of the body.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FBbt:00005070
database_cross_reference: PMID:26904543
database_cross_reference: PMID:30471994
has_exact_synonym: visceral muscle
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: visceral musculature
annotated property: definition
annotated target: Musculature surrounding internal organs of the body.
database_cross_reference: PMID:26904543
database_cross_reference: PMID:30471994

Axiom
annotated source: visceral musculature
annotated property: foaf depicted by
comment: 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

zeta neoblast
type: Class
subclass of: epidermal progenitor cell
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: integumental system
subclass of: Restriction
  on property: develops from
  some values from: sigma neoblast
definition: An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27542689
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28757112
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29158443
database_cross_reference: PMID:29557542
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
has_exact_synonym: zeta
has_exact_synonym: zeta class
has_exact_synonym: zeta class neoblast
has_exact_synonym: zeta-class neoblast
has_exact_synonym: zeta-neoblast
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: zeta neoblast
annotated property: definition
annotated target: An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s).
database_cross_reference: PMID:25017721

non ciliated epithelial cell
type: Class
subclass of: epithelial cell
definition: An epithelial cell lacking cilia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: XAO:0004225
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: non ciliated epithelial cell
annotated property: foaf depicted by
comment: 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.

pharynx
type: Class
subclass of: material entity
subclass of: organ
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16311336
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:17670787
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17942485
database_cross_reference: PMID:18063755
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:18456843
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19852954
database_cross_reference: PMID:19933103
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20511647
database_cross_reference: PMID:20599901
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20865784
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295483
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21747960
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21852957
database_cross_reference: PMID:21894189
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22371573
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22543868
database_cross_reference: PMID:22884275
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23123964
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23652002
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24238224
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24922054
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635

Axiom
annotated source: pharynx
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160

photoreceptor neuron
type: Class
subclass of: material entity
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: eye
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: develops from
  some values from: trail cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17390146
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17942485
database_cross_reference: PMID:18202849
database_cross_reference: PMID:19048075
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22884275
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23318641
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24922054
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25493551
database_cross_reference: PMID:25772472
database_cross_reference: PMID:26017970
database_cross_reference: PMID:26618653
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27606067
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28495872
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30143032
database_cross_reference: PMID:30399335
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30485821
database_cross_reference: UBERON:0006562
has_exact_synonym: PRN
has_exact_synonym: neuronal photoreceptive cell
has_exact_synonym: optical neuron
has_exact_synonym: photoreceptive neuron
has_exact_synonym: photoreceptor cell
has_exact_synonym: photosensitive cell
has_exact_synonym: visual neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: photoreceptor neuron
annotated property: definition
annotated target: Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain.
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22884275

Category 4 cell
type: Class
subclass of: material entity
subclass of: non ciliated epithelial cell
subclass of: epidermal progenitor cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: dorsal region of the epidermis
subclass of: Restriction
  on property: part of
  some values from: ventral epidermis
subclass of: Restriction
  on property: part of
  some values from: non-ciliated epidermis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: Category 3 cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 5
definition: Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18786419
database_cross_reference: PMID:22439894
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26457503
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Category 4 cell
annotated property: definition
annotated target: Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells.
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26457503

muscle progenitor cell
type: Class
subclass of: progenitor cell
subclass of: Restriction
  on property: part of
  some values from: musculature system
definition: Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30471994
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: muscle progenitor cell
annotated property: definition
annotated target: Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers.
database_cross_reference: PMID:25017721

protonephridia
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: renal system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: protonephridial progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:19852954
database_cross_reference: PMID:19933103
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24523458
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25254346
database_cross_reference: PMID:26057828
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26651295
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27501047
database_cross_reference: PMID:27551436
database_cross_reference: PMID:27612384
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29158443
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: UBERON:0006973
has_exact_synonym: excretory organ
has_exact_synonym: nephridia
has_exact_synonym: osmoregulatory duct
has_exact_synonym: protonephridial tubule
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: protonephridia
annotated property: definition
annotated target: Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:21828097
database_cross_reference: PMID:26057828

Axiom
annotated source: protonephridia
annotated property: foaf depicted by
comment: 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

biotype
type: Class
subclass of: Thing
definition: Organisms sharing a specified genotype or karyotype.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Category 5 cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: dorsal region of the epidermis
subclass of: Restriction
  on property: part of
  some values from: ventral epidermis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: Category 4 cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 6
definition: Post-mitotic, ciliated epidermal cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25017721
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Category 5 cell
annotated property: definition
annotated target: Post-mitotic, ciliated epidermal cells.
database_cross_reference: PMID:25017721

embryonic pharynx
type: Class
subclass of: material entity
subclass of: extraembryonic organ
subclass of: Restriction
  on property: part of
  some values from: embryonic digestive system
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FBbt:00001866
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:28072387
has_exact_synonym: temporary embryonic pharynx
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: embryonic pharynx
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms in on the embryonic pharynx.

Smed asexual biotype
type: Class
subclass of: biotype
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:11972158
database_cross_reference: PMID:28812561
has_exact_synonym: asexual
has_exact_synonym: asexual adult
has_exact_synonym: asexual biotype
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Smed asexual biotype
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:11972158
database_cross_reference: PMID:17376870

Axiom
annotated source: Smed asexual biotype
annotated property: foaf depicted by
comment: 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.

nervous system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
definition: 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].
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16311336
database_cross_reference: PMID:17251262
database_cross_reference: PMID:18202849
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21806978
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22696458
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25725068
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26556349
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27501047
database_cross_reference: PMID:27523733
database_cross_reference: PMID:27551436
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28292427
database_cross_reference: PMID:29357350
database_cross_reference: PMID:29557542
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30399335
database_cross_reference: UBERON:0001016
has_exact_synonym: nerve system
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nervous system
annotated property: definition
annotated target: 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].
database_cross_reference: UBERON:0001016

gut
type: Class
subclass of: material entity
subclass of: organ
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17942485
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19933103
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20865784
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21566195
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23903188
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24238224
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24950970
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26556349
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27122174
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27240733
database_cross_reference: PMID:27441386
database_cross_reference: PMID:27501047
database_cross_reference: PMID:27542689
database_cross_reference: PMID:27551436
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28686611
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29158443

Axiom
annotated source: gut
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:3490491

Smed sexual biotype
type: Class
subclass of: biotype
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:11972158
database_cross_reference: PMID:19022767
database_cross_reference: PMID:28812561
has_exact_synonym: hermaphroditic biotype
has_exact_synonym: sexual
has_exact_synonym: sexual hermaphrodite
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Smed sexual biotype
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:11972158
database_cross_reference: PMID:19022767

Axiom
annotated source: Smed sexual biotype
annotated property: foaf depicted by
comment: 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.

Category 2 cell
type: Class
subclass of: material entity
subclass of: epidermal progenitor cell
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: integumental system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: zeta neoblast
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 5
definition: Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18786419
database_cross_reference: PMID:20040488
database_cross_reference: PMID:21894189
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23629965
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24367277
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27542689
database_cross_reference: PMID:28072387
database_cross_reference: PMID:29674431
has_exact_synonym: Category 2 gene expressing cell
has_exact_synonym: NB.21.11e expressing cell
has_exact_synonym: Smed-NB.21.11e+ cell
has_exact_synonym: early division progeny
has_exact_synonym: early epidermal progenitor
has_exact_synonym: early neoblast progeny
has_exact_synonym: early post-mitotic progeny
has_exact_synonym: early progeny
has_exact_synonym: prog-1+ epidermal progenitor cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Category 2 cell
annotated property: definition
annotated target: Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts.
database_cross_reference: PMID:18786419
database_cross_reference: PMID:20040488
database_cross_reference: PMID:22385657
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26114597

primitive ectoderm
type: Class
subclass of: material entity
subclass of: extraembryonic organ
subclass of: Restriction
  on property: contained in
  some values from: aboral hemisphere
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:20423827
database_cross_reference: OCLC:464776945
database_cross_reference: OCLC:82522822
database_cross_reference: PMID:28072387
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primitive ectoderm
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:20423827
database_cross_reference: OCLC:464776945
database_cross_reference: OCLC:82522822
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md

midline
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The median line/ plane of bilateral symmetry along the anteroposterior axis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C81170
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: midline
annotated property: foaf depicted by
comment: Illustration of the midline (in green).

pigment cup cell
type: Class
subclass of: material entity
subclass of: neuron associated cell (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: part of
  some values from: optic cup
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: develops from
  some values from: trail cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17390146
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22884275
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23318641
database_cross_reference: PMID:24063805
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25493551
database_cross_reference: PMID:26017970
database_cross_reference: PMID:27122174
database_cross_reference: PMID:27551436
database_cross_reference: PMID:27606067
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28495872
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29158443
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30471994
has_exact_synonym: eye pigment cell
has_exact_synonym: eye pigment cup cell
has_exact_synonym: eye pigment producing cell
has_exact_synonym: eye pigmented cell
has_exact_synonym: melanin pigment cell
has_exact_synonym: optic cup cell
has_exact_synonym: photoceptor pigmented cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pigment cup cell
annotated property: definition
annotated target: Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22884275

dorsal midline
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: midline
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: midline
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal.
has_exact_synonym: dorsal region of midline
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000032

Axiom
annotated source: dorsal midline
annotated property: foaf depiction
comment: Illustration of the dorsal midline (in green).

epidermal progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: dorsal midline
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: dorsal midline
definition: 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.
has_exact_synonym: epithelial progenitor
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000033

Axiom
annotated source: epidermal progenitor cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27606067
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30282036

epidermis
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: integumental system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: epidermal progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
definition: A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16311336
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20511647
database_cross_reference: PMID:20599901
database_cross_reference: PMID:20865784
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295483
database_cross_reference: PMID:22252539
database_cross_reference: PMID:22549959
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24922054
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25772472
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26651295
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27240733
database_cross_reference: PMID:27501047
database_cross_reference: PMID:27612384
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28686611
database_cross_reference: PMID:28757112
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29158443
database_cross_reference: PMID:29273738
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
database_cross_reference: PMID:30194301
database_cross_reference: PMID:30282036
database_cross_reference: PMID:30962434
database_cross_reference: UBERON:0001003
has_exact_synonym: definitive epidermis
has_exact_synonym: epidermal layer
has_exact_synonym: epidermis
has_exact_synonym: epithelium
has_exact_synonym: mature epidermis
has_exact_synonym: tegument
has_obo_namespace: Planarian_Anatomy
comment: At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium).

Axiom
annotated source: epidermis
annotated property: definition
annotated target: A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
database_cross_reference: OCLC:16809160

Category 3 cell
type: Class
subclass of: material entity
subclass of: epidermal progenitor cell
subclass of: somatic cell
subclass of: Restriction
  on property: part of
  some values from: integumental system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: Category 2 cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 5
definition: Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18786419
database_cross_reference: PMID:20040488
database_cross_reference: PMID:21894189
database_cross_reference: PMID:22252539
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24367277
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27068018
database_cross_reference: PMID:28072387
has_exact_synonym: AGAT-1 expressing cell
has_exact_synonym: AGAT1 expressing cell
has_exact_synonym: Category 3 gene expressing cell
has_exact_synonym: Smed-AGAT-1+ cell
has_exact_synonym: late division progeny
has_exact_synonym: late epidermal progenitor
has_exact_synonym: late neoblast progeny
has_exact_synonym: late postmitotic progeny
has_exact_synonym: late progeny
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Category 3 cell
annotated property: definition
annotated target: Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells.
database_cross_reference: PMID:18786419
database_cross_reference: PMID:20040488
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503

eye
type: Class
subclass of: material entity
subclass of: organ
definition: An organ that detects light.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:15866156
database_cross_reference: PMID:15972844
database_cross_reference: PMID:16311336
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17942485
database_cross_reference: PMID:18063755
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:18456843
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19805089
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20040488
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20599901
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20865784
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21295483
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21566195
database_cross_reference: PMID:21747960
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21852957
database_cross_reference: PMID:21894189
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22884275
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24238224
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24922054
database_cross_reference: PMID:24950970
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25017721

Axiom
annotated source: eye
annotated property: definition
annotated target: An organ that detects light.
database_cross_reference: UBERON:0000970

obsolete definitive tissue
type: Class
term replaced by: tissue
comment: we will move forward using "tissue" instead. We have not listed anything as a regenerating or developing tissue, so this seems unnecessary
deprecated: true

ventral midline
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: midline
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: midline
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal.
has_exact_synonym: ventral region of midline
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000038

Axiom
annotated source: ventral midline
annotated property: foaf depiction
comment: Illustration of the ventral midline (in green).

gamma neoblast
type: Class
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: digestive system
definition: An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27542689
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28757112
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
has_exact_synonym: gamma
has_exact_synonym: gamma class neoblast
has_exact_synonym: gamma-neoblast
has_exact_synonym: gut progenitor cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gamma neoblast
annotated property: definition
annotated target: An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut.
database_cross_reference: PMID:25017721

obsolete Schmidtea mediterranea developmental stage
type: Class
comment: 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
deprecated: true

aboral hemisphere
type: Class
subclass of: independent continuant
subclass of: embryonic subdivision
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
database_cross_reference: UBERON:0008259
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: aboral hemisphere
annotated property: definition
annotated target: Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx.
database_cross_reference: PMID:28072387

anterior primary gut branch
type: Class
subclass of: material entity
subclass of: primary gut branch
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: The single, central gut branch of the triclad gut anterior to the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
database_cross_reference: PMID:3490491
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior primary gut branch
annotated property: definition
annotated target: The single, central gut branch of the triclad gut anterior to the pharynx.
database_cross_reference: PMID:3490491

Axiom
annotated source: anterior primary gut branch
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um

dorsal ventral margin of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal/ventral compartment boundary
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: dorsal/ventral compartment boundary
definition: Region along the edge of the animal where the dorsal and ventral surfaces meet.
has_exact_synonym: D/V boundary
has_exact_synonym: DV border
has_exact_synonym: DV boundary
has_exact_synonym: DV domain
has_exact_synonym: DV margin
has_exact_synonym: body edge
has_exact_synonym: body margin
has_exact_synonym: body periphery
has_exact_synonym: dorsal ventral boundary
has_exact_synonym: dorsal-ventral boundary
has_exact_synonym: dorsal/ventral compartment boundary of whole organism
has_exact_synonym: dorsoventral margin
has_exact_synonym: edge
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000043

Axiom
annotated source: dorsal ventral margin of the whole animal
annotated property: definition
annotated target: Region along the edge of the animal where the dorsal and ventral surfaces meet.
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:17905225
database_cross_reference: PMID:19174194
database_cross_reference: PMID:20865784
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21295483
database_cross_reference: PMID:21458439
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22696458
database_cross_reference: PMID:24415944
database_cross_reference: PMID:26457503
database_cross_reference: PMID:28216315
database_cross_reference: PMID:29357350
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30399335
database_cross_reference: PMID:30485821

cephalic ganglia
type: Class
subclass of: material entity
subclass of: organ
definition: The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16344473
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17670787
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17942485
database_cross_reference: PMID:17999079
database_cross_reference: PMID:18063755
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20844018
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21566195
database_cross_reference: PMID:21806978
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22549959
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23652002
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24238224
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25404302
database_cross_reference: PMID:25725068
database_cross_reference: PMID:25772472
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26017970
database_cross_reference: PMID:26884331
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28287248
database_cross_reference: PMID:29291974
database_cross_reference: PMID:29291981
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30194301
database_cross_reference: PMID:30237141

circular muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: body wall musculature
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: circular muscle progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:26904543
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
has_exact_synonym: circular muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: circular muscle cell
annotated property: definition
annotated target: Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema.
database_cross_reference: PMID:26904543
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md

Axiom
annotated source: circular muscle cell
annotated property: foaf depicted by
comment: 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.

clonogenic neoblast
type: Class
subclass of: neoblast
subclass of: somatic cell
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 6
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16344473
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20215344
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21852957
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22543868
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22884275
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23652002
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24173799
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27502555
database_cross_reference: PMID:27523733
database_cross_reference: PMID:27551436
database_cross_reference: PMID:28434803
database_cross_reference: PMID:29357350
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
database_cross_reference: PMID:30962434
has_exact_synonym: adult pluripotent stem cell
has_exact_synonym: cNeoblast
has_exact_synonym: clonogenic stem cell
has_exact_synonym: pluripotent stem cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: clonogenic neoblast
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:21566185

collecting duct
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: renal system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: adjacent to
  some values from: distal tubule
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:26057828
database_cross_reference: PMID:27068018
database_cross_reference: PMID:29674431
database_cross_reference: UBERON:0001232
has_exact_synonym: collection duct
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: collecting duct
annotated property: definition
annotated target: Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
database_cross_reference: PMID:26057828

Axiom
annotated source: collecting duct
annotated property: foaf depicted by
comment: 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.

diagonal muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: body wall musculature
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:23903188
database_cross_reference: PMID:26904543
database_cross_reference: PMID:27068018
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28807897
database_cross_reference: PMID:30471994
has_exact_synonym: diagonal fiber
has_exact_synonym: diagonal muscle
has_exact_synonym: diagonal muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: diagonal muscle cell
annotated property: definition
annotated target: Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
database_cross_reference: PMID:26904543

Axiom
annotated source: diagonal muscle cell
annotated property: foaf depicted by
comment: 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.

digestive system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16311336
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17390146
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19933103
database_cross_reference: PMID:20040488
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23079596
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24922054
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25558068
database_cross_reference: PMID:26556349
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27501047
database_cross_reference: PMID:29357350
database_cross_reference: UBERON:0001007
has_exact_synonym: gastrointestinal system
has_exact_synonym: gastrovascular system
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: digestive system
annotated property: definition
annotated target: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
database_cross_reference: UBERON:0001007

obsolete direct development
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

obsolete dispersed cleavage
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

distal tubule
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: protonephridia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: protonephridial progenitor cell
subclass of: Restriction
  on property: adjacent to
  some values from: collecting duct
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21828097
database_cross_reference: PMID:27068018
database_cross_reference: UBERON:0004135
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: distal tubule
annotated property: definition
annotated target: Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
database_cross_reference: PMID:21828097

Axiom
annotated source: distal tubule
annotated property: foaf depicted by
comment: 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.

dorsal region of the epidermis
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: epidermis
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: epidermis
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
has_exact_synonym: dorsal epithelium
has_exact_synonym: dorsal region of epidermis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000054

Axiom
annotated source: dorsal region of the epidermis
annotated property: definition
annotated target: Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:17942485
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20599901
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22479207
database_cross_reference: PMID:26457503
database_cross_reference: PMID:27612382
database_cross_reference: PMID:28292427

Axiom
annotated source: dorsal region of the epidermis
annotated property: foaf depiction
comment: 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.

dorsal stripe
type: Class
subclass of: material entity
subclass of: ciliated epithelium
subclass of: Restriction
  on property: part of
  some values from: dorsal region of the epidermis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Ciliated epithelial cells along the dorsal midline.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17553481
has_exact_synonym: racing stripe
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal stripe
annotated property: definition
annotated target: Ciliated epithelial cells along the dorsal midline.
database_cross_reference: PMID:17553481

Axiom
annotated source: dorsal stripe
annotated property: foaf depicted by
comment: 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.

ectolecithal embryo
type: Class
subclass of: embryo
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ectolecithal embryo
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md

obsolete embryonic cleavage
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

embryonic digestive system
type: Class
subclass of: independent continuant
subclass of: extraembryonic structure
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 7
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
database_cross_reference: UBERON:6001842
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic digestive system
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

embryonic gut cell
type: Class
subclass of: material entity
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: embryonic gut
subclass of: Restriction
  on property: contained in
  some values from: aboral hemisphere
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 4
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic gut cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

embryonic wall
type: Class
subclass of: independent continuant
subclass of: embryonic subdivision
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 5
definition: The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:12888018
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic wall
annotated property: definition
annotated target: The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:12888018

Axiom
annotated source: embryonic wall
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators.

enteric musculature
type: Class
subclass of: material entity
subclass of: visceral musculature
subclass of: Restriction
  on property: part of
  some values from: digestive system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: Visceral muscle surrounding the gut.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
database_cross_reference: PMID:22411224
database_cross_reference: PMID:23079596
database_cross_reference: PMID:26904543
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30962434
database_cross_reference: UBERON:2001324
has_exact_synonym: enteric muscle
has_exact_synonym: intestinal muscle
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: enteric musculature
annotated property: foaf depicted by
comment: 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.

esophagus
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Attachment between the triclad gut and the proximal end of the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:18063757
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21806978
database_cross_reference: PMID:24737865
database_cross_reference: PMID:27063937
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30485821
database_cross_reference: UBERON:0001043
has_exact_synonym: gut pharynx intersection
has_exact_synonym: pharynx root
has_exact_synonym: root of pharynx
has_obo_namespace: Planarian_Anatomy

extraembryonic structure
type: Class
subclass of: developing anatomical structure
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000478
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: extraembryonic structure
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0000478

flame bulb
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: protonephridia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: protonephridial progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Terminal structure of protonephridia unit; consists of flame cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21828097
database_cross_reference: PMID:26057828
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: flame bulb
annotated property: foaf depicted by
comment: 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.

flame cell
type: Class
subclass of: material entity
subclass of: terminally differentiated cell
subclass of: Restriction
  on property: part of
  some values from: flame bulb
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: adjacent to
  some values from: proximal tubule
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:17670787
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19852954
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21937596
database_cross_reference: PMID:24523458
database_cross_reference: PMID:26057828
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27542689
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: flame cell
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:21828097
database_cross_reference: PMID:26057828

Axiom
annotated source: flame cell
annotated property: foaf depicted by
comment: 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.

gastrodermis
type: Class
subclass of: material entity
subclass of: epithelium
subclass of: Restriction
  on property: part of
  some values from: gut
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: gamma neoblast
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0000509
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21664348
database_cross_reference: PMID:24120894
database_cross_reference: PMID:25558068
database_cross_reference: PMID:27441386
database_cross_reference: PMID:27501047
database_cross_reference: PMID:28287248
database_cross_reference: PMID:30608231
has_exact_synonym: gut epithelia
has_exact_synonym: gut epithelium
has_exact_synonym: intestinal epithelium
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gastrodermis
annotated property: definition
annotated target: The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
database_cross_reference: PMID:3490491

goblet cell
type: Class
subclass of: material entity
subclass of: secretory cell
subclass of: Restriction
  on property: part of
  some values from: gastrodermis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Secretory cells that release digestive enzymes into the lumen of the intestine.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0001540
database_cross_reference: PMID:20865784
database_cross_reference: PMID:21664348
database_cross_reference: PMID:23079596
database_cross_reference: PMID:27501047
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28287248
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: goblet cell
annotated property: definition
annotated target: Secretory cells that release digestive enzymes into the lumen of the intestine.
database_cross_reference: PMID:3490491

Axiom
annotated source: goblet cell
annotated property: foaf depicted by
comment: 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.

embryonic gut cavity
type: Class
subclass of: independent continuant
subclass of: anatomical cavity
subclass of: Restriction
  on property: part of
  some values from: embryonic gut
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 7
definition: Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic gut cavity
annotated property: definition
annotated target: Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut.
database_cross_reference: PMID:28072387

inner longitudinal muscle cell
type: Class
subclass of: material entity
subclass of: longitudinal muscle cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: longitudinal muscle progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:26904543
database_cross_reference: PMID:30962434
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md
has_exact_synonym: inner longitudinal muscle fiber
has_exact_synonym: inner longitudinal muscle layer
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: inner longitudinal muscle cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:26904543
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md

intestinal phagocyte
type: Class
subclass of: material entity
subclass of: terminally differentiated cell
subclass of: Restriction
  on property: part of
  some values from: gastrodermis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Absorptive digestive cells that engulf food particles for intracellular digestion.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19933103
database_cross_reference: PMID:21664348
database_cross_reference: PMID:23079596
database_cross_reference: PMID:27542689
database_cross_reference: PMID:28072387
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
has_exact_synonym: enterocyte
has_exact_synonym: gut enterocyte
has_exact_synonym: gut phagocyte
has_exact_synonym: intestinal epithelial cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intestinal phagocyte
annotated property: definition
annotated target: Absorptive digestive cells that engulf food particles for intracellular digestion.
database_cross_reference: PMID:3490491

longitudinal muscle cell
type: Class
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: body wall musculature
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:23903188
database_cross_reference: PMID:26904543
database_cross_reference: PMID:27551436
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28807897
database_cross_reference: PMID:30471994
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
has_exact_synonym: BW longitudinal fiber
has_exact_synonym: body wall longitudinal fiber
has_exact_synonym: longitudinal fiber
has_exact_synonym: longitudinal muscle
has_exact_synonym: longitudinal muscle cell
has_exact_synonym: longitudinal muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: longitudinal muscle cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:26904543
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md

Axiom
annotated source: longitudinal muscle cell
annotated property: foaf depicted by
comment: 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.

mouth
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: digestive system
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 6
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17905225
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21806978
database_cross_reference: PMID:23954785
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26556349
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27122174
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30399335
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30485821
database_cross_reference: UBERON:0000165
has_exact_synonym: anus
has_exact_synonym: manus
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: mouth
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160

Axiom
annotated source: mouth
annotated property: foaf depicted by
comment: 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.

oocyte
type: Class
subclass of: gamete
subclass of: female germ cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: develops from
  some values from: oogonial cell
subclass of: Restriction
  on property: produced by
  some values from: ovary
definition: A female germ cell that has entered meiosis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000023
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
database_cross_reference: PMID:27501047
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28812561
has_exact_synonym: egg
has_exact_synonym: female gamete
has_exact_synonym: ovum
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oocyte
annotated property: definition
annotated target: A female germ cell that has entered meiosis.
database_cross_reference: CL:0000023

optic cup
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: eye
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:15866156
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20865784
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22884275
database_cross_reference: PMID:25493551
database_cross_reference: PMID:26017970
database_cross_reference: PMID:26618653
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27240733
database_cross_reference: PMID:27542689
database_cross_reference: PMID:27606067
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28495872
database_cross_reference: PMID:29547123
database_cross_reference: PMID:30143032
database_cross_reference: PMID:30194301
database_cross_reference: UBERON:0003072
has_exact_synonym: eye cup
has_exact_synonym: photoreceptor pigment cup
has_exact_synonym: photoreceptor pigmentation
has_exact_synonym: pigment cup
has_exact_synonym: pigmented cell cup
has_exact_synonym: pigmented optic cup
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: optic cup
annotated property: definition
annotated target: A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22884275

oral hemisphere
type: Class
subclass of: independent continuant
subclass of: embryonic subdivision
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: Stage 3-5 embryo hemisphere centered around the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oral hemisphere
annotated property: definition
annotated target: Stage 3-5 embryo hemisphere centered around the embryonic pharynx.
database_cross_reference: PMID:28072387

Axiom
annotated source: oral hemisphere
annotated property: foaf depicted by
comment: Illustration of the oral hemispshere (in green).

outer longitudinal muscle cell
type: Class
subclass of: material entity
subclass of: longitudinal muscle cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: longitudinal muscle progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:26904543
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
has_exact_synonym: outer longitudinal muscle layer
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: outer longitudinal muscle cell
annotated property: definition
annotated target: Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.
database_cross_reference: PMID:26904543
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md

parenchymal musculature
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: musculature system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:30962434
has_exact_synonym: dorsoventral muscle fibers
has_exact_synonym: parenchymal muscle
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: parenchymal musculature
annotated property: definition
annotated target: Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles.
database_cross_reference: OCLC:16809160

Axiom
annotated source: parenchymal musculature
annotated property: foaf depicted by
comment: Image is an electron micrograph of the parenchyma. Three muscle cells have been notated with an arrowhead. Scale bar is 2 um.

peripheral nervous system
type: Class
subclass of: nervous system
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22339734
database_cross_reference: PMID:23903188
database_cross_reference: PMID:26017970
database_cross_reference: PMID:26884331
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27612382
database_cross_reference: PMID:29674431
database_cross_reference: UBERON:0000010
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: peripheral nervous system
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0000010

pharynx pouch
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: An epithelial structure housing the pharynx, connected to the esophagus and mouth.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
has_exact_synonym: pharyngeal pocket
has_exact_synonym: pharyngeal pouch
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx pouch
annotated property: definition
annotated target: An epithelial structure housing the pharynx, connected to the esophagus and mouth.
database_cross_reference: OCLC:16809160

obsolete racing stripe
type: Class
comment: racing stripe is now a synonym of PLANA:0000055 dorsal stripe
deprecated: true

posterior primary gut branch
type: Class
subclass of: material entity
subclass of: primary gut branch
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: gamma neoblast
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
database_cross_reference: PMID:23318641
database_cross_reference: PMID:24063805
has_exact_synonym: major posterior gut branch
has_exact_synonym: primary posterior intestinal branch
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior primary gut branch
annotated property: definition
annotated target: The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
database_cross_reference: PMID:3490491

Axiom
annotated source: posterior primary gut branch
annotated property: foaf depicted by
comment: 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

primitive gut cell
type: Class
subclass of: material entity
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: primitive gut
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 5
definition: A phagocytic cell closely associated with the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primitive gut cell
annotated property: definition
annotated target: A phagocytic cell closely associated with the embryonic pharynx.
database_cross_reference: PMID:28072387

obsolete protosphere
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

proximal tubule
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: protonephridia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: protonephridial progenitor cell
subclass of: Restriction
  on property: adjacent to
  some values from: distal tubule
subclass of: Restriction
  on property: adjacent to
  some values from: flame cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 6
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21937596
database_cross_reference: PMID:26057828
database_cross_reference: PMID:27068018
database_cross_reference: UBERON:0004134
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: proximal tubule
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:21828097

Axiom
annotated source: proximal tubule
annotated property: foaf depicted by
comment: 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.

renal system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:17670787
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22427692
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24523458
database_cross_reference: PMID:24737865
database_cross_reference: PMID:25254346
database_cross_reference: PMID:26057828
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27542689
database_cross_reference: PMID:28461239
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30297872
database_cross_reference: UBERON:0001008
has_exact_synonym: excretory system
has_exact_synonym: protonephridial system
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: renal system
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0001008

secondary gut branch
type: Class
subclass of: gut branch
definition: Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
database_cross_reference: PMID:27122174
database_cross_reference: PMID:28287248
database_cross_reference: PMID:30471994
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secondary gut branch
annotated property: definition
annotated target: Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
database_cross_reference: PMID:3490491

Axiom
annotated source: secondary gut branch
annotated property: foaf depicted by
comment: 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

sperm
type: Class
subclass of: gamete
subclass of: male germ cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: elongate spermatid
subclass of: Restriction
  on property: produced by
  some values from: testis
definition: A mature male germ cell that develops from a spermatid.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000019
database_cross_reference: PMID:17390146
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:28072387
database_cross_reference: PMID:29095551
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: mature sperm
has_exact_synonym: spermatozoa
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sperm
annotated property: definition
annotated target: A mature male germ cell that develops from a spermatid.
database_cross_reference: CL:0000019

obsolete sphere formation
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

yolk syncytium
type: Class
subclass of: material entity
subclass of: syncytium
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 1
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 1
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 2
subclass of: Restriction
  on property: produced by
  some values from: yolk cell
definition: Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:15599763
has_exact_synonym: syncytial yolk cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: yolk syncytium
annotated property: definition
annotated target: Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2.
database_cross_reference: PMID:15599763

tertiary gut branch
type: Class
subclass of: gut branch
definition: Gut branches originating from and connected to the secondary gut branches.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
database_cross_reference: PMID:23250205
database_cross_reference: PMID:27122174
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28287248
database_cross_reference: PMID:30194301
database_cross_reference: PMID:30471994
has_exact_synonym: tertiary branch
has_exact_synonym: tertiary intestinal branch
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tertiary gut branch
annotated property: definition
annotated target: Gut branches originating from and connected to the secondary gut branches.
database_cross_reference: PMID:3490491

Axiom
annotated source: tertiary gut branch
annotated property: foaf depicted by
comment: 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

obsolete tissue morphogenesis
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

trail cell
type: Class
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 6
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22884275
database_cross_reference: PMID:23250205
database_cross_reference: PMID:24040508
database_cross_reference: PMID:27606067
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28245923
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30485821
has_exact_synonym: eye progenitor
has_exact_synonym: eye progenitor cell
has_exact_synonym: ovo+ eye progenitor
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: trail cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22884275

ventral epidermis
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: epidermis
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: epidermis
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells
has_exact_synonym: cilated ventral epidermis
has_exact_synonym: ciliated ventral epithelium
has_exact_synonym: ventral epidermin
has_exact_synonym: ventral epithelia
has_exact_synonym: ventral epithelium
has_exact_synonym: ventral region of epidermis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000096

Axiom
annotated source: ventral epidermis
annotated property: definition
annotated target: Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:15866156
database_cross_reference: PMID:17942485
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20599901
database_cross_reference: PMID:21282632
database_cross_reference: PMID:23144623
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24523458
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26912790
database_cross_reference: PMID:27068018
database_cross_reference: PMID:28292427
database_cross_reference: PMID:29100657
database_cross_reference: PMID:30383829
database_cross_reference: PMID:30962434

ventral nerve cord
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: central nervous system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
definition: 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].
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0002328
database_cross_reference: EFO:0000896
database_cross_reference: FBbt:00001102
database_cross_reference: ISBN:9780070316607
database_cross_reference: MAT:0000339
database_cross_reference: MIAA:0000339
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17390146
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:18063755
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20599901
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25772472
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26017970
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26556349
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27612382
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29291974
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30143032
database_cross_reference: PMID:30471994
database_cross_reference: UBERON:0000934
database_cross_reference: WBbt:0005829
database_cross_reference: http://en.wikipedia.org/wiki/Ventral:nerve:cord
database_cross_reference: nlx:146329
has_exact_synonym: VNC
has_exact_synonym: nerve cord
has_exact_synonym: ventral cord
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral nerve cord
annotated property: definition
annotated target: 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].
database_cross_reference: UBERON:0000934

zygote
type: Class
subclass of: independent continuant
subclass of: whole organism
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 1
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 1
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 1
definition: Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ].
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0000854
database_cross_reference: CL:0000365
database_cross_reference: PMID:28812561
database_cross_reference: UBERON:0000106
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: zygote
annotated property: definition
annotated target: Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ].
database_cross_reference: CL:0000365

neuron
type: Class
subclass of: electrically signaling cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0000938
database_cross_reference: CL:0000540
database_cross_reference: NCIT:C12623
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:20215344
database_cross_reference: PMID:21566185
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22549959
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23903188
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24922054
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25558068
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27542689
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29184198
database_cross_reference: PMID:29291974
database_cross_reference: PMID:29291981
database_cross_reference: PMID:29357350
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30143032
database_cross_reference: PMID:30399335
database_cross_reference: WBbt:0003679
has_exact_synonym: differentiated neuron
has_exact_synonym: nerve cell
has_exact_synonym: neural cell
has_exact_synonym: neuronal cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neuron
annotated property: definition
annotated target: 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.
database_cross_reference: CL:0000540

epithelial cell
type: Class
subclass of: terminally differentiated cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000066
database_cross_reference: PMID:18202849
database_cross_reference: PMID:19048075
database_cross_reference: PMID:20865784
database_cross_reference: PMID:22479207
database_cross_reference: PMID:24737865
database_cross_reference: PMID:26114597
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28461239
has_exact_synonym: epidermis cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: epithelial cell
annotated property: definition
annotated target: 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.
database_cross_reference: CL:0000066

muscle cell
type: Class
subclass of: electrically responsive cell
definition: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000187
database_cross_reference: PMID:15972844
database_cross_reference: PMID:18202849
database_cross_reference: PMID:19174194
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20511647
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22252539
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24737865
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25558068
database_cross_reference: PMID:26062938
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27523733
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28686611
database_cross_reference: PMID:28807897
database_cross_reference: PMID:28893948
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30962434
has_exact_synonym: muscle fiber
has_exact_synonym: myocyte
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: muscle cell
annotated property: definition
annotated target: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
database_cross_reference: CL:0000187

Axiom
annotated source: muscle cell
annotated property: foaf depicted by
comment: 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.

anatomical region
type: Class
subclass of: organism subdivision
definition: A subdivision of an anatomical compartment.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BSPO:0000070
database_cross_reference: PMID:28292427
database_cross_reference: PMID:29547123
has_exact_synonym: body region
has_obo_namespace: Planarian_Anatomy

central nervous system
type: Class
subclass of: nervous system
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16344473
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17670787
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17942485
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19933103
database_cross_reference: PMID:20865784
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22252539
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22445864
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24367277
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24737865
database_cross_reference: PMID:24922054
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25493551
database_cross_reference: PMID:25772472
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26017970
database_cross_reference: PMID:26459857
database_cross_reference: PMID:26711341
database_cross_reference: PMID:26884331
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27240733
database_cross_reference: PMID:27523733
database_cross_reference: PMID:27542689
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27800171
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28807897
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29273738
database_cross_reference: PMID:29291981
database_cross_reference: PMID:30399335
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30729158
database_cross_reference: PMID:30962434
database_cross_reference: UBERON:0001017
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: CNS

Axiom
annotated source: central nervous system
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0001017

rhabdite
type: Class
subclass of: epithelial cell component
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: rhabdite
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160

Axiom
annotated source: rhabdite
annotated property: foaf depicted by
comment: 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.

secretory cell
type: Class
subclass of: terminally differentiated cell
definition: A cell that specializes in controlled release of one or more substances.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000151
database_cross_reference: NCIT:C13055
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secretory cell
annotated property: definition
annotated target: A cell that specializes in controlled release of one or more substances.
database_cross_reference: CL:0000151

Axiom
annotated source: secretory cell
annotated property: foaf depicted by
comment: 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.

ciliated epithelial cell
type: Class
subclass of: epithelial cell
definition: An epithelial cell that has cilia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000067
database_cross_reference: PMID:24737865
database_cross_reference: PMID:28461239
database_cross_reference: PMID:28807897
has_exact_synonym: ciliated epidermal cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ciliated epithelial cell
annotated property: definition
annotated target: An epithelial cell that has cilia.
database_cross_reference: CL:0000067

yolk cell
type: Class
subclass of: terminally differentiated cell
subclass of: reproductive system product
subclass of: Restriction
  on property: part of
  some values from: embryonic wall
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: produced by
  some values from: vitelline gland
definition: An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000428
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: PMID:29674431
has_exact_synonym: vitellocyte
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: yolk cell
annotated property: definition
annotated target: An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
database_cross_reference: PMID:27149082

obsolete anatomical compartment subdivision feature
type: Class
comment: extra layer of complexity not needed upon further examination
deprecated: true

pharynx progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: pharynx
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: pharynx
definition: foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000110

Axiom
annotated source: pharynx progenitor cell
annotated property: definition
annotated target: foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx.
database_cross_reference: PMID:24737865
database_cross_reference: PMID:25254346

proximal tubule epithelial cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: Restriction
  on property: part of
  some values from: proximal tubule
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Ciliated epithelial cells that assemble into proximal tubules.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0006154
database_cross_reference: PMID:21828097
database_cross_reference: PMID:29674431
has_exact_synonym: proximal tubule cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: proximal tubule epithelial cell
annotated property: definition
annotated target: Ciliated epithelial cells that assemble into proximal tubules.
database_cross_reference: PMID:21828097

Axiom
annotated source: proximal tubule epithelial cell
annotated property: foaf depicted by
comment: 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.

obsolete Schmidtea mediterranea developmental term
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

tissue
type: Class
subclass of: multicellular anatomical structure
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000479
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tissue
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0000479

anatomical system
type: Class
subclass of: multicellular anatomical structure
definition: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000467
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anatomical system
annotated property: definition
annotated target: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
database_cross_reference: UBERON:0000467

distal tubule epithelial cell
type: Class
subclass of: material entity
subclass of: non ciliated epithelial cell
subclass of: Restriction
  on property: part of
  some values from: distal tubule
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Nonciliated epithelial cells that assemble into protonephridial distal tubules.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21828097
database_cross_reference: PMID:29674431
has_exact_synonym: distal tubule cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: distal tubule epithelial cell
annotated property: definition
annotated target: Nonciliated epithelial cells that assemble into protonephridial distal tubules.
database_cross_reference: PMID:21828097

Axiom
annotated source: distal tubule epithelial cell
annotated property: foaf depicted by
comment: 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.

embryo
type: Class
subclass of: whole organism
subclass of: reproductive system product
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000922
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryo
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0000922

embryonic structure
type: Class
subclass of: developing anatomical structure
definition: Anatomical structure that is part of an embryo.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0000174
database_cross_reference: UBERON:0002050
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic structure
annotated property: definition
annotated target: Anatomical structure that is part of an embryo.
database_cross_reference: UBERON:0002050

collecting duct epithelial cell
type: Class
subclass of: material entity
subclass of: non ciliated epithelial cell
subclass of: Restriction
  on property: part of
  some values from: collecting duct
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Nonciliated epithelial cells that assemble into collecting ducts.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:26057828
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: collecting duct epithelial cell
annotated property: definition
annotated target: Nonciliated epithelial cells that assemble into collecting ducts.
database_cross_reference: PMID:26057828

Axiom
annotated source: collecting duct epithelial cell
annotated property: foaf depicted by
comment: 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.

terminally differentiated cell
type: Class
subclass of: somatic cell
definition: A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29674432
has_obo_namespace: Planarian_Anatomy

progenitor cell
type: Class
subclass of: independent continuant
subclass of: cell
subclass of: Restriction
  on property: develops from
  some values from: neoblast
definition: A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21852957
database_cross_reference: PMID:29674432
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: precursor cell
has_obo_namespace: Planarian_Anatomy

stem cell
type: Class
subclass of: cell
definition: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000034
database_cross_reference: PMID:17376870
database_cross_reference: PMID:19805089
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22385657
database_cross_reference: PMID:23123964
database_cross_reference: PMID:23318635
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24173799
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26651295
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27501047
database_cross_reference: PMID:29124009
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: stem cell
annotated property: definition
annotated target: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
database_cross_reference: CL:0000034

gamete
type: Class
subclass of: reproductive system product
subclass of: germ cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: produced by
  some values from: gonad
definition: A mature sexual reproductive cell having a single set of unpaired chromosomes.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000300
database_cross_reference: PMID:20844018
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:28434803
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gamete
annotated property: definition
annotated target: A mature sexual reproductive cell having a single set of unpaired chromosomes.
database_cross_reference: CL:0000300

embryonic cell
type: Class
subclass of: cell
definition: A cell of the embryo.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0002321
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic cell
annotated property: definition
annotated target: A cell of the embryo.
database_cross_reference: CL:0002321

visual system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: The sensory system subserving the sense of vision.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0002104
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: visual system
annotated property: definition
annotated target: The sensory system subserving the sense of vision.
database_cross_reference: UBERON:0002104

sensory system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0001032
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sensory system
annotated property: definition
annotated target: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
database_cross_reference: UBERON:0001032

reproductive system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
definition: Anatomical system that has as its parts the organs concerned with reproduction.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000990
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: reproductive system
annotated property: definition
annotated target: Anatomical system that has as its parts the organs concerned with reproduction.
database_cross_reference: UBERON:0000990

oviduct epithelial cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: Restriction
  on property: part of
  some values from: oviduct epithelium
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Ciliated epithelial cells that assemble into the oviduct.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:22074376
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oviduct epithelial cell
annotated property: definition
annotated target: Ciliated epithelial cells that assemble into the oviduct.
database_cross_reference: PMID:22074376

sperm duct epithelial cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: Restriction
  on property: part of
  some values from: sperm duct epithelium
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Ciliated epithelial cells comprising the sperm ducts.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sperm duct epithelial cell
annotated property: definition
annotated target: Ciliated epithelial cells comprising the sperm ducts.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376

obsolete anatomical structure
type: Class
term replaced by: anatomical structure
comment: replacing with UBERON term
deprecated: true

circular muscle progenitor cell
type: Class
subclass of: muscle progenitor cell
subclass of: neoblast
subclass of: somatic cell
definition: piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29168507
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: circular muscle progenitor cell
annotated property: definition
annotated target: piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers.
database_cross_reference: PMID:29168507

primordium
type: Class
subclass of: regenerating anatomical structure
definition: Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0001048
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primordium
annotated property: definition
annotated target: Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
database_cross_reference: UBERON:0001048

obsolete gametogenesis
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

mechanoreceptor cell
type: Class
subclass of: sensory neuron
definition: A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18202849
database_cross_reference: PMID:7466176
has_exact_synonym: mechanoreceptor
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: mechanoreceptor cell
annotated property: definition
annotated target: A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
database_cross_reference: PMID:18202849
database_cross_reference: PMID:7466176

longitudinal muscle progenitor cell
type: Class
subclass of: muscle progenitor cell
subclass of: neoblast
definition: piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29168507
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: longitudinal muscle progenitor cell
annotated property: definition
annotated target: piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
database_cross_reference: PMID:29168507

female primordial germ cell
type: Class
subclass of: material entity
subclass of: stem cell
subclass of: female germ cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17390146
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: female primordial germ cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:17390146

whole organism
type: Class
subclass of: anatomical structure
definition: Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17251262
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27502555
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29906446
database_cross_reference: UBERON:0000468
has_exact_synonym: WW
has_exact_synonym: intact animal
has_exact_synonym: intact planarian
has_exact_synonym: whole animal
has_exact_synonym: whole body
has_exact_synonym: whole worm
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: whole organism
annotated property: definition
annotated target: Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria.
database_cross_reference: UBERON:0000468

regeneration
type: Class
subclass of: anatomical structure development
definition: 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).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0031099
database_cross_reference: GOC:mah
database_cross_reference: GOC:pr
database_cross_reference: Wikipedia:Regeneration:(biology)
has_exact_synonym: regernative development
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: regeneration
annotated property: definition
annotated target: 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).
database_cross_reference: GO:0031099

Hyman vesicle
type: Class
subclass of: independent continuant
subclass of: intracellular granule
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29100657
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Hyman vesicle
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:29100657

Axiom
annotated source: Hyman vesicle
annotated property: foaf depicted by
comment: Image is an immunoelectron micrograph depicting hyman vesicles in the apical side of an epidermal cell. Scale bar is 1um.

anterior region of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus.
has_exact_synonym: anterior region of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000140

Axiom
annotated source: anterior region of the whole animal
annotated property: definition
annotated target: Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus.
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16311336
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18456843
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19805089
database_cross_reference: PMID:19852954
database_cross_reference: PMID:19933103
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20422023
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21852957
database_cross_reference: PMID:21894189
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22696458
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24367277
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24523458
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25493551
database_cross_reference: PMID:25558068
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26556349
database_cross_reference: PMID:26651295
database_cross_reference: PMID:26884331
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27240733
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28893948
database_cross_reference: PMID:29273738
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29557542
database_cross_reference: PMID:29906446
database_cross_reference: PMID:30143032
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30485821

Axiom
annotated source: anterior region of the whole animal
annotated property: foaf depiction
comment: Illustration of the anterior region of the whole animal (in green).

dorsal region of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes.
has_exact_synonym: dorsal region of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000141

Axiom
annotated source: dorsal region of the whole animal
annotated property: foaf depiction
comment: Illustration of the dorsal region of the whole animal (in green).

posterior region of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: 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.
has_exact_synonym: posterior compartment of the whole animal
has_exact_synonym: posterior region of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000142

Axiom
annotated source: posterior region of the whole animal
annotated property: foaf depiction
comment: Illustration of the posterior compartement of the whole animal (in green).

ventral region of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: Compartment along the dorsoventral axis that is below the anteroposterior axis.
has_exact_synonym: ventral region of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000143

Axiom
annotated source: ventral region of the whole animal
annotated property: foaf depiction
comment: Illustration of the ventral region of the whole animal (in green).

bursal canal
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: copulatory apparatus
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: bursal canal
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22074376

gonopore
type: Class
subclass of: independent continuant
subclass of: pore
subclass of: Restriction
  on property: part of
  some values from: copulatory apparatus
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21566185
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22899852
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: common gonopore
has_exact_synonym: genital pore
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gonopore
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22074376

ovary
type: Class
subclass of: material entity
subclass of: gonad
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: NCIT:C12404
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:18456843
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20844018
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22371573
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25404302
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28812561
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: female gonad
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ovary
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:17376870

oviduct
type: Class
subclass of: material entity
subclass of: reproductive organ
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20844018
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:28072387
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: ovovitilline duct
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oviduct
annotated property: definition
annotated target: Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
database_cross_reference: PMID:22074376

penis papilla
type: Class
subclass of: material entity
subclass of: reproductive organ
subclass of: Restriction
  on property: part of
  some values from: copulatory apparatus
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27074666
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: penis
has_exact_synonym: penis bulb
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: penis papilla
annotated property: definition
annotated target: A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal.
database_cross_reference: PMID:22074376

sperm duct
type: Class
subclass of: material entity
subclass of: reproductive organ
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:17390146
database_cross_reference: PMID:19022767
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20844018
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27304889
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: ZFA:0001268
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: seminal duct
has_exact_synonym: sperm ductule
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sperm duct
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376

testis
type: Class
subclass of: material entity
subclass of: gonad
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:18456843
database_cross_reference: PMID:19022767
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20844018
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22371573
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25404302
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28812561
database_cross_reference: PMID:29095551
database_cross_reference: UBERON:0000473
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: male gonad
has_exact_synonym: testis lobe
has_exact_synonym: testis lobule
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: testis
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19022767

obsolete developing anatomical structure
type: Class
term replaced by: developing anatomical structure
comment: replacing with UBERON term
deprecated: true

primitive ectoderm cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: primitive ectoderm
subclass of: Restriction
  on property: contained in
  some values from: aboral hemisphere
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
definition: Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:20423827
database_cross_reference: OCLC:464776945
database_cross_reference: OCLC:82522822
database_cross_reference: PMID:28072387
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primitive ectoderm cell
annotated property: definition
annotated target: Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2.
database_cross_reference: OCLC:20423827
database_cross_reference: OCLC:464776945
database_cross_reference: OCLC:82522822
database_cross_reference: PMID:28072387
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md

obsolete blastomere compartment
type: Class
term replaced by: blastomere
comment: replace with blastomere only
deprecated: true

juvenile stage
type: Class
subclass of: life cycle stage
definition: A postnatal stage of Smed development that initiates with hatching and proceeds until sexual maturity is reached. Reproductive structures develop during the juvenile stage.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0034919
has_obo_namespace: Planarian_Anatomy

reproductive system product
type: Class
subclass of: material entity
subclass of: anatomical structure
subclass of: Restriction
  on property: produced by
  some values from: reproductive system
definition: Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

egg capsule
type: Class
subclass of: reproductive system product
subclass of: Restriction
  on property: produced by
  some values from: sexual organism
definition: A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:18942102
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22371573
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28812561
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: capsule
has_exact_synonym: cocoon
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: egg capsule
annotated property: definition
annotated target: A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk.
database_cross_reference: PMID:18942102

gonad
type: Class
subclass of: reproductive organ
definition: Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22252538
database_cross_reference: PMID:22371573
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28976975
database_cross_reference: UBERON:0000991
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gonad
annotated property: definition
annotated target: Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
database_cross_reference: UBERON:0000991

male primordial germ cell
type: Class
subclass of: material entity
subclass of: stem cell
subclass of: male germ cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: male primordial germ cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146

spermatogonial stem cell
type: Class
subclass of: material entity
subclass of: stem cell
subclass of: male germ cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: neoblast
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085
has_exact_synonym: SSC
has_exact_synonym: male germline stem cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: spermatogonial stem cell
annotated property: definition
annotated target: gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085

spermatogonium
type: Class
subclass of: material entity
subclass of: progenitor cell
subclass of: male germ cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: spermatogonial stem cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000020
database_cross_reference: PMID:23629965
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: spermatogonial cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: spermatogonium
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085

spermatocyte
type: Class
subclass of: material entity
subclass of: male germ cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: spermatogonium
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000017
database_cross_reference: PMID:17376870
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25404302
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
database_cross_reference: PMID:29095551
has_exact_synonym: primary spermatocyte
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: spermatocyte
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27330085

spermatid
type: Class
subclass of: material entity
subclass of: male germ cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
definition: A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000018
database_cross_reference: PMID:17376870
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: PMID:25404302
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: spermatid
annotated property: definition
annotated target: A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
database_cross_reference: CL:0000018

oogonial stem cell
type: Class
subclass of: material entity
subclass of: stem cell
subclass of: female germ cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: develops from
  some values from: neoblast
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085
has_exact_synonym: female germ cell
has_exact_synonym: female germline cell
has_exact_synonym: female germline stem cell
has_exact_synonym: oogonial stem cell
has_exact_synonym: ovarian germline stem cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oogonial stem cell
annotated property: definition
annotated target: A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018

cement gland
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: copulatory apparatus
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:18942102
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:23652002
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
has_exact_synonym: shell gland
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cement gland
annotated property: definition
annotated target: Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk.
database_cross_reference: ASIN:B000M4NK9M
database_cross_reference: PMID:18942102
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082

obsolete oviparity
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

obsolete cross-fertilization
type: Class
comment: removing all processes. may bring back if PLANA expanded to cover processes.
deprecated: true

germ cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: reproductive system
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0000535
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: germ cell
annotated property: definition
annotated target: 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.
database_cross_reference: BTO:0000535

male germ cell
type: Class
subclass of: germ cell
definition: A male germ cell is a germ cell that supports male gamete production.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000015
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: male germ cell
annotated property: definition
annotated target: A male germ cell is a germ cell that supports male gamete production.
database_cross_reference: CL:0000015

female germ cell
type: Class
subclass of: germ cell
definition: Female germ cell is a germ cell that supports female gamete production.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000021
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: female germ cell
annotated property: definition
annotated target: Female germ cell is a germ cell that supports female gamete production.
database_cross_reference: CL:0000021

tuba
type: Class
subclass of: material entity
subclass of: reproductive organ
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:28434803
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tuba
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082

vitelline gland
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: produces
  some values from: yolk cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:16932928
database_cross_reference: PMID:17390146
database_cross_reference: PMID:18942102
database_cross_reference: PMID:19247960
database_cross_reference: PMID:22074376
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27501047
database_cross_reference: PMID:28072387
database_cross_reference: PMID:28434803
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: vitellaria
has_exact_synonym: vitellarium
has_exact_synonym: yolk gland
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: vitelline gland
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:16932928
database_cross_reference: PMID:18942102
database_cross_reference: PMID:27149082

copulatory apparatus
type: Class
subclass of: material entity
subclass of: reproductive structure
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: Accessory reproductive structures involved in copulation, egg capsule development and laying.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27163480
database_cross_reference: PMID:28434803
has_exact_synonym: copulatory complex
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: copulatory apparatus
annotated property: definition
annotated target: Accessory reproductive structures involved in copulation, egg capsule development and laying.
database_cross_reference: PMID:22074376

copulatory bursa
type: Class
subclass of: material entity
subclass of: reproductive organ
subclass of: Restriction
  on property: part of
  some values from: copulatory apparatus
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: An organ that receives and stores sperm from mating partners.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20967238
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: bursa
has_exact_synonym: male antrum
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: copulatory bursa
annotated property: definition
annotated target: An organ that receives and stores sperm from mating partners.
database_cross_reference: PMID:22074376

seminal vesicle
type: Class
subclass of: material entity
subclass of: reproductive organ
subclass of: Restriction
  on property: part of
  some values from: copulatory apparatus
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
definition: Glandular pouches adjoining the sperm ducts which produce seminal fluid.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C12787
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376
database_cross_reference: UBERON:0000998
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: seminal vesicle
annotated property: definition
annotated target: Glandular pouches adjoining the sperm ducts which produce seminal fluid.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376

round spermatid
type: Class
subclass of: spermatid
subclass of: Restriction
  on property: develops from
  some values from: spermatocyte
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20844018
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
database_cross_reference: PMID:29095551
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: round spermatid
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085

elongate spermatid
type: Class
subclass of: spermatid
subclass of: Restriction
  on property: develops from
  some values from: round spermatid
definition: Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20844018
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27304889
database_cross_reference: PMID:27330085
database_cross_reference: PMID:29095551
has_exact_synonym: elongating spermatid
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: elongate spermatid
annotated property: definition
annotated target: Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm.
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085

oogonial cell
type: Class
subclass of: material entity
subclass of: progenitor cell
subclass of: female germ cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: develops from
  some values from: oogonial stem cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FMA:83673
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oogonial cell
annotated property: definition
annotated target: An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
database_cross_reference: FMA:83673

body wall musculature
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: musculature system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Any collection of muscles that is part of a body wall [Automatically generated definition].
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BSA:0000058
database_cross_reference: BTO:0001863
database_cross_reference: FMA:86931
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22385657
database_cross_reference: PMID:24992682
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27074666
database_cross_reference: PMID:28171748
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30962434
database_cross_reference: UBERON:0004462
database_cross_reference: WBbt:0005813
has_exact_synonym: BWM
has_exact_synonym: body muscle
has_exact_synonym: body wall muscle
has_exact_synonym: body wall muscles
has_exact_synonym: body-wall muscle
has_exact_synonym: body-wall musculature
has_exact_synonym: muscle layer surrounding the body wall
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: body wall musculature
annotated property: definition
annotated target: Any collection of muscles that is part of a body wall [Automatically generated definition].
database_cross_reference: UBERON:0004462

Axiom
annotated source: body wall musculature
annotated property: foaf depicted by
comment: 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 longitudinal muscle cell
type: Class
subclass of: independent continuant
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: pharynx musculature
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Pharynx muscle fibers running anteroposterior (proximal to distal).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
has_exact_synonym: pharyngeal longitudinal muscle cell
has_exact_synonym: pharyngeal longitudinal muscle fiber
has_exact_synonym: pharynx longitudinal muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx longitudinal muscle cell
annotated property: definition
annotated target: Pharynx muscle fibers running anteroposterior (proximal to distal).
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx longitudinal muscle cell
annotated property: foaf depicted by
comment: 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.

obsolete anatomical cavity
type: Class
term replaced by: anatomical cavity
comment: replacing with UBERON term
deprecated: true

obsolete anatomical entity
type: Class
term replaced by: anatomical entity
comment: replacing with UBERON term
deprecated: true

obsolete immaterial anatomical entity
type: Class
term replaced by: UBERON_0000466
comment: replacing with UBERON term
deprecated: true

obsolete anatomical point
type: Class
term replaced by: UBERON_0006983
comment: replacing with UBERON term
deprecated: true

obsolete anatomical space
type: Class
term replaced by: UBERON_0000464
comment: replacing with UBERON term
deprecated: true

pharynx lumen
type: Class
subclass of: immaterial entity
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: immediately deep to
  some values from: pharynx inner epithelium surface
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: luminal space of
  some values from: pharynx
definition: Anatomical space enclosed by the pharynx inner epithelium.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17251262
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27502555
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29906446
database_cross_reference: UBERON:0000468
has_exact_synonym: cavity of pharynx
has_exact_synonym: pharyngeal lumen
has_exact_synonym: pharynx cavity
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx lumen
annotated property: definition
annotated target: Anatomical space enclosed by the pharynx inner epithelium.
database_cross_reference: UBERON:0000468

Axiom
annotated source: pharynx lumen
annotated property: foaf depicted by
comment: Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Cavity of pharynx is indicated by arrows. Scale bar = 250um

digestive tract lumen
type: Class
subclass of: immaterial entity
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: gut
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
subclass of: Restriction
  on property: luminal space of
  some values from: gut
definition: An anatomical space that is surrounded by a digestive tract.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17553481
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21828097
database_cross_reference: PMID:28072387
database_cross_reference: UBERON:0006909
has_exact_synonym: digestive system lumen
has_exact_synonym: gut cavity
has_exact_synonym: lumen of digestive tract
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: digestive tract lumen
annotated property: definition
annotated target: An anatomical space that is surrounded by a digestive tract.
database_cross_reference: PMID:21664348

Axiom
annotated source: digestive tract lumen
annotated property: foaf depicted by
comment: 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

oral opening
type: Class
subclass of: independent continuant
subclass of: anatomical cavity
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: part of
  some values from: mouth
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
definition: The orifice that connects the mouth to the exterior of the body.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17670787
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30399335
database_cross_reference: UBERON:0000166
has_exact_synonym: pharyngeal mouth opening
has_exact_synonym: pharynx opening
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oral opening
annotated property: definition
annotated target: The orifice that connects the mouth to the exterior of the body.
database_cross_reference: UBERON:0000166

pharynx pouch cavity
type: Class
subclass of: independent continuant
subclass of: anatomical cavity
subclass of: Restriction
  on property: part of
  some values from: pharynx pouch
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
has_exact_synonym: pharnygeal cavity
has_exact_synonym: pharyngeal pouch cavity
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx pouch cavity
annotated property: definition
annotated target: Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch.
database_cross_reference: OCLC:16809160

Axiom
annotated source: pharynx pouch cavity
annotated property: foaf depicted by
comment: 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

apical surface of the epidermis
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: epidermis
  intersection of: Restriction
    on property: overlaps
    some values from: apical surface
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: epidermis
subclass of: Restriction
  on property: overlaps
  some values from: apical surface
definition: The apical surface of the single layered epidermis that is in contact with the environment.
has_exact_synonym: apical surface of epidermis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000409

Axiom
annotated source: apical surface of the epidermis
annotated property: foaf depiction
comment: 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.

basal surface of the epidermis
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: epidermis
  intersection of: Restriction
    on property: overlaps
    some values from: basal surface
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: epidermis
subclass of: Restriction
  on property: overlaps
  some values from: basal surface
definition: The basal surface of the epidermis in direct contact with the basal lamina.
has_exact_synonym: basal surface of epidermis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0000410

Axiom
annotated source: basal surface of the epidermis
annotated property: foaf depiction
comment: Electron micrograph of the dorsal epidermis in a transverse plane. The basal epidermis surface is noted with magenta arrows. Scale bar is 5um.

gastrodermis surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: gut
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The surface of the gastrodermis in contact with the gut lumen.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
has_exact_synonym: lumen gut surface
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gastrodermis surface
annotated property: definition
annotated target: The surface of the gastrodermis in contact with the gut lumen.
database_cross_reference: PMID:21664348

Axiom
annotated source: gastrodermis surface
annotated property: foaf depicted by
comment: 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.

pharynx inner epithelium surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: pharynx inner epithelium
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The epithelial surface lining the interior of the pharynx, facing the lumen.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0001731
has_exact_synonym: pharyngeal inner epidermis surface
has_exact_synonym: pharyngeal inner epithelial surface
has_exact_synonym: pharyngeal lumen epithelial surface
has_exact_synonym: pharynx inner epidermis surface
has_exact_synonym: pharynx lumen epithelial surface
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx inner epithelium surface
annotated property: foaf depicted by
comment: 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 outer epithelium surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: pharynx outer epithelium
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Epithelial surface covering the outside of the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:24120894
database_cross_reference: PMID:29865769
database_cross_reference: doi:10.1002/jmor.1052060308
has_exact_synonym: pharyngeal outer epidermis surface
has_exact_synonym: pharyngeal outer epithelial surface
has_exact_synonym: pharynx outer epidermis surface
has_exact_synonym: pharynx outer side
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx outer epithelium surface
annotated property: definition
annotated target: Epithelial surface covering the outside of the pharynx.
database_cross_reference: PMID:29865769
database_cross_reference: doi:10.1002/jmor.1052060308

Axiom
annotated source: pharynx outer epithelium surface
annotated property: foaf depicted by
comment: 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.

pharynx pouch epithelial surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: pharynx pouch epithelium
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The surface of the parapharyngeal pouch facing the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
has_exact_synonym: pharyngeal pouch surface
has_exact_synonym: pharynx pouch surface
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx pouch epithelial surface
annotated property: definition
annotated target: The surface of the parapharyngeal pouch facing the pharynx.
database_cross_reference: OCLC:16809160

Axiom
annotated source: pharynx pouch epithelial surface
annotated property: foaf depicted by
comment: 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.

obsolete organism subdivision
type: Class
term replaced by: organism subdivision
comment: replacing with UBERON term
deprecated: true

definitive organism subdivision
type: Class
subclass of: organism subdivision
definition: Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

head region
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: anterior to
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000033
has_exact_synonym: head
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: head region
annotated property: foaf depicted by
comment: Depicted by field contains diagram representation of body region.

prepharyngeal region
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: anterior to
  some values from: parapharyngeal region
subclass of: Restriction
  on property: posterior to
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:17251262
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22339734
database_cross_reference: PMID:23318641
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24922054
database_cross_reference: PMID:26556349
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27150006
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28245923
database_cross_reference: PMID:28287248
database_cross_reference: PMID:28893948
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29674431
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: neck
has_exact_synonym: pre-pharyngeal region
has_exact_synonym: pre-pharynx region
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: prepharyngeal region
annotated property: definition
annotated target: Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx.
database_cross_reference: OCLC:16809160

Axiom
annotated source: prepharyngeal region
annotated property: foaf depicted by
comment: Depicted by field contains diagram representation of body region.

parapharyngeal region
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: anterior to
  some values from: tail region
subclass of: Restriction
  on property: anterior to
  some values from: copulatory region
subclass of: Restriction
  on property: posterior to
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Region of the animal lateral to and surrounding the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:22125640
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26651295
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30143032
has_exact_synonym: para-pharyngeal
has_exact_synonym: parapharyngeal
has_exact_synonym: peri-pharyngeal
has_exact_synonym: peripharyngeal region
has_exact_synonym: trunk
has_obo_namespace: Planarian_Anatomy
comment: 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.

Axiom
annotated source: parapharyngeal region
annotated property: foaf depicted by
comment: Depicted by field contains diagram representation of body region.

tail region
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: posterior to
  some values from: copulatory region
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Caudal region, beginning at the mouth and ending at posterior pole.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0002415
has_exact_synonym: tail
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tail region
annotated property: foaf depicted by
comment: Depicted by field contains diagram representation of body region.

tail stripe
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Medial region of the tail; the parenchymal space between the posterior primary gut branches.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tail stripe
annotated property: definition
annotated target: Medial region of the tail; the parenchymal space between the posterior primary gut branches.
database_cross_reference: PMID:29906446

embryonic subdivision
type: Class
subclass of: organism subdivision
definition: Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

obsolete material anatomical entity
type: Class
term replaced by: material anatomical entity
comment: replacing with UBERON term
deprecated: true

obsolete definitive anatomical structure
type: Class
comment: extra layer of complexity not needed upon further examination
deprecated: true

obsolete acellular anatomical structure
type: Class
term replaced by: acellular anatomical structure
comment: replacing with UBERON term
deprecated: true

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0010000
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: multicellular anatomical structure
annotated property: definition
annotated target: An anatomical structure that has more than one cell as a part.
database_cross_reference: UBERON:0010000

musculature system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: Total musculature of the planarian body.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:15866156
database_cross_reference: PMID:17942485
database_cross_reference: PMID:20707997
database_cross_reference: PMID:24950970
database_cross_reference: PMID:27068018
database_cross_reference: PMID:28137894
database_cross_reference: UBERON:0001015
has_exact_synonym: muscular system
has_exact_synonym: musculature
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: musculature system
annotated property: definition
annotated target: Total musculature of the planarian body.
database_cross_reference: UBERON:0001015

neoblast
type: Class
subclass of: material entity
subclass of: progenitor cell
subclass of: stem cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0006347
database_cross_reference: PMID:15866156
database_cross_reference: PMID:15972844
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16311336
database_cross_reference: PMID:16344473
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17670787
database_cross_reference: PMID:17905225
database_cross_reference: PMID:18063755
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:18456843
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19564616
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19805089
database_cross_reference: PMID:20040488
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20599901
database_cross_reference: PMID:20844018
database_cross_reference: PMID:21179477
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21747960
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21852957
database_cross_reference: PMID:21894189
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22223737
database_cross_reference: PMID:22252538
database_cross_reference: PMID:22252539
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22371573
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22543868
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22696458
database_cross_reference: PMID:22884275
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23903188
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894

Axiom
annotated source: neoblast
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:16311336
database_cross_reference: PMID:21566185
database_cross_reference: PMID:22899852
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md

Axiom
annotated source: neoblast
annotated property: foaf depicted by
comment: 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.

epithelial cell component
type: Class
subclass of: cellular_component
subclass of: Restriction
  on property: part of
  some values from: epithelial cell
definition: A part of an epithelial cell.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

organ
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that performs a specific function or group of functions.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29547123
database_cross_reference: UBERON:0000062
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: organ
annotated property: definition
annotated target: Anatomical structure that performs a specific function or group of functions.
database_cross_reference: UBERON:0000062

obsolete regenerating anatomical structure
type: Class
term replaced by: regenerating anatomical structure
comment: replacing with UBERON term
deprecated: true

obsolete cellular component
type: Class
term replaced by: cellular_component
comment: replacing with GO term
deprecated: true

optic chiasm
type: Class
subclass of: material entity
subclass of: neuron projection bundle
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A decussation of the diencephalon where the fibers of the optic nerve cross
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: AAO:0010622
database_cross_reference: BAMS:DC
database_cross_reference: BAMS:OC
database_cross_reference: BAMS:och
database_cross_reference: BAMS:ox
database_cross_reference: BM:Tel-OCX
database_cross_reference: C90609
database_cross_reference: DHBA:10644
database_cross_reference: DMBA:17783
database_cross_reference: EHDAA2:0001302
database_cross_reference: EHDAA:10227
database_cross_reference: EMAPA:17603
database_cross_reference: FMA:62045
database_cross_reference: GAID:832
database_cross_reference: HBA:9310
database_cross_reference: MA:0001098
database_cross_reference: MBA:117
database_cross_reference: MESH:D009897
database_cross_reference: NCIT:C90609
database_cross_reference: Optic:chiasm
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18466009
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19211673
database_cross_reference: PMID:21282632
database_cross_reference: PMID:22339734
database_cross_reference: PMID:22445864
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25493551
database_cross_reference: PMID:26618653
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28495872
database_cross_reference: PMID:30194301
database_cross_reference: PMID:30962434
database_cross_reference: TAO:0000556
database_cross_reference: UBERON:0000959
database_cross_reference: UMLS:C0029126
database_cross_reference: VHOG:0000190
database_cross_reference: XAO:0004071
database_cross_reference: ZFA:0000556
database_cross_reference: birnlex:1416
database_cross_reference: http://braininfo.rprc.washington.edu/centraldirectory.aspx
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0029126
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/244453006
has_exact_synonym: chiasm
has_exact_synonym: chiasma
has_exact_synonym: chiasma nervorum opticorum
has_exact_synonym: chiasma opticum
has_exact_synonym: decussation of optic nerve fibers
has_exact_synonym: optic chiasm (Rufus of Ephesus)
has_exact_synonym: optic chiasma
has_exact_synonym: optic chiasmata
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: optic chiasm
annotated property: definition
annotated target: A decussation of the diencephalon where the fibers of the optic nerve cross
database_cross_reference: PMID:18466009

anterior commissure
type: Class
subclass of: brain commissure
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A bundle of nerve fibers connecting the two cephalic ganglia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000935
has_exact_synonym: anterior brain commissure
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior commissure
annotated property: definition
annotated target: A bundle of nerve fibers connecting the two cephalic ganglia.
database_cross_reference: UBERON:0000935

lateral branch
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:12128224
database_cross_reference: PMID:18287199
database_cross_reference: PMID:18466009
database_cross_reference: PMID:20422023
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21806978
database_cross_reference: PMID:24922054
database_cross_reference: PMID:25254346
database_cross_reference: PMID:27612384
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30399335
database_cross_reference: PMID:4452894
database_cross_reference: PMID:9493832
has_exact_synonym: bilateral cephalic ganglia branch
has_exact_synonym: brain branch
has_exact_synonym: cephalic brain branch
has_exact_synonym: cephalic branch
has_exact_synonym: lateral brain branch
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: lateral branch
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:12128224
database_cross_reference: PMID:18466009
database_cross_reference: PMID:27612384
database_cross_reference: PMID:4452894
database_cross_reference: PMID:9493832

sensory cell
type: Class
subclass of: terminally differentiated cell
definition: A cell that performs a sensory function.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0001037
database_cross_reference: ISBN:9780070316607
database_cross_reference: NCIT:C12628
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17942485
has_obo_namespace: Planarian_Anatomy

cholinergic neuron
type: Class
subclass of: independent continuant
subclass of: neurosecretory neuron
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Neurons that express choline acetyltransferase.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20338223
database_cross_reference: PMID:21566185
database_cross_reference: PMID:23652002
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28137894
database_cross_reference: PMID:29291981
database_cross_reference: PMID:30143032
database_cross_reference: PMID:30194301
has_exact_synonym: acetylcholinergic neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cholinergic neuron
annotated property: definition
annotated target: Neurons that express choline acetyltransferase.
database_cross_reference: PMID:20338223

GABAergic neuron
type: Class
subclass of: independent continuant
subclass of: neurosecretory neuron
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Neurons that express glutamine decarboxylase.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000617
database_cross_reference: FBbt:00007228
database_cross_reference: PMID:18440152
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24922054
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28216315
database_cross_reference: PMID:29291981
database_cross_reference: PMID:30194301
database_cross_reference: PMID:30485821
database_cross_reference: WBbt:0005190
database_cross_reference: ZFA:0009276
has_exact_synonym: GABA neuron
has_exact_synonym: GABAergic cell
has_exact_synonym: gabanergic neuron
has_exact_synonym: inhibitory neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: GABAergic neuron
annotated property: definition
annotated target: Neurons that express glutamine decarboxylase.
database_cross_reference: PMID:18440152

pharynx nerve plexus
type: Class
subclass of: material entity
subclass of: nerve plexus
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Plexus of nerves located in the pharynx comprised of inner and outer wall rings.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17905225
database_cross_reference: PMID:20967238
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
has_exact_synonym: nerve ganglia of pharynx
has_exact_synonym: neural plexus of the pharynx
has_exact_synonym: pharyngeal nerve plexus
has_exact_synonym: pharyngeal nerve ring
has_exact_synonym: pharyngeal nervous system
has_exact_synonym: pharyngeal neural plexus
has_exact_synonym: pharynx nerve ring
has_obo_namespace: Planarian_Anatomy

subepidermal nerve plexus
type: Class
subclass of: material entity
subclass of: nerve plexus
subclass of: Restriction
  on property: part of
  some values from: integumental system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Plexus of nerves located just between the epidermis and the body wall musculature.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27612384
database_cross_reference: doi:10.1002/jmor.1051550208
has_obo_namespace: Planarian_Anatomy

submuscular nerve plexus
type: Class
subclass of: material entity
subclass of: nerve plexus
subclass of: Restriction
  on property: part of
  some values from: musculature system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Plexus of nerves that innervate the body wall musculature.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

gastrodermal plexus
type: Class
subclass of: material entity
subclass of: nerve plexus
subclass of: Restriction
  on property: part of
  some values from: digestive system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A thin net of single nerve fibers located around the gut.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17999079
database_cross_reference: doi.org/10.1002/jmor.1051550208
has_obo_namespace: Planarian_Anatomy

neuropil
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0005268
database_cross_reference: C12617
database_cross_reference: CALOHA:TS-2403
database_cross_reference: FBbt:00005139
database_cross_reference: FMA:261269
database_cross_reference: GAID:740
database_cross_reference: MESH:D019581
database_cross_reference: NIF:Subcellular:sao205380252
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17553481
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25356635
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:29291974
database_cross_reference: PMID:29291981
database_cross_reference: UBERON:0002606
database_cross_reference: UMLS:C0228081
database_cross_reference: birnlex:1142
database_cross_reference: http://en.wikipedia.org/wiki/Neuropil
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0228081
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/67146008
has_exact_synonym: central neuropil
has_exact_synonym: cephalic ganglia neuropil
has_exact_synonym: neuropilus
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neuropil
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27612384

pharynx outer epithelium
type: Class
subclass of: material entity
subclass of: ciliated epithelium
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: immediately superficial to
  some values from: pharynx outer longitudinal muscle cell
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
database_cross_reference: PMID:29674431
has_exact_synonym: epithelial pharynx lining
has_exact_synonym: outer pharyngeal epidermis
has_exact_synonym: outer pharyngeal epithelium
has_exact_synonym: outer pharynx epidermis
has_exact_synonym: outer pharynx epithelium
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx outer epithelium
annotated property: definition
annotated target: 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.
database_cross_reference: ASIN:B000M4NK9M

pharynx outer circular muscle cell
type: Class
subclass of: pharynx circular muscle cell
subclass of: Restriction
  on property: immediately deep to
  some values from: pharynx outer longitudinal muscle cell
definition: Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
database_cross_reference: ISBN:9780070316607
has_exact_synonym: outer circular muscle layer
has_exact_synonym: pharyneal outer circular muscle fiber
has_exact_synonym: pharyngeal outer circular muscle cell
has_exact_synonym: pharynx outer circular muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx outer circular muscle cell
annotated property: definition
annotated target: Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles.
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx outer circular muscle cell
annotated property: foaf depicted by
comment: 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 inner circular muscle cell
type: Class
subclass of: pharynx circular muscle cell
subclass of: Restriction
  on property: immediately deep to
  some values from: pharynx inner epithelium
subclass of: Restriction
  on property: immediately superficial to
  some values from: pharynx inner longitudinal muscle cell
definition: Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
has_exact_synonym: inner circular muscle layer
has_exact_synonym: pharyngeal inner circular muscle cell
has_exact_synonym: pharyngeal inner circular muscle fiber
has_exact_synonym: pharynx inner circular muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx inner circular muscle cell
annotated property: definition
annotated target: Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers.
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx inner circular muscle cell
annotated property: foaf depicted by
comment: 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 inner longitudinal muscle cell
type: Class
subclass of: pharynx longitudinal muscle cell
subclass of: Restriction
  on property: immediately deep to
  some values from: pharynx inner circular muscle cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
database_cross_reference: ISBN:9780070316607
has_exact_synonym: inner longitudinal muscle layer
has_exact_synonym: pharyngeal inner longitudinal muscle cell
has_exact_synonym: pharyngeal inner longitudinal muscle fiber
has_exact_synonym: pharynx inner longitudinal muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx inner longitudinal muscle cell
annotated property: definition
annotated target: 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.
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx inner longitudinal muscle cell
annotated property: foaf depicted by
comment: 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 outer longitudinal muscle cell
type: Class
subclass of: pharynx longitudinal muscle cell
subclass of: Restriction
  on property: immediately deep to
  some values from: pharynx outer epithelium
subclass of: Restriction
  on property: immediately superficial to
  some values from: pharynx outer circular muscle cell
definition: Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
has_exact_synonym: pharyngeal outer longitudinal muscle cell
has_exact_synonym: pharyngeal outer longitudinal muscle fiber
has_exact_synonym: pharynx outer longitudinal muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx outer longitudinal muscle cell
annotated property: definition
annotated target: Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx outer longitudinal muscle cell
annotated property: foaf depicted by
comment: 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 radial muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: pharynx musculature
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
database_cross_reference: PMID:28072387
has_exact_synonym: pharyngeal radial muscle cell
has_exact_synonym: pharyngeal radial muscle fiber
has_exact_synonym: pharynx radial muscle fiber
has_exact_synonym: radial muscle cell
has_exact_synonym: radial muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx radial muscle cell
annotated property: definition
annotated target: Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts.
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx radial muscle cell
annotated property: foaf depicted by
comment: 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.

pharynx musculature
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: part of
  some values from: musculature system
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The total musculature within the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:26904543
database_cross_reference: PMID:29674432
database_cross_reference: UBERON:0004467
has_exact_synonym: pharyngeal musculature
has_exact_synonym: pharynx muscle
has_exact_synonym: pharynx musculature
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx musculature
annotated property: definition
annotated target: The total musculature within the pharynx.
database_cross_reference: PMID:26904543

pharynx inner nerve plexus
type: Class
subclass of: pharynx nerve plexus
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
definition: Ring of the pharynx nerve plexus that is proximal to the lumen.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
has_exact_synonym: inner pharyngeal nerve ring
has_exact_synonym: inner pharynx nerve ring
has_exact_synonym: pharynx inner nerve plexus
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx inner nerve plexus
annotated property: definition
annotated target: Ring of the pharynx nerve plexus that is proximal to the lumen.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: pharynx inner nerve plexus
annotated property: foaf depicted by
comment: 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.

pharynx outer nerve plexus
type: Class
subclass of: pharynx nerve plexus
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
definition: Ring of the pharynx nerve plexus that is proximal to the exterior surface.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:27612384
database_cross_reference: doi:10.1002/jmor.1051550208
has_exact_synonym: outer pharyngeal nerve ring
has_exact_synonym: outer pharynx nerve plexus
has_exact_synonym: outer pharynx nerve ring
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx outer nerve plexus
annotated property: definition
annotated target: Ring of the pharynx nerve plexus that is proximal to the exterior surface.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: pharynx outer nerve plexus
annotated property: foaf depicted by
comment: 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.

serotonergic neuron
type: Class
subclass of: material entity
subclass of: neurosecretory neuron
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: part of
  some values from: ventral nerve cord
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: develops from
  some values from: serotonergic neural progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Neurons that express the neurotransmitter serotonin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000850
database_cross_reference: FBbt:00005133
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24922054
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28137894
database_cross_reference: PMID:29357350
database_cross_reference: PMID:30194301
database_cross_reference: WBbt:0006837
database_cross_reference: ZFA:0009361
has_exact_synonym: serotonergic cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: serotonergic neuron
annotated property: definition
annotated target: Neurons that express the neurotransmitter serotonin.
database_cross_reference: PMID:17624455

dopaminergic neuron
type: Class
subclass of: independent continuant
subclass of: neurosecretory neuron
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A neuron that expresses the neurotransmitter dopamine.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000700
database_cross_reference: FBbt:00005131
database_cross_reference: PMID:17565705
database_cross_reference: PMID:21458439
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24950970
database_cross_reference: PMID:25356635
database_cross_reference: PMID:27864883
database_cross_reference: PMID:30194301
database_cross_reference: WBbt:0006746
database_cross_reference: ZFA:0009301
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dopaminergic neuron
annotated property: definition
annotated target: A neuron that expresses the neurotransmitter dopamine.
database_cross_reference: PMID:17565705

octopaminergic neuron
type: Class
subclass of: independent continuant
subclass of: neurosecretory neuron
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Neurons that express the biogenic amine octopamine.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FBbt:00007364
database_cross_reference: PMID:18926867
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: octopaminergic neuron
annotated property: definition
annotated target: Neurons that express the biogenic amine octopamine.
database_cross_reference: PMID:18926867

secretory system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20865784
database_cross_reference: WBbt:0006850
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secretory system
annotated property: definition
annotated target: Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus.
database_cross_reference: PMID:20865784

gland cell
type: Class
subclass of: epithelial cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CLYH:1000090
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20865784
database_cross_reference: PMID:23318635
database_cross_reference: PMID:24737865
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30962434
database_cross_reference: WBbt:0003670
has_exact_synonym: secretory gland cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gland cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:20865784

Axiom
annotated source: gland cell
annotated property: foaf depicted by
comment: 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.

secretory pore
type: Class
subclass of: independent continuant
subclass of: pore
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The opening by which the gland cells secrete mucus to the exterior of the animal.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20865784
has_exact_synonym: pore
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secretory pore
annotated property: definition
annotated target: The opening by which the gland cells secrete mucus to the exterior of the animal.
database_cross_reference: PMID:20865784

Axiom
annotated source: secretory pore
annotated property: foaf depicted by
comment: 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.

acidophilic gland cell
type: Class
subclass of: gland cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20865784
has_exact_synonym: eosinophilic gland cell
has_exact_synonym: erythrophilous gland cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: acidophilic gland cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:20865784

basophilic gland cell
type: Class
subclass of: gland cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20865784
database_cross_reference: PMID:23405188
has_exact_synonym: cyanophilic gland cell
has_exact_synonym: cyanophilic secretory cell
has_exact_synonym: cyanophilous gland
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: basophilic gland cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:20865784

obsolete anatomical line
type: Class
term replaced by: anatomical line
comment: replacing with CARO term
deprecated: true

obsolete anatomical plane
type: Class
term replaced by: anatomical plane
comment: replacing with BSPO term
deprecated: true

obsolete plane of autonomy
type: Class
term replaced by: UBERON_0035086
comment: let odk import from BSPO if needed
comment: replacing with UBERON term
label: obsolete plane of autotomy
deprecated: true

nerve plexus
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
definition: 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].
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: AEO:0000138
database_cross_reference: BTO:0000205
database_cross_reference: C12929
database_cross_reference: EHDAA2:0003138
database_cross_reference: EHDAA:3780
database_cross_reference: FMA:5901
database_cross_reference: ISBN:9780070316607
database_cross_reference: MA:0002407
database_cross_reference: PMID:16311336
database_cross_reference: PMID:21566185
database_cross_reference: PMID:22899852
database_cross_reference: UBERON:0001810
database_cross_reference: UMLS:C0501403
database_cross_reference: http://en.wikipedia.org/wiki/Nervous:system:plexus
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0501403
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/122455009
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md
has_exact_synonym: neural network
has_exact_synonym: neural plexus
has_exact_synonym: plexus
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nerve plexus
annotated property: definition
annotated target: 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].
database_cross_reference: UBERON:0001810

obsolete nervous system commissure
type: Class
term replaced by: commissural neuron
comment: we will just use commissural neuron moving forward
deprecated: true

brain commissure
type: Class
subclass of: material entity
subclass of: commissure
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
definition: any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0005970
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: brain commissure
annotated property: definition
annotated target: any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
database_cross_reference: UBERON:0005970

blastema
type: Class
subclass of: regenerating anatomical structure
definition: A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: AEO:0000192
database_cross_reference: BTO:0001638
database_cross_reference: CARO:0000010
database_cross_reference: EFO:0003658
database_cross_reference: FMA:50705
database_cross_reference: PMID:15866156
database_cross_reference: PMID:15972844
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17670787
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17942485
database_cross_reference: PMID:18063755
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18456843
database_cross_reference: PMID:19048075
database_cross_reference: PMID:19174194
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20040488
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20599901
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21295483
database_cross_reference: PMID:21356107
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21566195
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22252539
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22411224
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22549959
database_cross_reference: PMID:22884275
database_cross_reference: PMID:22899852
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23629965
database_cross_reference: PMID:23652002
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24523458
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24922054
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25725068
database_cross_reference: PMID:25772472
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26459857
database_cross_reference: PMID:26525673
database_cross_reference: PMID:26711341
database_cross_reference: PMID:26884331
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27240733
database_cross_reference: PMID:27542689
database_cross_reference: PMID:27551436
database_cross_reference: PMID:27606067

Axiom
annotated source: blastema
annotated property: definition
annotated target: A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise.
database_cross_reference: UBERON:0005306

obsolete anatomical boundary
type: Class
term replaced by: UBERON_0000015
comment: replacing with UBERON term
deprecated: true

obsolete anatomical junction
type: Class
term replaced by: UBERON_0007651
comment: replacing with UBERON term
deprecated: true

obsolete main body axis
type: Class
term replaced by: anterior-posterior axis of the whole animal
comment: replacing duplicate PLANA term
deprecated: true

cell
type: Class
subclass of: anatomical structure
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CALOHA:TS-2035
database_cross_reference: CL:0000000
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
has_obo_namespace: Planarian_Anatomy
comment: 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).

Axiom
annotated source: cell
annotated property: definition
annotated target: 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.
database_cross_reference: CL:0000000

obsolete cell part
type: Class
term replaced by: cellular_component
comment: PLANA:0000500 child terms moved to cellular component (GO:0005575) term and we think better serves interoperability and searchability
deprecated: true

cell projection
type: Class
subclass of: cellular_component
definition: A prolongation or process extending from a cell.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0042995
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cell projection
annotated property: definition
annotated target: A prolongation or process extending from a cell.
database_cross_reference: GO:0042995

actin-based cell projection
type: Class
subclass of: cell projection
definition: A cell projection supported by an assembly of actin filaments.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0098858
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: actin-based cell projection
annotated property: definition
annotated target: A cell projection supported by an assembly of actin filaments.
database_cross_reference: GO:0098858

obsolete cilium
type: Class
term replaced by: cilium
comment: inadvertently duplicated, going with ID that is best annotated
deprecated: true

microvillus
type: Class
subclass of: actin-based cell projection
definition: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005902
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: microvillus
annotated property: definition
annotated target: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments.
database_cross_reference: GO:0005902

Axiom
annotated source: microvillus
annotated property: foaf depicted by
comment: 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.

cell-cell contact zone
type: Class
subclass of: cellular_component
definition: Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044291
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cell-cell contact zone
annotated property: definition
annotated target: Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions.
database_cross_reference: GO:0044291

cell junction
type: Class
subclass of: cell-cell contact zone
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0030054
database_cross_reference: PMID:20511647
database_cross_reference: PMID:21458439
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cell junction
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0030054

Axiom
annotated source: cell junction
annotated property: foaf depicted by
comment: 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.

cell-cell junction
type: Class
subclass of: cell junction
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005911
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cell-cell junction
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005911

Axiom
annotated source: cell-cell junction
annotated property: foaf depicted by
comment: 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.

cell-cell adhesion
type: Class
subclass of: cell-cell contact zone
definition: The attachment of one cell to another cell via adhesion molecules.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0098609
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cell-cell adhesion
annotated property: definition
annotated target: The attachment of one cell to another cell via adhesion molecules.
database_cross_reference: GO:0098609

Axiom
annotated source: cell-cell adhesion
annotated property: foaf depicted by
comment: 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.

intracellular part
type: Class
subclass of: cellular_component
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044424
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intracellular part
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0044424

cytoplasm
type: Class
subclass of: intracellular part
definition: All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005737
database_cross_reference: PMID:16890156
database_cross_reference: PMID:28976975
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cytoplasm
annotated property: definition
annotated target: All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
database_cross_reference: GO:0005737

Axiom
annotated source: cytoplasm
annotated property: foaf depicted by
comment: 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.

obsolete acidophilic cytoplasm
type: Class
comment: term is not needed.
deprecated: true

obsolete basophilic cytoplasm
type: Class
comment: term is not needed.
deprecated: true

cytoplasmic part
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044444
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cytoplasmic part
annotated property: definition
annotated target: Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
database_cross_reference: GO:0044444

cytoplasmic vesicle part
type: Class
subclass of: cytoplasmic part
definition: Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044433
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cytoplasmic vesicle part
annotated property: definition
annotated target: Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
database_cross_reference: GO:0044433

vacuole
type: Class
subclass of: membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005773
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: vacuole
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005773

obsolete cytoskeleton organization
type: Class
comment: term is not needed.
deprecated: true

intracellular organelle
type: Class
subclass of: intracellular part
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043229
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intracellular organelle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0043229

intracellular non-membrane-bounded organelle
type: Class
subclass of: intracellular organelle
subclass of: non-membrane-bounded organelle
definition: 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
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043232
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intracellular non-membrane-bounded organelle
annotated property: definition
annotated target: 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
database_cross_reference: GO:0043232

membrane
type: Class
subclass of: cellular_component
definition: A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0016020
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: membrane
annotated property: definition
annotated target: A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
database_cross_reference: GO:0016020

bounding membrane of organelle
type: Class
subclass of: membrane
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0098588
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: bounding membrane of organelle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0098588

membrane part
type: Class
subclass of: cellular_component
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044425
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: membrane part
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0044425

plasma membrane part
type: Class
subclass of: membrane part
subclass of: Restriction
  on property: part of
  some values from: plasma membrane
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044459
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: plasma membrane part
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0044459

organelle membrane
type: Class
subclass of: membrane
subclass of: Restriction
  on property: part of
  some values from: membrane-bounded organelle
definition: A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0031090
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: organelle membrane
annotated property: definition
annotated target: A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
database_cross_reference: GO:0031090

organelle
type: Class
subclass of: cellular_component
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043226
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: organelle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0043226

membrane-bounded organelle
type: Class
subclass of: organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043227
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: membrane-bounded organelle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0043227

intracellular membrane-bounded organelle
type: Class
subclass of: intracellular organelle
subclass of: membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043231
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intracellular membrane-bounded organelle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0043231

Golgi apparatus
type: Class
subclass of: intracellular membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005794
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Golgi apparatus
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005794

Axiom
annotated source: Golgi apparatus
annotated property: foaf depicted by
comment: 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.

nucleus
type: Class
subclass of: intracellular membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005634
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:23405188
database_cross_reference: PMID:25404302
database_cross_reference: PMID:26457503
database_cross_reference: PMID:28976975
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29357350
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nucleus
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005634

Axiom
annotated source: nucleus
annotated property: foaf depicted by
comment: 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.

secretory vesicle
type: Class
subclass of: intracellular membrane-bounded organelle
definition: A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0099503
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secretory vesicle
annotated property: definition
annotated target: A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
database_cross_reference: GO:0099503

Axiom
annotated source: secretory vesicle
annotated property: foaf depicted by
comment: 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.

non-membrane-bounded organelle
type: Class
subclass of: organelle
definition: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043228
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: non-membrane-bounded organelle
annotated property: definition
annotated target: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
database_cross_reference: GO:0043228

nuclear part
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044428
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear part
annotated property: definition
annotated target: Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
database_cross_reference: GO:0044428

nucleolus
type: Class
subclass of: nuclear part
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044428
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nucleolus
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0044428

Axiom
annotated source: nucleolus
annotated property: foaf depicted by
comment: Image is an electron micrograph depicting a nucleus. Inside, the nucleolus has been labeled with arrowheads. Scale bar is 1 um.

chromatin
type: Class
subclass of: nuclear part
definition: The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0000785
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chromatin
annotated property: definition
annotated target: The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome.
database_cross_reference: GO:0000785

Axiom
annotated source: chromatin
annotated property: foaf depicted by
comment: Image is an electron micrograph showing a mitotic cell with condensed chromatin (arrowhead). Scale bar is 1um.

heterochromatin
type: Class
subclass of: chromatin
definition: A compact and highly condensed form of chromatin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0000792
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: heterochromatin
annotated property: definition
annotated target: A compact and highly condensed form of chromatin.
database_cross_reference: GO:0000792

euchromatin
type: Class
subclass of: chromatin
definition: A dispersed and relatively uncompacted form of chromatin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0000791
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: euchromatin
annotated property: definition
annotated target: A dispersed and relatively uncompacted form of chromatin.
database_cross_reference: GO:0000791

ribosome
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: 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 ]
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005840
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ribosome
annotated property: definition
annotated target: 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 ]
database_cross_reference: GO:0005840

Axiom
annotated source: ribosome
annotated property: foaf depicted by
comment: 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.

axon tract
type: Class
subclass of: tissue
definition: A group of axons linking two or more neuropils and having a common origin, termination
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:22884275
database_cross_reference: PMID:24950970
database_cross_reference: PMID:28137894
database_cross_reference: UBERON:0001018
has_exact_synonym: axon bundle
has_exact_synonym: axon bundles
has_exact_synonym: axon tracts
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: axon tract
annotated property: definition
annotated target: A group of axons linking two or more neuropils and having a common origin, termination
database_cross_reference: UBERON:0001018

electrically responsive cell
type: Class
subclass of: terminally differentiated cell
definition: A cell whose function is determined by its response to an electric signal.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000393
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: electrically responsive cell
annotated property: definition
annotated target: A cell whose function is determined by its response to an electric signal.
database_cross_reference: CL:0000393

electrically signaling cell
type: Class
subclass of: terminally differentiated cell
definition: A cell that initiates an electrical signal and passes that signal to another cell.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000404
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: electrically signaling cell
annotated property: definition
annotated target: A cell that initiates an electrical signal and passes that signal to another cell.
database_cross_reference: CL:0000404

nerve
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27800171
database_cross_reference: UBERON:0001021
has_exact_synonym: nerve bundle
has_exact_synonym: nerves
has_exact_synonym: neural subtree
has_exact_synonym: peripheral nerve
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nerve
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0001021

neuron projection bundle
type: Class
subclass of: axon tract
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CARO:0001001
database_cross_reference: UBERON:0000122
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neuron projection bundle
annotated property: definition
annotated target: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
database_cross_reference: CARO:0001001

afferent neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A neuron which conveys sensory information centrally from the periphery.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000526
database_cross_reference: FMA:87653
has_exact_synonym: input neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: afferent neuron
annotated property: definition
annotated target: A neuron which conveys sensory information centrally from the periphery.
database_cross_reference: CL:0000526

bipolar neuron
type: Class
subclass of: interneuron
subclass of: Restriction
  on property: part of
  some values from: subepidermal nerve plexus
subclass of: Restriction
  on property: part of
  some values from: submuscular nerve plexus
subclass of: Restriction
  on property: part of
  some values from: transverse commissure
definition: A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000103
database_cross_reference: FMA:67282
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:16033796
database_cross_reference: PMID:18202849
database_cross_reference: PMID:21458439
database_cross_reference: PMID:22445864
database_cross_reference: PMID:24173799
database_cross_reference: PMID:25493551
has_exact_synonym: bipolar nerve cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: bipolar neuron
annotated property: definition
annotated target: A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
database_cross_reference: CL:0000103

commissural neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A neuron that has an axon which crosses the midline.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000678
database_cross_reference: PMID:22339734
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: commissural neuron
annotated property: definition
annotated target: A neuron that has an axon which crosses the midline.
database_cross_reference: CL:0000678

efferent neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: A neuron which sends impulses peripherally to activate muscles or secretory cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000527
has_exact_synonym: output neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: efferent neuron
annotated property: definition
annotated target: A neuron which sends impulses peripherally to activate muscles or secretory cells.
database_cross_reference: CL:0000527

excitatory motor neuron
type: Class
subclass of: motor neuron
subclass of: peripheral nervous system neuron
definition: A motor neuron that is capable of directly inducing muscle contraction.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0008014
database_cross_reference: PMID:25356635
has_exact_synonym: excitatory neuron
has_obo_namespace: Planarian_Anatomy
comment: In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates.

Axiom
annotated source: excitatory motor neuron
annotated property: definition
annotated target: A motor neuron that is capable of directly inducing muscle contraction.
database_cross_reference: CL:0008014

interneuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0003811
database_cross_reference: CL:0000099
database_cross_reference: FBbt:00005125
database_cross_reference: FMA:67313
database_cross_reference: WBbt:0005113
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: interneuron
annotated property: definition
annotated target: 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.
database_cross_reference: CL:0000099

sensory neuron
type: Class
subclass of: sensory cell
subclass of: afferent neuron
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0001037
database_cross_reference: CL:0000101
database_cross_reference: FBbt:00005124
database_cross_reference: FMA:84649
database_cross_reference: WBbt:0005759
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sensory neuron
annotated property: definition
annotated target: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
database_cross_reference: CL:0000101

motor neuron
type: Class
subclass of: efferent neuron
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0000312
database_cross_reference: CL:0000100
database_cross_reference: FMA:83617
database_cross_reference: WBbt:0005409
has_exact_synonym: motoneuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: motor neuron
annotated property: definition
annotated target: 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.
database_cross_reference: CL:0000100

neurosecretory neuron
type: Class
subclass of: neuron
subclass of: secretory cell
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Neuronal cells which synthesize, store and release neurohormones.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000381
database_cross_reference: FBbt:00005130
database_cross_reference: PMID:24173799
has_exact_synonym: neurosecretory cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neurosecretory neuron
annotated property: definition
annotated target: Neuronal cells which synthesize, store and release neurohormones.
database_cross_reference: CL:0000381

sympathetic neuron
type: Class
subclass of: neuron
definition: Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0011103
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sympathetic neuron
annotated property: definition
annotated target: Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides.
database_cross_reference: CL:0011103

unipolar neuron
type: Class
subclass of: sensory neuron
definition: Neuron with one neurite that extends from the cell body.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000106
database_cross_reference: FMA:67278
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:18499291
database_cross_reference: PMID:24173799
has_exact_synonym: unipolar nerve cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: unipolar neuron
annotated property: definition
annotated target: Neuron with one neurite that extends from the cell body.
database_cross_reference: CL:0000106

multipolar neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: central nervous system
subclass of: Restriction
  on property: part of
  some values from: subepidermal nerve plexus
definition: Neuron with an axon and two or more dendrites.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000104
database_cross_reference: FMA:67287
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:18499291
has_exact_synonym: multipolar nerve cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: multipolar neuron
annotated property: definition
annotated target: Neuron with an axon and two or more dendrites.
database_cross_reference: CL:0000104

neuron associated cell (sensu Nematoda and Protostomia)
type: Class
subclass of: terminally differentiated cell
definition: Cells that are in close proximity to neurons.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000130
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neuron associated cell (sensu Nematoda and Protostomia)
annotated property: definition
annotated target: Cells that are in close proximity to neurons.
database_cross_reference: CL:0000130

central nervous system neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Any neuron that is part of a central nervous system.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:2000029
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: central nervous system neuron
annotated property: definition
annotated target: Any neuron that is part of a central nervous system.
database_cross_reference: CL:2000029

peripheral nervous system neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: Any neuron that is part of a peripheral nervous system.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:2000032
database_cross_reference: PMID:23123964
database_cross_reference: PMID:23954785
database_cross_reference: PMID:25254346
database_cross_reference: PMID:26711341
database_cross_reference: PMID:29184198
has_exact_synonym: peripheral neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: peripheral nervous system neuron
annotated property: definition
annotated target: Any neuron that is part of a peripheral nervous system.
database_cross_reference: CL:2000032

autonomic neuron
type: Class
subclass of: peripheral nervous system neuron
definition: A neruon whose cell body is within an autonomic ganglion.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000107
database_cross_reference: FMA:80121
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: autonomic neuron
annotated property: definition
annotated target: A neruon whose cell body is within an autonomic ganglion.
database_cross_reference: CL:0000107

enteric neuron
type: Class
subclass of: autonomic neuron
definition: A neruon contained within with the enteric nervous system (gastrodermal plexus).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0007011
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: enteric neuron
annotated property: definition
annotated target: A neruon contained within with the enteric nervous system (gastrodermal plexus).
database_cross_reference: CL:0007011

basal lamina of epidermis
type: Class
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: integumental system
subclass of: Restriction
  on property: immediately deep to
  some values from: epidermis
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: AAO:0010269
database_cross_reference: AEO:0000065
database_cross_reference: BILA:0000065
database_cross_reference: C32186
database_cross_reference: CARO:0000065
database_cross_reference: EHDAA2:0003065
database_cross_reference: FMA:62918
database_cross_reference: HAO:0000065
database_cross_reference: ISBN:9780070316607
database_cross_reference: MESH:D001485
database_cross_reference: NIF_Subcellular:sao1397492660
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23079596
database_cross_reference: PMID:23405188
database_cross_reference: PMID:23903188
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26057828
database_cross_reference: PMID:26457503
database_cross_reference: PMID:27551436
database_cross_reference: PMID:29100657
database_cross_reference: PMID:30383829
database_cross_reference: PMID:30962434
database_cross_reference: TAO:0001485
database_cross_reference: TGMA:0001850
database_cross_reference: UMLS:C0085872
database_cross_reference: VHOG:0001592
database_cross_reference: WBbt:0005756
database_cross_reference: XAO:0003163
database_cross_reference: ZFA:0001485
has_exact_synonym: basal lamina
has_exact_synonym: basal lamina of epithelium
has_exact_synonym: basement membrane
has_obo_namespace: Planarian_Anatomy
comment: 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.

Axiom
annotated source: basal lamina of epidermis
annotated property: definition
annotated target: 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.
database_cross_reference: CARO:0000065

Axiom
annotated source: basal lamina of epidermis
annotated property: foaf depicted by
comment: 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.

adenal rhabdite
type: Class
subclass of: independent continuant
subclass of: rhabdite
subclass of: Restriction
  on property: part of
  some values from: dorsal epidermis progenitor cell
subclass of: Restriction
  on property: part of
  some values from: ventral epidermis progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
has_obo_namespace: Planarian_Anatomy
comment: 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.

Axiom
annotated source: adenal rhabdite
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: adenal rhabdite
annotated property: foaf depicted by
comment: 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.

adherens junction
type: Class
subclass of: cell junction
subclass of: Restriction
  on property: part of
  some values from: cell-cell adhesion
definition: A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005912
database_cross_reference: PMID:26556349
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: adherens junction
annotated property: definition
annotated target: A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
database_cross_reference: GO:0005912

Axiom
annotated source: adherens junction
annotated property: foaf depicted by
comment: 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.

adhesive papilla
type: Class
subclass of: material entity
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: viscid gland cell
subclass of: Restriction
  on property: part of
  some values from: releasing gland cell
subclass of: Restriction
  on property: contained in
  some values from: dorsal ventral margin of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: marginal adhesive zone
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
has_exact_synonym: adhesive papillae
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: adhesive papilla
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: adhesive papilla
annotated property: foaf depicted by
comment: 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.

amputation
type: Class
subclass of: cut
definition: A wound resulting in two or more separate tissue fragments.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

anterior gut branch
type: Class
subclass of: material entity
subclass of: gut branch
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: A branch of the triclad gut located anterior to the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19174194
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21458439
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23318635
database_cross_reference: PMID:24063805
database_cross_reference: PMID:28287248
database_cross_reference: PMID:30194301
has_exact_synonym: anterior branch
has_exact_synonym: anterior intestinal branch
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior gut branch
annotated property: definition
annotated target: A branch of the triclad gut located anterior to the pharynx.
database_cross_reference: PMID:21664348

anterior tip
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The anterior-medial region of the head margin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:15866156
database_cross_reference: PMID:18063755
database_cross_reference: PMID:22479207
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24992682
database_cross_reference: PMID:27063937
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28216315
database_cross_reference: PMID:29547123
database_cross_reference: PMID:30962434
has_exact_synonym: head tip
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior tip
annotated property: definition
annotated target: The anterior-medial region of the head margin.
database_cross_reference: PMID:22479207

Axiom
annotated source: anterior tip
annotated property: foaf depicted by
comment: Illustration of the anterior tip in green.

antrum
type: Class
subclass of: anatomical cavity
definition: A chamber formation in an organ.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: NCIT:C97102
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: antrum
annotated property: definition
annotated target: A chamber formation in an organ.
database_cross_reference: ISBN:9780070316607

auricle
type: Class
subclass of: material entity
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: sensory system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28495872
database_cross_reference: PMID:30399335
database_cross_reference: PMID:30485821
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: auricle
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: auricle
annotated property: foaf depicted by
comment: 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.

axon
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: neurite
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0030424
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17553481
database_cross_reference: PMID:18202849
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21566185
database_cross_reference: PMID:22445864
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23903188
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25493551
database_cross_reference: PMID:25772472
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28495872
has_exact_synonym: nerve fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: axon
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0030424

Axiom
annotated source: axon
annotated property: foaf depicted by
comment: 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.

axoneme
type: Class
subclass of: independent continuant
subclass of: intracellular non-membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cilium
subclass of: Restriction
  on property: part of
  some values from: flagellum
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005930
database_cross_reference: PMID:23144623
database_cross_reference: PMID:26057828
database_cross_reference: PMID:26912790
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: axoneme
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005930

Axiom
annotated source: axoneme
annotated property: foaf depicted by
comment: 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.

basal body
type: Class
subclass of: independent continuant
subclass of: intracellular non-membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cilium
subclass of: Restriction
  on property: part of
  some values from: flagellum
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0036064
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21937596
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: basal body
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0036064

Axiom
annotated source: basal body
annotated property: foaf depicted by
comment: Image is an electron micrograph showing a cross-section of a cilium, revealing the basal body (arrowhead). Scale bar is 0.5um.

brain visual center
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16033796
database_cross_reference: PMID:26618653
has_exact_synonym: visual center
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: brain visual center
annotated property: definition
annotated target: Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons).
database_cross_reference: PMID:16033796

bulbar cavity
type: Class
subclass of: independent continuant
subclass of: anatomical cavity
subclass of: Restriction
  on property: part of
  some values from: seminal vesicle
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
definition: An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: bulbar lumen
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: bulbar cavity
annotated property: definition
annotated target: An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla.
database_cross_reference: ISBN:9780070316607

Category 1 cell
type: Class
subclass of: material entity
subclass of: somatic cell
subclass of: parenchymal cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18786419
database_cross_reference: PMID:21894189
database_cross_reference: PMID:22439894
has_exact_synonym: Category 1 gene expressing cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Category 1 cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18786419

cell body
type: Class
subclass of: cellular_component
definition: The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0044297
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16033796
database_cross_reference: PMID:20865784
database_cross_reference: PMID:27612384
database_cross_reference: PMID:28495872
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cell body
annotated property: definition
annotated target: The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
database_cross_reference: GO:0044297

cephalic ganglia lobe
type: Class
subclass of: material entity
subclass of: tissue
definition: One of two bilaterally symmetric structures comprising the planarian brain.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:15866156
database_cross_reference: PMID:16033796
database_cross_reference: PMID:16890156
database_cross_reference: PMID:17251262
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17670787
database_cross_reference: PMID:17905225
database_cross_reference: PMID:17999079
database_cross_reference: PMID:18063757
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:19211673
database_cross_reference: PMID:19247960
database_cross_reference: PMID:19766622
database_cross_reference: PMID:19852954
database_cross_reference: PMID:20223763
database_cross_reference: PMID:20422023
database_cross_reference: PMID:20707997
database_cross_reference: PMID:20967238
database_cross_reference: PMID:21179478
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21566185
database_cross_reference: PMID:21806978
database_cross_reference: PMID:21828097
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22125640
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22371573
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22445864
database_cross_reference: PMID:22451003
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22884275
database_cross_reference: PMID:23123964
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318635
database_cross_reference: PMID:23652002
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24063805
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24131630
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24238224
database_cross_reference: PMID:24523458
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24950970
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25017721
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25356635
database_cross_reference: PMID:25493551
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25772472
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26525673
database_cross_reference: PMID:26556349
database_cross_reference: PMID:26618653
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27034770
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27149082
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27523733
database_cross_reference: PMID:27606067
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384

Axiom
annotated source: cephalic ganglia lobe
annotated property: definition
annotated target: One of two bilaterally symmetric structures comprising the planarian brain.
database_cross_reference: PMID:17999079

cephalic ganglia neuron
type: Class
subclass of: material entity
subclass of: central nervous system neuron
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
definition: A central nervous system neuron located within the planarian brain.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17999079
database_cross_reference: PMID:24173799
database_cross_reference: PMID:27612382
has_exact_synonym: brain neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cephalic ganglia neuron
annotated property: definition
annotated target: A central nervous system neuron located within the planarian brain.
database_cross_reference: PMID:17999079

chemical amputation
type: Class
subclass of: wound
definition: Amputation carried out by application of chemicals.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:24737865
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chemical amputation
annotated property: definition
annotated target: Amputation carried out by application of chemicals.
database_cross_reference: PMID:24737865

chemical pharynx amputation
type: Class
subclass of: chemical amputation
definition: Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:24737865
has_exact_synonym: chemical pharyngeal amputation
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chemical pharynx amputation
annotated property: definition
annotated target: Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide.
database_cross_reference: PMID:24737865

chemosensory neuron
type: Class
subclass of: sensory neuron
subclass of: Restriction
  on property: part of
  some values from: sensory system
definition: Any neuron that capable of some detection of chemical stimulus involved in sensory perception.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FBbt:00005922
database_cross_reference: PMID:18202849
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27612382
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28686611
database_cross_reference: PMID:29547123
has_exact_synonym: chemoreceptive neuron
has_exact_synonym: chemoreceptor neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chemosensory neuron
annotated property: definition
annotated target: Any neuron that capable of some detection of chemical stimulus involved in sensory perception.
database_cross_reference: FBbt:00005922

chromatoid body
type: Class
subclass of: non-membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0033391
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20215344
database_cross_reference: PMID:21356107
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22439894
database_cross_reference: PMID:22543868
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24367277
database_cross_reference: PMID:24903754
database_cross_reference: PMID:25017721
database_cross_reference: PMID:27523733
has_exact_synonym: nuage
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chromatoid body
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22318224
database_cross_reference: PMID:24903754

Axiom
annotated source: chromatoid body
annotated property: foaf depicted by
comment: 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.

chromosome
type: Class
subclass of: non-membrane-bounded organelle
subclass of: nuclear part
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005694
database_cross_reference: PMID:25404302
database_cross_reference: PMID:28757112
database_cross_reference: PMID:28812561
database_cross_reference: PMID:29364871
database_cross_reference: PMID:30143032
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chromosome
annotated property: definition
annotated target: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
database_cross_reference: GO:0005694

Axiom
annotated source: chromosome
annotated property: foaf depicted by
comment: Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um.

chromosome arm
type: Class
subclass of: chromosome part
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C13355
database_cross_reference: PMID:25404302
database_cross_reference: SO:0000105
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chromosome arm
annotated property: definition
annotated target: 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.
database_cross_reference: NCIT:C13355

Axiom
annotated source: chromosome arm
annotated property: foaf depicted by
comment: Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um.

ciliated epithelium
type: Class
subclass of: epithelium
definition: Epithelium bearing vibratile cilia on the free surface.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26711341
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28292427
database_cross_reference: UBERON:0007601
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ciliated epithelium
annotated property: definition
annotated target: Epithelium bearing vibratile cilia on the free surface.
database_cross_reference: UBERON:0007601

Axiom
annotated source: ciliated epithelium
annotated property: foaf depicted by
comment: Image is an electron micrograph of an outer epidermal cell of the pharynx. These cells are heavily ciliated. Scale bar is 2um.

cilium
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: ciliated epithelial cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005929
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cilium
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005929

Axiom
annotated source: cilium
annotated property: foaf depicted by
comment: Image is an electron micrograph depicting several cilia (arrowheads) emerging from a ventral epidermis cell. Scale bar is 0.5um.

commissure
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C32349
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: commissure
annotated property: definition
annotated target: A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord.
database_cross_reference: NCIT:C32349

cut
type: Class
subclass of: surgical wound
definition: A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C50518
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cut
annotated property: definition
annotated target: A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument.
database_cross_reference: NCIT:C50518

dendrite
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: neurite
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0030425
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17553481
database_cross_reference: PMID:22445864
database_cross_reference: PMID:25493551
database_cross_reference: PMID:28495872
has_exact_synonym: cell dendrite
has_exact_synonym: dendritic process
has_exact_synonym: dendritic projection
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dendrite
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0030425

dorsal-ventral muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: parenchymal musculature
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30962434
has_exact_synonym: DVM
has_exact_synonym: dorsal-ventral muscle
has_exact_synonym: dorsal-ventral muscle fibers
has_exact_synonym: dorsoventral muscle
has_exact_synonym: dorsoventralmuscle fibers
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal-ventral muscle cell
annotated property: definition
annotated target: A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal.
database_cross_reference: PMID:30962434

Axiom
annotated source: dorsal-ventral muscle cell
annotated property: foaf depicted by
comment: 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.

early female germ cell
type: Class
subclass of: material entity
subclass of: female germ cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: A premeiotic female germ cell (i.e., a diploid female germline stem cell or transit amplifying oogonial cell).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

early male germ cell
type: Class
subclass of: material entity
subclass of: male germ cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27330085
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: early male germ cell
annotated property: definition
annotated target: A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell).
database_cross_reference: PMID:27330085

embryonic gut
type: Class
subclass of: material entity
subclass of: extraembryonic organ
subclass of: Restriction
  on property: part of
  some values from: embryonic digestive system
subclass of: Restriction
  on property: contained in
  some values from: aboral hemisphere
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 4
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: A cryptic digestive cavity comprised of phagocytic embryonic gut cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic gut
annotated property: definition
annotated target: A cryptic digestive cavity comprised of phagocytic embryonic gut cells.
database_cross_reference: PMID:28072387

epidermal cell
type: Class
subclass of: epithelial cell
definition: An epithelial cell of the integument (the outer layer of an organism).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000362
database_cross_reference: PMID:21458439
database_cross_reference: PMID:24922054
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26457503
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28686611
database_cross_reference: PMID:28807897
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29357350
database_cross_reference: PMID:30399335
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: epidermal cell
annotated property: definition
annotated target: An epithelial cell of the integument (the outer layer of an organism).
database_cross_reference: CL:0000362

Axiom
annotated source: epidermal cell
annotated property: foaf depicted by
comment: 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.

epidermal rhabdite
type: Class
subclass of: independent continuant
subclass of: rhabdite
subclass of: Restriction
  on property: part of
  some values from: ventral epidermis cell
subclass of: Restriction
  on property: part of
  some values from: dorsal epidermis cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Rhabdites located within epidermal cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
has_obo_namespace: Planarian_Anatomy
comment: 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

Axiom
annotated source: epidermal rhabdite
annotated property: definition
annotated target: Rhabdites located within epidermal cells.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: epidermal rhabdite
annotated property: foaf depicted by
comment: 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.

ER membrane
type: Class
subclass of: bounding membrane of organelle
subclass of: Restriction
  on property: part of
  some values from: endoplasmic reticulum
definition: The lipid bilayer surrounding the endoplasmic reticulum.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005789
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ER membrane
annotated property: definition
annotated target: The lipid bilayer surrounding the endoplasmic reticulum.
database_cross_reference: GO:0005789

Axiom
annotated source: ER membrane
annotated property: foaf depicted by
comment: 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.

eumelanin
type: Class
subclass of: independent continuant
subclass of: cellular_component
subclass of: Restriction
  on property: part of
  some values from: melanosome
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CHEBI:24009
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26017970
database_cross_reference: PMID:27240733
has_exact_synonym: eye cell pigment
has_exact_synonym: eye pigment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: eumelanin
annotated property: definition
annotated target: The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color.
database_cross_reference: PMID:15760337
database_cross_reference: PMID:26017970
database_cross_reference: PMID:8812261

excretory cell
type: Class
subclass of: terminally differentiated cell
subclass of: Restriction
  on property: part of
  some values from: renal system
definition: A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000424
database_cross_reference: PMID:21566185
database_cross_reference: PMID:24173799
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: excretory cell
annotated property: definition
annotated target: A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
database_cross_reference: CL:0000424

Axiom
annotated source: excretory cell
annotated property: foaf depicted by
comment: 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.

extracellular matrix
type: Class
subclass of: independent continuant
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0031012
database_cross_reference: PMID:19048075
database_cross_reference: PMID:28126842
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28807897
database_cross_reference: PMID:30962434
has_exact_synonym: ECM
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: extracellular matrix
annotated property: definition
annotated target: A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
database_cross_reference: GO:0031012

Axiom
annotated source: extracellular matrix
annotated property: foaf depicted by
comment: Image is an electron micrograph showing the extracellular matrix (arrowheads) between two cells. Scale bar is 0.2um.

extracellular space
type: Class
subclass of: acellular anatomical structure
definition: That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005615
database_cross_reference: PMID:21828097
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: extracellular space
annotated property: definition
annotated target: That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
database_cross_reference: GO:0005615

fission
type: Class
subclass of: wound
definition: A form of asexual reproduction resulting in self-amputation of posterior tissue, generating an anterior fragment and a fission fragment.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

flagellum
type: Class
subclass of: independent continuant
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: sperm
definition: 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).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29095551
database_cross_reference: PMID:4190073
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: flagellum
annotated property: definition
annotated target: 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).
database_cross_reference: PMID:4190073

gap junction
type: Class
subclass of: cell-cell junction
definition: A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005921
database_cross_reference: PMID:17670787
database_cross_reference: PMID:22125640
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: gap junction
annotated property: definition
annotated target: A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
database_cross_reference: GO:0005921

genital atrium
type: Class
subclass of: independent continuant
subclass of: anatomical cavity
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID: 22074376
has_exact_synonym: atrium
has_exact_synonym: female antrum
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: genital atrium
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22074376

germ cell cyst
type: Class
subclass of: reproductive structure
subclass of: syncytium
subclass of: Restriction
  on property: part of
  some values from: gonad
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17376870
database_cross_reference: PMID:22318224
has_exact_synonym: germ cell cluster
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: germ cell cyst
annotated property: definition
annotated target: A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells.
database_cross_reference: PMID:17376870

germline stem cell
type: Class
subclass of: independent continuant
subclass of: stem cell
subclass of: Restriction
  on property: part of
  some values from: gonad
subclass of: Restriction
  on property: develops from
  some values from: neoblast
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Stem cell that is the precursor of gametes.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000014
database_cross_reference: FBbt:00004861
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:17390146
database_cross_reference: PMID:18456843
database_cross_reference: PMID:19247960
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22252538
database_cross_reference: PMID:22318224
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22543868
database_cross_reference: PMID:23652002
database_cross_reference: PMID:24173799
database_cross_reference: PMID:24367277
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27013241
database_cross_reference: PMID:28434803
database_cross_reference: PMID:28812561
database_cross_reference: https://doi.org/10.1101/279364
has_exact_synonym: germ cell
has_exact_synonym: germ stem cell
has_exact_synonym: germline cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: germline stem cell
annotated property: definition
annotated target: Stem cell that is the precursor of gametes.
database_cross_reference: FBbt:00004861

glycogen granule
type: Class
subclass of: intracellular granule
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0042587
database_cross_reference: PMID:30608231
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: glycogen granule
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0042587

Axiom
annotated source: glycogen granule
annotated property: foaf depicted by
comment: Image is an electron micrograph depicting glycogen granules (arrowheads) within the cytoplasm of a cell. Scale bar is 200 nm.

incision
type: Class
subclass of: cut
definition: A surgical cut that breaches the epidermis, made with a defined edge.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

pharynx inner epidermal cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: pharynx epithelium
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20511647
has_exact_synonym: inner pharynx epidermal cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx inner epidermal cell
annotated property: definition
annotated target: Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: pharynx inner epidermal cell
annotated property: foaf depicted by
comment: 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.

inner zone of gland cells
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: inner zone of gland cells
annotated property: definition
annotated target: Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: inner zone of gland cells
annotated property: foaf depicted by
comment: 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.

intercellular junction
type: Class
subclass of: cell-cell junction
definition: A cell junction that forms a connection between two or more cells in a multicellular organism.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005911
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intercellular junction
annotated property: definition
annotated target: A cell junction that forms a connection between two or more cells in a multicellular organism.
database_cross_reference: GO:0005911

linear amputation
type: Class
subclass of: amputation
definition: An amputation performed with a transverse, oblique or longitudinal cut.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

linear incision
type: Class
subclass of: incision
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: scratch
has_obo_namespace: Planarian_Anatomy

lipid droplet
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005811
database_cross_reference: PMID:30608231
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: lipid droplet
annotated property: definition
annotated target: An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
database_cross_reference: GO:0005811

Axiom
annotated source: lipid droplet
annotated property: foaf depicted by
comment: 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.

lumen
type: Class
subclass of: anatomical cavity
definition: The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C94478
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: lumen
annotated property: definition
annotated target: The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine.
database_cross_reference: NCIT:C94478

marginal adhesive zone
type: Class
subclass of: anatomical compartment
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20865784
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: marginal adhesive zone
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: marginal adhesive zone
annotated property: foaf depicted by
comment: 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.

mechanosensory neuron
type: Class
subclass of: sensory neuron
subclass of: Restriction
  on property: part of
  some values from: sensory system
definition: Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FBbt:00005919
database_cross_reference: PMID:25725068
database_cross_reference: PMID:28216315
database_cross_reference: WBbt:0008431
has_exact_synonym: mechanosensory cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: mechanosensory neuron
annotated property: definition
annotated target: Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception.
database_cross_reference: FBbt:00005919

medial muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: parenchymal musculature
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Subset of dorsal-ventral muscle cells located in the medial body region.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30962434
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: medial muscle cell
annotated property: definition
annotated target: Subset of dorsal-ventral muscle cells located in the medial body region.
database_cross_reference: PMID:30962434

Axiom
annotated source: medial muscle cell
annotated property: foaf depicted by
comment: 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.

meiotic germ cell
type: Class
subclass of: independent continuant
subclass of: germ cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: A germ cell undergoing meiosis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27330085
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: meiotic germ cell
annotated property: definition
annotated target: A germ cell undergoing meiosis.
database_cross_reference: PMID:27330085

melanosome
type: Class
subclass of: material entity
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: pigment cup cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 7
definition: A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0042470
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: melanosome
annotated property: definition
annotated target: A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
database_cross_reference: GO:0042470

mucus
type: Class
subclass of: material entity
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: secretory system
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
subclass of: Restriction
  on property: produced by
  some values from: secretory cell
definition: A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21282632
database_cross_reference: PMID:22653920
database_cross_reference: UBERON:0000912
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: mucus
annotated property: definition
annotated target: A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance.
database_cross_reference: PMID:22653920

Axiom
annotated source: mucus
annotated property: foaf depicted by
comment: 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.

nephridiopore
type: Class
subclass of: independent continuant
subclass of: pore
subclass of: Restriction
  on property: part of
  some values from: flame cell
definition: The external opening and terminus of a protonephridium made by a terminal cell.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:21828097
database_cross_reference: UBERON:0006972
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nephridiopore
annotated property: definition
annotated target: The external opening and terminus of a protonephridium made by a terminal cell.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: nephridiopore
annotated property: foaf depicted by
comment: 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.

neurite
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: neuron
definition: Cell appendage of the neuron which includes the axon and the dendrite.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: FBbt:00005113
database_cross_reference: FMA:61814
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:27612382
database_cross_reference: PMID:29547123
has_exact_synonym: neuronal process
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neurite
annotated property: definition
annotated target: Cell appendage of the neuron which includes the axon and the dendrite.
database_cross_reference: FMA:61814

neuropeptidergic neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A neuron that produces and releases neuropeptides at chemical synapses.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:24173799
database_cross_reference: PMID:25356635
database_cross_reference: PMID:27163480
has_exact_synonym: cns peptidergic cell
has_exact_synonym: peptidergic neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: neuropeptidergic neuron
annotated property: definition
annotated target: A neuron that produces and releases neuropeptides at chemical synapses.
database_cross_reference: PMID:24173799

non-ciliated epidermis
type: Class
subclass of: epidermis
definition: Differentiating, immature epidermal cells lacking cilia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:26457503
database_cross_reference: PMID:28292427
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: non-ciliated epidermis
annotated property: definition
annotated target: Differentiating, immature epidermal cells lacking cilia.
database_cross_reference: PMID:26457503

nuclear envelope
type: Class
subclass of: membrane
definition: 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).
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005635
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear envelope
annotated property: definition
annotated target: 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).
database_cross_reference: GO:0005635

Axiom
annotated source: nuclear envelope
annotated property: foaf depicted by
comment: 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.

nuclear inner membrane
type: Class
subclass of: membrane part
subclass of: Restriction
  on property: part of
  some values from: nuclear envelope
definition: The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005637
has_exact_synonym: inner leaflet
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear inner membrane
annotated property: definition
annotated target: The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
database_cross_reference: GO:0005637

Axiom
annotated source: nuclear inner membrane
annotated property: foaf depicted by
comment: 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.

nuclear lumen
type: Class
subclass of: nuclear part
definition: The volume enclosed by the nuclear inner membrane.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0031981
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear lumen
annotated property: definition
annotated target: The volume enclosed by the nuclear inner membrane.
database_cross_reference: GO:0031981

nuclear outer membrane
type: Class
subclass of: membrane part
subclass of: Restriction
  on property: part of
  some values from: nuclear envelope
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005640
has_exact_synonym: outer leaflet
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear outer membrane
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0005640

Axiom
annotated source: nuclear outer membrane
annotated property: foaf depicted by
comment: 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.

nuclear periphery
type: Class
subclass of: nuclear part
definition: The portion of the nuclear lumen proximal to the inner nuclear membrane.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0034399
database_cross_reference: PMID:25404302
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear periphery
annotated property: definition
annotated target: The portion of the nuclear lumen proximal to the inner nuclear membrane.
database_cross_reference: GO:0034399

ommochrome pigment cell
type: Class
subclass of: material entity
subclass of: pigment cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Parenchymal cells that synthesize and contain brown ommonchrome pigment.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27240733
has_exact_synonym: non-melanin pigment cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ommochrome pigment cell
annotated property: definition
annotated target: Parenchymal cells that synthesize and contain brown ommonchrome pigment.
database_cross_reference: PMID:27240733

optic nerve
type: Class
subclass of: material entity
subclass of: nerve
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27800171
database_cross_reference: UBERON:0004904
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: optic nerve
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0004904

pharynx outer epidermal cell
type: Class
subclass of: material entity
subclass of: ciliated epithelial cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: pharynx epithelium
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:20511647
has_exact_synonym: outer pharynx epidermal cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx outer epidermal cell
annotated property: definition
annotated target: Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature.
database_cross_reference: ISBN:9780070316607

Axiom
annotated source: pharynx outer epidermal cell
annotated property: foaf depicted by
comment: 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.

phagocytic cell
type: Class
subclass of: terminally differentiated cell
definition: A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000234
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:25956527
database_cross_reference: PMID:27501047
database_cross_reference: PMID:30471994
has_exact_synonym: phagocyte
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: phagocytic cell
annotated property: definition
annotated target: A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome.
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:30471994

pharynx tip
type: Class
subclass of: independent continuant
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The distal-most end of the pharnyx containing an opening to the pharynx lumen.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx tip
annotated property: foaf depicted by
comment: 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.

pigment cell
type: Class
subclass of: terminally differentiated cell
definition: A pigment cell is a cell that contains pigment granules.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000147
database_cross_reference: PMID:26618653
has_exact_synonym: pigment producing cell
has_exact_synonym: pigmented cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pigment cell
annotated property: definition
annotated target: A pigment cell is a cell that contains pigment granules.
database_cross_reference: CL:0000147

pigment granule
type: Class
subclass of: membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: pigment cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0048770
database_cross_reference: ISBN:9780070316607
database_cross_reference: PMID:27551436
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pigment granule
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0048770

plug amputation
type: Class
subclass of: amputation
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: plug amputation
annotated property: foaf depicted by
comment: Illustration of an example of a plug amputation showing resultant fragment and donor wound.

point incision
type: Class
subclass of: incision
definition: A breach of the epidermis made with a sharp pointed object, like a needle or an insect pin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: poke
has_obo_namespace: Planarian_Anatomy

pore
type: Class
subclass of: anatomical cavity
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0008915
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pore
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0008915

post-meiotic germ cell
type: Class
subclass of: independent continuant
subclass of: germ cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: develops from
  some values from: premeiotic germ cell
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
definition: A haploid gamete undergoing terminal differentiation.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

postsynaptic cell
type: Class
subclass of: independent continuant
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: part of
  some values from: asexual organism
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0045211
database_cross_reference: PMID:24950970
has_exact_synonym: post-synaptic cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: postsynaptic cell
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0045211

premeiotic germ cell
type: Class
subclass of: independent continuant
subclass of: germ cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A diploid germline stem cell or transit amplifying germ cell that has not committed to undergoing meiotic DNA replication, reductive divisions or terminal differentiation.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

presynaptic cell
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: The part of a synapse that is part of the presynaptic cell.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0098793
database_cross_reference: PMID:24950970
has_exact_synonym: pre-synaptic cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: presynaptic cell
annotated property: definition
annotated target: The part of a synapse that is part of the presynaptic cell.
database_cross_reference: GO:0098793

presynaptic terminal
type: Class
subclass of: cellular_component
subclass of: Restriction
  on property: part of
  some values from: axon
subclass of: Restriction
  on property: part of
  some values from: presynaptic cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043195
database_cross_reference: PMID:23903188
has_exact_synonym: pre-synaptic terminal
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: presynaptic terminal
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0043195

presynaptic vesicle
type: Class
subclass of: membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: presynaptic cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0008021
database_cross_reference: PMID:23903188
has_exact_synonym: pre-synaptic vesicle
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: presynaptic vesicle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0008021

primary gut branch
type: Class
subclass of: gut branch
definition: The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17553481
database_cross_reference: PMID:20865784
database_cross_reference: PMID:21664348
database_cross_reference: PMID:27122174
database_cross_reference: PMID:28137894
database_cross_reference: PMID:29674431
has_exact_synonym: main gut branch
has_exact_synonym: primary intestine branch
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primary gut branch
annotated property: definition
annotated target: The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature.
database_cross_reference: PMID:21664348

primitive gut
type: Class
subclass of: material entity
subclass of: extraembryonic organ
subclass of: Restriction
  on property: part of
  some values from: embryonic digestive system
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: Four large phagocytic cells associated with the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_exact_synonym: primitive endoderm
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primitive gut
annotated property: definition
annotated target: Four large phagocytic cells associated with the embryonic pharynx.
database_cross_reference: PMID:28072387

quarternary gut branch
type: Class
subclass of: gut branch
definition: Gut branches originating from and connected to the tertiary gut branches.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21664348
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: quarternary gut branch
annotated property: definition
annotated target: Gut branches originating from and connected to the tertiary gut branches.
database_cross_reference: PMID:21664348

reproductive organ
type: Class
subclass of: independent continuant
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: An organ involved in reproduction
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16344473
database_cross_reference: PMID:17376870
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:25278423
database_cross_reference: PMID:27074666
database_cross_reference: UBERON:0003133
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: reproductive organ
annotated property: definition
annotated target: An organ involved in reproduction
database_cross_reference: UBERON:0003133

reproductive structure
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Any anatomical structure that is part of the reproductive system.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17376870
database_cross_reference: UBERON:0005156
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: reproductive structure
annotated property: definition
annotated target: Any anatomical structure that is part of the reproductive system.
database_cross_reference: UBERON:0005156

rhabdome
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: eye
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:15760337
database_cross_reference: PMID:16033796
database_cross_reference: PMID:21852957
database_cross_reference: PMID:26017970
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: rhabdome
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:15760337
database_cross_reference: PMID:16033796
database_cross_reference: PMID:21852957

rhabdomere
type: Class
subclass of: material entity
subclass of: cell projection
subclass of: Restriction
  on property: part of
  some values from: photoreceptor neuron
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0016028
database_cross_reference: PMID:15760337
database_cross_reference: PMID:16033796
database_cross_reference: PMID:18202849
database_cross_reference: PMID:20865784
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22445864
database_cross_reference: PMID:25772472
database_cross_reference: PMID:26618653
database_cross_reference: PMID:27800171
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: rhabdomere
annotated property: definition
annotated target: The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light.
database_cross_reference: PMID:15760337
database_cross_reference: PMID:16033796
database_cross_reference: PMID:21852957

secretory duct
type: Class
subclass of: independent continuant
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: secretory system
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A tubular structure that transports secreted or excreted substances.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:30383829
database_cross_reference: UBERON:0000058
has_exact_synonym: secretory canal
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secretory duct
annotated property: definition
annotated target: A tubular structure that transports secreted or excreted substances.
database_cross_reference: UBERON:0000058

Axiom
annotated source: secretory duct
annotated property: foaf depicted by
comment: 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.

secretory granule
type: Class
subclass of: membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: secretory cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0030141
database_cross_reference: PMID:29100657
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: secretory granule
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0030141

somatic cell
type: Class
subclass of: cell
definition: One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: BTO:0001268
database_cross_reference: CL:0002371
database_cross_reference: PMID:20599901
database_cross_reference: PMID:21852957
database_cross_reference: PMID:22074376
database_cross_reference: PMID:22371573
database_cross_reference: PMID:22385657
database_cross_reference: PMID:25404302
database_cross_reference: PMID:27606067
database_cross_reference: PMID:28757112
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: somatic cell
annotated property: definition
annotated target: One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
database_cross_reference: BTO:0001268

somatic gonadal cell
type: Class
subclass of: independent continuant
subclass of: terminally differentiated cell
subclass of: Restriction
  on property: part of
  some values from: gonad
definition: A non-germline cell within the ovary or testis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085
database_cross_reference: WBbt:0007815
has_exact_synonym: gonadal niche cell
has_exact_synonym: somatic gonadal niche cell
has_exact_synonym: somatic gonadal support cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: somatic gonadal cell
annotated property: definition
annotated target: A non-germline cell within the ovary or testis.
database_cross_reference: PMID:27163480
database_cross_reference: PMID:27330085

specialized neoblast
type: Class
subclass of: neoblast
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25254346
database_cross_reference: PMID:26651295
database_cross_reference: PMID:27542689
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30962434
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: specialized neoblast
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:23404104

stalk
type: Class
subclass of: material entity
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: egg capsule
subclass of: Restriction
  on property: produced by
  some values from: cement gland
definition: A thin, flexible rod that anchors an egg capsule to a solid substrate.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: stalk
annotated property: definition
annotated target: A thin, flexible rod that anchors an egg capsule to a solid substrate.
database_cross_reference: ISBN:9780070316607

surgical wound
type: Class
subclass of: wound
definition: A wound produced by non-autonomous physical means.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

synapse
type: Class
subclass of: cell-cell junction
subclass of: Restriction
  on property: part of
  some values from: neuron
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0045202
database_cross_reference: PMID:18202849
database_cross_reference: PMID:18287199
database_cross_reference: PMID:21282632
has_exact_synonym: neural synapse
has_exact_synonym: neuronal synapse
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: synapse
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0045202

synaptic cleft
type: Class
subclass of: extracellular space
subclass of: Restriction
  on property: part of
  some values from: neuron
subclass of: Restriction
  on property: part of
  some values from: electrically responsive cell
definition: The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043083
database_cross_reference: PMID:23903188
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: synaptic cleft
annotated property: definition
annotated target: The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.
database_cross_reference: GO:0043083

synaptic vesicle
type: Class
subclass of: membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: neuron
definition: 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]
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0008021
database_cross_reference: PMID:24950970
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: synaptic vesicle
annotated property: definition
annotated target: 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]
database_cross_reference: GO:0008021

synaptonemal complex
type: Class
subclass of: chromosomal_structural_element
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0000795
database_cross_reference: PMID:25404302
has_obo_namespace: Planarian_Anatomy

tail tip
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The posterior-medial region of the tail margin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tail tip
annotated property: foaf depicted by
comment: Illustration of the tail tip (in green).

telomere
type: Class
subclass of: chromosome part
subclass of: Restriction
  on property: part of
  some values from: chromosome arm
definition: The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0000781
database_cross_reference: PMID:22371573
database_cross_reference: PMID:25404302
database_cross_reference: https://doi.org/10.1101/279364
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: telomere
annotated property: definition
annotated target: The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
database_cross_reference: GO:0000781

septate junction
type: Class
subclass of: cell-cell junction
subclass of: Restriction
  on property: part of
  some values from: epithelium
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0070160
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: septate junction
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0070160

Axiom
annotated source: septate junction
annotated property: foaf depicted by
comment: 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.

wedge amputation
type: Class
subclass of: amputation
definition: A wound resulting from a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: wedge amputation
annotated property: foaf depicted by
comment: Illustration of a wedge amputation depicting the resultant donor wound and wedge fragment.

wound
type: Class
subclass of: perturbation
definition: An injury that breaches the epidermis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: injury
has_obo_namespace: Planarian_Anatomy

X1 cell
type: Class
subclass of: cell
subclass of: FACS sorted cell population
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16872450
database_cross_reference: PMID:17670787
database_cross_reference: PMID:18456843
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:21937596
database_cross_reference: PMID:22385657
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22543868
database_cross_reference: PMID:22549959
database_cross_reference: PMID:23235145
database_cross_reference: PMID:23629965
database_cross_reference: PMID:24120894
database_cross_reference: PMID:24367277
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27068018
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27502555
database_cross_reference: PMID:27523733
database_cross_reference: PMID:27551436
database_cross_reference: PMID:28137894
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29557542
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
database_cross_reference: PMID:30194301
has_exact_synonym: X1
has_exact_synonym: X1 cell population
has_exact_synonym: X1 neoblast
has_exact_synonym: X1 population
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: X1 cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:16872450

X1(FS) cell
type: Class
subclass of: cell
subclass of: FACS sorted cell population
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:21566185
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: X1(FS) cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:21566185

X2 cell
type: Class
subclass of: cell
subclass of: FACS sorted cell population
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16872450
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22543868
database_cross_reference: PMID:23629965
database_cross_reference: PMID:24367277
database_cross_reference: PMID:25017721
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27150006
database_cross_reference: PMID:27502555
database_cross_reference: PMID:27606067
database_cross_reference: PMID:27864883
database_cross_reference: PMID:28137894
database_cross_reference: PMID:29674432
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: X2 cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:16872450

Xins cell
type: Class
subclass of: cell
subclass of: FACS sorted cell population
definition: A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16872450
database_cross_reference: PMID:17670787
database_cross_reference: PMID:18456843
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19048075
database_cross_reference: PMID:20215344
database_cross_reference: PMID:20223763
database_cross_reference: PMID:22427692
database_cross_reference: PMID:22479207
database_cross_reference: PMID:22543868
database_cross_reference: PMID:23629965
database_cross_reference: PMID:24367277
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25558068
database_cross_reference: PMID:25956527
database_cross_reference: PMID:26114597
database_cross_reference: PMID:26457503
database_cross_reference: PMID:26711341
database_cross_reference: PMID:27013241
database_cross_reference: PMID:27502555
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29674432
database_cross_reference: PMID:29906446
database_cross_reference: PMID:30194301
has_exact_synonym: Xins
has_exact_synonym: Xins cell population
has_exact_synonym: Xins cells
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: Xins cell
annotated property: definition
annotated target: A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types.
database_cross_reference: PMID:16872450

postpharyngeal region
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Posterior to the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: post pharyngeal
has_exact_synonym: post-pharyngeal
has_exact_synonym: post-pharyngeal region
has_exact_synonym: postpharyngeal region
has_obo_namespace: Planarian_Anatomy

post-blastema region
type: Class
subclass of: anatomical region
definition: Adjacent to blastema, or proximal to blastema.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: post-blastema
has_exact_synonym: postblastema
has_exact_synonym: postblastema region
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: post-blastema region
annotated property: foaf depicted by
comment: Illustration of the post-blastema region(in green) in the anterior region of a regenerating tail fragment.

fission fragment
type: Class
subclass of: fragment
definition: A fragment derived from a spontaneous or induced fission event.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

obsolete oblique
type: Class
comment: term is not needed.
deprecated: true

epithelium
type: Class
subclass of: tissue
definition: The avascular cellular layers that cover body surfaces and cavities and may form glands.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: NCIT:C12710
database_cross_reference: UBERON:0000483
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: epithelium
annotated property: definition
annotated target: The avascular cellular layers that cover body surfaces and cavities and may form glands.
database_cross_reference: NCIT:C12710

Axiom
annotated source: epithelium
annotated property: foaf depicted by
comment: 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.

gut branch
type: Class
subclass of: independent continuant
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: gut
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: The triclad planarian gut is serially bifrucated into connected lumens where each bifrucation is a branch.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

extraembryonic organ
type: Class
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: embryo
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

chromosome part
type: Class
subclass of: nuclear part
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: SO:0000830
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chromosome part
annotated property: definition
annotated target: 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.
database_cross_reference: SO:0000830

perturbation
type: Class
subclass of: Thing
definition: An event or occurrence that causes damage to a tissue or organ.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: insult
has_obo_namespace: Planarian_Anatomy

chromosomal_structural_element
type: Class
subclass of: chromosome part
definition: structural element of a chromosome, for example, a telomere and a centromere
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: SO:0000628
has_exact_synonym: chromosomal structural element
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: chromosomal_structural_element
annotated property: definition
annotated target: structural element of a chromosome, for example, a telomere and a centromere
database_cross_reference: SO:0000628

thick fragment
type: Class
subclass of: longitudinal fragment
definition: A longitudinal fragment containing the preexisting midline and medial structures.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: thick fragment
annotated property: foaf depicted by
comment: Illustration of a thick fragment (in green).

thin fragment
type: Class
subclass of: longitudinal fragment
definition: A longitudinal fragment lacking a midline and medial structures.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: thin fragment
annotated property: foaf depicted by
comment: Illustration of a thin fragment (in green).

fragment
type: Class
subclass of: regenerating anatomical structure
definition: A piece of tissue isolated from the body.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: piece
has_obo_namespace: Planarian_Anatomy

longitudinal region
type: Class
subclass of: anatomical region
definition: 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
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: longitudinal region
annotated property: foaf depicted by
comment: Illustration of a longitudinal region (green).

chemical wound
type: Class
subclass of: wound
definition: An intentional wound produced by non-autonomous chemical means.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

plug wound
type: Class
subclass of: wound
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: plug wound
annotated property: foaf depicted by
comment: Illustration of a wound left in a donor animal resulting from a plug amputation.

wedge wound
type: Class
subclass of: wound
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: wedge wound
annotated property: foaf depicted by
comment: Illustration of a wedge wound.

regenerating fragment
type: Class
subclass of: fragment
definition: A fragment that has undergone wound healing and is undergoing tissue replacement and morphallaxis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

sagittal orientation
type: Class
subclass of: longitudinal orientation
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: longitudinal orientation
has_obo_namespace: Planarian_Anatomy

parasagittal orientation
type: Class
subclass of: sagittal orientation
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PATO:0005023
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: parasagittal orientation
annotated property: definition
annotated target: 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.
database_cross_reference: PATO:0005023

syncytium
type: Class
subclass of: anatomical structure
definition: An anatomical entity consisting of a single or a few multinucleated structures
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: AEO:0000203
database_cross_reference: BTO:0005784
database_cross_reference: PMID:27330085
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: syncytium
annotated property: definition
annotated target: An anatomical entity consisting of a single or a few multinucleated structures
database_cross_reference: AEO:0000203

intracellular granule
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: MICRO:0000215
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: intracellular granule
annotated property: definition
annotated target: Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy.
database_cross_reference: MICRO:0000215

Axiom
annotated source: intracellular granule
annotated property: foaf depicted by
comment: Image is an electron micrograph depicting a cell with many intracellular granules (arrowheads) visible in the cytoplasm. The scale bar is 1um.

FACS sorted cell population
type: Class
subclass of: derived cell population
definition: Any number of cells from dissociated planarian tissue sorted via a FACS sorter for any parameter.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

derived cell population
type: Class
subclass of: material anatomical entity
definition: Cells isolated from dissociated planarian tissue.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

pharynx pouch epithelium
type: Class
subclass of: material entity
subclass of: epithelium
subclass of: Restriction
  on property: part of
  some values from: pharynx pouch
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: An epithelial monolayer lining the pharynx pouch cavity.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx pouch epithelium
annotated property: definition
annotated target: An epithelial monolayer lining the pharynx pouch cavity.
database_cross_reference: OCLC:16809160

Axiom
annotated source: pharynx pouch epithelium
annotated property: foaf depicted by
comment: 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.

sperm duct epithelial surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: sperm duct epithelium
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Epithelial surface lining the sperm duct.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sperm duct epithelial surface
annotated property: definition
annotated target: Epithelial surface lining the sperm duct.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376

parenchyma
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
has_exact_synonym: mesenchyme
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: parenchyma
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160

dorsal region of tail
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: tail region
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of the tail.
has_exact_synonym: dorsal region of tail region
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003000

Axiom
annotated source: dorsal region of tail
annotated property: foaf depiction
comment: Illustration of the dorsal region of the tail (in green).

lateral region of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: lateral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: lateral region
definition: The lateral region of the medio-lateral axis of the whole animal.
has_exact_synonym: lateral region of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003001

anterior region of the eye
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: eye
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: eye
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of the eye.
has_exact_synonym: anterior region of eye
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003002

posterior region of the eye
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: eye
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: eye
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of the eye.
has_exact_synonym: posterior region of eye
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003003

prepharyngeal midline
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: midline
  intersection of: Restriction
    on property: overlaps
    some values from: prepharyngeal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: midline
subclass of: Restriction
  on property: overlaps
  some values from: prepharyngeal region
definition: The center-most region just anterior to the pharynx
has_exact_synonym: prepharyngeal region of midline
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003004

testis cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: testis
definition: cell which is part of the testis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003100

Axiom
annotated source: testis cell
annotated property: definition
annotated target: cell which is part of the testis
database_cross_reference: PMID:29674431

ventral epidermis cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: ventral epidermis
definition: cell which is part of the ventral epidermis
has_exact_synonym: ventral ciliated cell
has_exact_synonym: ventral epithelial cell
has_exact_synonym: ventral motile ciliated cell
has_exact_synonym: ventral multiciliated cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003101

Axiom
annotated source: ventral epidermis cell
annotated property: definition
annotated target: cell which is part of the ventral epidermis
database_cross_reference: PMID:22479207
database_cross_reference: PMID:23144623

visual system cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: visual system
definition: cell which is part of the visual system
has_exact_synonym: visual cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003102

Axiom
annotated source: visual system cell
annotated property: definition
annotated target: cell which is part of the visual system
database_cross_reference: PMID:17905225
database_cross_reference: PMID:24922054

eye cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: eye
definition: cell which is part of the eye
has_exact_synonym: photoreceptor cell
has_exact_synonym: photosensitive cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003103

Axiom
annotated source: eye cell
annotated property: definition
annotated target: cell which is part of the eye
database_cross_reference: PMID:29357350

enteric muscle cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: enteric musculature
definition: cell which is part of the enteric musculature
has_exact_synonym: gut muscle cell
has_exact_synonym: intestinal muscle cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003104

Axiom
annotated source: enteric muscle cell
annotated property: definition
annotated target: cell which is part of the enteric musculature
database_cross_reference: PMID:23954785
database_cross_reference: PMID:25558068

dorsal epidermis cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: dorsal region of the epidermis
definition: cell which is part of the dorsal region of the epidermis
has_exact_synonym: dorsal epithelial cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003105

Axiom
annotated source: dorsal epidermis cell
annotated property: definition
annotated target: cell which is part of the dorsal region of the epidermis
database_cross_reference: PMID:22479207

adhesion gland cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: adhesion gland
definition: cell which is part of the adhesion gland
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003106

Axiom
annotated source: adhesion gland cell
annotated property: definition
annotated target: cell which is part of the adhesion gland
database_cross_reference: PMID:16890156
database_cross_reference: PMID:28976975

body wall muscle cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: body wall musculature
definition: cell which is part of the body wall musculature
has_exact_synonym: body wall muscle fiber
has_exact_synonym: body-wall muscle cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003107

Axiom
annotated source: body wall muscle cell
annotated property: definition
annotated target: cell which is part of the body wall musculature
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25725068
database_cross_reference: PMID:26525673

gastrodermal cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: gastrodermis
definition: cell which is part of the gastrodermis
has_exact_synonym: gut cell
has_exact_synonym: intestinal cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003108

Axiom
annotated source: gastrodermal cell
annotated property: definition
annotated target: cell which is part of the gastrodermis
database_cross_reference: PMID:19174194
database_cross_reference: PMID:22479207
database_cross_reference: PMID:27122174

anterior pole cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: anterior pole
definition: cell which is part of the anterior pole
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003109

Axiom
annotated source: anterior pole cell
annotated property: definition
annotated target: cell which is part of the anterior pole
database_cross_reference: PMID:24992682
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30471994

pharynx neuron
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: neuron
  intersection of: Restriction
    on property: part of
    some values from: pharynx
definition: neuron which is part of the pharynx
has_exact_synonym: pharyngeal neuron
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003110

Axiom
annotated source: pharynx neuron
annotated property: definition
annotated target: neuron which is part of the pharynx
database_cross_reference: PMID:18202849
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30485821

pharynx epithelial cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: pharynx
definition: epithelial cell which is part of the pharynx
has_exact_synonym: pharynx epithelial cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003111

Axiom
annotated source: pharynx epithelial cell
annotated property: definition
annotated target: epithelial cell which is part of the pharynx
database_cross_reference: PMID:20511647

pharynx muscle cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: part of
    some values from: pharynx
definition: muscle cell which is part of the pharynx
has_exact_synonym: pharynx muscle fiber
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003112

Axiom
annotated source: pharynx muscle cell
annotated property: definition
annotated target: muscle cell which is part of the pharynx
database_cross_reference: PMID:27068018

pharynx pouch epithelial cell
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: pharynx pouch
definition: epithelial cell which is part of the pharynx pouch
has_exact_synonym: pharyngeal cavity epithelial cell
has_exact_synonym: pharynx cavity epithelial cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003113

melanin pigment granule
type: Class
subclass of: independent continuant
subclass of: Class
  intersection of: pigment granule
  intersection of: Restriction
    on property: part of
    some values from: eumelanin
definition: pigment granule which is part of the eumelanin
has_exact_synonym: melanin
has_exact_synonym: melanosome
has_exact_synonym: photoreceptor pigment
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003114

Axiom
annotated source: melanin pigment granule
annotated property: definition
annotated target: pigment granule which is part of the eumelanin
database_cross_reference: PMID:25356635
database_cross_reference: PMID:26017970
database_cross_reference: PMID:27551436

ommochrome pigment granule
type: Class
subclass of: Class
  intersection of: pigment granule
  intersection of: Restriction
    on property: part of
    some values from: ommochrome pigment cell
definition: pigment granule which is part of the ommochrome pigment cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003115

parenchymal cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: parenchyma
definition: cell which is part of the parenchyma
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003116

Axiom
annotated source: parenchymal cell
annotated property: definition
annotated target: cell which is part of the parenchyma
database_cross_reference: PMID:19247960
database_cross_reference: PMID:29674431

parapharyngeal cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: parapharyngeal region
definition: cell which is part of the parapharyngeal region
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003117

prepharyngeal cell
type: Class
subclass of: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: prepharyngeal region
definition: cell which is part of the prepharyngeal region
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003118

G1 phase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G1 phase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic G1 phase
definition: neoblast undergoing mitotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003200

S phase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic S phase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic S phase
definition: neoblast undergoing mitotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003201

G2 phase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G2 phase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic G2 phase
definition: neoblast undergoing mitotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003202

prophase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic prophase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic prophase
definition: neoblast undergoing mitotic prophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003203

Axiom
annotated source: prophase neoblast
annotated property: foaf depicted by
comment: 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.

metaphase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic metaphase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic metaphase
definition: neoblast undergoing mitotic metaphase
has_exact_synonym: M phase neoblast
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003204

Axiom
annotated source: metaphase neoblast
annotated property: foaf depicted by
comment: 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.

anaphase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic anaphase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic anaphase
definition: neoblast undergoing mitotic anaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003205

Axiom
annotated source: anaphase neoblast
annotated property: foaf depicted by
comment: 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.

telophase neoblast
type: Class
equivalent class: Class
  intersection of: neoblast
  intersection of: Restriction
    on property: contains process
    some values from: mitotic telophase
subclass of: neoblast
subclass of: Restriction
  on property: contains process
  some values from: mitotic telophase
definition: neoblast undergoing mitotic telophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003206

Axiom
annotated source: telophase neoblast
annotated property: foaf depicted by
comment: 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.

G1 phase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G1 phase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic G1 phase
definition: spermatogonial stem cell undergoing mitotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003207

S phase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic S phase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic S phase
definition: spermatogonial stem cell undergoing mitotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003208

G2 phase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G2 phase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic G2 phase
definition: spermatogonial stem cell undergoing mitotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003209

prophase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic prophase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic prophase
definition: spermatogonial stem cell undergoing mitotic prophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003210

metaphase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic metaphase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic metaphase
definition: spermatogonial stem cell undergoing mitotic metaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003211

anaphase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic anaphase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic anaphase
definition: spermatogonial stem cell undergoing mitotic anaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003212

telophase spermatogonial stem cell
type: Class
equivalent class: Class
  intersection of: spermatogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic telophase
subclass of: spermatogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic telophase
definition: spermatogonial stem cell undergoing mitotic telophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003213

G1 phase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G1 phase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic G1 phase
definition: oogonial stem cell undergoing mitotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003214

S phase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic S phase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic S phase
definition: oogonial stem cell undergoing mitotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003215

G2 phase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G2 phase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic G2 phase
definition: oogonial stem cell undergoing mitotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003216

prophase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic prophase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic prophase
definition: oogonial stem cell undergoing mitotic prophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003217

metaphase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic metaphase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic metaphase
definition: oogonial stem cell undergoing mitotic metaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003218

anaphase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic anaphase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic anaphase
definition: oogonial stem cell undergoing mitotic anaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003219

telophase oogonial stem cell
type: Class
equivalent class: Class
  intersection of: oogonial stem cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic telophase
subclass of: oogonial stem cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic telophase
definition: oogonial stem cell undergoing mitotic telophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003220

G1 phase spermatogonium
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G1 phase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic G1 phase
definition: spermatogonium undergoing mitotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003221

S phase spermatogonium
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic S phase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic S phase
definition: spermatogonium undergoing mitotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003222

G2 phase spermatogonium
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G2 phase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic G2 phase
definition: spermatogonium undergoing mitotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003223

prophase spermatogonium
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic prophase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic prophase
definition: spermatogonium undergoing mitotic prophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003224

metaphase spermatogonia
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic metaphase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic metaphase
definition: spermatogonium undergoing mitotic metaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003225

anaphase spermatogonia
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic anaphase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic anaphase
definition: spermatogonium undergoing mitotic anaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003226

telophase spermatogonium
type: Class
equivalent class: Class
  intersection of: spermatogonium
  intersection of: Restriction
    on property: contains process
    some values from: mitotic telophase
subclass of: spermatogonium
subclass of: Restriction
  on property: contains process
  some values from: mitotic telophase
definition: spermatogonium undergoing mitotic telophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003227

G1 phase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G1 phase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic G1 phase
definition: oogonial cell undergoing mitotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003228

S phase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic S phase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic S phase
definition: oogonial cell undergoing mitotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003229

G2 phase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G2 phase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic G2 phase
definition: oogonial cell undergoing mitotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003230

prophase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic prophase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic prophase
definition: oogonial cell undergoing mitotic prophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003231

metaphase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic metaphase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic metaphase
definition: oogonial cell undergoing mitotic metaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003232

anaphase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic anaphase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic anaphase
definition: oogonial cell undergoing mitotic anaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003233

telophase oogonial cell
type: Class
equivalent class: Class
  intersection of: oogonial cell
  intersection of: Restriction
    on property: contains process
    some values from: mitotic telophase
subclass of: oogonial cell
subclass of: Restriction
  on property: contains process
  some values from: mitotic telophase
definition: oogonial cell undergoing mitotic telophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003234

G1 phase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G1 phase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic G1 phase
definition: germ cell cyst undergoing mitotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003235

S phase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic S phase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic S phase
definition: germ cell cyst undergoing mitotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003236

G2 phase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic G2 phase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic G2 phase
definition: germ cell cyst undergoing mitotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003237

prophase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic prophase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic prophase
definition: germ cell cyst undergoing mitotic prophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003238

metaphase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic metaphase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic metaphase
definition: germ cell cyst undergoing mitotic metaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003239

anaphase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic anaphase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic anaphase
definition: germ cell cyst undergoing mitotic anaphase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003240

telophase germ cell cyst
type: Class
equivalent class: Class
  intersection of: germ cell cyst
  intersection of: Restriction
    on property: contains process
    some values from: mitotic telophase
subclass of: germ cell cyst
subclass of: Restriction
  on property: contains process
  some values from: mitotic telophase
definition: germ cell cyst undergoing mitotic telophase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003241

meiotic S phase spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic S phase
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic S phase
definition: spermatocyte undergoing meiotic S phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003242

meiotic G1 phase spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic G1 phase
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic G1 phase
definition: spermatocyte undergoing meiotic G1 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003243

meiotic G2 phase spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic G2 phase
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic G2 phase
definition: spermatocyte undergoing meiotic G2 phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003244

meiotic prophase I spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic prophase I
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic prophase I
definition: spermatocyte undergoing meiotic prophase I
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003245

leptotene stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: leptotene
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: leptotene
definition: spermatocyte undergoing leptotene
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003246

zygotene stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: zygotene
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: zygotene
definition: spermatocyte undergoing zygotene
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003247

Axiom
annotated source: zygotene stage spermatocyte
annotated property: definition
annotated target: spermatocyte undergoing zygotene
database_cross_reference: https://doi.org/10.1101/279364

pachytene stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: pachytene
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: pachytene
definition: spermatocyte undergoing pachytene
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003248

Axiom
annotated source: pachytene stage spermatocyte
annotated property: definition
annotated target: spermatocyte undergoing pachytene
database_cross_reference: https://doi.org/10.1101/279364

diplotene stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: diplotene
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: diplotene
definition: spermatocyte undergoing diplotene
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003249

diakinesis stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: diakinesis
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: diakinesis
definition: spermatocyte undergoing diakinesis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003250

meiotic metaphase 1 stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic metaphase I
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic metaphase I
definition: spermatocyte undergoing meiotic metaphase I
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003251

meiotic anaphase I stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic anaphase I
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic anaphase I
definition: spermatocyte undergoing meiotic anaphase I
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003252

meiotic telophase I spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic telophase I
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic telophase I
definition: spermatocyte undergoing meiotic telophase I
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003253

meiosis II stage spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiosis II cell cycle phase
subclass of: spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiosis II cell cycle phase
definition: spermatocyte undergoing meiosis II cell cycle phase
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003254

meiotic prophase II spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic prophase II
subclass of: meiosis II stage spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic prophase II
definition: spermatocyte undergoing meiotic prophase II
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003255

meiotic metaphase 2 spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic metaphase II
subclass of: meiosis II stage spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic metaphase II
definition: spermatocyte undergoing meiotic metaphase II
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003256

meiotic anaphase II spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic anaphase II
subclass of: meiosis II stage spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic anaphase II
definition: spermatocyte undergoing meiotic anaphase II
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003257

meiotic telophase II spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: contains process
    some values from: meiotic telophase II
subclass of: meiosis II stage spermatocyte
subclass of: Restriction
  on property: contains process
  some values from: meiotic telophase II
definition: spermatocyte undergoing meiotic telophase II
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003258

cephalic ganglia primordium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: cephalic ganglia
subclass of: anatomical entity
subclass of: primordium
subclass of: Restriction
  on property: develops into
  some values from: cephalic ganglia
definition: This primordium develops into cephalic ganglia
database_cross_reference: PMID:16033796
database_cross_reference: PMID:17553481
database_cross_reference: PMID:17905225
database_cross_reference: PMID:19174194
database_cross_reference: PMID:21806978
database_cross_reference: PMID:22339734
database_cross_reference: PMID:23318635
database_cross_reference: PMID:25772472
database_cross_reference: PMID:26525673
has_exact_synonym: brain primordia
has_exact_synonym: brain primordium
has_exact_synonym: brain primoridia
has_exact_synonym: brain rudiment
has_exact_synonym: cephalic ganglia primordia
has_exact_synonym: cephalic ganglia primordium
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003300

eye primordium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: eye
subclass of: anatomical entity
subclass of: primordium
subclass of: Restriction
  on property: develops into
  some values from: eye
definition: This primordium develops into eye
database_cross_reference: PMID:22884275
has_exact_synonym: eye aggregate
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003301

pharynx primordium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: pharynx
subclass of: anatomical entity
subclass of: primordium
subclass of: Restriction
  on property: develops into
  some values from: pharynx
definition: This primordium develops into pharynx
database_cross_reference: PMID:18202849
database_cross_reference: PMID:21282632
database_cross_reference: PMID:25254346
database_cross_reference: PMID:26556349
database_cross_reference: PMID:27074666
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003302

pigment cup primordium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: optic cup
subclass of: anatomical entity
subclass of: primordium
subclass of: Restriction
  on property: develops into
  some values from: optic cup
definition: This primordium develops into optic cup
database_cross_reference: PMID:21852957
has_exact_synonym: optic cup primordium
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003303

testis primordium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: testis
subclass of: gonad primoridium
subclass of: Restriction
  on property: develops into
  some values from: testis
definition: This primordium develops into testis
database_cross_reference: PMID:23652002
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003304

gonad primoridium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: gonad
subclass of: anatomical entity
subclass of: primordium
subclass of: Restriction
  on property: develops into
  some values from: gonad
definition: This primordium develops into gonad
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003305

ovary primordium
type: Class
equivalent class: Class
  intersection of: primordium
  intersection of: Restriction
    on property: develops into
    some values from: ovary
subclass of: gonad primoridium
subclass of: Restriction
  on property: develops into
  some values from: ovary
definition: This primordium develops into ovary
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003306

protonephridial lumen
type: Class
equivalent class: Class
  intersection of: lumen
  intersection of: Restriction
    on property: part of
    some values from: protonephridia
subclass of: independent continuant
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: protonephridia
definition: lumen which is part of the protonephridia
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003400

Axiom
annotated source: protonephridial lumen
annotated property: definition
annotated target: lumen which is part of the protonephridia
database_cross_reference: PMID:26057828

testis lumen
type: Class
equivalent class: Class
  intersection of: lumen
  intersection of: Restriction
    on property: part of
    some values from: testis
subclass of: independent continuant
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: testis
definition: lumen which is part of the testis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003401

Axiom
annotated source: testis lumen
annotated property: definition
annotated target: lumen which is part of the testis
database_cross_reference: PMID:17390146

ovary lumen
type: Class
equivalent class: Class
  intersection of: lumen
  intersection of: Restriction
    on property: part of
    some values from: ovary
subclass of: independent continuant
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: ovary
definition: lumen which is part of the ovary
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003402

Axiom
annotated source: ovary lumen
annotated property: definition
annotated target: lumen which is part of the ovary
database_cross_reference: PMID:19247960

flame cell lumen
type: Class
equivalent class: Class
  intersection of: lumen
  intersection of: Restriction
    on property: part of
    some values from: flame cell
subclass of: protonephridial lumen
subclass of: Restriction
  on property: part of
  some values from: flame cell
definition: lumen which is part of the flame cell
has_exact_synonym: flame cell barrel lumen
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003403

Axiom
annotated source: flame cell lumen
annotated property: definition
annotated target: lumen which is part of the flame cell
database_cross_reference: PMID:21828097

cephalic ganglia progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: cephalic ganglia
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: cephalic ganglia
definition: A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system.
has_exact_synonym: brain progenitor
has_exact_synonym: brain progentitor cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cephalic ganglia progenitor cell
annotated property: definition
annotated target: A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system.
database_cross_reference: PMID:26525673

dorsal epidermis progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: dorsal region of the epidermis
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: dorsal region of the epidermis
definition: A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis.
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal epidermis progenitor cell
annotated property: definition
annotated target: A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis.
database_cross_reference: PMID:28292427

optic cup progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: optic cup
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: optic cup
definition: A progenitor cell that gives rise to optic cup cells of the eye.
has_exact_synonym: optic cup trail cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: optic cup progenitor cell
annotated property: definition
annotated target: A progenitor cell that gives rise to optic cup cells of the eye.
database_cross_reference: PMID:21852957

ventral epidermis progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: ventral epidermis
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: ventral epidermis
definition: A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003503

Axiom
annotated source: ventral epidermis progenitor cell
annotated property: definition
annotated target: A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis.
database_cross_reference: PMID:28292427

testis somatic gonadal cell progenitor cell
type: Class
equivalent class: Class
  intersection of: progenitor cell
  intersection of: Restriction
    on property: develops into
    some values from: testis somatic gonadal cell
subclass of: anatomical entity
subclass of: progenitor cell
subclass of: Restriction
  on property: develops into
  some values from: testis somatic gonadal cell
definition: This progenitor cell develops into testis somatic gonadal cell
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003504

Axiom
annotated source: testis somatic gonadal cell progenitor cell
annotated property: definition
annotated target: This progenitor cell develops into testis somatic gonadal cell
database_cross_reference: PMID: 23652002

head fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: head region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: head region
definition: A fragment derived from a prepharyngeal amputation encompassing the head.
has_exact_synonym: head piece
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003600

Axiom
annotated source: head fragment
annotated property: foaf depicted by
comment: A fragment derived from a prepharyngeal amputation encompassing the head.

trunk fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: parapharyngeal region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: parapharyngeal region
definition: A fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
has_exact_synonym: trunk piece
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003601

Axiom
annotated source: trunk fragment
annotated property: foaf depicted by
comment: Illustration of a trunk fragment (in green).

tail fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: tail region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: tail region
definition: A fragment derived from a postpharyngeal amputation encompassing the tail.
has_exact_synonym: tail piece
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003602

Axiom
annotated source: tail fragment
annotated property: foaf depicted by
comment: A fragment derived from a postpharyngeal amputation encompassing the tail.

prepharyngeal fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: prepharyngeal region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: prepharyngeal region
definition: A fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
has_exact_synonym: neck fragment
has_exact_synonym: neck piece
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003603

Axiom
annotated source: prepharyngeal fragment
annotated property: foaf depicted by
comment: Illustration of a prepharyngeal fragment (in green).

postpharyngeal fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: postpharyngeal region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: postpharyngeal region
definition: A fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
has_exact_synonym: post-pharyngeal fragment
has_exact_synonym: post-pharyngeal piece
has_exact_synonym: postpharyngeal piece
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003604

Axiom
annotated source: postpharyngeal fragment
annotated property: foaf depicted by
comment: Illustration of a postpharyngeal fragment (in green).

anterior fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: anterior region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: anterior region
definition: A fragment encompassing all or part of the anterior region of the animal.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003605

Axiom
annotated source: anterior fragment
annotated property: foaf depicted by
comment: A fragment encompassing all or part of the anterior region of the animal.

posterior fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: posterior region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: posterior region
definition: A fragment encompassing all or part of the posterior region of the animal.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003606

Axiom
annotated source: posterior fragment
annotated property: foaf depicted by
comment: Illustration of an example of a posterior fragment (in green).

lateral fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: lateral side
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: lateral side
definition: 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]
has_exact_synonym: edge fragment
has_exact_synonym: longitudinal fragment
has_exact_synonym: sagittal fragment
has_exact_synonym: side fragment
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003607

Axiom
annotated source: lateral fragment
annotated property: foaf depicted by
comment: 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]

longitudinal fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: longitudinal region
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: longitudinal region
definition: a fragment derived from an amputation parallel to the midline.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003608

Axiom
annotated source: longitudinal fragment
annotated property: foaf depicted by
comment: a fragment derived from an amputation parallel to the midline.

plug fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: plug shaped
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: plug shaped
definition: 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.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003609

Axiom
annotated source: plug fragment
annotated property: foaf depicted by
comment: Illustration of an example plug fragment in green.

wedge fragment
type: Class
equivalent class: Class
  intersection of: fragment
  intersection of: Restriction
    on property: derives from
    some values from: cuneate
subclass of: fragment
subclass of: Restriction
  on property: derives from
  some values from: cuneate
definition: A piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003610

Axiom
annotated source: wedge fragment
annotated property: foaf depicted by
comment: Illustration of an example wedge fragment in green.

dorsal region of head fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: head fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: head fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment derived from a prepharyngeal amputation encompassing the head.
has_exact_synonym: dorsal region of head fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of head fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a head fragment (green).

ventral region of head fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: head fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: head fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment derived from a prepharyngeal amputation encompassing the head.
has_exact_synonym: ventral region of head fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of head fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a head fragment (green).

anterior region of head fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: head fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: head fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment derived from a prepharyngeal amputation encompassing the head.
has_exact_synonym: anterior region of head fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of head fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a head fragment (green).

posterior region of head fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: head fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: head fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment derived from a prepharyngeal amputation encompassing the head.
has_exact_synonym: posterior region of head fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of head fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a head fragment (green).

dorsal region of trunk fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: trunk fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: trunk fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
has_exact_synonym: dorsal region of trunk fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of trunk fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a trunk fragment (green).

ventral region of trunk fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: trunk fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: trunk fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
has_exact_synonym: ventral region of trunk fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of trunk fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a trunk fragment (green).

anterior region of trunk fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: trunk fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: trunk fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
has_exact_synonym: anterior region of trunk fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of trunk fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a trunk fragment (green).

posterior region of trunk fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: trunk fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: trunk fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
has_exact_synonym: posterior region of trunk fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of trunk fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a trunk fragment (green).

dorsal region of tail fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: tail fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: tail fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment derived from a postpharyngeal amputation encompassing the tail.
has_exact_synonym: dorsal region of tail fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of tail fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a tail fragment (green).

ventral region of tail fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: tail fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: tail fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment derived from a postpharyngeal amputation encompassing the tail.
has_exact_synonym: ventral region of tail fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of tail fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a tail fragment (green).

anterior region of tail fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: tail fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: tail fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment derived from a postpharyngeal amputation encompassing the tail.
has_exact_synonym: anterior region of tail fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of tail fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a tail fragment (green).

posterior region of tail fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: tail fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: tail fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment derived from a postpharyngeal amputation encompassing the tail.
has_exact_synonym: posterior region of tail fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of tail fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a tail fragment (green).

dorsal region of prepharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: prepharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
has_exact_synonym: dorsal region of prepharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of prepharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a prepharyngeal fragment (green).

ventral region of prepharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: prepharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
has_exact_synonym: ventral region of prepharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of prepharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a prepharyngeal fragment (green).

anterior region of prepharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: prepharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
has_exact_synonym: anterior region of prepharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of prepharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a prepharyngeal fragment (green).

posterior region of prepharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: prepharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
has_exact_synonym: posterior region of prepharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of prepharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a prepharyngeal fragment (green).

dorsal region of postpharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: postpharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: postpharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
has_exact_synonym: dorsal region of postpharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of postpharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a postpharyngeal fragment (green).

ventral region of postpharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: postpharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: postpharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
has_exact_synonym: ventral region of postpharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of postpharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a postpharyngeal fragment (green).

anterior region of postpharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: postpharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: postpharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
has_exact_synonym: anterior region of postpharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of postpharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a postpharyngeal fragment (green).

posterior region of postpharyngeal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: postpharyngeal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: postpharyngeal fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
has_exact_synonym: posterior region of postpharyngeal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of postpharyngeal fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a postpharyngeal fragment (green).

dorsal region of anterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: anterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: anterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment encompassing all or part of the anterior region of the animal.
has_exact_synonym: dorsal region of anterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of anterior fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of an anterior fragment (green).

ventral region of anterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: anterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: anterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment encompassing all or part of the anterior region of the animal.
has_exact_synonym: ventral region of anterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of anterior fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of an anterior fragment (green).

anterior region of anterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: anterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: anterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment encompassing all or part of the anterior region of the animal.
has_exact_synonym: anterior region of anterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of anterior fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of an anterior fragment (green).

posterior region of anterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: anterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: anterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment encompassing all or part of the anterior region of the animal.
has_exact_synonym: posterior region of anterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of anterior fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of an anterior fragment (green).

dorsal region of posterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: posterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: posterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment encompassing all or part of the posterior region of the animal.
has_exact_synonym: dorsal region of posterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of posterior fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a posterior fragment (green).

ventral region of posterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: posterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: posterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment encompassing all or part of the posterior region of the animal.
has_exact_synonym: ventral region of posterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of posterior fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a posterior fragment (green).

anterior region of posterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: posterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: posterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment encompassing all or part of the posterior region of the animal.
has_exact_synonym: anterior region of posterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of posterior fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a posterior fragment (green).

posterior region of posterior fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: posterior fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: posterior fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment encompassing all or part of the posterior region of the animal.
has_exact_synonym: posterior region of posterior fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of posterior fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a posterior fragment (green).

dorsal region of lateral fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: lateral fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: lateral fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: 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.
has_exact_synonym: dorsal region of lateral fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of lateral fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a lateral fragment (green).

ventral region of lateral fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: lateral fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: lateral fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: 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.
has_exact_synonym: ventral region of lateral fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of lateral fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a lateral fragment (green).

anterior region of lateral fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: lateral fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: lateral fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: 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.
has_exact_synonym: anterior region of lateral fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of lateral fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a lateral fragment (green).

posterior region of lateral fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: lateral fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: lateral fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: 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.
has_exact_synonym: posterior region of lateral fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of lateral fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a lateral fragment (green).

dorsal region of longitudinal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: longitudinal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: longitudinal fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a fragment derived from an amputation parallel to the midline.
has_exact_synonym: dorsal region of longitudinal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of longitudinal fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a longitudinal fragment (green).

ventral region of longitudinal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: longitudinal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: longitudinal fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a fragment derived from an amputation parallel to the midline.
has_exact_synonym: ventral region of longitudinal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of longitudinal fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a longitudinal fragment (green).

anterior region of longitudinal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: longitudinal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: longitudinal fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a fragment derived from an amputation parallel to the midline.
has_exact_synonym: anterior region of longitudinal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of longitudinal fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a longitudinal fragment (green).

posterior region of longitudinal fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: longitudinal fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: longitudinal fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a fragment derived from an amputation parallel to the midline.
has_exact_synonym: posterior region of longitudinal fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of longitudinal fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a longitudinal fragment (green).

dorsal region of plug fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: plug fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: plug fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: 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.
has_exact_synonym: dorsal region of plug fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of plug fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a plug fragment (green).

ventral region of plug fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: plug fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: plug fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: 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.
has_exact_synonym: ventral region of plug fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of plug fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a plug fragment (green).

anterior region of plug fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: plug fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: plug fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: 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.
has_exact_synonym: anterior region of plug fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of plug fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a plug fragment (green).

posterior region of plug fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: plug fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: plug fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: 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.
has_exact_synonym: posterior region of plug fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of plug fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a plug fragment (green).

dorsal region of wedge fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: wedge fragment
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: wedge fragment
subclass of: Restriction
  on property: overlaps
  some values from: dorsal region
definition: The dorsal region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
has_exact_synonym: dorsal region of wedge fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: dorsal region of wedge fragment
annotated property: foaf depiction
comment: Illustration of the dorsal region of a plug fragment (green).

ventral region of wedge fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: wedge fragment
  intersection of: Restriction
    on property: overlaps
    some values from: ventral region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: wedge fragment
subclass of: Restriction
  on property: overlaps
  some values from: ventral region
definition: The ventral region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
has_exact_synonym: ventral region of wedge fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ventral region of wedge fragment
annotated property: foaf depiction
comment: Illustration of the ventral region of a plug fragment (green).

anterior region of wedge fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: wedge fragment
  intersection of: Restriction
    on property: overlaps
    some values from: anterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: wedge fragment
subclass of: Restriction
  on property: overlaps
  some values from: anterior region
definition: The anterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
has_exact_synonym: anterior region of wedge fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior region of wedge fragment
annotated property: foaf depiction
comment: Illustration of the anterior region of a wedge fragment (green).

posterior region of wedge fragment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: wedge fragment
  intersection of: Restriction
    on property: overlaps
    some values from: posterior region
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: wedge fragment
subclass of: Restriction
  on property: overlaps
  some values from: posterior region
definition: The posterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
has_exact_synonym: posterior region of wedge fragment
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior region of wedge fragment
annotated property: foaf depiction
comment: Illustration of the posterior region of a wedge fragment (green).

anterior photoreceptor neuron
type: Class
equivalent class: Class
  intersection of: photoreceptor neuron
  intersection of: Restriction
    on property: contained in
    some values from: anterior region of the eye
subclass of: photoreceptor neuron
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the eye
definition: photoreceptor neuron is contained in the anterior region of the eye
has_exact_synonym: photoreceptor neuron contained in anterior region of the eye
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior photoreceptor neuron
annotated property: definition
annotated target: photoreceptor neuron is contained in the anterior region of the eye
database_cross_reference: PMID: 20967238

posterior photoreceptor neuron
type: Class
equivalent class: Class
  intersection of: photoreceptor neuron
  intersection of: Restriction
    on property: contained in
    some values from: posterior region of the eye
subclass of: photoreceptor neuron
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the eye
definition: photoreceptor neuron is contained in the posterior region of the eye
has_exact_synonym: photoreceptor neuron contained in posterior region of the eye
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior photoreceptor neuron
annotated property: definition
annotated target: photoreceptor neuron is contained in the posterior region of the eye
database_cross_reference: PMID: 20967238

lateral muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: contained in
    some values from: lateral region
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: contained in
  some values from: lateral region
definition: muscle cell is contained in the lateral region
has_exact_synonym: muscle cell contained in lateral region
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: lateral muscle cell
annotated property: definition
annotated target: muscle cell is contained in the lateral region
database_cross_reference: PMID: 29674431

anterior muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: contained in
    some values from: anterior region
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: contained in
  some values from: anterior region
definition: muscle cell is contained in the anterior region
has_exact_synonym: muscle cell contained in anterior region
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior muscle cell
annotated property: definition
annotated target: muscle cell is contained in the anterior region
database_cross_reference: PMID: 29674432

posterior muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: contained in
    some values from: posterior region
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: contained in
  some values from: posterior region
definition: muscle cell is contained in the posterior region
has_exact_synonym: muscle cell contained in posterior region
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior muscle cell
annotated property: definition
annotated target: muscle cell is contained in the posterior region
database_cross_reference: PMID: 29674433

head blastema
type: Class
equivalent class: Class
  intersection of: blastema
  intersection of: Restriction
    on property: develops into
    some values from: head region
subclass of: anatomical entity
subclass of: blastema
subclass of: Restriction
  on property: develops into
  some values from: head region
definition: blastema which develops into head region
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003900

tail blastema
type: Class
equivalent class: Class
  intersection of: blastema
  intersection of: Restriction
    on property: develops into
    some values from: tail region
subclass of: anatomical entity
subclass of: blastema
subclass of: Restriction
  on property: develops into
  some values from: tail region
definition: blastema which develops into tail region
has_obo_namespace: Planarian_Anatomy
id: PLANA:0003901

regenerating head fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: head fragment
subclass of: regenerating fragment
subclass of: head fragment
definition: a head fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating trunk fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: trunk fragment
subclass of: regenerating fragment
subclass of: trunk fragment
definition: a trunk fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating tail fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: tail fragment
subclass of: regenerating fragment
subclass of: tail fragment
definition: a tail fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating prepharyngeal fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: prepharyngeal fragment
subclass of: regenerating fragment
subclass of: prepharyngeal fragment
definition: a prepharyngeal fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating postpharyngeal fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: postpharyngeal fragment
subclass of: regenerating fragment
subclass of: postpharyngeal fragment
definition: a postpharyngeal fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating anterior fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: anterior fragment
subclass of: regenerating fragment
subclass of: anterior fragment
definition: a anterior fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating posterior fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: posterior fragment
subclass of: regenerating fragment
subclass of: posterior fragment
definition: a posterior fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating lateral fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: lateral fragment
subclass of: regenerating fragment
subclass of: lateral fragment
definition: a lateral fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating longitudinal fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: longitudinal fragment
subclass of: regenerating fragment
subclass of: longitudinal fragment
definition: a longitudinal fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating plug fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: plug fragment
subclass of: regenerating fragment
subclass of: plug fragment
definition: a plug fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

regenerating wedge fragment
type: Class
equivalent class: Class
  intersection of: regenerating fragment
  intersection of: wedge fragment
subclass of: regenerating fragment
subclass of: wedge fragment
definition: a wedge fragment that is regenerating
has_obo_namespace: Planarian_Anatomy

adult hermaphrodite
type: Class
subclass of: life cycle stage
definition: A fully formed, sexually mature organism that reproduces through cross-fertilization.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:11972158
database_cross_reference: PMID:19022767
has_exact_synonym: sexual adult
has_exact_synonym: sexually mature adult
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: adult hermaphrodite
annotated property: definition
annotated target: A fully formed, sexually mature organism that reproduces through cross-fertilization.
database_cross_reference: PMID:11972158
database_cross_reference: PMID:19022767

Axiom
annotated source: adult hermaphrodite
annotated property: foaf depicted by
comment: Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm.

asexual adult
type: Class
subclass of: life cycle stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:11972158
database_cross_reference: PMID:17376870
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: asexual adult
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:11972158
database_cross_reference: PMID:17376870

Axiom
annotated source: asexual adult
annotated property: foaf depicted by
comment: Depicted by field shows an asexual adult with a scale bar of 500um

testis somatic gonadal cell
type: Class
subclass of: material entity
subclass of: somatic gonadal cell
subclass of: Restriction
  on property: part of
  some values from: testis
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27163480
has_exact_synonym: somatic gonadal cell of the testis
has_exact_synonym: somatic niche cell of the testis
has_exact_synonym: somatic testis cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: testis somatic gonadal cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:23652002
database_cross_reference: PMID:27163480

ovarian somatic gonadal cell
type: Class
subclass of: material entity
subclass of: terminally differentiated cell
subclass of: Restriction
  on property: part of
  some values from: ovary
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27163480
has_exact_synonym: somatic follicular cell of the ovary
has_exact_synonym: somatic ovarian cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ovarian somatic gonadal cell
annotated property: definition
annotated target: ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia.
database_cross_reference: PMID:27163480

oral-aboral axis of the embryo
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: embryo
  intersection of: Restriction
    on property: overlaps
    some values from: oral-aboral axis
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: embryo
subclass of: Restriction
  on property: overlaps
  some values from: oral-aboral axis
definition: 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.
has_exact_synonym: oral-aboral axis of embryo
has_obo_namespace: Planarian_Anatomy
id: PLANA:0004511

Axiom
annotated source: oral-aboral axis of the embryo
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

Axiom
annotated source: oral-aboral axis of the embryo
annotated property: foaf depiction
comment: Illustration noting the oral-aboral axis in cyan double headed arrow. It starts at the embryonic pharynx and extends to opposite pole.

primitive ectoderm surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: primitive ectoderm
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
definition: The apical surface of the single layered primitive ectoderm that is in contact with the environment.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:20423827
database_cross_reference: OCLC:464776945
database_cross_reference: OCLC:82522822
database_cross_reference: PMID:28072387
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primitive ectoderm surface
annotated property: definition
annotated target: The apical surface of the single layered primitive ectoderm that is in contact with the environment.
database_cross_reference: OCLC:20423827
database_cross_reference: OCLC:464776945
database_cross_reference: OCLC:82522822
database_cross_reference: PMID:28072387
database_cross_reference: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md

primtive gut cell surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: primitive gut cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 5
definition: The surface of the primitive gut cells in contact with the embryonic wall.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: primtive gut cell surface
annotated property: definition
annotated target: The surface of the primitive gut cells in contact with the embryonic wall.
database_cross_reference: PMID:28072387

embryonic gut cell surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: embryonic gut cell
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 4
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic gut cell surface
annotated property: definition
annotated target: The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
database_cross_reference: PMID:28072387

embryonic pharynx lumen epithelial surface
type: Class
subclass of: anatomical surface
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: The epithelial cell surface lining the embryonic pharynx lumen.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20100474
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx lumen epithelial surface
annotated property: definition
annotated target: The epithelial cell surface lining the embryonic pharynx lumen.
database_cross_reference: PMID:28072387

blastomere
type: Class
subclass of: material entity
subclass of: embryonic cell
subclass of: Restriction
  on property: part of
  some values from: ectolecithal embryo
subclass of: Restriction
  on property: contained in
  some values from: aboral hemisphere
subclass of: Restriction
  on property: contained in
  some values from: embryonic wall
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: zygote
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 1
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 1
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 5
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000353
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: blastomere
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:28072387

extraembryonic cell
type: Class
subclass of: terminally differentiated cell
definition: Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000349
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: extraembryonic cell
annotated property: definition
annotated target: Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
database_cross_reference: PMID:28072387

embryonic pharynx neuron
type: Class
subclass of: material entity
subclass of: neuron
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx neuron
annotated property: definition
annotated target: A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
database_cross_reference: PMID:28072387

embryonic pharynx radial muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: Differentiated radial muscle cell present in the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16932928
has_exact_synonym: embryonic pharynx radial muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx radial muscle cell
annotated property: definition
annotated target: Differentiated radial muscle cell present in the embryonic pharynx.
database_cross_reference: PMID:16932928

embryonic pharynx epithelial cell
type: Class
subclass of: material entity
subclass of: epithelial cell
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: foxA1+ epithelial cell contained in the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:20100474
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx epithelial cell
annotated property: definition
annotated target: foxA1+ epithelial cell contained in the embryonic pharynx.
database_cross_reference: PMID:28072387

embryonic pharynx circular muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: contained in
  some values from: oral hemisphere
subclass of: Restriction
  on property: develops from
  some values from: blastomere
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 2
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 2
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
definition: Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:16932928
has_exact_synonym: embryonic pharynx circular muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx circular muscle cell
annotated property: definition
annotated target: Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx.
database_cross_reference: PMID:16932928

copulatory region
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: posterior to
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:22074376
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: copulatory region
annotated property: definition
annotated target: Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus.
database_cross_reference: PMID:22074376

Axiom
annotated source: copulatory region
annotated property: foaf depicted by
comment: Depicted by field contains diagram representation of body region.

pharynx epithelium
type: Class
subclass of: material entity
subclass of: epithelium
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Epithelia associated with the pharynx organ.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0003351
has_exact_synonym: pharnyx epidermis
has_exact_synonym: pharyngeal epidermis
has_exact_synonym: pharyngeal epithelium
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx epithelium
annotated property: foaf depicted by
comment: 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.

integumental system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: sexual organism
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0002416
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: integumental system
annotated property: definition
annotated target: 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.
database_cross_reference: UBERON:0002416

oviduct lumen
type: Class
subclass of: immaterial entity
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: oviduct
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: luminal space of
  some values from: oviduct
definition: Anatomical space enclosed by the oviduct epithelium.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:22074376
database_cross_reference: TADS:0000435
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oviduct lumen
annotated property: definition
annotated target: Anatomical space enclosed by the oviduct epithelium.
database_cross_reference: PMID:22074376

sperm duct lumen
type: Class
subclass of: immaterial entity
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: sperm duct
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: luminal space of
  some values from: sperm duct
definition: Anatomical space enclosed by the sperm duct epithelium.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sperm duct lumen
annotated property: definition
annotated target: Anatomical space enclosed by the sperm duct epithelium.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376

oviduct epithelium
type: Class
subclass of: material entity
subclass of: ciliated epithelium
subclass of: Restriction
  on property: part of
  some values from: oviduct
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Ciliated epithelium lining the oviduct.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:2000064
database_cross_reference: PMID:22074376
database_cross_reference: UBERON:0004804
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: oviduct epithelium
annotated property: definition
annotated target: Ciliated epithelium lining the oviduct.
database_cross_reference: PMID:22074376

sperm duct epithelium
type: Class
subclass of: material entity
subclass of: ciliated epithelium
subclass of: Restriction
  on property: part of
  some values from: sperm duct
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Ciliated epithelium lining the sperm duct.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: sperm duct epithelium
annotated property: definition
annotated target: Ciliated epithelium lining the sperm duct.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:22074376

tuba lumen
type: Class
subclass of: immaterial entity
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: tuba
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: luminal space of
  some values from: tuba
definition: Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: tuba lumen
annotated property: definition
annotated target: Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct.
database_cross_reference: PMID:19022767
database_cross_reference: PMID:20844018
database_cross_reference: PMID:22074376
database_cross_reference: PMID:27149082

obsolete coronal plane
type: Class
comment: let odk import from BSPO if needed
deprecated: true

sagittal plane of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: sagittal plane
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: sagittal plane
definition: 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.
has_exact_synonym: sagittal plane of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0007503

Axiom
annotated source: sagittal plane of the whole animal
annotated property: foaf depiction
comment: Illustration of a sagittal plane of the whole animal (in green).

obsolete dorsal compartment
type: Class
term replaced by: dorsal region of the whole animal
comment: replaced by dorsal region PLANA:0000141
deprecated: true

obsolete ventral compartment
type: Class
comment: now using patterned term ventral region PLANA:0000143
deprecated: true

obsolete anterior compartment
type: Class
term replaced by: anterior region of the whole animal
comment: now using patterned term anterior region
deprecated: true

obsolete posterior compartment
type: Class
term replaced by: posterior region of the whole animal
comment: replaced
comment: replacing duplicate PLANA term
deprecated: true

obsolete extracellular component
type: Class
term replaced by: acellular anatomical structure
comment: choosing to use UBERON:0000476, acellular anatomical structure instead
deprecated: true

plasma membrane
type: Class
subclass of: membrane
definition: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005886
database_cross_reference: PMID:20511647
database_cross_reference: PMID:27523733
has_exact_synonym: cell membrane
has_exact_synonym: cytoplasmic membrane
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: plasma membrane
annotated property: definition
annotated target: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
database_cross_reference: GO:0005886

Axiom
annotated source: plasma membrane
annotated property: foaf depicted by
comment: Image is an electron micrograph showing several cells. Arrowheads label the plasma membrane, the boundary between cells. Scale bar is 1um.

extracellular organelle
type: Class
subclass of: organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0043230
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: extracellular organelle
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0043230

mitochondrion
type: Class
subclass of: intracellular membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005739
database_cross_reference: PMID:21828097
database_cross_reference: PMID:22318224
database_cross_reference: PMID:26516985
database_cross_reference: PMID:29100657
has_exact_synonym: mitochondria
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: mitochondrion
annotated property: foaf depicted by
comment: 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.

endoplasmic reticulum
type: Class
subclass of: intracellular membrane-bounded organelle
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005783
database_cross_reference: PMID:30143032
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: endoplasmic reticulum
annotated property: foaf depicted by
comment: Image is an electron micrograph depicting endoplasmic reticulum (magenta) in multiple cells. Scale bar is 0.5um.

rough endoplasmic reticulum
type: Class
subclass of: endoplasmic reticulum
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005791
database_cross_reference: PMID:30143032
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: rough endoplasmic reticulum
annotated property: foaf depicted by
comment: 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.

smooth endoplasmic reticulum
type: Class
subclass of: endoplasmic reticulum
definition: Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005790
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: smooth endoplasmic reticulum
annotated property: foaf depicted by
comment: 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.

nuclear pore
type: Class
subclass of: nuclear part
subclass of: pore
definition: Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005643
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nuclear pore
annotated property: definition
annotated target: Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
database_cross_reference: GO:0005643

Axiom
annotated source: nuclear pore
annotated property: foaf depicted by
comment: 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.

lysosome
type: Class
subclass of: intracellular membrane-bounded organelle
definition: The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: GO:0005764
database_cross_reference: ISBN:0-71677033-4
database_cross_reference: PMID:4853064
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: lysosome
annotated property: foaf depicted by
comment: 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.

anterior-posterior axis of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: anterior-posterior axis
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: anterior-posterior axis
definition: 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.
has_exact_synonym: anterior-posterior axis
has_exact_synonym: anterior-posterior axis of whole organism
has_exact_synonym: body axis
has_exact_synonym: longitudinal axis
has_exact_synonym: main body axis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0007519

Axiom
annotated source: anterior-posterior axis of the whole animal
annotated property: foaf depiction
comment: Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um

dorsal-ventral axis of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal-ventral axis
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: dorsal-ventral axis
definition: 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.
has_exact_synonym: D/V axis
has_exact_synonym: DV axis
has_exact_synonym: dorsal-ventral axis
has_exact_synonym: dorsal-ventral axis of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0007520

Axiom
annotated source: dorsal-ventral axis of the whole animal
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18287199
database_cross_reference: PMID:18786419
database_cross_reference: PMID:19174194
database_cross_reference: PMID:21295481
database_cross_reference: PMID:21295483
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:22445864
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24523458
database_cross_reference: PMID:25017721
database_cross_reference: PMID:27063937
database_cross_reference: PMID:27523733
database_cross_reference: PMID:27612382
database_cross_reference: PMID:28137894
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28686611
database_cross_reference: PMID:29100657
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29674431
database_cross_reference: PMID:30471994

left-right axis of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: left-right axis
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: left-right axis
definition: 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.
has_exact_synonym: dextro-sinister axis
has_exact_synonym: left-right axis
has_exact_synonym: left-right axis of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0007521

Axiom
annotated source: left-right axis of the whole animal
annotated property: foaf depiction
comment: Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um

medial-lateral axis of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: medial-lateral axis
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: medial-lateral axis
definition: 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.
has_exact_synonym: medial-lateral axis
has_exact_synonym: medial-lateral axis of whole organism
has_exact_synonym: mediolateral
has_exact_synonym: mediolateral axis
has_obo_namespace: Planarian_Anatomy
id: PLANA:0007522

Axiom
annotated source: medial-lateral axis of the whole animal
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:20707997
database_cross_reference: PMID:21282632
database_cross_reference: PMID:21295483
database_cross_reference: PMID:21664348
database_cross_reference: PMID:21806978
database_cross_reference: PMID:23250205
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23903188
database_cross_reference: PMID:23954785
database_cross_reference: PMID:25017721
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27523733
database_cross_reference: PMID:28287248
database_cross_reference: PMID:29291981
database_cross_reference: PMID:29547123
database_cross_reference: PMID:30471994
database_cross_reference: PMID:30962434

Axiom
annotated source: medial-lateral axis of the whole animal
annotated property: foaf depiction
comment: Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um

proximal-distal axis of the whole animal
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: contained in
    some values from: whole organism
  intersection of: Restriction
    on property: overlaps
    some values from: proximal-distal axis
subclass of: material entity
subclass of: Restriction
  on property: contained in
  some values from: whole organism
subclass of: Restriction
  on property: overlaps
  some values from: proximal-distal axis
definition: 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.
has_exact_synonym: proximal-distal axis
has_exact_synonym: proximal-distal axis of whole organism
has_obo_namespace: Planarian_Anatomy
id: PLANA:0007523

Axiom
annotated source: proximal-distal axis of the whole animal
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:21828097

Axiom
annotated source: proximal-distal axis of the whole animal
annotated property: foaf depiction
comment: Pharynx of an asexual adult exposed by tricaine treatment. The proximodistal axis is denoted with the double headed magenta arrow.

anterior pole
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: contained in
  some values from: midline
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18063755
database_cross_reference: PMID:21566195
database_cross_reference: PMID:23297191
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23903188
database_cross_reference: PMID:23954785
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24523458
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24992682
database_cross_reference: PMID:25254346
database_cross_reference: PMID:25725068
database_cross_reference: PMID:26062938
database_cross_reference: PMID:26525673
database_cross_reference: PMID:27074666
database_cross_reference: PMID:27800171
database_cross_reference: PMID:28216315
database_cross_reference: PMID:28292427
database_cross_reference: PMID:28893948
database_cross_reference: PMID:29547123
database_cross_reference: PMID:29906446
database_cross_reference: PMID:30485821
has_exact_synonym: anterior signaling center
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior pole
annotated property: definition
annotated target: Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD.
database_cross_reference: PMID:21566195
database_cross_reference: PMID:23297191
database_cross_reference: PMID:24040508
database_cross_reference: PMID:24415944
database_cross_reference: PMID:24704339
database_cross_reference: PMID:24992682

Axiom
annotated source: anterior pole
annotated property: foaf depicted by
comment: Illustration of the anterior pole (green).

posterior pole
type: Class
subclass of: material entity
subclass of: anatomical region
subclass of: Restriction
  on property: contained in
  some values from: midline
subclass of: Restriction
  on property: contained in
  some values from: tail tip
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 7
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 8
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Distinct posterior cluster of muscle cells located at the midline which express wnt1.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:18063755
database_cross_reference: PMID:19805089
database_cross_reference: PMID:21566195
database_cross_reference: PMID:23318641
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24415944
database_cross_reference: PMID:25725068
database_cross_reference: PMID:26062938
database_cross_reference: PMID:27074666
database_cross_reference: PMID:30485821
has_exact_synonym: posterior regeneration pole
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: posterior pole
annotated property: definition
annotated target: Distinct posterior cluster of muscle cells located at the midline which express wnt1.
database_cross_reference: PMID:18063755
database_cross_reference: PMID:21680047

Axiom
annotated source: posterior pole
annotated property: foaf depicted by
comment: Illustration of the posterior pole (in green).

glial cell
type: Class
subclass of: material entity
subclass of: neuron associated cell (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: part of
  some values from: neuropil
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000125
database_cross_reference: PMID:27612382
database_cross_reference: PMID:27612384
database_cross_reference: PMID:28137894
database_cross_reference: PMID:29674431
database_cross_reference: PMID:29674432
database_cross_reference: PMID:30471994
has_exact_synonym: glia
has_exact_synonym: glia cell
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: glial cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27612384

Axiom
annotated source: glial cell
annotated property: foaf depicted by
comment: 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.

ganglion
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A biological tissue mass of nerve cell bodies.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: UBERON:0000045
has_exact_synonym: ganglia
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ganglion
annotated property: definition
annotated target: A biological tissue mass of nerve cell bodies.
database_cross_reference: UBERON:0000045

pharynx inner epithelium
type: Class
subclass of: material entity
subclass of: ciliated epithelium
subclass of: Restriction
  on property: part of
  some values from: pharynx
subclass of: Restriction
  on property: immediately superficial to
  some values from: pharynx inner circular muscle cell
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:24120894
database_cross_reference: doi:10.1002/jmor.1051550208
has_exact_synonym: epithelial pharynx lining
has_exact_synonym: epithelium lining the lumen of the pharynx
has_exact_synonym: inner epithelium
has_exact_synonym: inner pharyngeal epidermis
has_exact_synonym: inner pharyngeal epithelium
has_exact_synonym: inner pharynx epidermis
has_exact_synonym: inner pharynx epithelium
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx inner epithelium
annotated property: definition
annotated target: Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
database_cross_reference: OCLC:16809160
database_cross_reference: doi:10.1002/jmor.1051550208

Axiom
annotated source: pharynx inner epithelium
annotated property: foaf depicted by
comment: 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 circular muscle cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: pharynx musculature
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Pharynx muscle fibers running circumferentially about the pharynx.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ASIN:B000M4NK9M
has_exact_synonym: pharyngeal circular muscle cell
has_exact_synonym: pharynx circular muscle cell
has_exact_synonym: pharynx circular muscle fiber
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pharynx circular muscle cell
annotated property: definition
annotated target: Pharynx muscle fibers running circumferentially about the pharynx.
database_cross_reference: ASIN:B000M4NK9M

Axiom
annotated source: pharynx circular muscle cell
annotated property: foaf depicted by
comment: 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.

obsolete specific_to
type: Class
comment: using part of instead
deprecated: true

obsolete brain
type: Class
term replaced by: cephalic ganglia
comment: replacing duplicate PLANA term
deprecated: true

adhesion gland
type: Class
subclass of: material entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: secretory system
subclass of: Restriction
  on property: contained in
  some values from: dorsal ventral margin of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: ISBN:9780070316607
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784
has_exact_synonym: marginal adhesive gland
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: adhesion gland
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784

Axiom
annotated source: adhesion gland
annotated property: foaf depicted by
comment: 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.

anchor cell
type: Class
subclass of: material entity
subclass of: acidophilic gland cell
subclass of: Restriction
  on property: part of
  some values from: adhesion gland
subclass of: Restriction
  on property: contained in
  some values from: dorsal ventral margin of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anchor cell
annotated property: definition
annotated target: Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784

Axiom
annotated source: anchor cell
annotated property: foaf depicted by
comment: 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.

viscid gland cell
type: Class
subclass of: material entity
subclass of: acidophilic gland cell
subclass of: Restriction
  on property: part of
  some values from: adhesion gland
subclass of: Restriction
  on property: contained in
  some values from: dorsal ventral margin of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: viscid gland cell
annotated property: definition
annotated target: 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.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784

Axiom
annotated source: viscid gland cell
annotated property: foaf depicted by
comment: 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.

releasing gland cell
type: Class
subclass of: material entity
subclass of: acidophilic gland cell
subclass of: Restriction
  on property: part of
  some values from: adhesion gland
subclass of: Restriction
  on property: contained in
  some values from: dorsal ventral margin of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: releasing gland cell
annotated property: definition
annotated target: Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:20865784

Axiom
annotated source: releasing gland cell
annotated property: foaf depicted by
comment: 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.

TrpA+ central nervous system neuron
type: Class
subclass of: material entity
subclass of: central nervous system neuron
subclass of: Restriction
  on property: part of
  some values from: cephalic ganglia
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: develops from
  some values from: TrpA+ neural progenitor cell
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25254346
has_exact_synonym: TrpA+ neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: TrpA+ central nervous system neuron
annotated property: definition
annotated target: A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2.
database_cross_reference: PMID:25254346

cintillo+ sensory neuron
type: Class
subclass of: material entity
subclass of: sensory neuron
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: head region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A subset of sensory neurons located along the dorsal head margin.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:12557210
database_cross_reference: PMID:25254346
database_cross_reference: PMID:29674431
has_exact_synonym: cintillo+ neuron
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cintillo+ sensory neuron
annotated property: definition
annotated target: A subset of sensory neurons located along the dorsal head margin.
database_cross_reference: PMID:12557210
database_cross_reference: PMID:25254346
database_cross_reference: PMID:29674431

obsolete epidermal compartment
type: Class
comment: no longer designating mediolateral regions using the contained_in object property
deprecated: true

TrpA+ neural progenitor cell
type: Class
subclass of: neural progenitor cell
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25254346
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: TrpA+ neural progenitor cell
annotated property: definition
annotated target: piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
database_cross_reference: PMID:25254346

anterior pole progenitor cell
type: Class
subclass of: neoblast
definition: piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:24415944
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: anterior pole progenitor cell
annotated property: definition
annotated target: piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole.
database_cross_reference: PMID:24415944

transverse commissure
type: Class
subclass of: independent continuant
subclass of: commissure
subclass of: Restriction
  on property: part of
  some values from: ventral nerve cord
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17999079
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: transverse commissure
annotated property: definition
annotated target: Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords.
database_cross_reference: PMID:17999079

obsolete body wall musculature compartment
type: Class
comment: no longer designating mediolateral regions using the contained_in object property
deprecated: true

serotonergic neural progenitor cell
type: Class
subclass of: neural progenitor cell
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:25254346
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: serotonergic neural progenitor cell
annotated property: definition
annotated target: piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons.
database_cross_reference: PMID:23903188
database_cross_reference: PMID:24131630
database_cross_reference: PMID:25254346

klf+ sensory neuron progenitor cell
type: Class
subclass of: neural progenitor cell
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: asexual organism
definition: piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25254346
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: klf+ sensory neuron progenitor cell
annotated property: definition
annotated target: piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons.
database_cross_reference: PMID:25254346

nu neoblast
type: Class
subclass of: neural progenitor cell
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:27150006
has_exact_synonym: vNeoblast
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: nu neoblast
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27150006

lateral nerve
type: Class
subclass of: independent continuant
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: part of
  some values from: asexual organism
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17999079
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: lateral nerve
annotated property: definition
annotated target: A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus.
database_cross_reference: PMID:17999079

obsolete parenchymal compartment
type: Class
comment: no longer designating mediolateral regions using the contained_in object property
deprecated: true

pax3/7+ neural progenitor cell
type: Class
subclass of: neural progenitor cell
subclass of: neoblast
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:25254346
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: pax3/7+ neural progenitor cell
annotated property: definition
annotated target: piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
database_cross_reference: PMID:25254346

embryonic pharynx lumen
type: Class
subclass of: immaterial entity
subclass of: lumen
subclass of: Restriction
  on property: part of
  some values from: embryonic pharynx
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 3
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 4
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 5
subclass of: Restriction
  on property: existence overlaps
  some values from: Stage 6
subclass of: Restriction
  on property: existence starts during or after
  some values from: Stage 3
subclass of: Restriction
  on property: existence ends during or before
  some values from: Stage 6
subclass of: Restriction
  on property: luminal space of
  some values from: embryonic pharynx
definition: A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:28072387
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: embryonic pharynx lumen
annotated property: definition
annotated target: A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity.
database_cross_reference: PMID:28072387

testis nerve plexus
type: Class
subclass of: material entity
subclass of: nerve plexus
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: dorsal region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: posterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: parapharyngeal region
subclass of: Restriction
  on property: contained in
  some values from: tail region
subclass of: Restriction
  on property: contained in
  some values from: copulatory region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Nerve plexus surrounding the testis.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17999079
database_cross_reference: PMID:7833618
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: testis nerve plexus
annotated property: definition
annotated target: Nerve plexus surrounding the testis.
database_cross_reference: PMID:17999079
database_cross_reference: PMID:7833618

fission plane
type: Class
subclass of: anatomical plane
definition: Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:11972158
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: fission plane
annotated property: definition
annotated target: Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs.
database_cross_reference: OCLC:16809160
database_cross_reference: PMID:11972158

ovary nerve plexus
type: Class
subclass of: material entity
subclass of: nerve plexus
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: contained in
  some values from: anterior region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: ventral region of the whole animal
subclass of: Restriction
  on property: contained in
  some values from: prepharyngeal region
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
definition: Nerve plexus surrounding the ovary.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: PMID:17999079
database_cross_reference: PMID:7833618
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: ovary nerve plexus
annotated property: definition
annotated target: Nerve plexus surrounding the ovary.
database_cross_reference: PMID:17999079
database_cross_reference: PMID:7833618

obsolete gastrovascular compartment
type: Class
comment: no longer designating mediolateral regions using the contained_in object property
deprecated: true

head margin
type: Class
subclass of: dorsal ventral margin of the whole animal
definition: Peripheral region of the head.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

glutamatergic neuron
type: Class
subclass of: independent continuant
subclass of: neurosecretory neuron
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence overlaps
  some values from: adult hermaphrodite
subclass of: Restriction
  on property: existence overlaps
  some values from: asexual adult
definition: Neurons that express the biogenic amine glutamate.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CL:0000679
database_cross_reference: PMID:24131630
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: glutamatergic neuron
annotated property: definition
annotated target: Neurons that express the biogenic amine glutamate.
database_cross_reference: PMID:24131630

sexual organism
type: Class
subclass of: independent continuant
subclass of: whole organism
subclass of: Restriction
  on property: develops from
  some values from: embryo
definition: An individual member of the sexual biotype of Schmidtea mediterranea.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

asexual organism
type: Class
subclass of: independent continuant
subclass of: whole organism
subclass of: Restriction
  on property: develops from
  some values from: asexual organism
definition: An individual member of the asexual biotype of Schmidtea mediterranea.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: CARO:0000030
has_obo_namespace: Planarian_Anatomy

non-ciliated neuron
type: Class
subclass of: neuron
definition: A neuron cell that does not have cilia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: non cilated neuron
has_exact_synonym: uncilated neuon
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: non-ciliated neuron
annotated property: definition
annotated target: A neuron cell that does not have cilia.
database_cross_reference: PMID:29674431

cilated neuron
type: Class
subclass of: neuron
definition: A neuron that has cilia.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
database_cross_reference: WBbt:0006816
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: cilated neuron
annotated property: definition
annotated target: A neuron that has cilia.
database_cross_reference: PMID:29674431

guidepost cell
type: Class
subclass of: material entity
subclass of: muscle cell
subclass of: Restriction
  on property: part of
  some values from: visual system cell
subclass of: Restriction
  on property: contained in
  some values from: head region
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: guidepost cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:32586989

NME cell
type: Class
subclass of: guidepost cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: NME cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:32586989

NMC cell
type: Class
subclass of: NME cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: NMC cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:32586989

NBC cell
type: Class
subclass of: NMC cell
definition: 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.
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_obo_namespace: Planarian_Anatomy

Axiom
annotated source: NBC cell
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:32586989

juvenile organism
type: Class
subclass of: independent continuant
subclass of: whole organism
subclass of: Restriction
  on property: existence overlaps
  some values from: juvenile stage
subclass of: Restriction
  on property: existence starts during or after
  some values from: juvenile stage
subclass of: Restriction
  on property: existence ends during or before
  some values from: juvenile stage
definition: A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype
created by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
has_exact_synonym: juvenile
has_obo_namespace: Planarian_Anatomy

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FBbt:00007001
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: SCTID:362889002
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
database_cross_reference: http://dbpedia.org/ontology/AnatomicalStructure
has_exact_synonym: biological structure
has_exact_synonym: connected biological structure
has_obo_namespace: uberon
id: UBERON:0000061
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: has_exact_synonym
annotated target: connected biological structure
database_cross_reference: CARO:0000003

embryo stage
type: Class
subclass of: life cycle stage
definition: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
database_cross_reference: BilaDO:0000002
database_cross_reference: EV:0300001
database_cross_reference: FBdv:00005289
database_cross_reference: FMA:72652
database_cross_reference: HsapDv:0000002
database_cross_reference: MmusDv:0000002
database_cross_reference: OGES:000000
database_cross_reference: OGES:000022
database_cross_reference: SCTID:296280003
database_cross_reference: WBls:0000003
database_cross_reference: WBls:0000092
database_cross_reference: WBls:0000102
database_cross_reference: XAO:1000012
has_exact_synonym: embryonic stage
has_obo_namespace: uberon
has_related_synonym: embryogenesis
id: UBERON:0000068

Axiom
annotated source: embryo stage
annotated property: definition
annotated target: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
database_cross_reference: http://orcid.org/0000-0002-6601-2165

life cycle stage
type: Class
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
editor note: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
external_ontology_notes: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
external_ontology_notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
database_cross_reference: BILS:0000105
database_cross_reference: EFO:0000399
database_cross_reference: FBdv:00007012
database_cross_reference: FMA:24120
database_cross_reference: HsapDv:0000000
database_cross_reference: MESH:D008018
database_cross_reference: MmusDv:0000000
database_cross_reference: OlatDv:0000010
database_cross_reference: PdumDv:0000090
database_cross_reference: WBls:0000002
database_cross_reference: XAO:1000000
database_cross_reference: ZFS:0000000
database_cross_reference: ZFS:0100000
database_cross_reference: ncithesaurus:Developmental_Stage
has_narrow_synonym: developmental stage
has_narrow_synonym: stage
has_obo_namespace: uberon
id: UBERON:0000105
in_subset: common anatomy
in_subset: efo slim
in_subset: upper level

Axiom
annotated source: life cycle stage
annotated property: definition
annotated target: A spatiotemporal region encompassing some part of the life cycle of an organism.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FBbt:00007016
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: Anatomical entity that has mass.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

organism subdivision
type: Class
subclass of: anatomical structure
definition: 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.
editor note: Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
database_cross_reference: AAO:0010053
database_cross_reference: AEO:0000032
database_cross_reference: BILA:0000032
database_cross_reference: BIRNLEX:7
database_cross_reference: CALOHA:TS-2084
database_cross_reference: CARO:0000032
database_cross_reference: EFO:0000808
database_cross_reference: EHDAA2:0003032
database_cross_reference: EMAPA:36031
database_cross_reference: FBbt:00007009
database_cross_reference: FMA:7153
database_cross_reference: HAO:0000032
database_cross_reference: MA:0002433
database_cross_reference: MAT:0000293
database_cross_reference: MESH:D001829
database_cross_reference: MIAA:0000293
database_cross_reference: NCIT:C32221
database_cross_reference: TAO:0001308
database_cross_reference: TGMA:0001840
database_cross_reference: VHOG:0001758
database_cross_reference: Wikipedia:Body_part
database_cross_reference: XAO:0003013
database_cross_reference: ZFA:0001308
database_cross_reference: galen:BodyPart
has_exact_synonym: anatomic region
has_obo_namespace: uberon
has_related_synonym: body part
has_related_synonym: body region
has_related_synonym: cardinal body part
id: UBERON:0000475
in_subset: common anatomy
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: upper level

Axiom
annotated source: organism subdivision
annotated property: definition
annotated target: 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.
database_cross_reference: CARO:0000032
database_cross_reference: CARO:DOS
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: organism subdivision
annotated property: has_exact_synonym
annotated target: anatomic region
database_cross_reference: MA:0002433

Axiom
annotated source: organism subdivision
annotated property: has_related_synonym
annotated target: body region
database_cross_reference: FMA:7153

Axiom
annotated source: organism subdivision
annotated property: has_related_synonym
annotated target: cardinal body part
database_cross_reference: FMA:7153

acellular anatomical structure
type: Class
subclass of: anatomical structure
definition: Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
database_cross_reference: AAO:0010268
database_cross_reference: AEO:0000040
database_cross_reference: BILA:0000040
database_cross_reference: CARO:0000040
database_cross_reference: EHDAA2:0003040
database_cross_reference: FBbt:00007013
database_cross_reference: FMA:63863
database_cross_reference: HAO:0000040
database_cross_reference: TAO:0000382
database_cross_reference: TGMA:0001841
database_cross_reference: XAO:0003162
database_cross_reference: ZFA:0000382
has_obo_namespace: uberon
has_related_synonym: acellular anatomical structures
id: UBERON:0000476
in_subset: common anatomy
in_subset: vertebrate core

Axiom
annotated source: acellular anatomical structure
annotated property: definition
annotated target: Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: acellular anatomical structure
annotated property: has_related_synonym
annotated target: acellular anatomical structures
database_cross_reference: ZFA:0000382
has_synonym_type: PLURAL

anatomical entity
type: Class
definition: 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.
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has_obo_namespace: uberon
id: UBERON:0001062
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: 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.
database_cross_reference: FMA:62955
database_cross_reference: http://orcid.org/0000-0001-9114-8737

anatomical cavity
type: Class
subclass of: anatomical entity
definition: 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.
has_broad_synonym: cavity
database_cross_reference: BIRNLEX:1011
database_cross_reference: FMA:67552
database_cross_reference: MA:0002447
database_cross_reference: NCIT:C34007
database_cross_reference: galen:Cavity
has_obo_namespace: uberon
id: UBERON:0002553
in_subset: upper level

Axiom
annotated source: anatomical cavity
annotated property: definition
annotated target: 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.
database_cross_reference: FMA:67552

developing anatomical structure
type: Class
subclass of: material anatomical entity
database_cross_reference: AEO:0000125
database_cross_reference: CALOHA:TS-2122
database_cross_reference: EHDAA2:0003125
database_cross_reference: FBbt:00007006
database_cross_reference: FMA:292313
database_cross_reference: MIAA:0000019
has_obo_namespace: uberon
has_related_synonym: developing structure
has_related_synonym: developmental structure
has_related_synonym: developmental tissue
id: UBERON:0005423
in_subset: common anatomy

Axiom
annotated source: developing anatomical structure
annotated property: has_related_synonym
annotated target: developmental tissue
database_cross_reference: MIAA:0000019

regenerating anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that is undergoing regeneration.
editor note: we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure.
database_cross_reference: AEO:0000200
database_cross_reference: EHDAA2:0003233
database_cross_reference: TAO:0005147
database_cross_reference: XAO:0004059
database_cross_reference: ZFA:0005147
has_obo_namespace: uberon
has_related_synonym: regenerating tissue
has_related_synonym: regenerating tissues
has_related_synonym: regenerative tissue
id: UBERON:0007567

Axiom
annotated source: regenerating anatomical structure
annotated property: definition
annotated target: An anatomical structure that is undergoing regeneration.
database_cross_reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: regenerating anatomical structure
annotated property: has_related_synonym
annotated target: regenerating tissue
database_cross_reference: ZFA:0005147

Axiom
annotated source: regenerating anatomical structure
annotated property: has_related_synonym
annotated target: regenerating tissues
database_cross_reference: ZFA:0005147
has_synonym_type: PLURAL

example to be eventually removed
type: NamedIndividual
type: curation status specification
IAO_0000111: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
IAO_0000117: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
type: curation status specification
IAO_0000111: metadata complete
definition: 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.

organizational term
type: NamedIndividual
type: curation status specification
IAO_0000111: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
IAO_0000111: ready for release
definition: 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."

metadata incomplete
type: NamedIndividual
type: curation status specification
IAO_0000111: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
IAO_0000111: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
IAO_0000111: pending final vetting
definition: 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.

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: term imported
editor note: 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 split
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: term split
editor note: 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.

universal
type: NamedIndividual
type: denotator type
IAO_0000111: universal
editor note: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000119: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
IAO_0000111: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "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.
IAO_0000117: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
IAO_0000111: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: 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
IAO_0000117: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
IAO_0000111: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
IAO_0000111: requires discussion
definition: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

out of scope
type: NamedIndividual
type: obsolescence reason specification
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: 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.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/77
IAO_0000234: https://orcid.org/0000-0001-5208-3432

infer input from direct reg
is rule enabled: true
comment: 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
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: 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'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: 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'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

Imp
comment: This can't be added as a property chain because it causes a circularity violation for 'part of'.
body: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: in left side of
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: in left side of
  argument1: x
  argument2: z

Imp
comment: This can't be added as a property chain because it causes a circularity violation for 'part of'.
body: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: in right side of
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: in right side of
  argument1: x
  argument2: z

Imp
comment: This can't be added as a property chain because it causes a circularity violation for 'part of'.
body: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: in lateral side of
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: in lateral side of
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: 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.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2