format-version: 1.2 data-version: releases/2023-03-13 subsetdef: attribute_slim "" subsetdef: cell_quality "" subsetdef: common_anatomy "" subsetdef: efo_slim "" subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_manually_annotate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" subsetdef: goslim_drosophila "" subsetdef: goslim_flybase_ribbon "" subsetdef: goslim_generic "" subsetdef: goslim_metagenomics "" subsetdef: goslim_mouse "" subsetdef: goslim_pir "" subsetdef: goslim_plant "" subsetdef: goslim_pombe "" subsetdef: goslim_yeast "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: pheno_slim "" subsetdef: relational_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: uberon_slim "" subsetdef: upper_level "" subsetdef: value_slim "" subsetdef: vertebrate_core "" synonymtypedef: human "synonym typically used in the context of human anatomy" NARROW synonymtypedef: PLURAL "" synonymtypedef: vertebrate "synonym typically used in the context of vertebrate anatomy" NARROW default-namespace: Planarian_Anatomy treat-xrefs-as-genus-differentia: CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 ontology: plana property_value: dc-description "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea." xsd:string property_value: dc-title "Planarian Anatomy Ontology (PLANA)" xsd:string property_value: dcterms-license https://creativecommons.org/licenses/by/3.0/ property_value: owl:versionInfo "2023-03-13" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant def: "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." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 {all_only="true"} ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity relationship: part_of BFO:0000003 {all_only="true"} ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string property_value: IAO:0000112 "a heart" xsd:string property_value: IAO:0000112 "a leg" xsd:string property_value: IAO:0000112 "a molecule" xsd:string property_value: IAO:0000112 "a spatial region" xsd:string property_value: IAO:0000112 "an atom" xsd:string property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "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)" xsd:string property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role property_value: BFO:0000179 "disposition" xsd:string property_value: BFO:0000180 "Disposition" xsd:string property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 name: realizable entity def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant relationship: part_of BFO:0000019 {all_only="true"} ! quality property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string property_value: IAO:0000112 "the color of a tomato" xsd:string property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "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." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: 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." xsd:string property_value: 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" xsd:string property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role def: "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." [] is_a: BFO:0000017 ! realizable entity property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string property_value: 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." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: 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." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition property_value: BFO:0000179 "function" xsd:string property_value: BFO:0000180 "Function" xsd:string property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 name: material entity def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string property_value: IAO:0000112 "a hurricane" xsd:string property_value: IAO:0000112 "a photon" xsd:string property_value: IAO:0000112 "a puff of smoke" xsd:string property_value: IAO:0000112 "a sea wave" xsd:string property_value: IAO:0000112 "a tornado" xsd:string property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string property_value: 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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: 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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant [Term] id: BSPO:0000005 name: anatomical surface namespace: spatial def: "A 2D surface of an anatomical continuant." [BSPO:cjm] comment: to be merged into CARO synonym: "surface" EXACT [] xref: FMA:24137 is_a: CARO:0000010 ! anatomical boundary [Term] id: BSPO:0000010 name: anatomical axis namespace: spatial def: "A straight line through space, intersecting an anatomical entity." [BSPO:cjm] comment: Axis directions are defined in terms of axes. xref: http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG is_a: CARO:0000008 ! anatomical line relationship: passes_through CARO:0000000 ! anatomical entity [Term] id: BSPO:0000013 name: anterior-posterior axis namespace: spatial def: "An axis that extends through an organism from head end to opposite end of body or tail." [BSPO:cjm] 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] synonym: "A-P axis" EXACT [] synonym: "anteroposterior axis" EXACT [] synonym: "AP axis" EXACT [] synonym: "cephalocaudal axis" NARROW [http://en.wikipedia.org/wiki/Anatomical_terms_of_location] synonym: "craniocaudal axis" NARROW vertebrate [] synonym: "longitudinal axis" RELATED [] synonym: "rostral/caudal" NARROW vertebrate [] synonym: "rostrocaudal axis" NARROW vertebrate [] is_a: BSPO:0000010 ! anatomical axis intersection_of: BSPO:0000010 ! anatomical axis intersection_of: orthogonal_to BSPO:0000018 ! transverse plane relationship: approximately_perpendicular_to BSPO:0000016 ! dorsal-ventral axis relationship: orthogonal_to BSPO:0000018 ! transverse plane [Term] id: BSPO:0000014 name: apical-basal axis relative to substrate namespace: spatial def: "An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure." [BSPO:mah] synonym: "apical/basal" EXACT [] synonym: "longitudinal axis" RELATED [] is_a: BSPO:0000010 ! anatomical axis [Term] id: BSPO:0000015 name: proximal-distal axis namespace: spatial def: "An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal)." [BSPO:curators, http://en.wikipedia.org/wiki/Anatomical_terms_of_location] 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. synonym: "proximal/distal" EXACT [] synonym: "proximodistal" EXACT [] is_a: BSPO:0000010 ! anatomical axis [Term] id: BSPO:0000016 name: dorsal-ventral axis namespace: spatial def: "An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body." [BSPO:curators] synonym: "anterior-posterior axis" NARROW human [] synonym: "D-V axis" EXACT [] synonym: "dorsoventral axis" EXACT [] synonym: "DV axis" EXACT [] is_a: BSPO:0000010 ! anatomical axis intersection_of: BSPO:0000010 ! anatomical axis intersection_of: orthogonal_to BSPO:0000019 ! horizontal plane relationship: orthogonal_to BSPO:0000019 ! horizontal plane [Term] id: BSPO:0000017 name: left-right axis namespace: spatial def: "An axis that bisects an organism from left to right sides of body, through a sagittal plane." [BSPO:cjm] synonym: "dextro-sinister axis" EXACT [] synonym: "L-R axis" EXACT [] synonym: "left to right axis" EXACT [] synonym: "LR axis" EXACT [] synonym: "R-L axis" EXACT [] synonym: "right to left axis" EXACT [] synonym: "right-left axis" EXACT [] synonym: "RL axis" EXACT [] is_a: BSPO:0000010 ! anatomical axis intersection_of: BSPO:0000010 ! anatomical axis intersection_of: orthogonal_to BSPO:0000417 ! sagittal plane relationship: orthogonal_to BSPO:0000417 ! sagittal plane [Term] id: BSPO:0000018 name: transverse plane namespace: spatial def: "Anatomical plane that divides body into anterior and posterior parts." [BSPO:mah] synonym: "axial plane" EXACT [] synonym: "axial section" EXACT [] synonym: "cross-section" RELATED [] synonym: "transverse section" EXACT [] xref: FMA:12247 is_a: BSPO:0000400 ! anatomical plane [Term] id: BSPO:0000019 name: horizontal plane namespace: spatial def: "Anatomical plane that divides bilateral body into dorsal and ventral parts." [BSPO:mah] synonym: "coronal section" RELATED [] synonym: "frontal plane" EXACT [] synonym: "frontal section" RELATED [] synonym: "horizontal anatomical plane" EXACT [FMA:52810] synonym: "horizontal section" EXACT [] xref: FMA:52810 is_a: BSPO:0000400 ! anatomical plane [Term] id: BSPO:0000026 name: antero-dorsal region namespace: spatial def: "Anatomical region that overlaps the anterior and dorsal regions of a body or body part." [BSPO:wd] synonym: "anterodorsal region " EXACT [] is_a: BSPO:0000071 ! anterior region is_a: BSPO:0000079 ! dorsal region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000055 ! anterior side intersection_of: overlaps BSPO:0000063 ! dorsal side created_by: Melissa Haendel creation_date: 2009-06-15T01:01:38Z [Term] id: BSPO:0000027 name: antero-ventral region namespace: spatial def: "Anatomical region that overlaps the anterior and ventral regions of a body or body part." [BSPO:wd] synonym: "anteroventral region " EXACT [] is_a: BSPO:0000071 ! anterior region is_a: BSPO:0000084 ! ventral region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000055 ! anterior side intersection_of: overlaps BSPO:0000068 ! ventral side created_by: Melissa Haendel creation_date: 2009-06-15T01:04:59Z [Term] id: BSPO:0000028 name: postero-lateral region namespace: spatial def: "Anatomical region that overlaps the posterior and lateral regions of the body or body part." [BSPO:wd] synonym: "posterolateral region" EXACT [] is_a: BSPO:0000072 ! posterior region is_a: BSPO:0000082 ! lateral region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000056 ! posterior side intersection_of: overlaps BSPO:0000066 ! lateral side created_by: Melissa Haendel creation_date: 2009-06-15T01:06:01Z [Term] id: BSPO:0000029 name: antero-lateral region namespace: spatial def: "Anatomical region that overlaps the anterior and lateral regions of a body or body part." [BSPO:wd] synonym: "anterolateral region" EXACT [] is_a: BSPO:0000071 ! anterior region is_a: BSPO:0000082 ! lateral region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000055 ! anterior side intersection_of: overlaps BSPO:0000066 ! lateral side created_by: Melissa Haendel creation_date: 2009-06-15T01:07:18Z [Term] id: BSPO:0000030 name: postero-dorsal region namespace: spatial def: "Anatomical region that overlaps the posterior and dorsal regions of the body or body part." [BSPO:wd] synonym: "posterodorsal region" EXACT [] is_a: BSPO:0000072 ! posterior region is_a: BSPO:0000079 ! dorsal region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000056 ! posterior side intersection_of: overlaps BSPO:0000063 ! dorsal side created_by: Melissa Haendel creation_date: 2009-06-15T01:08:13Z [Term] id: BSPO:0000035 name: postero-ventral region namespace: spatial def: "Anatomical region that overlaps the posterior and ventral regions of a body or body part." [BSPO:wd] synonym: "posteroventral region" EXACT [] is_a: BSPO:0000072 ! posterior region is_a: BSPO:0000084 ! ventral region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000056 ! posterior side intersection_of: overlaps BSPO:0000068 ! ventral side created_by: Melissa Haendel creation_date: 2009-06-15T01:08:38Z [Term] id: BSPO:0000054 name: anatomical side namespace: spatial def: "An anatomical region bounded by a plane perpendicular to an axis through the middle." [BSPO:cjm] xref: FBql:00005841 is_a: BSPO:0000070 ! anatomical region [Term] id: BSPO:0000055 name: anterior side namespace: spatial def: "An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane." [BSPO:RW] synonym: "anterior" EXACT [] synonym: "rostral" EXACT [] xref: FBcv:0000053 xref: FBql:00005848 is_a: BSPO:0000054 ! anatomical side relationship: anterior_to BSPO:0000056 ! posterior side relationship: opposite_to BSPO:0000056 ! posterior side relationship: starts_axis BSPO:0000013 ! anterior-posterior axis [Term] id: BSPO:0000056 name: posterior side namespace: spatial def: "An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane." [BSPO:RW, BSPO:wd] synonym: "caudal" NARROW vertebrate [] synonym: "posterior" EXACT [] xref: FBcv:0000065 xref: FBql:00005849 is_a: BSPO:0000054 ! anatomical side relationship: finishes_axis BSPO:0000013 ! anterior-posterior axis relationship: posterior_to BSPO:0000055 ! anterior side [Term] id: BSPO:0000057 name: apical side namespace: spatial def: "Anatomical side that is located on the apical end of an organism or structure." [BSPO:wd] synonym: "apical" EXACT [] xref: FBcv:0000054 xref: FBql:00005854 is_a: BSPO:0000054 ! anatomical side relationship: opposite_to BSPO:0000058 ! basal side relationship: starts_axis BSPO:0000014 ! apical-basal axis relative to substrate [Term] id: BSPO:0000058 name: basal side namespace: spatial def: "Anatomical side that is located on the basal end of an organism or structure." [BSPO:wd] comment: The part of the organism attached to a substrate. Axis of symmetry. synonym: "basal" EXACT [] xref: FBcv:0000055 xref: FBql:00005855 is_a: BSPO:0000054 ! anatomical side relationship: finishes_axis BSPO:0000014 ! apical-basal axis relative to substrate [Term] id: BSPO:0000063 name: dorsal side namespace: spatial def: "An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane." [BSPO:wd] synonym: "dorsal" EXACT [] xref: FBcv:0000059 xref: FBql:00005842 is_a: BSPO:0000054 ! anatomical side relationship: dorsal_to BSPO:0000066 ! lateral side relationship: opposite_to BSPO:0000068 ! ventral side relationship: starts_axis BSPO:0000016 ! dorsal-ventral axis [Term] id: BSPO:0000066 name: lateral side namespace: spatial synonym: "lateral" EXACT [] xref: FBcv:0000063 xref: FBql:00005844 is_a: BSPO:0000054 ! anatomical side [Term] id: BSPO:0000068 name: ventral side namespace: spatial def: "An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane." [BSPO:RW, BSPO:wd] synonym: "ventral" EXACT [] xref: FBcv:0000070 xref: FBql:00005843 is_a: BSPO:0000054 ! anatomical side relationship: finishes_axis BSPO:0000016 ! dorsal-ventral axis [Term] id: BSPO:0000070 name: anatomical region namespace: spatial def: "A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm." [BSPO:cjm] comment: to be merged into CARO xref: FBql:00005841 is_a: CARO:0000003 ! anatomical structure [Term] id: BSPO:0000071 name: anterior region namespace: spatial def: "Anatomical region anteriorly located on the body or body part." [BSPO:wd] xref: FBql:00005848 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000055 ! anterior side relationship: overlaps BSPO:0000055 ! anterior side [Term] id: BSPO:0000072 name: posterior region namespace: spatial def: "Anatomical region posteriorly located on the body or body part." [BSPO:wd] xref: FBql:00005849 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000056 ! posterior side relationship: overlaps BSPO:0000056 ! posterior side [Term] id: BSPO:0000073 name: apical region namespace: spatial def: "Anatomical region located on the apical end on the body or body part." [BSPO:wd] xref: FBql:00005854 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000057 ! apical side relationship: overlaps BSPO:0000057 ! apical side [Term] id: BSPO:0000074 name: basal region namespace: spatial def: "Anatomical region located basally on the body or body part." [BSPO:wd] xref: FBql:00005855 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000058 ! basal side relationship: overlaps BSPO:0000058 ! basal side [Term] id: BSPO:0000079 name: dorsal region namespace: spatial def: "Anatomical region dorsally located on the body or body part." [BSPO:wd] xref: FBql:00005842 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000063 ! dorsal side relationship: overlaps BSPO:0000063 ! dorsal side [Term] id: BSPO:0000080 name: dorso-lateral region namespace: spatial def: "Anatomical region that overlaps the dorsal and lateral regions of a body or body part." [BSPO:wd] synonym: "dorsolateral region" EXACT [] xref: FBql:00005845 is_a: BSPO:0000079 ! dorsal region is_a: BSPO:0000082 ! lateral region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000063 ! dorsal side intersection_of: overlaps BSPO:0000066 ! lateral side [Term] id: BSPO:0000082 name: lateral region namespace: spatial def: "Anatomical region laterally located on the body or body part." [BSPO:wd] xref: FBql:00005844 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000066 ! lateral side relationship: overlaps BSPO:0000066 ! lateral side [Term] id: BSPO:0000084 name: ventral region namespace: spatial def: "Anatomical region ventrally located on the body or body part." [BSPO:wd] xref: FBql:00005843 is_a: BSPO:0000070 ! anatomical region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000068 ! ventral side relationship: overlaps BSPO:0000068 ! ventral side [Term] id: BSPO:0000085 name: ventro-lateral region namespace: spatial def: "Anatomical region that overlaps the ventral and lateral regions of a body or body part." [BSPO:wd] comment: This is an example of a composition of two axis positions. synonym: "ventrolateral region" EXACT [] xref: FBql:00005846 is_a: BSPO:0000082 ! lateral region is_a: BSPO:0000084 ! ventral region intersection_of: BSPO:0000070 ! anatomical region intersection_of: overlaps BSPO:0000066 ! lateral side intersection_of: overlaps BSPO:0000068 ! ventral side [Term] id: BSPO:0000086 name: anatomical compartment namespace: spatial comment: to be merged into CARO xref: FBql:00005873 xref: FMA:9647 is_a: CARO:0000003 ! anatomical structure [Term] id: BSPO:0000092 name: anatomical compartment boundary namespace: spatial comment: to be merged into CARO xref: FBql:00005881 is_a: CARO:0000010 ! anatomical boundary [Term] id: BSPO:0000094 name: dorsal/ventral compartment boundary namespace: spatial xref: FBcv:0000034 xref: FBql:00005879 is_a: BSPO:0000092 ! anatomical compartment boundary [Term] id: BSPO:0000196 name: medial-external axis namespace: spatial def: "An anatomical axis that extends from the center of the body outwards or externally." [BSPO:curators] comment: The medial-external axis could apply to a sphere-shaped body. synonym: "proximal-distal axis" RELATED [] is_a: BSPO:0000010 ! anatomical axis created_by: wasila.dahdul creation_date: 2013-07-02T11:21:42Z [Term] id: BSPO:0000198 name: oral-aboral axis namespace: spatial def: "An axis that extends from the oral opening to the furthest point in an organism that is directly opposite." [BSPO:PM] is_a: BSPO:0000010 ! anatomical axis created_by: wasila.dahdul creation_date: 2013-07-02T11:29:33Z [Term] id: BSPO:0000371 name: anterior surface namespace: spatial def: "Anatomical surface that is located on the anterior side of the body or body part." [BSPO:wd] xref: FBql:00005848 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000055 ! anterior side relationship: surface_of BSPO:0000055 ! anterior side [Term] id: BSPO:0000372 name: posterior surface namespace: spatial def: "Anatomical surface that is located on the posterior side of the body or body part." [BSPO:wd] xref: FBql:00005849 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000056 ! posterior side relationship: surface_of BSPO:0000056 ! posterior side [Term] id: BSPO:0000373 name: apical surface namespace: spatial def: "Anatomical surface that is located on the apical side of the body or body part." [BSPO:wd] xref: FBql:00005854 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000057 ! apical side relationship: surface_of BSPO:0000057 ! apical side [Term] id: BSPO:0000374 name: basal surface namespace: spatial def: "Anatomical surface that is located on the basal side of the body or body part." [BSPO:wd] xref: FBql:00005855 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000058 ! basal side relationship: surface_of BSPO:0000058 ! basal side [Term] id: BSPO:0000379 name: dorsal surface namespace: spatial def: "Anatomical surface that located on the dorsal side of the body or body part." [BSPO:wd] xref: FBql:00005842 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000063 ! dorsal side relationship: surface_of BSPO:0000063 ! dorsal side [Term] id: BSPO:0000382 name: lateral surface namespace: spatial def: "Anatomical surface that located on the lateral side of the body or body part." [BSPO:wd] xref: FBql:00005844 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000066 ! lateral side relationship: surface_of BSPO:0000066 ! lateral side [Term] id: BSPO:0000384 name: ventral surface namespace: spatial def: "Anatomical surface that is located on the ventral side of the body or body part." [BSPO:wd] xref: FBql:00005843 is_a: BSPO:0000005 ! anatomical surface intersection_of: BSPO:0000005 ! anatomical surface intersection_of: surface_of BSPO:0000068 ! ventral side relationship: surface_of BSPO:0000068 ! ventral side [Term] id: BSPO:0000400 name: anatomical plane namespace: spatial def: "A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions." [BSPO:cjm] 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. synonym: "anatomical cross-section" EXACT [] synonym: "anatomical section" EXACT [] synonym: "cross-section" RELATED [] synonym: "plane" EXACT [] synonym: "section" EXACT [] xref: FMA:242982 is_a: CARO:0000010 ! anatomical boundary [Term] id: BSPO:0000417 name: sagittal plane namespace: spatial def: "Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size." [BSPO:cjm, BSPO:DOS, BSPO:mah] synonym: "left/right plane" EXACT [] synonym: "median plane" EXACT [] synonym: "sagittal section" EXACT [] xref: FMA:11361 is_a: BSPO:0000010 ! anatomical axis is_a: BSPO:0000400 ! anatomical plane intersection_of: BSPO:0000400 ! anatomical plane intersection_of: BSPO:0001102 BSPO:0000013 ! parallel to anterior-posterior axis intersection_of: BSPO:0001102 BSPO:0000016 ! parallel to dorsal-ventral axis intersection_of: orthogonal_to BSPO:0000017 ! left-right axis relationship: BSPO:0001102 BSPO:0000013 ! parallel to anterior-posterior axis relationship: BSPO:0001102 BSPO:0000016 ! parallel to dorsal-ventral axis relationship: orthogonal_to BSPO:0000017 ! left-right axis [Term] id: BSPO:0001001 name: medial-lateral axis namespace: spatial def: "An axis that extends from the center of organism to one or other side." [BSPO:cjm] 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. synonym: "M-L axis" EXACT [] synonym: "medio-lateral axis" EXACT [] synonym: "mediolateral axis" EXACT [] synonym: "ML axis" EXACT [] synonym: "proximal-distal axis " RELATED [] xref: http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG is_a: BSPO:0000196 ! medial-external axis [Term] id: CARO:0000000 name: anatomical entity namespace: spatial def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [CAROC:Brownsville2014] def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [CARO:MAH] 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. is_a: CARO:0030000 ! biological entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000003 name: anatomical structure name: connected anatomical structure namespace: spatial def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CC:DOS] is_a: CARO:0000006 ! material anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000006 name: material anatomical entity namespace: spatial def: "An anatomical entity that has mass." [CC:DOS] is_a: BFO:0000040 ! material entity is_a: CARO:0000000 ! anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000007 name: immaterial anatomical entity namespace: spatial def: "An anatomical entity that has no mass." [CC:DOS] is_a: BFO:0000141 ! immaterial entity is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0000008 name: anatomical line namespace: spatial def: "A one dimensional, immaterial anatomical entity." [CC:DOS] is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000010 name: anatomical boundary namespace: spatial def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CC:DOS] is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0030000 name: biological entity is_a: BFO:0000004 ! independent continuant [Term] id: GO:0000003 name: reproduction namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732] subset: goslim_agr subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_pir subset: goslim_plant synonym: "reproductive physiological process" EXACT [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase [Term] id: GO:0000080 name: mitotic G1 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "G1 phase of mitotic cell cycle" EXACT [] is_a: GO:0051318 ! G1 phase relationship: part_of GO:0051329 ! mitotic interphase [Term] id: GO:0000084 name: mitotic S phase namespace: biological_process def: "The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "S phase of mitotic cell cycle" EXACT [] synonym: "S-phase of mitotic cell cycle" EXACT [] is_a: GO:0051320 ! S phase relationship: part_of GO:0051329 ! mitotic interphase [Term] id: GO:0000085 name: mitotic G2 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "G2 phase of mitotic cell cycle" EXACT [] is_a: GO:0051319 ! G2 phase relationship: part_of GO:0051329 ! mitotic interphase [Term] id: GO:0000087 name: mitotic M phase namespace: biological_process def: "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "M phase of mitotic cell cycle" EXACT [] synonym: "M-phase of mitotic cell cycle" EXACT [] is_a: GO:0000279 ! M phase is_a: GO:0098763 ! mitotic cell cycle phase intersection_of: GO:0000279 ! M phase intersection_of: happens_during GO:0000278 ! mitotic cell cycle [Term] id: GO:0000088 name: mitotic prophase namespace: biological_process def: "The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051324 ! prophase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000089 name: mitotic metaphase namespace: biological_process def: "The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051323 ! metaphase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000090 name: mitotic anaphase namespace: biological_process def: "The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051322 ! anaphase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000093 name: mitotic telophase namespace: biological_process def: "The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051326 ! telophase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000237 name: leptotene namespace: biological_process def: "The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Leptotene xref: Wikipedia:Meiosis#Leptotene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000238 name: zygotene namespace: biological_process def: "The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Meiosis#Zygotene xref: Wikipedia:Zygotene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000239 name: pachytene namespace: biological_process def: "The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Meiosis#Pachytene xref: Wikipedia:Pachytene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000240 name: diplotene namespace: biological_process def: "The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Diplotene xref: Wikipedia:Meiosis#Diplotene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000241 name: diakinesis namespace: biological_process def: "The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Diakinesis xref: Wikipedia:Meiosis#Diakinesis is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] 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. subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_yeast synonym: "mitosis" RELATED [] xref: Wikipedia:Mitosis is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division [Term] id: GO:0000279 name: M phase namespace: biological_process def: "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "M-phase" EXACT [] xref: Wikipedia:M_phase is_a: GO:0022403 ! cell cycle phase [Term] id: GO:0000280 name: nuclear division namespace: biological_process def: "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah] subset: goslim_pir synonym: "karyokinesis" RELATED [] is_a: GO:0048285 ! organelle fission [Term] id: GO:0003006 name: developmental process involved in reproduction namespace: biological_process def: "A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring." [GOC:dph, GOC:isa_complete] synonym: "puberty" NARROW [GOC:dph] synonym: "reproductive developmental process" RELATED [GOC:dph, GOC:tb] is_a: GO:0022414 ! reproductive process is_a: GO:0032502 ! developmental process intersection_of: GO:0032502 ! developmental process intersection_of: part_of GO:0000003 ! reproduction [Term] id: GO:0003674 name: molecular_function def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt] 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. synonym: "molecular function" EXACT [] is_a: BFO:0000015 ! process property_value: IAO:0000589 "molecular process" xsd:string [Term] id: GO:0003824 name: catalytic activity is_a: GO:0003674 ! molecular_function [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao1337158144] 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. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell or subcellular entity" EXACT [] synonym: "cellular component" EXACT [] synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] xref: NIF_Subcellular:sao1337158144 [Term] id: GO:0006996 name: organelle organization namespace: biological_process alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] subset: goslim_candida subset: goslim_pir synonym: "organelle organisation" EXACT [] synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah] synonym: "single organism organelle organization" EXACT [GOC:TermGenie] synonym: "single-organism organelle organization" RELATED [] is_a: GO:0016043 ! cellular component organization created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] id: GO:0007049 name: cell cycle namespace: biological_process def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle] subset: gocheck_do_not_manually_annotate subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_pir subset: goslim_plant synonym: "cell-division cycle" EXACT [] xref: Wikipedia:Cell_cycle is_a: GO:0009987 ! cellular process [Term] id: GO:0007128 name: meiotic prophase I namespace: biological_process def: "The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051324 ! prophase is_a: GO:0098764 ! meiosis I cell cycle phase [Term] id: GO:0007132 name: meiotic metaphase I namespace: biological_process def: "The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051323 ! metaphase is_a: GO:0098764 ! meiosis I cell cycle phase [Term] id: GO:0007133 name: meiotic anaphase I namespace: biological_process def: "The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051322 ! anaphase is_a: GO:0098764 ! meiosis I cell cycle phase [Term] id: GO:0007134 name: meiotic telophase I namespace: biological_process def: "The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051326 ! telophase is_a: GO:0098764 ! meiosis I cell cycle phase [Term] id: GO:0007136 name: meiotic prophase II namespace: biological_process def: "The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051324 ! prophase is_a: GO:0098765 ! meiosis II cell cycle phase [Term] id: GO:0007137 name: meiotic metaphase II namespace: biological_process def: "The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051323 ! metaphase is_a: GO:0098765 ! meiosis II cell cycle phase [Term] id: GO:0007138 name: meiotic anaphase II namespace: biological_process def: "The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051322 ! anaphase is_a: GO:0098765 ! meiosis II cell cycle phase [Term] id: GO:0007139 name: meiotic telophase II namespace: biological_process def: "The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0051326 ! telophase is_a: GO:0098765 ! meiosis II cell cycle phase [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] 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. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0009987 name: cellular process namespace: biological_process alt_id: GO:0008151 alt_id: GO:0044763 alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] 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. subset: gocheck_do_not_annotate subset: goslim_plant synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] id: GO:0016043 name: cellular component organization namespace: biological_process alt_id: GO:0044235 alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: goslim_agr subset: goslim_mouse subset: goslim_pir subset: goslim_plant synonym: "cell organisation" EXACT [] synonym: "cell organization and biogenesis" RELATED [GOC:mah] synonym: "cellular component organisation at cellular level" EXACT [GOC:mah] synonym: "cellular component organisation in other organism" EXACT [GOC:mah] synonym: "cellular component organization at cellular level" EXACT [] synonym: "cellular component organization in other organism" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis [Term] id: GO:0016301 name: kinase activity def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] 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. synonym: "phosphokinase activity" EXACT [] xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups [Term] id: GO:0016740 name: transferase activity is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016772 name: transferase activity, transferring phosphorus-containing groups is_a: GO:0016740 ! transferase activity [Term] id: GO:0019953 name: sexual reproduction namespace: biological_process def: "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid)." [Wikipedia:Sexual_reproduction] 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. xref: Wikipedia:Sexual_reproduction is_a: GO:0000003 ! reproduction property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI [Term] id: GO:0022402 name: cell cycle process namespace: biological_process def: "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation." [GOC:isa_complete, GOC:mtg_cell_cycle] subset: gocheck_do_not_annotate is_a: GO:0009987 ! cellular process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0007049 ! cell cycle relationship: part_of GO:0007049 ! cell cycle [Term] id: GO:0022403 name: cell cycle phase namespace: biological_process def: "One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate is_a: GO:0044848 ! biological phase [Term] id: GO:0022414 name: reproductive process namespace: biological_process alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: goslim_generic synonym: "single organism reproductive process" RELATED [] is_a: GO:0008150 ! biological_process intersection_of: GO:0008150 ! biological_process intersection_of: part_of GO:0000003 ! reproduction disjoint_from: GO:0044848 ! biological phase relationship: part_of GO:0000003 ! reproduction created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] id: GO:0032502 name: developmental process namespace: biological_process alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0043473 name: pigmentation namespace: biological_process def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process [Term] id: GO:0044848 name: biological phase namespace: biological_process def: "A distinct period or stage in a biological process or cycle." [GOC:jl] 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. subset: gocheck_do_not_manually_annotate is_a: GO:0008150 ! biological_process disjoint_from: GO:0071840 ! cellular component organization or biogenesis created_by: jl creation_date: 2014-07-16T13:12:40Z [Term] id: GO:0048285 name: organelle fission namespace: biological_process def: "The creation of two or more organelles by division of one organelle." [GOC:jid] subset: goslim_pir subset: goslim_yeast is_a: GO:0006996 ! organelle organization [Term] id: GO:0048856 name: anatomical structure development namespace: biological_process def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021] subset: goslim_chembl subset: goslim_generic subset: goslim_plant synonym: "development of an anatomical structure" EXACT [] is_a: GO:0032502 ! developmental process [Term] id: GO:0051301 name: cell division namespace: biological_process def: "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:di, GOC:go_curators, GOC:pr] comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. subset: goslim_chembl subset: goslim_drosophila subset: goslim_pir xref: Wikipedia:Cell_division is_a: GO:0009987 ! cellular process [Term] id: GO:0051318 name: G1 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:G1_phase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0051325 ! interphase [Term] id: GO:0051319 name: G2 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis)." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:G2_phase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0051325 ! interphase [Term] id: GO:0051320 name: S phase namespace: biological_process def: "The cell cycle phase, following G1, during which DNA synthesis takes place." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "S-phase" EXACT [] xref: Wikipedia:S_phase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0051325 ! interphase [Term] id: GO:0051321 name: meiotic cell cycle namespace: biological_process alt_id: GO:0007126 def: "Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions." [GOC:ai] 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. subset: goslim_drosophila subset: goslim_yeast synonym: "meiosis" RELATED [] xref: Wikipedia:Meiosis is_a: GO:0007049 ! cell cycle is_a: GO:0022414 ! reproductive process intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140013 ! meiotic nuclear division relationship: has_part GO:0140013 ! meiotic nuclear division relationship: part_of GO:0019953 ! sexual reproduction property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24599" xsd:anyURI [Term] id: GO:0051322 name: anaphase namespace: biological_process def: "The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Anaphase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0000279 ! M phase [Term] id: GO:0051323 name: metaphase namespace: biological_process def: "The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Metaphase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0000279 ! M phase [Term] id: GO:0051324 name: prophase namespace: biological_process def: "The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Prophase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0000279 ! M phase [Term] id: GO:0051325 name: interphase namespace: biological_process def: "The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "karyostasis" EXACT [] synonym: "resting phase" BROAD [] xref: Wikipedia:Interphase is_a: GO:0022403 ! cell cycle phase [Term] id: GO:0051326 name: telophase namespace: biological_process def: "The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate xref: Wikipedia:Telophase is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0000279 ! M phase [Term] id: GO:0051327 name: meiotic M phase namespace: biological_process def: "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "M phase of meiotic cell cycle" EXACT [] is_a: GO:0000279 ! M phase is_a: GO:0098762 ! meiotic cell cycle phase intersection_of: GO:0000279 ! M phase intersection_of: happens_during GO:0051321 ! meiotic cell cycle [Term] id: GO:0051328 name: meiotic interphase namespace: biological_process def: "The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "interphase of meiotic cell cycle" EXACT [] is_a: GO:0051325 ! interphase is_a: GO:0098762 ! meiotic cell cycle phase intersection_of: GO:0051325 ! interphase intersection_of: happens_during GO:0051321 ! meiotic cell cycle [Term] id: GO:0051329 name: mitotic interphase namespace: biological_process def: "The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "interphase of mitotic cell cycle" EXACT [] is_a: GO:0051325 ! interphase is_a: GO:0098763 ! mitotic cell cycle phase intersection_of: GO:0051325 ! interphase intersection_of: happens_during GO:0000278 ! mitotic cell cycle [Term] id: GO:0051330 name: meiotic G1 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "G1 phase of meiotic cell cycle" EXACT [] is_a: GO:0051318 ! G1 phase relationship: part_of GO:0051328 ! meiotic interphase [Term] id: GO:0051331 name: meiotic G2 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "G2 phase of meiotic cell cycle" EXACT [] is_a: GO:0051319 ! G2 phase relationship: part_of GO:0051328 ! meiotic interphase [Term] id: GO:0051332 name: meiotic S phase namespace: biological_process def: "The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle." [GOC:mtg_cell_cycle] 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). subset: gocheck_do_not_annotate synonym: "premeiotic S-phase" EXACT [] synonym: "S phase of meiotic cell cycle" EXACT [] synonym: "S-phase of meiotic cell cycle" EXACT [] is_a: GO:0051320 ! S phase relationship: part_of GO:0051328 ! meiotic interphase [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] subset: goslim_flybase_ribbon subset: goslim_metagenomics synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah] synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah] synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] id: GO:0098762 name: meiotic cell cycle phase namespace: biological_process def: "One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:dos] 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). subset: gocheck_do_not_annotate is_a: GO:0022403 ! cell cycle phase intersection_of: GO:0022403 ! cell cycle phase intersection_of: happens_during GO:0051321 ! meiotic cell cycle relationship: happens_during GO:0051321 ! meiotic cell cycle [Term] id: GO:0098763 name: mitotic cell cycle phase namespace: biological_process def: "One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:dos] 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). subset: gocheck_do_not_annotate is_a: GO:0022403 ! cell cycle phase intersection_of: GO:0022403 ! cell cycle phase intersection_of: happens_during GO:0000278 ! mitotic cell cycle relationship: happens_during GO:0000278 ! mitotic cell cycle [Term] id: GO:0098764 name: meiosis I cell cycle phase namespace: biological_process def: "A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs." [GOC:dos] 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). subset: gocheck_do_not_annotate is_a: GO:0098762 ! meiotic cell cycle phase [Term] id: GO:0098765 name: meiosis II cell cycle phase namespace: biological_process def: "A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division)." [GOC:dos] 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). subset: gocheck_do_not_annotate is_a: GO:0098762 ! meiotic cell cycle phase [Term] id: GO:0140013 name: meiotic nuclear division namespace: biological_process def: "One of the two nuclear divisions that occur as part of the meiotic cell cycle." [PMID:9334324] subset: goslim_generic synonym: "meiosis" EXACT [] is_a: GO:0000280 ! nuclear division is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0051321 ! meiotic cell cycle property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI created_by: pg creation_date: 2017-03-23T09:40:00Z [Term] id: GO:0140014 name: mitotic nuclear division namespace: biological_process def: "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [ISBN:0198547684] subset: goslim_chembl subset: goslim_generic synonym: "mitosis" EXACT [] is_a: GO:0000280 ! nuclear division is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] id: GO:1903046 name: meiotic cell cycle process namespace: biological_process def: "A process that is part of the meiotic cell cycle." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie] subset: gocheck_do_not_annotate subset: goslim_pombe is_a: GO:0022402 ! cell cycle process is_a: GO:0022414 ! reproductive process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0051321 ! meiotic cell cycle disjoint_from: GO:1903047 ! mitotic cell cycle process relationship: part_of GO:0051321 ! meiotic cell cycle created_by: jl creation_date: 2014-05-22T14:22:28Z [Term] id: GO:1903047 name: mitotic cell cycle process namespace: biological_process def: "A process that is part of the mitotic cell cycle." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie] subset: gocheck_do_not_annotate is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] id: IAO:0000027 name: data item def: "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." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string [Term] id: IAO:0000028 name: symbol def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "symbol" xsd:string property_value: IAO:0000112 "a serial number such as \"12324X\"" xsd:string property_value: IAO:0000112 "a stop sign" xsd:string property_value: IAO:0000112 "a written proper name such as \"OBI\"" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000119 "based on Oxford English Dictionary" xsd:string [Term] id: IAO:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] is_a: BFO:0000031 ! generically dependent continuant relationship: IAO:0000136 BFO:0000001 ! is about entity property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000116 "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).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000119 "OBI_0000142" xsd:string [Term] id: IAO:0000078 name: curation status specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 "GROUP:OBI:" xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: IAO:0000102 name: data about an ontology part def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000225 name: obsolescence reason specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "denotator type" xsd:string property_value: 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." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [Term] id: IAO:0000577 name: centrally registered identifier symbol def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." [] is_a: IAO:0000028 ! symbol relationship: part_of IAO:0000578 ! centrally registered identifier property_value: 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." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID symbol" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string [Term] id: IAO:0000578 name: centrally registered identifier def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." [] is_a: IAO:0020000 ! identifier relationship: has_part IAO:0000577 ! centrally registered identifier symbol property_value: 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." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "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')." xsd:string property_value: IAO:0000116 "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation." xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string [Term] id: IAO:0000579 name: centrally registered identifier registry def: "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." [] is_a: IAO:0020020 ! code set property_value: IAO:0000112 "PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID registry" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020000 name: identifier def: "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." [] 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) is_a: IAO:0000030 ! information content entity intersection_of: IAO:0000030 ! information content entity intersection_of: IAO:0000219 BFO:0000001 ! denotes entity intersection_of: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process relationship: IAO:0000219 BFO:0000001 ! denotes entity relationship: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process property_value: dc-creator "Mathias Brochhausen" xsd:string property_value: IAO:0000111 "identifier" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "proper name" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020010 name: identifier creating process def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000299 IAO:0020000 ! has_specified_output identifier relationship: OBI:0000299 IAO:0020000 ! has_specified_output identifier property_value: dc-creator "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "dubbing process" xsd:string property_value: IAO:0000118 "naming" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020020 name: code set def: "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." [] 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.\n\nWhen 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 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: 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: 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. is_a: IAO:0000030 ! information content entity relationship: has_part IAO:0020000 ! identifier property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Clint Dowland" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matt Diller" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "code map" xsd:string property_value: IAO:0000118 "code system" xsd:string property_value: IAO:0000118 "codeset" xsd:string property_value: IAO:0000118 "coding system" xsd:string property_value: IAO:0000118 "controlled vocabulary" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: OBI:0000011 name: planned process def: "A process that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] is_a: BFO:0000020 ! specifically dependent continuant property_value: IAO:0000589 "quality (PATO)" xsd:string [Term] id: PATO:0000051 name: morphology namespace: quality def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0000052 name: shape namespace: quality alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] 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. subset: attribute_slim synonym: "relational shape quality" EXACT [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000133 name: orientation namespace: quality alt_id: PATO:0000137 def: "A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object." [PATOC:JE] subset: attribute_slim subset: relational_slim synonym: "amount of rotation" RELATED [] synonym: "angle" RELATED [] synonym: "angular magnitude" RELATED [] synonym: "angular placement" EXACT [] synonym: "plane angle" RELATED [] is_a: PATO:0000140 ! position [Term] id: PATO:0000140 name: position namespace: quality alt_id: PATO:0001032 alt_id: PATO:0001631 def: "A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity." [PATOC:GVG] subset: attribute_slim synonym: "location" EXACT [] synonym: "placement" EXACT [] synonym: "relational spatial quality" EXACT [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001018 name: physical quality namespace: quality alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] xref: Wikipedia:Physical_property is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001241 name: physical object quality namespace: quality alt_id: PATO:0001237 alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] 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. synonym: "monadic quality of a continuant" EXACT [] synonym: "monadic quality of an object" NARROW [] synonym: "monadic quality of continuant" NARROW [] synonym: "multiply inhering quality of a physical entity" EXACT [] synonym: "quality of a continuant" EXACT [] synonym: "quality of a single physical entity" EXACT [] synonym: "quality of an object" EXACT [] synonym: "quality of continuant" EXACT [] xref: snap:Quality is_a: PATO:0000001 ! quality [Term] id: PATO:0001875 name: triangular namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's having three angles." [wordreference:wordreference] subset: cell_quality subset: value_slim synonym: "delta shaped" RELATED [] synonym: "deltoid" EXACT [] synonym: "triangle" RELATED [] synonym: "triangle-shaped" RELATED [] is_a: PATO:0002006 ! 2-D shape [Term] id: PATO:0001955 name: cuneate namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base." [wordreference:wordreference] subset: value_slim synonym: "wedge-shaped" EXACT [] is_a: PATO:0001875 ! triangular [Term] id: PATO:0002006 name: 2-D shape namespace: quality def: "A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity." [PATOC:CJM] subset: attribute_slim synonym: "2-D projection" RELATED [] synonym: "cross-sectional" RELATED [] is_a: PATO:0000052 ! shape [Term] id: PATO:0005024 name: longitudinal orientation namespace: quality def: "An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis." [PATOC:WD] subset: value_slim is_a: PATO:0000133 ! orientation property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 creation_date: 2014-10-17T14:24:19Z [Term] id: PATO:0040012 name: plug shaped namespace: quality def: "A shape that is in the form of a plug, being tube-like and expanded on one end." [https://orcid.org/0000-0003-3162-7490] synonym: "plug like" EXACT [] is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/elements/1.1/date "2018-11-12T18:24:41Z" xsd:dateTime property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: PLANA:0000001 name: Stage 1 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium." [PMID:28072387] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000002 name: Stage 2 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall." [PMID:28072387] synonym: "protosphere" EXACT [] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/Stage2.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000003 name: Stage 3 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity." [PMID:28072387] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/Stage3.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000004 name: Stage 4 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation." [PMID:28072387] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/stage4.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000005 name: Stage 5 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity." [PMID:28072387] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/stage5.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000006 name: Stage 6 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation." [PMID:28072387] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/stage6.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000007 name: Stage 7 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility." [PMID:28072387] xref: PMID:28072387 xref: PMID:28812561 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/stage7.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000008 name: Stage 8 namespace: Schmidtea_mediterranea_Developmental_Stages def: "A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching." [PMID:28072387] synonym: "hatchling" EXACT [] synonym: "newborn hatchling" EXACT [] xref: PMID:28072387 is_a: UBERON:0000068 ! embryo stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/stage8.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000009 name: sigma neoblast def: "A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors." [PMID:25017721] synonym: "sigma class neoblast" EXACT [] synonym: "sigma-class neoblast" EXACT [] xref: PMID:15972844 xref: PMID:25017721 xref: PMID:25956527 xref: PMID:26457503 xref: PMID:26651295 xref: PMID:27013241 xref: PMID:27150006 xref: PMID:27542689 xref: PMID:28287248 xref: PMID:28686611 xref: PMID:28757112 xref: PMID:29557542 xref: PMID:29674432 xref: PMID:29906446 is_a: PLANA:0000429 ! neoblast created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000011 name: protonephridial progenitor cell def: "Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr,required for maintenance and regeneration of protonephridial cell types." [PMID:24523458, PMID:28072387] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000020 ! develops into protonephridia relationship: RO:0002203 PLANA:0000020 ! develops into protonephridia [Term] id: PLANA:0000012 name: neural progenitor cell def: "Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system." [PMID:21282632, PMID:24173799, PMID:25356635, PMID:26057828, PMID:26525673, PMID:28072387, PMID:29674432] synonym: "neural committed stem cell" EXACT [] synonym: "neural precursor cell" EXACT [] synonym: "neural progenitor cell" EXACT [] synonym: "neuronal progenitor" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000025 ! develops into nervous system relationship: RO:0002203 PLANA:0000025 ! develops into nervous system [Term] id: PLANA:0000013 name: visceral musculature def: "Musculature surrounding internal organs of the body." [PMID:26904543, PMID:30471994] synonym: "visceral muscle" EXACT [] xref: FBbt:00005070 xref: PMID:26904543 xref: PMID:30471994 is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000428 ! musculature system property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/visceralmusculature.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000014 name: zeta neoblast def: "An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s)." [PMID:25017721] synonym: "zeta" EXACT [] synonym: "zeta class" EXACT [] synonym: "zeta class neoblast" EXACT [] synonym: "zeta-class neoblast" EXACT [] synonym: "zeta-neoblast" EXACT [] xref: PMID:25017721 xref: PMID:25956527 xref: PMID:26457503 xref: PMID:26651295 xref: PMID:27013241 xref: PMID:27150006 xref: PMID:27542689 xref: PMID:28292427 xref: PMID:28757112 xref: PMID:28807897 xref: PMID:29158443 xref: PMID:29557542 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:29906446 is_a: PLANA:0000033 ! epidermal progenitor cell is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0004529 ! integumental system relationship: RO:0002202 PLANA:0000009 ! develops from sigma neoblast created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000015 name: non ciliated epithelial cell def: "An epithelial cell lacking cilia." [] xref: XAO:0004225 is_a: PLANA:0000100 ! epithelial cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nonciliatedepithelialcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000016 name: pharynx def: "A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types." [OCLC:16809160] synonym: "definitive pharynx" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:15866156 xref: PMID:16033796 xref: PMID:16311336 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17376870 xref: PMID:17390146 xref: PMID:17670787 xref: PMID:17905225 xref: PMID:17942485 xref: PMID:18063755 xref: PMID:18063757 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:18456843 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:19211673 xref: PMID:19247960 xref: PMID:19766622 xref: PMID:19852954 xref: PMID:19933103 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:20422023 xref: PMID:20511647 xref: PMID:20599901 xref: PMID:20707997 xref: PMID:20865784 xref: PMID:20967238 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21295483 xref: PMID:21356107 xref: PMID:21458439 xref: PMID:21664348 xref: PMID:21747960 xref: PMID:21806978 xref: PMID:21828097 xref: PMID:21852957 xref: PMID:21894189 xref: PMID:21937596 xref: PMID:22125640 xref: PMID:22339734 xref: PMID:22371573 xref: PMID:22385657 xref: PMID:22411224 xref: PMID:22439894 xref: PMID:22451003 xref: PMID:22543868 xref: PMID:22884275 xref: PMID:23079596 xref: PMID:23123964 xref: PMID:23250205 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23405188 xref: PMID:23629965 xref: PMID:23652002 xref: PMID:23954785 xref: PMID:24040508 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24238224 xref: PMID:24704339 xref: PMID:24737865 xref: PMID:24922054 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25558068 xref: PMID:25725068 xref: PMID:25956527 xref: PMID:26062938 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26459857 xref: PMID:26525673 xref: PMID:26711341 xref: PMID:27034770 xref: PMID:27063937 xref: PMID:27074666 xref: PMID:27122174 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27240733 xref: PMID:27441386 xref: PMID:27501047 xref: PMID:27551436 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:27654173 xref: PMID:28072387 xref: PMID:28126842 xref: PMID:28171748 xref: PMID:28245923 xref: PMID:28287248 xref: PMID:28292427 xref: PMID:28434803 xref: PMID:28461239 xref: PMID:28495872 xref: PMID:28686611 xref: PMID:28807897 xref: PMID:28893948 xref: PMID:29291981 xref: PMID:29674431 xref: PMID:29906446 xref: PMID:30194301 xref: PMID:30237141 xref: PMID:30282036 xref: PMID:30383829 xref: PMID:30399335 xref: PMID:30471994 xref: PMID:30485821 xref: PMID:30729158 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000049 ! digestive system relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000017 name: photoreceptor neuron def: "Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain." [PMID:21852957, PMID:22884275] synonym: "neuronal photoreceptive cell" EXACT [] synonym: "optical neuron" EXACT [] synonym: "photoreceptive neuron" EXACT [] synonym: "photoreceptor cell" EXACT [] synonym: "photosensitive cell" EXACT [] synonym: "PRN" EXACT [] synonym: "visual neuron" EXACT [] xref: ISBN:9780070316607 xref: PMID:16033796 xref: PMID:17251262 xref: PMID:17390146 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:17942485 xref: PMID:18202849 xref: PMID:19048075 xref: PMID:20967238 xref: PMID:21282632 xref: PMID:21852957 xref: PMID:22339734 xref: PMID:22411224 xref: PMID:22427692 xref: PMID:22445864 xref: PMID:22549959 xref: PMID:22884275 xref: PMID:23250205 xref: PMID:23318641 xref: PMID:24063805 xref: PMID:24922054 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25493551 xref: PMID:25772472 xref: PMID:26017970 xref: PMID:26618653 xref: PMID:27068018 xref: PMID:27606067 xref: PMID:27612384 xref: PMID:27800171 xref: PMID:28137894 xref: PMID:28216315 xref: PMID:28245923 xref: PMID:28495872 xref: PMID:28976975 xref: PMID:29547123 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:30143032 xref: PMID:30399335 xref: PMID:30471994 xref: PMID:30485821 xref: UBERON:0006562 is_a: BFO:0000040 ! material entity is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000036 ! eye relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002202 PLANA:0000095 ! develops from trail cell relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000018 name: Category 4 cell def: "Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells." [PMID:25017721, PMID:26457503] xref: PMID:18786419 xref: PMID:22439894 xref: PMID:25017721 xref: PMID:26457503 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000015 ! non ciliated epithelial cell is_a: PLANA:0000033 ! epidermal progenitor cell is_a: PLANA:0002032 ! epidermal cell relationship: part_of PLANA:0000054 ! dorsal region of the epidermis relationship: part_of PLANA:0000096 ! ventral epidermis relationship: part_of PLANA:0002063 ! non-ciliated epidermis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000035 ! develops from Category 3 cell relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000019 name: muscle progenitor cell def: "Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers." [PMID:25017721] xref: PMID:29674431 xref: PMID:29674432 xref: PMID:30471994 is_a: PLANA:0000120 ! progenitor cell relationship: part_of PLANA:0000428 ! musculature system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000020 name: protonephridia def: "Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct." [OCLC:16809160, PMID:21828097, PMID:26057828] synonym: "excretory organ" EXACT [] synonym: "nephridia" EXACT [] synonym: "osmoregulatory duct" EXACT [] synonym: "protonephridial tubule" EXACT [] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:19852954 xref: PMID:19933103 xref: PMID:21828097 xref: PMID:21937596 xref: PMID:22479207 xref: PMID:23318635 xref: PMID:23318641 xref: PMID:23954785 xref: PMID:24063805 xref: PMID:24523458 xref: PMID:24737865 xref: PMID:24992682 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:26057828 xref: PMID:26457503 xref: PMID:26651295 xref: PMID:26711341 xref: PMID:27068018 xref: PMID:27150006 xref: PMID:27501047 xref: PMID:27551436 xref: PMID:27612384 xref: PMID:28245923 xref: PMID:28292427 xref: PMID:28807897 xref: PMID:29100657 xref: PMID:29158443 xref: PMID:29674431 xref: PMID:29674432 xref: UBERON:0006973 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000088 ! renal system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000011 ! develops from protonephridial progenitor cell relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/protonephridia.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000021 name: biotype def: "Organisms sharing a specified genotype or karyotype." [] created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000022 name: Category 5 cell def: "Post-mitotic, ciliated epidermal cells." [PMID:25017721] xref: PMID:25017721 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell is_a: PLANA:0002032 ! epidermal cell relationship: part_of PLANA:0000054 ! dorsal region of the epidermis relationship: part_of PLANA:0000096 ! ventral epidermis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000018 ! develops from Category 4 cell relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000023 name: embryonic pharynx def: "An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7." [PMID:28072387] synonym: "temporary embryonic pharynx" EXACT [] xref: FBbt:00001866 xref: ISBN:9780070316607 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0002120 ! extraembryonic organ relationship: part_of PLANA:0000058 ! embryonic digestive system relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/temporaryembryonicpharynx.gif {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms in on the embryonic pharynx."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000024 name: Smed asexual biotype def: "Asexual animal strains that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed." [PMID:11972158, PMID:17376870] synonym: "asexual" EXACT [] synonym: "asexual adult" EXACT [] synonym: "asexual biotype" EXACT [] xref: PMID:11972158 xref: PMID:28812561 is_a: PLANA:0000021 ! biotype property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/asexualadult.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000025 name: nervous system def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [UBERON:0001016] synonym: "nerve system" EXACT [] xref: ISBN:9780070316607 xref: PMID:16033796 xref: PMID:16311336 xref: PMID:17251262 xref: PMID:18202849 xref: PMID:19048075 xref: PMID:19211673 xref: PMID:19247960 xref: PMID:20223763 xref: PMID:20707997 xref: PMID:20967238 xref: PMID:21806978 xref: PMID:22339734 xref: PMID:22427692 xref: PMID:22445864 xref: PMID:22549959 xref: PMID:22696458 xref: PMID:23079596 xref: PMID:23250205 xref: PMID:23297191 xref: PMID:23318641 xref: PMID:23903188 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24737865 xref: PMID:24950970 xref: PMID:25254346 xref: PMID:25278423 xref: PMID:25725068 xref: PMID:26062938 xref: PMID:26114597 xref: PMID:26556349 xref: PMID:27013241 xref: PMID:27068018 xref: PMID:27163480 xref: PMID:27501047 xref: PMID:27523733 xref: PMID:27551436 xref: PMID:27612384 xref: PMID:27864883 xref: PMID:28292427 xref: PMID:29357350 xref: PMID:29557542 xref: PMID:29674431 xref: PMID:30399335 xref: UBERON:0001016 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000026 name: gut def: "The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the gut through the pharynx." [PMID:3490491] synonym: "adult gut" EXACT [] synonym: "blind gut" EXACT [] synonym: "definitive gut" EXACT [] synonym: "digestive tract" EXACT [] synonym: "gastrovascular digestive tract" EXACT [] synonym: "gastrovascular tract" EXACT [] synonym: "intestinal tract" EXACT [] synonym: "intestine" EXACT [] synonym: "three-branched gut" EXACT [] synonym: "triclad gut" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:17553481 xref: PMID:17942485 xref: PMID:18063757 xref: PMID:18287199 xref: PMID:19174194 xref: PMID:19247960 xref: PMID:19933103 xref: PMID:20707997 xref: PMID:20865784 xref: PMID:20967238 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21356107 xref: PMID:21458439 xref: PMID:21566185 xref: PMID:21566195 xref: PMID:21664348 xref: PMID:21806978 xref: PMID:21828097 xref: PMID:22411224 xref: PMID:22439894 xref: PMID:22451003 xref: PMID:22899852 xref: PMID:23079596 xref: PMID:23235145 xref: PMID:23250205 xref: PMID:23318635 xref: PMID:23318641 xref: PMID:23405188 xref: PMID:23903188 xref: PMID:23954785 xref: PMID:24040508 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24173799 xref: PMID:24238224 xref: PMID:24415944 xref: PMID:24737865 xref: PMID:24950970 xref: PMID:24992682 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25558068 xref: PMID:25956527 xref: PMID:26062938 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26556349 xref: PMID:26651295 xref: PMID:27034770 xref: PMID:27063937 xref: PMID:27074666 xref: PMID:27122174 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27240733 xref: PMID:27441386 xref: PMID:27501047 xref: PMID:27542689 xref: PMID:27551436 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:27864883 xref: PMID:28072387 xref: PMID:28216315 xref: PMID:28245923 xref: PMID:28287248 xref: PMID:28292427 xref: PMID:28461239 xref: PMID:28686611 xref: PMID:28807897 xref: PMID:29100657 xref: PMID:29158443 xref: PMID:29547123 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:29906446 xref: PMID:30143032 xref: PMID:30194301 xref: PMID:30282036 xref: PMID:30297872 xref: PMID:30383829 xref: PMID:30471994 xref: PMID:30962434 xref: UBERON:0000160 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000049 ! digestive system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000039 ! develops from gamma neoblast relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000027 name: Smed sexual biotype def: "Strains of cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids." [PMID:11972158, PMID:19022767] synonym: "hermaphroditic biotype" EXACT [] synonym: "sexual" EXACT [] synonym: "sexual hermaphrodite" EXACT [] xref: PMID:11972158 xref: PMID:19022767 xref: PMID:28812561 is_a: PLANA:0000021 ! biotype property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/smedsexualbiotype.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000028 name: Category 2 cell def: "Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts." [PMID:18786419, PMID:20040488, PMID:22385657, PMID:25017721, PMID:26114597] synonym: "Category 2 gene expressing cell" EXACT [] synonym: "early division progeny" EXACT [] synonym: "early epidermal progenitor" EXACT [] synonym: "early neoblast progeny" EXACT [] synonym: "early post-mitotic progeny" EXACT [] synonym: "early progeny" EXACT [] synonym: "NB.21.11e expressing cell" EXACT [] synonym: "prog-1+ epidermal progenitor cell" EXACT [] synonym: "Smed-NB.21.11e+ cell" EXACT [] xref: PMID:18786419 xref: PMID:20040488 xref: PMID:21894189 xref: PMID:22385657 xref: PMID:22427692 xref: PMID:22439894 xref: PMID:22899852 xref: PMID:23318635 xref: PMID:23629965 xref: PMID:24063805 xref: PMID:24173799 xref: PMID:24367277 xref: PMID:25017721 xref: PMID:26114597 xref: PMID:26651295 xref: PMID:27013241 xref: PMID:27068018 xref: PMID:27542689 xref: PMID:28072387 xref: PMID:29674431 is_a: BFO:0000040 ! material entity is_a: PLANA:0000033 ! epidermal progenitor cell is_a: PLANA:0002095 ! somatic cell relationship: part_of PLANA:0004529 ! integumental system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000014 ! develops from zeta neoblast relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000029 name: primitive ectoderm def: "A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md, OCLC:20423827, OCLC:464776945, OCLC:82522822] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md xref: OCLC:20423827 xref: OCLC:464776945 xref: OCLC:82522822 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0002120 ! extraembryonic organ relationship: RO:0001018 PLANA:0000041 ! contained in aboral hemisphere relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000030 name: midline def: "The median line/ plane of bilateral symmetry along the anteroposterior axis." [] xref: NCIT:C81170 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000102 ! anatomical region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/midline.png {comment="Illustration of the midline (in green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000031 name: pigment cup cell def: "Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup." [PMID:21852957, PMID:22884275] synonym: "eye pigment cell" EXACT [] synonym: "eye pigment cup cell" EXACT [] synonym: "eye pigment producing cell" EXACT [] synonym: "eye pigmented cell" EXACT [] synonym: "melanin pigment cell" EXACT [] synonym: "optic cup cell" EXACT [] synonym: "photoceptor pigmented cell" EXACT [] xref: PMID:17251262 xref: PMID:17390146 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:20967238 xref: PMID:21282632 xref: PMID:21458439 xref: PMID:21852957 xref: PMID:22339734 xref: PMID:22445864 xref: PMID:22884275 xref: PMID:23250205 xref: PMID:23318641 xref: PMID:24063805 xref: PMID:25254346 xref: PMID:25493551 xref: PMID:26017970 xref: PMID:27122174 xref: PMID:27551436 xref: PMID:27606067 xref: PMID:28137894 xref: PMID:28245923 xref: PMID:28287248 xref: PMID:28495872 xref: PMID:28976975 xref: PMID:29158443 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:30471994 is_a: BFO:0000040 ! material entity is_a: PLANA:0000561 ! neuron associated cell (sensu Nematoda and Protostomia) relationship: part_of PLANA:0000075 ! optic cup relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002202 PLANA:0000095 ! develops from trail cell relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000032 name: dorsal midline def: "The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal." [] synonym: "dorsal region of midline" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0000030 ! contained in midline relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0000030 ! contained in midline property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalmidline.png {comment="Illustration of the dorsal midline (in green)."} [Term] id: PLANA:0000033 name: epidermal progenitor cell def: "Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs." [PMID:27150006, PMID:27606067, PMID:29674432, PMID:30282036] synonym: "epithelial progenitor" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000032 ! develops into dorsal midline relationship: RO:0002203 PLANA:0000032 ! develops into dorsal midline [Term] id: PLANA:0000034 name: epidermis def: "A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal." [OCLC:16809160] comment: At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium). synonym: "definitive epidermis" EXACT [] synonym: "epidermal layer" EXACT [] synonym: "epidermis" EXACT [] synonym: "epithelium" EXACT [] synonym: "mature epidermis" EXACT [] synonym: "tegument" EXACT [] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:15866156 xref: PMID:16311336 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:19247960 xref: PMID:19852954 xref: PMID:20215344 xref: PMID:20511647 xref: PMID:20599901 xref: PMID:20865784 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21295483 xref: PMID:22252539 xref: PMID:22549959 xref: PMID:23235145 xref: PMID:23297191 xref: PMID:23954785 xref: PMID:24120894 xref: PMID:24173799 xref: PMID:24922054 xref: PMID:24950970 xref: PMID:25558068 xref: PMID:25772472 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26651295 xref: PMID:26711341 xref: PMID:27034770 xref: PMID:27074666 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27240733 xref: PMID:27501047 xref: PMID:27612384 xref: PMID:28137894 xref: PMID:28216315 xref: PMID:28245923 xref: PMID:28292427 xref: PMID:28686611 xref: PMID:28757112 xref: PMID:28976975 xref: PMID:29100657 xref: PMID:29158443 xref: PMID:29273738 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:29906446 xref: PMID:30194301 xref: PMID:30282036 xref: PMID:30962434 xref: UBERON:0001003 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0004529 ! integumental system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000033 ! develops from epidermal progenitor cell relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000035 name: Category 3 cell def: "Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells." [PMID:18786419, PMID:20040488, PMID:26114597, PMID:26457503] synonym: "AGAT-1 expressing cell" EXACT [] synonym: "AGAT1 expressing cell" EXACT [] synonym: "Category 3 gene expressing cell" EXACT [] synonym: "late division progeny" EXACT [] synonym: "late epidermal progenitor" EXACT [] synonym: "late neoblast progeny" EXACT [] synonym: "late postmitotic progeny" EXACT [] synonym: "late progeny" EXACT [] synonym: "Smed-AGAT-1+ cell" EXACT [] xref: PMID:18786419 xref: PMID:20040488 xref: PMID:21894189 xref: PMID:22252539 xref: PMID:22427692 xref: PMID:22439894 xref: PMID:22899852 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23629965 xref: PMID:23954785 xref: PMID:24063805 xref: PMID:24173799 xref: PMID:24367277 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26651295 xref: PMID:27013241 xref: PMID:27068018 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000033 ! epidermal progenitor cell is_a: PLANA:0002095 ! somatic cell relationship: part_of PLANA:0004529 ! integumental system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000028 ! develops from Category 2 cell relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/epidermis.png created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000036 name: eye def: "An organ that detects light." [UBERON:0000970] comment: Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um synonym: "cerebral eye" EXACT [] synonym: "eye spot" EXACT [] synonym: "eye-spot" EXACT [] synonym: "eyespot" EXACT [] synonym: "ocelli" EXACT [] synonym: "photoreceptor" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:15866156 xref: PMID:15972844 xref: PMID:16311336 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:17942485 xref: PMID:18063755 xref: PMID:18063757 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:18456843 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:19211673 xref: PMID:19247960 xref: PMID:19766622 xref: PMID:19805089 xref: PMID:19852954 xref: PMID:20040488 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:20422023 xref: PMID:20599901 xref: PMID:20707997 xref: PMID:20865784 xref: PMID:20967238 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21295481 xref: PMID:21295483 xref: PMID:21356107 xref: PMID:21458439 xref: PMID:21566185 xref: PMID:21566195 xref: PMID:21747960 xref: PMID:21806978 xref: PMID:21828097 xref: PMID:21852957 xref: PMID:21894189 xref: PMID:21937596 xref: PMID:22125640 xref: PMID:22318224 xref: PMID:22339734 xref: PMID:22385657 xref: PMID:22411224 xref: PMID:22439894 xref: PMID:22445864 xref: PMID:22479207 xref: PMID:22549959 xref: PMID:22884275 xref: PMID:22899852 xref: PMID:23235145 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23318641 xref: PMID:23405188 xref: PMID:23629965 xref: PMID:23903188 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24238224 xref: PMID:24415944 xref: PMID:24704339 xref: PMID:24737865 xref: PMID:24922054 xref: PMID:24950970 xref: PMID:24992682 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25493551 xref: PMID:25558068 xref: PMID:25725068 xref: PMID:25772472 xref: PMID:25956527 xref: PMID:26017970 xref: PMID:26062938 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26525673 xref: PMID:26556349 xref: PMID:26618653 xref: PMID:26711341 xref: PMID:26884331 xref: PMID:27034770 xref: PMID:27063937 xref: PMID:27150006 xref: PMID:27240733 xref: PMID:27542689 xref: PMID:27551436 xref: PMID:27606067 xref: PMID:27654173 xref: PMID:27800171 xref: PMID:28171748 xref: PMID:28216315 xref: PMID:28287248 xref: PMID:28292427 xref: PMID:28495872 xref: PMID:28686611 xref: PMID:28893948 xref: PMID:28976975 xref: PMID:29100657 xref: PMID:29158443 xref: PMID:29273738 xref: PMID:29291974 xref: PMID:29291981 xref: PMID:29357350 xref: PMID:29547123 xref: PMID:29674431 xref: PMID:30237141 xref: PMID:30282036 xref: PMID:30297872 xref: PMID:30383829 xref: PMID:30485821 xref: PMID:30962434 xref: UBERON:0000970 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000103 ! central nervous system relationship: part_of PLANA:0000124 ! visual system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002202 PLANA:0000095 ! develops from trail cell relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/eye.png created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000037 name: obsolete definitive tissue comment: we will move forward using "tissue" instead. We have not listed anything as a regenerating or developing tissue, so this seems unnecessary is_obsolete: true replaced_by: PLANA:0000113 [Term] id: PLANA:0000038 name: ventral midline def: "The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal." [] synonym: "ventral region of midline" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0000030 ! contained in midline relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0000030 ! contained in midline property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralmidline.png {comment="Illustration of the ventral midline (in green)."} [Term] id: PLANA:0000039 name: gamma neoblast def: "An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut." [PMID:25017721] synonym: "gamma" EXACT [] synonym: "gamma class neoblast" EXACT [] synonym: "gamma-neoblast" EXACT [] synonym: "gut progenitor cell" EXACT [] xref: PMID:25017721 xref: PMID:26651295 xref: PMID:27013241 xref: PMID:27150006 xref: PMID:27542689 xref: PMID:28287248 xref: PMID:28757112 xref: PMID:28807897 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:29906446 is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000049 ! digestive system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000040 name: obsolete Schmidtea mediterranea developmental stage 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 is_obsolete: true [Term] id: PLANA:0000041 name: aboral hemisphere def: "Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx." [PMID:28072387] xref: PMID:28072387 xref: UBERON:0008259 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000423 ! embryonic subdivision relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000042 name: anterior primary gut branch def: "The single, central gut branch of the triclad gut anterior to the pharynx." [PMID:3490491] xref: PMID:21664348 xref: PMID:3490491 is_a: BFO:0000040 ! material entity is_a: PLANA:0002086 ! primary gut branch relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorprimarygutbranch.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000043 name: dorsal ventral margin of the whole animal def: "Region along the edge of the animal where the dorsal and ventral surfaces meet." [ISBN:9780070316607, PMID:17905225, PMID:19174194, PMID:20865784, PMID:21295481, PMID:21295483, PMID:21458439, PMID:22549959, PMID:22696458, PMID:24415944, PMID:26457503, PMID:28216315, PMID:29357350, PMID:29674431, PMID:29674432, PMID:30399335, PMID:30485821] synonym: "body edge" EXACT [] synonym: "body margin" EXACT [] synonym: "body periphery" EXACT [] synonym: "D/V boundary" EXACT [] synonym: "dorsal ventral boundary" EXACT [] synonym: "dorsal-ventral boundary" EXACT [] synonym: "dorsal/ventral compartment boundary of whole organism" EXACT [] synonym: "dorsoventral margin" EXACT [] synonym: "DV border" EXACT [] synonym: "DV boundary" EXACT [] synonym: "DV domain" EXACT [] synonym: "DV margin" EXACT [] synonym: "edge" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000094 ! dorsal/ventral compartment boundary intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000094 ! dorsal/ventral compartment boundary relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalventralmarginofthewholeanimal.png [Term] id: PLANA:0000044 name: cephalic ganglia def: "The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head." [] synonym: "bi-lobed brain" EXACT [] synonym: "bi-lobed cephalic ganglia" EXACT [] synonym: "brain" EXACT [] synonym: "cerebral ganglia" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:15866156 xref: PMID:16033796 xref: PMID:16344473 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17376870 xref: PMID:17553481 xref: PMID:17670787 xref: PMID:17905225 xref: PMID:17942485 xref: PMID:17999079 xref: PMID:18063755 xref: PMID:18063757 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:19211673 xref: PMID:19247960 xref: PMID:19766622 xref: PMID:20215344 xref: PMID:20422023 xref: PMID:20844018 xref: PMID:20967238 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21295481 xref: PMID:21458439 xref: PMID:21566195 xref: PMID:21806978 xref: PMID:22074376 xref: PMID:22125640 xref: PMID:22339734 xref: PMID:22411224 xref: PMID:22445864 xref: PMID:22451003 xref: PMID:22549959 xref: PMID:23235145 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23318641 xref: PMID:23405188 xref: PMID:23652002 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24238224 xref: PMID:24415944 xref: PMID:24950970 xref: PMID:25254346 xref: PMID:25278423 xref: PMID:25356635 xref: PMID:25404302 xref: PMID:25725068 xref: PMID:25772472 xref: PMID:25956527 xref: PMID:26017970 xref: PMID:26884331 xref: PMID:27013241 xref: PMID:27074666 xref: PMID:27163480 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:27800171 xref: PMID:28072387 xref: PMID:28126842 xref: PMID:28216315 xref: PMID:28287248 xref: PMID:29291974 xref: PMID:29291981 xref: PMID:29547123 xref: PMID:29674431 xref: PMID:30194301 xref: PMID:30237141 xref: UBERON:0000955 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000103 ! central nervous system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000045 name: circular muscle cell def: "Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md, PMID:26904543] synonym: "circular muscle fiber" EXACT [] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md xref: PMID:26904543 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000240 ! body wall musculature relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000130 ! develops from circular muscle progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/circularmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000046 name: clonogenic neoblast def: "Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm." [PMID:21566185] synonym: "adult pluripotent stem cell" EXACT [] synonym: "clonogenic stem cell" EXACT [] synonym: "cNeoblast" EXACT [] synonym: "pluripotent stem cell" EXACT [] xref: PMID:16344473 xref: PMID:19247960 xref: PMID:20215344 xref: PMID:21566185 xref: PMID:21852957 xref: PMID:21937596 xref: PMID:22318224 xref: PMID:22385657 xref: PMID:22411224 xref: PMID:22543868 xref: PMID:22549959 xref: PMID:22884275 xref: PMID:22899852 xref: PMID:23079596 xref: PMID:23297191 xref: PMID:23318641 xref: PMID:23652002 xref: PMID:23954785 xref: PMID:24040508 xref: PMID:24120894 xref: PMID:24173799 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:26711341 xref: PMID:27063937 xref: PMID:27074666 xref: PMID:27149082 xref: PMID:27150006 xref: PMID:27502555 xref: PMID:27523733 xref: PMID:27551436 xref: PMID:28434803 xref: PMID:29357350 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:29906446 xref: PMID:30962434 is_a: PLANA:0000429 ! neoblast is_a: PLANA:0002095 ! somatic cell relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000047 name: collecting duct def: "Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis." [PMID:26057828] synonym: "collection duct" EXACT [] xref: PMID:26057828 xref: PMID:27068018 xref: PMID:29674431 xref: UBERON:0001232 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: adjacent_to PLANA:0000053 ! distal tubule relationship: part_of PLANA:0000088 ! renal system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/collectingduct.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000048 name: diagonal muscle cell def: "Body wall muscle fibers arrayed diagonally along the anteroposterior axis." [PMID:26904543] synonym: "diagonal fiber" EXACT [] synonym: "diagonal muscle" EXACT [] synonym: "diagonal muscle fiber" EXACT [] xref: ISBN:9780070316607 xref: PMID:23903188 xref: PMID:26904543 xref: PMID:27068018 xref: PMID:28461239 xref: PMID:28807897 xref: PMID:30471994 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000240 ! body wall musculature relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/diagonalmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000049 name: digestive system def: "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [UBERON:0001007] synonym: "gastrointestinal system" EXACT [] synonym: "gastrovascular system" EXACT [] xref: ISBN:9780070316607 xref: PMID:15866156 xref: PMID:16311336 xref: PMID:16344473 xref: PMID:17390146 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:18063757 xref: PMID:18287199 xref: PMID:19048075 xref: PMID:19247960 xref: PMID:19766622 xref: PMID:19933103 xref: PMID:20040488 xref: PMID:20215344 xref: PMID:20707997 xref: PMID:21356107 xref: PMID:21664348 xref: PMID:21806978 xref: PMID:22451003 xref: PMID:22479207 xref: PMID:23079596 xref: PMID:24737865 xref: PMID:24922054 xref: PMID:25254346 xref: PMID:25558068 xref: PMID:26556349 xref: PMID:27068018 xref: PMID:27501047 xref: PMID:29357350 xref: UBERON:0001007 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000051 name: obsolete direct development comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000052 name: obsolete dispersed cleavage comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000053 name: distal tubule def: "Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells." [PMID:21828097] xref: PMID:21828097 xref: PMID:27068018 xref: UBERON:0004135 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: adjacent_to PLANA:0000047 ! collecting duct relationship: part_of PLANA:0000020 ! protonephridia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000011 ! develops from protonephridial progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/distaltubule.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000054 name: dorsal region of the epidermis def: "Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe." [ISBN:9780070316607, PMID:17942485, PMID:19048075, PMID:19852954, PMID:20599901, PMID:20844018, PMID:22385657, PMID:22479207, PMID:26457503, PMID:27612382, PMID:28292427] synonym: "dorsal epithelium" EXACT [] synonym: "dorsal region of epidermis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0000034 ! contained in epidermis relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0000034 ! contained in epidermis property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalepidermis.png {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."} [Term] id: PLANA:0000055 name: dorsal stripe def: "Ciliated epithelial cells along the dorsal midline." [PMID:17553481] synonym: "racing stripe" EXACT [] xref: PMID:17553481 is_a: BFO:0000040 ! material entity is_a: PLANA:0002023 ! ciliated epithelium relationship: part_of PLANA:0000054 ! dorsal region of the epidermis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalstripe.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000056 name: ectolecithal embryo def: "Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md, PMID:22074376, PMID:27149082] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md xref: PMID:22074376 xref: PMID:27149082 is_a: PLANA:0000116 ! embryo created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000057 name: obsolete embryonic cleavage comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000058 name: embryonic digestive system def: "A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals." [PMID:28072387] xref: PMID:28072387 xref: UBERON:6001842 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000063 ! extraembryonic structure relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000007 ! existence ends during or before Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000059 name: embryonic gut cell def: "Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0002031 ! embryonic gut relationship: RO:0001018 PLANA:0000041 ! contained in aboral hemisphere relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000004 ! existence starts during or after Stage 4 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000060 name: embryonic wall def: "The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos." [OCLC:16809160, PMID:12888018] xref: OCLC:16809160 xref: PMID:12888018 xref: PMID:28072387 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000423 ! embryonic subdivision relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000005 ! existence ends during or before Stage 5 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/embryonicwall.png {comment="Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000061 name: enteric musculature def: "Visceral muscle surrounding the gut." [] synonym: "enteric muscle" EXACT [] synonym: "intestinal muscle" EXACT [] xref: PMID:21664348 xref: PMID:22411224 xref: PMID:23079596 xref: PMID:26904543 xref: PMID:30471994 xref: PMID:30962434 xref: UBERON:2001324 is_a: BFO:0000040 ! material entity is_a: PLANA:0000013 ! visceral musculature relationship: part_of PLANA:0000049 ! digestive system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/entericmusculature.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000062 name: esophagus def: "Attachment between the triclad gut and the proximal end of the pharynx." [] synonym: "gut pharynx intersection" EXACT [] synonym: "pharynx root" EXACT [] synonym: "root of pharynx" EXACT [] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:18063757 xref: PMID:20707997 xref: PMID:21806978 xref: PMID:24737865 xref: PMID:27063937 xref: PMID:29674431 xref: PMID:30485821 xref: UBERON:0001043 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000063 name: extraembryonic structure def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [UBERON:0000478] xref: UBERON:0000478 is_a: UBERON:0005423 ! developing anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000064 name: flame bulb def: "Terminal structure of protonephridia unit; consists of flame cells." [] xref: PMID:21828097 xref: PMID:26057828 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000020 ! protonephridia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000011 ! develops from protonephridial progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/flamebulb.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000065 name: flame cell def: "Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin." [OCLC:16809160, PMID:21828097, PMID:26057828] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:17670787 xref: PMID:19247960 xref: PMID:19852954 xref: PMID:21828097 xref: PMID:21937596 xref: PMID:24523458 xref: PMID:26057828 xref: PMID:26711341 xref: PMID:27068018 xref: PMID:27542689 xref: PMID:29674431 xref: PMID:29674432 is_a: BFO:0000040 ! material entity is_a: PLANA:0000119 ! terminally differentiated cell relationship: adjacent_to PLANA:0000087 ! proximal tubule relationship: part_of PLANA:0000064 ! flame bulb relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/flamecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000066 name: gastrodermis def: "The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle." [PMID:3490491] synonym: "gut epithelia" EXACT [] synonym: "gut epithelium" EXACT [] synonym: "intestinal epithelium" EXACT [] xref: BTO:0000509 xref: ISBN:9780070316607 xref: PMID:21282632 xref: PMID:21664348 xref: PMID:24120894 xref: PMID:25558068 xref: PMID:27441386 xref: PMID:27501047 xref: PMID:28287248 xref: PMID:30608231 is_a: BFO:0000040 ! material entity is_a: PLANA:0002118 ! epithelium relationship: part_of PLANA:0000026 ! gut relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000039 ! develops from gamma neoblast relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000067 name: goblet cell def: "Secretory cells that release digestive enzymes into the lumen of the intestine." [PMID:3490491] xref: BTO:0001540 xref: PMID:20865784 xref: PMID:21664348 xref: PMID:23079596 xref: PMID:27501047 xref: PMID:28137894 xref: PMID:28287248 xref: PMID:29674431 xref: PMID:29674432 is_a: BFO:0000040 ! material entity is_a: PLANA:0000105 ! secretory cell relationship: part_of PLANA:0000066 ! gastrodermis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/gobletcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000068 name: embryonic gut cavity def: "Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0002553 ! anatomical cavity relationship: part_of PLANA:0002031 ! embryonic gut relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000007 ! existence ends during or before Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000069 name: inner longitudinal muscle cell def: "Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md, PMID:26904543] synonym: "inner longitudinal muscle fiber" EXACT [] synonym: "inner longitudinal muscle layer" EXACT [] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md xref: ISBN:9780070316607 xref: PMID:26904543 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000071 ! longitudinal muscle cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000134 ! develops from longitudinal muscle progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000070 name: intestinal phagocyte def: "Absorptive digestive cells that engulf food particles for intracellular digestion." [PMID:3490491] synonym: "enterocyte" EXACT [] synonym: "gut enterocyte" EXACT [] synonym: "gut phagocyte" EXACT [] synonym: "intestinal epithelial cell" EXACT [] xref: PMID:19933103 xref: PMID:21664348 xref: PMID:23079596 xref: PMID:27542689 xref: PMID:28072387 xref: PMID:29674431 xref: PMID:29674432 is_a: BFO:0000040 ! material entity is_a: PLANA:0000119 ! terminally differentiated cell relationship: part_of PLANA:0000066 ! gastrodermis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000071 name: longitudinal muscle cell def: "Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md, PMID:26904543] synonym: "body wall longitudinal fiber" EXACT [] synonym: "BW longitudinal fiber" EXACT [] synonym: "longitudinal fiber" EXACT [] synonym: "longitudinal muscle" EXACT [] synonym: "longitudinal muscle cell" EXACT [] synonym: "longitudinal muscle fiber" EXACT [] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md xref: ISBN:9780070316607 xref: PMID:23903188 xref: PMID:26904543 xref: PMID:27551436 xref: PMID:28461239 xref: PMID:28807897 xref: PMID:30471994 is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000240 ! body wall musculature property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/longitudinalmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000072 name: mouth def: "The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells." [OCLC:16809160] synonym: "anus" EXACT [] synonym: "manus" EXACT [] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:17251262 xref: PMID:17905225 xref: PMID:18287199 xref: PMID:19174194 xref: PMID:19211673 xref: PMID:20707997 xref: PMID:21295481 xref: PMID:21458439 xref: PMID:21806978 xref: PMID:23954785 xref: PMID:26457503 xref: PMID:26556349 xref: PMID:27034770 xref: PMID:27063937 xref: PMID:27074666 xref: PMID:27122174 xref: PMID:28807897 xref: PMID:29674431 xref: PMID:30399335 xref: PMID:30471994 xref: PMID:30485821 xref: UBERON:0000165 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000049 ! digestive system relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/mouth.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000074 name: oocyte def: "A female germ cell that has entered meiosis." [CL:0000023] synonym: "egg" EXACT [] synonym: "female gamete" EXACT [] synonym: "ovum" EXACT [] xref: CL:0000023 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27330085 xref: PMID:27501047 xref: PMID:28072387 xref: PMID:28434803 xref: PMID:28812561 is_a: PLANA:0000122 ! gamete is_a: PLANA:0000229 ! female germ cell relationship: part_of PLANA:0000204 ! ovary relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002202 PLANA:0000239 ! develops from oogonial cell relationship: RO:0003001 PLANA:0000204 ! produced by ovary created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000075 name: optic cup def: "A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons." [PMID:21852957, PMID:22884275] synonym: "eye cup" EXACT [] synonym: "photoreceptor pigment cup" EXACT [] synonym: "photoreceptor pigmentation" EXACT [] synonym: "pigment cup" EXACT [] synonym: "pigmented cell cup" EXACT [] synonym: "pigmented optic cup" EXACT [] xref: ISBN:9780070316607 xref: PMID:15866156 xref: PMID:20707997 xref: PMID:20865784 xref: PMID:21458439 xref: PMID:21828097 xref: PMID:21852957 xref: PMID:22411224 xref: PMID:22427692 xref: PMID:22445864 xref: PMID:22549959 xref: PMID:22884275 xref: PMID:25493551 xref: PMID:26017970 xref: PMID:26618653 xref: PMID:27068018 xref: PMID:27240733 xref: PMID:27542689 xref: PMID:27606067 xref: PMID:27800171 xref: PMID:28495872 xref: PMID:29547123 xref: PMID:30143032 xref: PMID:30194301 xref: UBERON:0003072 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000036 ! eye relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000076 name: oral hemisphere def: "Stage 3-5 embryo hemisphere centered around the embryonic pharynx." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000423 ! embryonic subdivision relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/oralhemisphere.png {comment="Illustration of the oral hemispshere (in green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000078 name: outer longitudinal muscle cell def: "Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md, PMID:26904543] synonym: "outer longitudinal muscle layer" EXACT [] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md xref: ISBN:9780070316607 xref: PMID:26904543 is_a: BFO:0000040 ! material entity is_a: PLANA:0000071 ! longitudinal muscle cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000134 ! develops from longitudinal muscle progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000079 name: parenchymal musculature def: "Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles." [OCLC:16809160] synonym: "dorsoventral muscle fibers" EXACT [] synonym: "parenchymal muscle" EXACT [] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000428 ! musculature system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/parenchymalmusculature.png {comment="Image is an electron micrograph of the parenchyma. Three muscle cells have been notated with an arrowhead. Scale bar is 2 um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000080 name: peripheral nervous system def: "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [UBERON:0000010] xref: PMID:20967238 xref: PMID:22339734 xref: PMID:23903188 xref: PMID:26017970 xref: PMID:26884331 xref: PMID:27150006 xref: PMID:27612382 xref: PMID:29674431 xref: UBERON:0000010 is_a: PLANA:0000025 ! nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000081 name: pharynx pouch def: "An epithelial structure housing the pharynx, connected to the esophagus and mouth." [OCLC:16809160] synonym: "pharyngeal pocket" EXACT [] synonym: "pharyngeal pouch" EXACT [] xref: OCLC:16809160 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000082 name: obsolete racing stripe comment: racing stripe is now a synonym of PLANA:0000055 dorsal stripe is_obsolete: true [Term] id: PLANA:0000084 name: posterior primary gut branch def: "The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch." [PMID:3490491] synonym: "major posterior gut branch" EXACT [] synonym: "primary posterior intestinal branch" EXACT [] xref: PMID:21664348 xref: PMID:23318641 xref: PMID:24063805 is_a: BFO:0000040 ! material entity is_a: PLANA:0002086 ! primary gut branch relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000039 ! develops from gamma neoblast relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorprimarygutbranch.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000085 name: primitive gut cell def: "A phagocytic cell closely associated with the embryonic pharynx." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0002087 ! primitive gut relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000005 ! existence ends during or before Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000086 name: obsolete protosphere comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000087 name: proximal tubule def: "Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma." [PMID:21828097] xref: PMID:21828097 xref: PMID:21937596 xref: PMID:26057828 xref: PMID:27068018 xref: UBERON:0004134 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: adjacent_to PLANA:0000053 ! distal tubule relationship: adjacent_to PLANA:0000065 ! flame cell relationship: part_of PLANA:0000020 ! protonephridia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000011 ! develops from protonephridial progenitor cell relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/proximaltubule.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000088 name: renal system def: "The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products." [UBERON:0001008] synonym: "excretory system" EXACT [] synonym: "protonephridial system" EXACT [] xref: ISBN:9780070316607 xref: PMID:17670787 xref: PMID:19048075 xref: PMID:19247960 xref: PMID:19852954 xref: PMID:20707997 xref: PMID:21828097 xref: PMID:21937596 xref: PMID:22427692 xref: PMID:23079596 xref: PMID:23235145 xref: PMID:23903188 xref: PMID:24173799 xref: PMID:24523458 xref: PMID:24737865 xref: PMID:25254346 xref: PMID:26057828 xref: PMID:26711341 xref: PMID:27068018 xref: PMID:27542689 xref: PMID:28461239 xref: PMID:29674431 xref: PMID:30297872 xref: UBERON:0001008 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000089 name: secondary gut branch def: "Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge." [PMID:3490491] xref: PMID:21664348 xref: PMID:27122174 xref: PMID:28287248 xref: PMID:30471994 is_a: PLANA:0002119 ! gut branch property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/secondarygutbranch.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000090 name: sperm def: "A mature male germ cell that develops from a spermatid." [CL:0000019] synonym: "mature sperm" EXACT [] synonym: "spermatozoa" EXACT [] xref: CL:0000019 xref: https://doi.org/10.1101/279364 xref: PMID:17390146 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:28072387 xref: PMID:29095551 is_a: PLANA:0000122 ! gamete is_a: PLANA:0000228 ! male germ cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000238 ! develops from elongate spermatid relationship: RO:0003001 PLANA:0000208 ! produced by testis created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000091 name: obsolete sphere formation comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000092 name: yolk syncytium def: "Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2." [PMID:15599763] synonym: "syncytial yolk cell" EXACT [] xref: PMID:15599763 is_a: BFO:0000040 ! material entity is_a: PLANA:0002136 ! syncytium relationship: RO:0002490 PLANA:0000001 ! existence overlaps Stage 1 relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002496 PLANA:0000001 ! existence starts during or after Stage 1 relationship: RO:0002497 PLANA:0000002 ! existence ends during or before Stage 2 relationship: RO:0003001 PLANA:0000107 ! produced by yolk cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000093 name: tertiary gut branch def: "Gut branches originating from and connected to the secondary gut branches." [PMID:3490491] synonym: "tertiary branch" EXACT [] synonym: "tertiary intestinal branch" EXACT [] xref: PMID:21664348 xref: PMID:23250205 xref: PMID:27122174 xref: PMID:28137894 xref: PMID:28287248 xref: PMID:30194301 xref: PMID:30471994 is_a: PLANA:0002119 ! gut branch property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/tertiarygutbranch.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000094 name: obsolete tissue morphogenesis comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000095 name: trail cell def: "Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup." [PMID:22884275] synonym: "eye progenitor" EXACT [] synonym: "eye progenitor cell" EXACT [] synonym: "ovo+ eye progenitor" EXACT [] xref: PMID:21852957 xref: PMID:22884275 xref: PMID:23250205 xref: PMID:24040508 xref: PMID:27606067 xref: PMID:28072387 xref: PMID:28245923 xref: PMID:29674431 xref: PMID:30485821 is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000124 ! visual system relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000096 name: ventral epidermis def: "Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells" [ISBN:9780070316607, PMID:15866156, PMID:17942485, PMID:19852954, PMID:20599901, PMID:21282632, PMID:23144623, PMID:23903188, PMID:24523458, PMID:25017721, PMID:26457503, PMID:26912790, PMID:27068018, PMID:28292427, PMID:29100657, PMID:30383829, PMID:30962434] synonym: "cilated ventral epidermis" EXACT [] synonym: "ciliated ventral epithelium" EXACT [] synonym: "ventral epidermin" EXACT [] synonym: "ventral epithelia" EXACT [] synonym: "ventral epithelium" EXACT [] synonym: "ventral region of epidermis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0000034 ! contained in epidermis relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0000034 ! contained in epidermis [Term] id: PLANA:0000097 name: ventral nerve cord def: "The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]." [UBERON:0000934] synonym: "nerve cord" EXACT [] synonym: "ventral cord" EXACT [] synonym: "VNC" EXACT [] xref: BTO:0002328 xref: EFO:0000896 xref: FBbt:00001102 xref: http://en.wikipedia.org/wiki/Ventral\:nerve\:cord xref: ISBN:9780070316607 xref: MAT:0000339 xref: MIAA:0000339 xref: nlx:146329 xref: PMID:16033796 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17390146 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:18063755 xref: PMID:18063757 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:19174194 xref: PMID:19211673 xref: PMID:19247960 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:20422023 xref: PMID:20599901 xref: PMID:20707997 xref: PMID:20967238 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21566185 xref: PMID:21806978 xref: PMID:21828097 xref: PMID:22074376 xref: PMID:22125640 xref: PMID:22339734 xref: PMID:22479207 xref: PMID:23250205 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23954785 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24950970 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25558068 xref: PMID:25772472 xref: PMID:25956527 xref: PMID:26017970 xref: PMID:26062938 xref: PMID:26457503 xref: PMID:26556349 xref: PMID:27013241 xref: PMID:27034770 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27612382 xref: PMID:28072387 xref: PMID:28126842 xref: PMID:28245923 xref: PMID:28807897 xref: PMID:29291974 xref: PMID:29674431 xref: PMID:30143032 xref: PMID:30471994 xref: UBERON:0000934 xref: WBbt:0005829 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000103 ! central nervous system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000098 name: zygote def: "Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]." [CL:0000365] xref: BTO:0000854 xref: CL:0000365 xref: PMID:28812561 xref: UBERON:0000106 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000136 ! whole organism relationship: RO:0002490 PLANA:0000001 ! existence overlaps Stage 1 relationship: RO:0002496 PLANA:0000001 ! existence starts during or after Stage 1 relationship: RO:0002497 PLANA:0000001 ! existence ends during or before Stage 1 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000099 name: neuron def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [CL:0000540] synonym: "differentiated neuron" EXACT [] synonym: "nerve cell" EXACT [] synonym: "neural cell" EXACT [] synonym: "neuronal cell" EXACT [] xref: BTO:0000938 xref: CL:0000540 xref: NCIT:C12623 xref: PMID:16033796 xref: PMID:16890156 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:19211673 xref: PMID:20215344 xref: PMID:21566185 xref: PMID:22411224 xref: PMID:22439894 xref: PMID:22479207 xref: PMID:22549959 xref: PMID:23297191 xref: PMID:23903188 xref: PMID:23954785 xref: PMID:24040508 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24737865 xref: PMID:24922054 xref: PMID:24950970 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25558068 xref: PMID:26457503 xref: PMID:26525673 xref: PMID:27013241 xref: PMID:27063937 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27542689 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:27864883 xref: PMID:28072387 xref: PMID:28126842 xref: PMID:28137894 xref: PMID:28245923 xref: PMID:28292427 xref: PMID:28461239 xref: PMID:28807897 xref: PMID:29100657 xref: PMID:29184198 xref: PMID:29291974 xref: PMID:29291981 xref: PMID:29357350 xref: PMID:29674432 xref: PMID:30143032 xref: PMID:30399335 xref: WBbt:0003679 is_a: PLANA:0000540 ! electrically signaling cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000100 name: epithelial cell def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina." [CL:0000066] synonym: "epidermis cell" EXACT [] xref: CL:0000066 xref: PMID:18202849 xref: PMID:19048075 xref: PMID:20865784 xref: PMID:22479207 xref: PMID:24737865 xref: PMID:26114597 xref: PMID:28072387 xref: PMID:28461239 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000101 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [CL:0000187] synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: CL:0000187 xref: PMID:15972844 xref: PMID:18202849 xref: PMID:19174194 xref: PMID:20422023 xref: PMID:20511647 xref: PMID:21458439 xref: PMID:21828097 xref: PMID:22252539 xref: PMID:22479207 xref: PMID:23318641 xref: PMID:23405188 xref: PMID:23954785 xref: PMID:24415944 xref: PMID:24737865 xref: PMID:25254346 xref: PMID:25558068 xref: PMID:26062938 xref: PMID:27063937 xref: PMID:27523733 xref: PMID:28216315 xref: PMID:28287248 xref: PMID:28292427 xref: PMID:28461239 xref: PMID:28686611 xref: PMID:28807897 xref: PMID:28893948 xref: PMID:30471994 xref: PMID:30962434 is_a: PLANA:0000539 ! electrically responsive cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/musclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000102 name: anatomical region def: "A subdivision of an anatomical compartment." [] synonym: "body region" EXACT [] xref: BSPO:0000070 xref: PMID:28292427 xref: PMID:29547123 is_a: UBERON:0000475 ! organism subdivision created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000103 name: central nervous system def: "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord." [UBERON:0001017] synonym: "CNS" EXACT [] synonym: "head-restricted nervous system" EXACT [] xref: https://doi.org/10.1101/279364 xref: PMID:16033796 xref: PMID:16344473 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17553481 xref: PMID:17670787 xref: PMID:17905225 xref: PMID:17942485 xref: PMID:18063757 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:19174194 xref: PMID:19247960 xref: PMID:19933103 xref: PMID:20865784 xref: PMID:20967238 xref: PMID:21282632 xref: PMID:21295481 xref: PMID:21458439 xref: PMID:21664348 xref: PMID:21806978 xref: PMID:21828097 xref: PMID:22125640 xref: PMID:22252539 xref: PMID:22339734 xref: PMID:22385657 xref: PMID:22411224 xref: PMID:22427692 xref: PMID:22439894 xref: PMID:22445864 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23318641 xref: PMID:23903188 xref: PMID:24063805 xref: PMID:24173799 xref: PMID:24367277 xref: PMID:24704339 xref: PMID:24737865 xref: PMID:24922054 xref: PMID:24950970 xref: PMID:25356635 xref: PMID:25493551 xref: PMID:25772472 xref: PMID:25956527 xref: PMID:26017970 xref: PMID:26459857 xref: PMID:26711341 xref: PMID:26884331 xref: PMID:27013241 xref: PMID:27063937 xref: PMID:27068018 xref: PMID:27074666 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27240733 xref: PMID:27523733 xref: PMID:27542689 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:27800171 xref: PMID:27864883 xref: PMID:28126842 xref: PMID:28434803 xref: PMID:28461239 xref: PMID:28807897 xref: PMID:28976975 xref: PMID:29273738 xref: PMID:29291981 xref: PMID:30399335 xref: PMID:30471994 xref: PMID:30729158 xref: PMID:30962434 xref: UBERON:0001017 is_a: PLANA:0000025 ! nervous system relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000104 name: rhabdite def: "Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions." [OCLC:16809160] xref: OCLC:16809160 is_a: PLANA:0000430 ! epithelial cell component property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/rhabdite.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000105 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [CL:0000151] xref: CL:0000151 xref: NCIT:C13055 is_a: PLANA:0000119 ! terminally differentiated cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/secretorycell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000106 name: ciliated epithelial cell def: "An epithelial cell that has cilia." [CL:0000067] synonym: "ciliated epidermal cell" EXACT [] xref: CL:0000067 xref: PMID:24737865 xref: PMID:28461239 xref: PMID:28807897 is_a: PLANA:0000100 ! epithelial cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000107 name: yolk cell def: "An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo." [PMID:27149082] synonym: "vitellocyte" EXACT [] xref: CL:0000428 xref: ISBN:9780070316607 xref: PMID:22074376 xref: PMID:27149082 xref: PMID:28072387 xref: PMID:28434803 xref: PMID:29674431 is_a: PLANA:0000119 ! terminally differentiated cell is_a: PLANA:0000215 ! reproductive system product relationship: part_of PLANA:0000060 ! embryonic wall relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0003001 PLANA:0000231 ! produced by vitelline gland created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000109 name: obsolete anatomical compartment subdivision feature comment: extra layer of complexity not needed upon further examination is_obsolete: true [Term] id: PLANA:0000110 name: pharynx progenitor cell def: "foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx." [PMID:24737865, PMID:25254346] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000016 ! develops into pharynx relationship: RO:0002203 PLANA:0000016 ! develops into pharynx [Term] id: PLANA:0000111 name: proximal tubule epithelial cell def: "Ciliated epithelial cells that assemble into proximal tubules." [PMID:21828097] synonym: "proximal tubule cell" EXACT [] xref: BTO:0006154 xref: PMID:21828097 xref: PMID:29674431 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell relationship: part_of PLANA:0000087 ! proximal tubule relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/proximaltubuleepithelialcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000112 name: obsolete Schmidtea mediterranea developmental term comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000113 name: tissue def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [UBERON:0000479] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md xref: UBERON:0000479 is_a: PLANA:0000427 ! multicellular anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000114 name: anatomical system def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [UBERON:0000467] xref: UBERON:0000467 is_a: PLANA:0000427 ! multicellular anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000115 name: distal tubule epithelial cell def: "Nonciliated epithelial cells that assemble into protonephridial distal tubules." [PMID:21828097] synonym: "distal tubule cell" EXACT [] xref: PMID:21828097 xref: PMID:29674431 is_a: BFO:0000040 ! material entity is_a: PLANA:0000015 ! non ciliated epithelial cell relationship: part_of PLANA:0000053 ! distal tubule relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/distaltubuleepithelialcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000116 name: embryo def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [UBERON:0000922] xref: UBERON:0000922 is_a: PLANA:0000136 ! whole organism is_a: PLANA:0000215 ! reproductive system product created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000117 name: embryonic structure def: "Anatomical structure that is part of an embryo." [UBERON:0002050] xref: BTO:0000174 xref: UBERON:0002050 is_a: UBERON:0005423 ! developing anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000118 name: collecting duct epithelial cell def: "Nonciliated epithelial cells that assemble into collecting ducts." [PMID:26057828] xref: PMID:26057828 is_a: BFO:0000040 ! material entity is_a: PLANA:0000015 ! non ciliated epithelial cell relationship: part_of PLANA:0000047 ! collecting duct relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/collectingduct.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000119 name: terminally differentiated cell def: "A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals." [] xref: PMID:29674432 is_a: PLANA:0002095 ! somatic cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000120 name: progenitor cell def: "A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program" [] synonym: "precursor cell" EXACT [] xref: https://doi.org/10.1101/279364 xref: PMID:21852957 xref: PMID:29674432 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000499 ! cell relationship: RO:0002202 PLANA:0000429 ! develops from neoblast created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000121 name: stem cell def: "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [CL:0000034] xref: CL:0000034 xref: https://doi.org/10.1101/279364 xref: PMID:17376870 xref: PMID:19805089 xref: PMID:20422023 xref: PMID:20707997 xref: PMID:21937596 xref: PMID:22385657 xref: PMID:23123964 xref: PMID:23318635 xref: PMID:24063805 xref: PMID:24173799 xref: PMID:26062938 xref: PMID:26651295 xref: PMID:26711341 xref: PMID:27013241 xref: PMID:27034770 xref: PMID:27501047 xref: PMID:29124009 is_a: PLANA:0000499 ! cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000122 name: gamete def: "A mature sexual reproductive cell having a single set of unpaired chromosomes." [CL:0000300] xref: CL:0000300 xref: PMID:20844018 xref: PMID:23652002 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:28434803 is_a: PLANA:0000215 ! reproductive system product is_a: PLANA:0000227 ! germ cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0003001 PLANA:0000217 ! produced by gonad created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000123 name: embryonic cell def: "A cell of the embryo." [CL:0002321] xref: CL:0002321 is_a: PLANA:0000499 ! cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000124 name: visual system def: "The sensory system subserving the sense of vision." [UBERON:0002104] xref: UBERON:0002104 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000125 name: sensory system def: "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." [UBERON:0001032] xref: UBERON:0001032 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000126 name: reproductive system def: "Anatomical system that has as its parts the organs concerned with reproduction." [UBERON:0000990] xref: UBERON:0000990 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000127 name: oviduct epithelial cell def: "Ciliated epithelial cells that assemble into the oviduct." [PMID:22074376] xref: PMID:22074376 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell relationship: part_of PLANA:0004532 ! oviduct epithelium relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000128 name: sperm duct epithelial cell def: "Ciliated epithelial cells comprising the sperm ducts." [PMID:19022767, PMID:22074376] xref: PMID:19022767 xref: PMID:22074376 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell relationship: part_of PLANA:0004533 ! sperm duct epithelium relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000129 name: obsolete anatomical structure comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000061 [Term] id: PLANA:0000130 name: circular muscle progenitor cell def: "piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers." [PMID:29168507] xref: PMID:29168507 is_a: PLANA:0000019 ! muscle progenitor cell is_a: PLANA:0000429 ! neoblast is_a: PLANA:0002095 ! somatic cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000131 name: primordium def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue." [UBERON:0001048] xref: UBERON:0001048 is_a: UBERON:0007567 ! regenerating anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000132 name: obsolete gametogenesis comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000133 name: mechanoreceptor cell def: "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." [PMID:18202849, PMID:7466176] synonym: "mechanoreceptor" EXACT [] xref: PMID:18202849 xref: PMID:7466176 is_a: PLANA:0000552 ! sensory neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000134 name: longitudinal muscle progenitor cell def: "piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers." [PMID:29168507] xref: PMID:29168507 is_a: PLANA:0000019 ! muscle progenitor cell is_a: PLANA:0000429 ! neoblast created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000135 name: female primordial germ cell def: "Cells expressing nanos that are located ventrally in the location that the ovaries form. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with oogonial stem cell." [PMID:17390146] xref: PMID:17390146 is_a: BFO:0000040 ! material entity is_a: PLANA:0000121 ! stem cell is_a: PLANA:0000229 ! female germ cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000136 name: whole organism def: "Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria." [UBERON:0000468] synonym: "intact animal" EXACT [] synonym: "intact planarian" EXACT [] synonym: "whole animal" EXACT [] synonym: "whole body" EXACT [] synonym: "whole worm" EXACT [] synonym: "WW" EXACT [] xref: PMID:17251262 xref: PMID:26711341 xref: PMID:27502555 xref: PMID:28976975 xref: PMID:29906446 xref: UBERON:0000468 is_a: UBERON:0000061 ! anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000137 name: regeneration def: "The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass)." [GO:0031099] synonym: "regernative development" EXACT [] xref: GO:0031099 xref: GOC:mah xref: GOC:pr xref: Wikipedia:Regeneration\:(biology) is_a: GO:0048856 ! anatomical structure development created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000138 name: Hyman vesicle def: "PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites." [PMID:29100657] xref: PMID:29100657 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002137 ! intracellular granule relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/hymanvesicle.png {comment="Image is an immunoelectron micrograph depicting hyman vesicles in the apical side of an epidermal cell. Scale bar is 1um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000140 name: anterior region of the whole animal def: "Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus." [ISBN:9780070316607, OCLC:16809160, PMID:16033796, PMID:16311336, PMID:17251262, PMID:17376870, PMID:17390146, PMID:18063757, PMID:18456843, PMID:18786419, PMID:19048075, PMID:19174194, PMID:19211673, PMID:19247960, PMID:19766622, PMID:19805089, PMID:19852954, PMID:19933103, PMID:20215344, PMID:20422023, PMID:21282632, PMID:21295481, PMID:21356107, PMID:21566185, PMID:21806978, PMID:21828097, PMID:21852957, PMID:21894189, PMID:21937596, PMID:22339734, PMID:22385657, PMID:22439894, PMID:22479207, PMID:22696458, PMID:22899852, PMID:23250205, PMID:23297191, PMID:23318635, PMID:23405188, PMID:23629965, PMID:23903188, PMID:24040508, PMID:24063805, PMID:24367277, PMID:24415944, PMID:24523458, PMID:24950970, PMID:25017721, PMID:25278423, PMID:25356635, PMID:25493551, PMID:25558068, PMID:26062938, PMID:26114597, PMID:26556349, PMID:26651295, PMID:26884331, PMID:27013241, PMID:27034770, PMID:27063937, PMID:27074666, PMID:27150006, PMID:27240733, PMID:27612382, PMID:27612384, PMID:27800171, PMID:28072387, PMID:28287248, PMID:28893948, PMID:29273738, PMID:29547123, PMID:29557542, PMID:29906446, PMID:30143032, PMID:30471994, PMID:30485821, PMID:30962434] synonym: "anterior region of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofthewholeanimal.png {comment="Illustration of the anterior region of the whole animal (in green)."} [Term] id: PLANA:0000141 name: dorsal region of the whole animal def: "Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes." [] synonym: "dorsal region of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofthewholeanimal.png {comment="Illustration of the dorsal region of the whole animal (in green)."} [Term] id: PLANA:0000142 name: posterior region of the whole animal def: "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." [] synonym: "posterior compartment of the whole animal" EXACT [] synonym: "posterior region of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorcompartmentofthewholeanimal.png {comment="Illustration of the posterior compartement of the whole animal (in green)."} [Term] id: PLANA:0000143 name: ventral region of the whole animal def: "Compartment along the dorsoventral axis that is below the anteroposterior axis." [] synonym: "ventral region of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofthewholeanimal.png {comment="Illustration of the ventral region of the whole animal (in green)."} [Term] id: PLANA:0000201 name: bursal canal def: "The passageway connecting the genital atrium to the copulatory bursa. Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the copulatory bursa before travelling up the oviducts to the tuba." [PMID:22074376] xref: ISBN:9780070316607 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:25278423 xref: PMID:27149082 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000232 ! copulatory apparatus relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000203 name: gonopore def: "The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying." [PMID:22074376] synonym: "common gonopore" EXACT [] synonym: "genital pore" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:19247960 xref: PMID:20967238 xref: PMID:21566185 xref: PMID:22074376 xref: PMID:22899852 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:28072387 xref: PMID:28434803 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002079 ! pore relationship: part_of PLANA:0000232 ! copulatory apparatus relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000204 name: ovary def: "A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development." [PMID:17376870] synonym: "female gonad" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: NCIT:C12404 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:17390146 xref: PMID:18456843 xref: PMID:19247960 xref: PMID:20844018 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:22318224 xref: PMID:22371573 xref: PMID:23652002 xref: PMID:25278423 xref: PMID:25404302 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27330085 xref: PMID:28072387 xref: PMID:28434803 xref: PMID:28812561 is_a: BFO:0000040 ! material entity is_a: PLANA:0000217 ! gonad relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000205 name: oviduct def: "Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium." [PMID:22074376] synonym: "ovovitilline duct" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:19247960 xref: PMID:20844018 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:23652002 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0002089 ! reproductive organ relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000206 name: penis papilla def: "A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal." [PMID:22074376] synonym: "penis" EXACT [] synonym: "penis bulb" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:23652002 xref: PMID:25278423 xref: PMID:27074666 xref: PMID:28072387 xref: PMID:28434803 is_a: BFO:0000040 ! material entity is_a: PLANA:0002089 ! reproductive organ relationship: part_of PLANA:0000232 ! copulatory apparatus relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000207 name: sperm duct def: "A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles." [PMID:19022767, PMID:22074376] synonym: "seminal duct" EXACT [] synonym: "sperm ductule" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:17390146 xref: PMID:19022767 xref: PMID:19247960 xref: PMID:20844018 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:23652002 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:27304889 xref: PMID:28072387 xref: PMID:28434803 xref: ZFA:0001268 is_a: BFO:0000040 ! material entity is_a: PLANA:0002089 ! reproductive organ relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000208 name: testis def: "A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration." [PMID:19022767] synonym: "male gonad" EXACT [] synonym: "testis lobe" EXACT [] synonym: "testis lobule" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:18456843 xref: PMID:19022767 xref: PMID:19247960 xref: PMID:20844018 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:22318224 xref: PMID:22371573 xref: PMID:23629965 xref: PMID:23652002 xref: PMID:25278423 xref: PMID:25404302 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27330085 xref: PMID:28072387 xref: PMID:28434803 xref: PMID:28812561 xref: PMID:29095551 xref: UBERON:0000473 is_a: BFO:0000040 ! material entity is_a: PLANA:0000217 ! gonad relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000209 name: obsolete developing anatomical structure comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0005423 [Term] id: PLANA:0000211 name: primitive ectoderm cell def: "Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md, OCLC:20423827, OCLC:464776945, OCLC:82522822, PMID:28072387] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md xref: OCLC:20423827 xref: OCLC:464776945 xref: OCLC:82522822 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0000029 ! primitive ectoderm relationship: RO:0001018 PLANA:0000041 ! contained in aboral hemisphere relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000212 name: obsolete blastomere compartment comment: replace with blastomere only is_obsolete: true replaced_by: PLANA:0004517 [Term] id: PLANA:0000214 name: juvenile stage def: "A postnatal stage of Smed development that initiates with hatching and proceeds until sexual maturity is reached. Reproductive structures develop during the juvenile stage." [] xref: UBERON:0034919 is_a: UBERON:0000105 ! life cycle stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000215 name: reproductive system product def: "Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules." [] is_a: BFO:0000040 ! material entity is_a: UBERON:0000061 ! anatomical structure relationship: RO:0003001 PLANA:0000126 ! produced by reproductive system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000216 name: egg capsule def: "A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk." [PMID:18942102] synonym: "capsule" EXACT [] synonym: "cocoon" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:18942102 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:22371573 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:28072387 xref: PMID:28434803 xref: PMID:28812561 is_a: PLANA:0000215 ! reproductive system product relationship: RO:0003001 PLANA:0007564 ! produced by sexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000217 name: gonad def: "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." [UBERON:0000991] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:17390146 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:22252538 xref: PMID:22371573 xref: PMID:23652002 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:28434803 xref: PMID:28976975 xref: UBERON:0000991 is_a: PLANA:0002089 ! reproductive organ created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000218 name: male primordial germ cell def: "Cells coexpressing piwi-1 and nanos that are required for male gonad formation. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with spermatogonial stem cell." [PMID:17376870, PMID:17390146] xref: PMID:17376870 xref: PMID:17390146 is_a: BFO:0000040 ! material entity is_a: PLANA:0000121 ! stem cell is_a: PLANA:0000228 ! male germ cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000219 name: spermatogonial stem cell def: "gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm." [PMID:19022767, PMID:20844018, PMID:27163480, PMID:27330085] synonym: "male germline stem cell" EXACT [] synonym: "SSC" EXACT [] xref: PMID:19022767 xref: PMID:20844018 xref: PMID:27163480 xref: PMID:27330085 is_a: BFO:0000040 ! material entity is_a: PLANA:0000121 ! stem cell is_a: PLANA:0000228 ! male germ cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000429 ! develops from neoblast relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000220 name: spermatogonium def: "An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation." [PMID:27163480, PMID:27330085] synonym: "spermatogonial cell" EXACT [] xref: CL:0000020 xref: https://doi.org/10.1101/279364 xref: PMID:23629965 xref: PMID:27163480 xref: PMID:27330085 is_a: BFO:0000040 ! material entity is_a: PLANA:0000120 ! progenitor cell is_a: PLANA:0000228 ! male germ cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000219 ! develops from spermatogonial stem cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000221 name: spermatocyte def: "A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." [PMID:27330085] synonym: "primary spermatocyte" EXACT [] xref: CL:0000017 xref: PMID:17376870 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:25278423 xref: PMID:25404302 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27330085 xref: PMID:29095551 is_a: BFO:0000040 ! material entity is_a: PLANA:0000228 ! male germ cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0000220 ! develops from spermatogonium relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000222 name: spermatid def: "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." [CL:0000018] xref: CL:0000018 xref: PMID:17376870 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:25278423 xref: PMID:25404302 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27330085 is_a: BFO:0000040 ! material entity is_a: PLANA:0000228 ! male germ cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000223 name: oogonial stem cell def: "A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes." [PMID:19022767, PMID:20844018] synonym: "female germ cell" EXACT [] synonym: "female germline cell" EXACT [] synonym: "female germline stem cell" EXACT [] synonym: "oogonial stem cell" EXACT [] synonym: "ovarian germline stem cell" EXACT [] xref: PMID:23652002 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27330085 is_a: BFO:0000040 ! material entity is_a: PLANA:0000121 ! stem cell is_a: PLANA:0000229 ! female germ cell relationship: part_of PLANA:0000204 ! ovary relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002202 PLANA:0000429 ! develops from neoblast relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000224 name: cement gland def: "Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk." [ASIN:B000M4NK9M, PMID:18942102, PMID:22074376, PMID:27149082] synonym: "shell gland" EXACT [] xref: ASIN:B000M4NK9M xref: ISBN:9780070316607 xref: PMID:18942102 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:23652002 xref: PMID:25278423 xref: PMID:27149082 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000232 ! copulatory apparatus relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000225 name: obsolete oviparity comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000226 name: obsolete cross-fertilization comment: removing all processes. may bring back if PLANA expanded to cover processes. is_obsolete: true [Term] id: PLANA:0000227 name: germ cell def: "1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex." [BTO:0000535] xref: BTO:0000535 is_a: PLANA:0000499 ! cell relationship: part_of PLANA:0000126 ! reproductive system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000228 name: male germ cell def: "A male germ cell is a germ cell that supports male gamete production." [CL:0000015] xref: CL:0000015 xref: PMID:23652002 xref: PMID:27304889 xref: PMID:27330085 is_a: PLANA:0000227 ! germ cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000229 name: female germ cell def: "Female germ cell is a germ cell that supports female gamete production." [CL:0000021] xref: CL:0000021 is_a: PLANA:0000227 ! germ cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000230 name: tuba def: "A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct." [PMID:19022767, PMID:20844018, PMID:22074376, PMID:27149082] xref: PMID:19022767 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:25278423 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:28434803 is_a: BFO:0000040 ! material entity is_a: PLANA:0002089 ! reproductive organ relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000231 name: vitelline gland def: "Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules." [PMID:16932928, PMID:18942102, PMID:27149082] synonym: "vitellaria" EXACT [] synonym: "vitellarium" EXACT [] synonym: "yolk gland" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:16932928 xref: PMID:17390146 xref: PMID:18942102 xref: PMID:19247960 xref: PMID:22074376 xref: PMID:23652002 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:27501047 xref: PMID:28072387 xref: PMID:28434803 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000126 ! reproductive system relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0003000 PLANA:0000107 ! produces yolk cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000232 name: copulatory apparatus def: "Accessory reproductive structures involved in copulation, egg capsule development and laying." [PMID:22074376] synonym: "copulatory complex" EXACT [] xref: ISBN:9780070316607 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:17390146 xref: PMID:19247960 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:23652002 xref: PMID:27149082 xref: PMID:27163480 xref: PMID:28434803 is_a: BFO:0000040 ! material entity is_a: PLANA:0002090 ! reproductive structure relationship: part_of PLANA:0000126 ! reproductive system relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000233 name: copulatory bursa def: "An organ that receives and stores sperm from mating partners." [PMID:22074376] synonym: "bursa" EXACT [] synonym: "male antrum" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 xref: PMID:20967238 xref: PMID:22074376 xref: PMID:25278423 is_a: BFO:0000040 ! material entity is_a: PLANA:0002089 ! reproductive organ relationship: part_of PLANA:0000232 ! copulatory apparatus relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000234 name: seminal vesicle def: "Glandular pouches adjoining the sperm ducts which produce seminal fluid." [PMID:19022767, PMID:22074376] xref: NCIT:C12787 xref: PMID:19022767 xref: PMID:22074376 xref: UBERON:0000998 is_a: BFO:0000040 ! material entity is_a: PLANA:0002089 ! reproductive organ relationship: part_of PLANA:0000232 ! copulatory apparatus relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000237 name: round spermatid def: "A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, andundergo morphogenesis to produce mature sperm." [PMID:27163480, PMID:27330085] xref: https://doi.org/10.1101/279364 xref: PMID:20844018 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27330085 xref: PMID:29095551 is_a: PLANA:0000222 ! spermatid relationship: RO:0002202 PLANA:0000221 ! develops from spermatocyte created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000238 name: elongate spermatid def: "Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm." [PMID:27163480, PMID:27330085] synonym: "elongating spermatid" EXACT [] xref: PMID:20844018 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27330085 xref: PMID:29095551 is_a: PLANA:0000222 ! spermatid relationship: RO:0002202 PLANA:0000237 ! develops from round spermatid created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000239 name: oogonial cell def: "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." [FMA:83673] xref: FMA:83673 is_a: BFO:0000040 ! material entity is_a: PLANA:0000120 ! progenitor cell is_a: PLANA:0000229 ! female germ cell relationship: part_of PLANA:0000204 ! ovary relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002202 PLANA:0000223 ! develops from oogonial stem cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000240 name: body wall musculature def: "Any collection of muscles that is part of a body wall [Automatically generated definition]." [UBERON:0004462] synonym: "body muscle" EXACT [] synonym: "body wall muscle" EXACT [] synonym: "body wall muscles" EXACT [] synonym: "body-wall muscle" EXACT [] synonym: "body-wall musculature" EXACT [] synonym: "BWM" EXACT [] synonym: "muscle layer surrounding the body wall" EXACT [] xref: BSA:0000058 xref: BTO:0001863 xref: FMA:86931 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:21828097 xref: PMID:22385657 xref: PMID:24992682 xref: PMID:27063937 xref: PMID:27074666 xref: PMID:28171748 xref: PMID:29100657 xref: PMID:29547123 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:30471994 xref: PMID:30962434 xref: UBERON:0004462 xref: WBbt:0005813 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000428 ! musculature system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/bodywallmusculature.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000241 name: pharynx longitudinal muscle cell def: "Pharynx muscle fibers running anteroposterior (proximal to distal)." [ASIN:B000M4NK9M] synonym: "pharyngeal longitudinal muscle cell" EXACT [] synonym: "pharyngeal longitudinal muscle fiber" EXACT [] synonym: "pharynx longitudinal muscle fiber" EXACT [] xref: ASIN:B000M4NK9M is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000478 ! pharynx musculature relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxlongitudinalmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000242 name: obsolete anatomical cavity comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0002553 [Term] id: PLANA:0000400 name: obsolete anatomical entity comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0001062 [Term] id: PLANA:0000401 name: obsolete immaterial anatomical entity comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000466 [Term] id: PLANA:0000402 name: obsolete anatomical point comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0006983 [Term] id: PLANA:0000403 name: obsolete anatomical space comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000464 [Term] id: PLANA:0000404 name: pharynx lumen def: "Anatomical space enclosed by the pharynx inner epithelium." [UBERON:0000468] synonym: "cavity of pharynx" EXACT [] synonym: "pharyngeal lumen" EXACT [] synonym: "pharynx cavity" EXACT [] xref: PMID:17251262 xref: PMID:26711341 xref: PMID:27502555 xref: PMID:28976975 xref: PMID:29906446 xref: UBERON:0000468 is_a: BFO:0000141 ! immaterial entity is_a: PLANA:0002053 ! lumen relationship: immediately_deep_to PLANA:0000412 ! pharynx inner epithelium surface relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002572 PLANA:0000016 ! luminal space of pharynx property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/cavityofpharynx.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000405 name: digestive tract lumen def: "An anatomical space that is surrounded by a digestive tract." [PMID:21664348] synonym: "digestive system lumen" EXACT [] synonym: "gut cavity" EXACT [] synonym: "lumen of digestive tract" EXACT [] xref: PMID:17553481 xref: PMID:21664348 xref: PMID:21828097 xref: PMID:28072387 xref: UBERON:0006909 is_a: BFO:0000141 ! immaterial entity is_a: PLANA:0002053 ! lumen relationship: part_of PLANA:0000026 ! gut relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 relationship: RO:0002572 PLANA:0000026 ! luminal space of gut property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/lumenofdigestivetract.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000406 name: oral opening def: "The orifice that connects the mouth to the exterior of the body." [UBERON:0000166] synonym: "pharyngeal mouth opening" EXACT [] synonym: "pharynx opening" EXACT [] xref: PMID:17670787 xref: PMID:29674431 xref: PMID:30399335 xref: UBERON:0000166 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0002553 ! anatomical cavity relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: part_of PLANA:0000072 ! mouth relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000407 name: pharynx pouch cavity def: "Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch." [OCLC:16809160] synonym: "pharnygeal cavity" EXACT [] synonym: "pharyngeal pouch cavity" EXACT [] xref: OCLC:16809160 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0002553 ! anatomical cavity relationship: part_of PLANA:0000081 ! pharynx pouch relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/parapharyngealpouchcavity.png {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"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000409 name: apical surface of the epidermis def: "The apical surface of the single layered epidermis that is in contact with the environment." [] synonym: "apical surface of epidermis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000373 ! apical surface intersection_of: RO:0001018 PLANA:0000034 ! contained in epidermis relationship: overlaps BSPO:0000373 ! apical surface relationship: RO:0001018 PLANA:0000034 ! contained in epidermis property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/apicalepidermissurface.png {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."} [Term] id: PLANA:0000410 name: basal surface of the epidermis def: "The basal surface of the epidermis in direct contact with the basal lamina." [] synonym: "basal surface of epidermis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000374 ! basal surface intersection_of: RO:0001018 PLANA:0000034 ! contained in epidermis relationship: overlaps BSPO:0000374 ! basal surface relationship: RO:0001018 PLANA:0000034 ! contained in epidermis property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/basalepidermissurface.png {comment="Electron micrograph of the dorsal epidermis in a transverse plane. The basal epidermis surface is noted with magenta arrows. Scale bar is 5um."} [Term] id: PLANA:0000411 name: gastrodermis surface def: "The surface of the gastrodermis in contact with the gut lumen." [PMID:21664348] synonym: "lumen gut surface" EXACT [] xref: PMID:21664348 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0000026 ! gut relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/lumengutsurface.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000412 name: pharynx inner epithelium surface def: "The epithelial surface lining the interior of the pharynx, facing the lumen." [] synonym: "pharyngeal inner epidermis surface" EXACT [] synonym: "pharyngeal inner epithelial surface" EXACT [] synonym: "pharyngeal lumen epithelial surface" EXACT [] synonym: "pharynx inner epidermis surface" EXACT [] synonym: "pharynx lumen epithelial surface" EXACT [] xref: UBERON:0001731 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0007534 ! pharynx inner epithelium relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxinnerepitheliumsurface.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000413 name: pharynx outer epithelium surface def: "Epithelial surface covering the outside of the pharynx." [doi:10.1002/jmor.1052060308, PMID:29865769] synonym: "pharyngeal outer epidermis surface" EXACT [] synonym: "pharyngeal outer epithelial surface" EXACT [] synonym: "pharynx outer epidermis surface" EXACT [] synonym: "pharynx outer side" EXACT [] xref: doi:10.1002/jmor.1052060308 xref: PMID:24120894 xref: PMID:29865769 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0000472 ! pharynx outer epithelium relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxouterepithelium.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000414 name: pharynx pouch epithelial surface def: "The surface of the parapharyngeal pouch facing the pharynx." [OCLC:16809160] synonym: "pharyngeal pouch surface" EXACT [] synonym: "pharynx pouch surface" EXACT [] xref: OCLC:16809160 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0002140 ! pharynx pouch epithelium relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/parapharyngealpouchsurface.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000416 name: obsolete organism subdivision comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000475 [Term] id: PLANA:0000417 name: definitive organism subdivision def: "Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems." [] is_a: UBERON:0000475 ! organism subdivision created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000418 name: head region def: "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)." [] synonym: "head" EXACT [] xref: UBERON:0000033 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000102 ! anatomical region relationship: anterior_to PLANA:0000419 ! prepharyngeal region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/head.png {comment="Depicted by field contains diagram representation of body region."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000419 name: prepharyngeal region def: "Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx." [OCLC:16809160] synonym: "neck" EXACT [] synonym: "pre-pharyngeal region" EXACT [] synonym: "pre-pharynx region" EXACT [] xref: https://doi.org/10.1101/279364 xref: OCLC:16809160 xref: PMID:17251262 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:21295481 xref: PMID:21852957 xref: PMID:22339734 xref: PMID:23318641 xref: PMID:24120894 xref: PMID:24922054 xref: PMID:26556349 xref: PMID:27063937 xref: PMID:27150006 xref: PMID:28216315 xref: PMID:28245923 xref: PMID:28287248 xref: PMID:28893948 xref: PMID:29547123 xref: PMID:29674431 is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: anterior_to PLANA:0000420 ! parapharyngeal region relationship: posterior_to PLANA:0000418 ! head region relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/neck.png {comment="Depicted by field contains diagram representation of body region."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000420 name: parapharyngeal region def: "Region of the animal lateral to and surrounding the pharynx." [] 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. synonym: "para-pharyngeal" EXACT [] synonym: "parapharyngeal" EXACT [] synonym: "peri-pharyngeal" EXACT [] synonym: "peripharyngeal region" EXACT [] synonym: "trunk" EXACT [] xref: PMID:22125640 xref: PMID:25956527 xref: PMID:26651295 xref: PMID:28807897 xref: PMID:29674431 xref: PMID:30143032 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000102 ! anatomical region relationship: anterior_to PLANA:0000421 ! tail region relationship: anterior_to PLANA:0004527 ! copulatory region relationship: posterior_to PLANA:0000419 ! prepharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/parapharyngealregion.png {comment="Depicted by field contains diagram representation of body region."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000421 name: tail region def: "Caudal region, beginning at the mouth and ending at posterior pole." [] synonym: "tail" EXACT [] xref: UBERON:0002415 is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: posterior_to PLANA:0004527 ! copulatory region relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/tail.png {comment="Depicted by field contains diagram representation of body region."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000422 name: tail stripe def: "Medial region of the tail; the parenchymal space between the posterior primary gut branches." [PMID:29906446] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000102 ! anatomical region relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000423 name: embryonic subdivision def: "Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems." [] is_a: UBERON:0000475 ! organism subdivision created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000424 name: obsolete material anatomical entity comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000465 [Term] id: PLANA:0000425 name: obsolete definitive anatomical structure comment: extra layer of complexity not needed upon further examination is_obsolete: true [Term] id: PLANA:0000426 name: obsolete acellular anatomical structure comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000476 [Term] id: PLANA:0000427 name: multicellular anatomical structure def: "An anatomical structure that has more than one cell as a part." [UBERON:0010000] xref: UBERON:0010000 is_a: UBERON:0000061 ! anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000428 name: musculature system def: "Total musculature of the planarian body." [UBERON:0001015] synonym: "muscular system" EXACT [] synonym: "musculature" EXACT [] xref: ISBN:9780070316607 xref: PMID:15866156 xref: PMID:17942485 xref: PMID:20707997 xref: PMID:24950970 xref: PMID:27068018 xref: PMID:28137894 xref: UBERON:0001015 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000429 name: neoblast def: "A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md, PMID:16311336, PMID:21566185, PMID:22899852] synonym: "adult somatic stem cell" EXACT [] synonym: "adult stem cell" EXACT [] synonym: "ASC" EXACT [] synonym: "cycling cell" EXACT [] synonym: "irradiation-sensitive cell" EXACT [] synonym: "neoblast compartment" EXACT [] synonym: "pASC" EXACT [] synonym: "planarian adult stem cell" EXACT [] synonym: "planarian stem cell" EXACT [] synonym: "somatic stem cell" EXACT [] xref: BTO:0006347 xref: https://doi.org/10.1101/279364 xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md xref: PMID:15866156 xref: PMID:15972844 xref: PMID:16033796 xref: PMID:16311336 xref: PMID:16344473 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17376870 xref: PMID:17390146 xref: PMID:17553481 xref: PMID:17670787 xref: PMID:17905225 xref: PMID:18063755 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:18456843 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:19247960 xref: PMID:19564616 xref: PMID:19766622 xref: PMID:19805089 xref: PMID:20040488 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:20599901 xref: PMID:20844018 xref: PMID:21179477 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21356107 xref: PMID:21458439 xref: PMID:21566185 xref: PMID:21664348 xref: PMID:21747960 xref: PMID:21806978 xref: PMID:21852957 xref: PMID:21894189 xref: PMID:21937596 xref: PMID:22125640 xref: PMID:22223737 xref: PMID:22252538 xref: PMID:22252539 xref: PMID:22318224 xref: PMID:22339734 xref: PMID:22371573 xref: PMID:22385657 xref: PMID:22411224 xref: PMID:22427692 xref: PMID:22439894 xref: PMID:22445864 xref: PMID:22451003 xref: PMID:22479207 xref: PMID:22543868 xref: PMID:22549959 xref: PMID:22696458 xref: PMID:22884275 xref: PMID:22899852 xref: PMID:23079596 xref: PMID:23235145 xref: PMID:23250205 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23318641 xref: PMID:23405188 xref: PMID:23629965 xref: PMID:23903188 xref: PMID:23954785 xref: PMID:24040508 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24238224 xref: PMID:24367277 xref: PMID:24415944 xref: PMID:24523458 xref: PMID:24704339 xref: PMID:24737865 xref: PMID:24903754 xref: PMID:24922054 xref: PMID:24992682 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:25278423 xref: PMID:25356635 xref: PMID:25956527 xref: PMID:26057828 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26459857 xref: PMID:26516985 xref: PMID:26525673 xref: PMID:26556349 xref: PMID:26618653 xref: PMID:26651295 xref: PMID:26884331 xref: PMID:27013241 xref: PMID:27063937 xref: PMID:27068018 xref: PMID:27122174 xref: PMID:27149082 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27304889 xref: PMID:27441386 xref: PMID:27501047 xref: PMID:27502555 xref: PMID:27523733 xref: PMID:27542689 xref: PMID:27551436 xref: PMID:27606067 xref: PMID:27612384 xref: PMID:27654173 xref: PMID:27864883 xref: PMID:28072387 xref: PMID:28137894 xref: PMID:28171748 xref: PMID:28216315 xref: PMID:28287248 xref: PMID:28292427 xref: PMID:28461239 xref: PMID:28686611 xref: PMID:28757112 xref: PMID:28893948 xref: PMID:29095551 xref: PMID:29100657 xref: PMID:29124009 xref: PMID:29273738 xref: PMID:29291974 xref: PMID:29364871 xref: PMID:29547123 xref: PMID:29557542 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:29906446 xref: PMID:30143032 xref: PMID:30194301 xref: PMID:30237141 xref: PMID:30282036 xref: PMID:30297872 xref: PMID:30471994 xref: PMID:30485821 xref: PMID:30729158 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000120 ! progenitor cell is_a: PLANA:0000121 ! stem cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000005 ! existence starts during or after Stage 5 property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/neoblast.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000430 name: epithelial cell component def: "A part of an epithelial cell." [] is_a: GO:0005575 ! cellular_component relationship: part_of PLANA:0000100 ! epithelial cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000431 name: organ def: "Anatomical structure that performs a specific function or group of functions." [UBERON:0000062] xref: PMID:29547123 xref: UBERON:0000062 is_a: PLANA:0000427 ! multicellular anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000432 name: obsolete regenerating anatomical structure comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0007567 [Term] id: PLANA:0000433 name: obsolete cellular component comment: replacing with GO term is_obsolete: true replaced_by: GO:0005575 [Term] id: PLANA:0000459 name: optic chiasm def: "A decussation of the diencephalon where the fibers of the optic nerve cross" [PMID:18466009] synonym: "chiasm" EXACT [] synonym: "chiasma" EXACT [] synonym: "chiasma nervorum opticorum" EXACT [] synonym: "chiasma opticum" EXACT [] synonym: "decussation of optic nerve fibers" EXACT [] synonym: "optic chiasm (Rufus of Ephesus)" EXACT [] synonym: "optic chiasma" EXACT [] synonym: "optic chiasmata" EXACT [] xref: AAO:0010622 xref: BAMS:DC xref: BAMS:OC xref: BAMS:och xref: BAMS:ox xref: birnlex:1416 xref: BM:Tel-OCX xref: C90609 xref: DHBA:10644 xref: DMBA:17783 xref: EHDAA2:0001302 xref: EHDAA:10227 xref: EMAPA:17603 xref: FMA:62045 xref: GAID:832 xref: HBA:9310 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 xref: http://linkedlifedata.com/resource/umls/id/C0029126 xref: http://www.snomedbrowser.com/Codes/Details/244453006 xref: MA:0001098 xref: MBA:117 xref: MESH:D009897 xref: NCIT:C90609 xref: Optic:chiasm xref: PMID:15866156 xref: PMID:16033796 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:18202849 xref: PMID:18466009 xref: PMID:19048075 xref: PMID:19211673 xref: PMID:21282632 xref: PMID:22339734 xref: PMID:22445864 xref: PMID:25356635 xref: PMID:25493551 xref: PMID:26618653 xref: PMID:27800171 xref: PMID:28495872 xref: PMID:30194301 xref: PMID:30962434 xref: TAO:0000556 xref: UBERON:0000959 xref: UMLS:C0029126 xref: VHOG:0000190 xref: XAO:0004071 xref: ZFA:0000556 is_a: BFO:0000040 ! material entity is_a: PLANA:0000543 ! neuron projection bundle relationship: part_of PLANA:0000124 ! visual system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000460 name: anterior commissure def: "A bundle of nerve fibers connecting the two cephalic ganglia." [UBERON:0000935] synonym: "anterior brain commissure" EXACT [] xref: UBERON:0000935 is_a: PLANA:0000494 ! brain commissure relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000461 name: lateral branch def: "Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation." [PMID:12128224, PMID:18466009, PMID:27612384, PMID:4452894, PMID:9493832] synonym: "bilateral cephalic ganglia branch" EXACT [] synonym: "brain branch" EXACT [] synonym: "cephalic brain branch" EXACT [] synonym: "cephalic branch" EXACT [] synonym: "lateral brain branch" EXACT [] xref: ISBN:9780070316607 xref: PMID:12128224 xref: PMID:18287199 xref: PMID:18466009 xref: PMID:20422023 xref: PMID:21282632 xref: PMID:21806978 xref: PMID:24922054 xref: PMID:25254346 xref: PMID:27612384 xref: PMID:29674431 xref: PMID:30399335 xref: PMID:4452894 xref: PMID:9493832 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000462 name: sensory cell def: "A cell that performs a sensory function." [] xref: BTO:0001037 xref: ISBN:9780070316607 xref: NCIT:C12628 xref: PMID:17251262 xref: PMID:17942485 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000463 name: cholinergic neuron def: "Neurons that express choline acetyltransferase." [PMID:20338223] synonym: "acetylcholinergic neuron" EXACT [] xref: PMID:20338223 xref: PMID:21566185 xref: PMID:23652002 xref: PMID:23903188 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24950970 xref: PMID:25356635 xref: PMID:26525673 xref: PMID:27163480 xref: PMID:27612382 xref: PMID:27864883 xref: PMID:28126842 xref: PMID:28137894 xref: PMID:29291981 xref: PMID:30143032 xref: PMID:30194301 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000556 ! neurosecretory neuron relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000464 name: GABAergic neuron def: "Neurons that express glutamine decarboxylase." [PMID:18440152] synonym: "GABA neuron" EXACT [] synonym: "GABAergic cell" EXACT [] synonym: "gabanergic neuron" EXACT [] synonym: "inhibitory neuron" EXACT [] xref: CL:0000617 xref: FBbt:00007228 xref: PMID:18440152 xref: PMID:23903188 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24922054 xref: PMID:24950970 xref: PMID:25356635 xref: PMID:26525673 xref: PMID:27864883 xref: PMID:28216315 xref: PMID:29291981 xref: PMID:30194301 xref: PMID:30485821 xref: WBbt:0005190 xref: ZFA:0009276 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000556 ! neurosecretory neuron relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000465 name: pharynx nerve plexus def: "Plexus of nerves located in the pharynx comprised of inner and outer wall rings." [] synonym: "nerve ganglia of pharynx" EXACT [] synonym: "neural plexus of the pharynx" EXACT [] synonym: "pharyngeal nerve plexus" EXACT [] synonym: "pharyngeal nerve ring" EXACT [] synonym: "pharyngeal nervous system" EXACT [] synonym: "pharyngeal neural plexus" EXACT [] synonym: "pharynx nerve ring" EXACT [] xref: PMID:16033796 xref: PMID:17905225 xref: PMID:20967238 xref: PMID:23250205 xref: PMID:23297191 is_a: BFO:0000040 ! material entity is_a: PLANA:0000492 ! nerve plexus relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000466 name: subepidermal nerve plexus def: "Plexus of nerves located just between the epidermis and the body wall musculature." [] xref: doi:10.1002/jmor.1051550208 xref: PMID:27612384 is_a: BFO:0000040 ! material entity is_a: PLANA:0000492 ! nerve plexus relationship: part_of PLANA:0004529 ! integumental system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000467 name: submuscular nerve plexus def: "Plexus of nerves that innervate the body wall musculature." [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000492 ! nerve plexus relationship: part_of PLANA:0000428 ! musculature system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000468 name: gastrodermal plexus def: "A thin net of single nerve fibers located around the gut." [] xref: doi.org/10.1002/jmor.1051550208 xref: PMID:17999079 is_a: BFO:0000040 ! material entity is_a: PLANA:0000492 ! nerve plexus relationship: part_of PLANA:0000049 ! digestive system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000470 name: neuropil def: "A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur." [PMID:27612384] synonym: "central neuropil" EXACT [] synonym: "cephalic ganglia neuropil" EXACT [] synonym: "neuropilus" EXACT [] xref: birnlex:1142 xref: BTO:0005268 xref: C12617 xref: CALOHA:TS-2403 xref: FBbt:00005139 xref: FMA:261269 xref: GAID:740 xref: http://en.wikipedia.org/wiki/Neuropil xref: http://linkedlifedata.com/resource/umls/id/C0228081 xref: http://www.snomedbrowser.com/Codes/Details/67146008 xref: MESH:D019581 xref: NIF:Subcellular\:sao205380252 xref: PMID:16033796 xref: PMID:17553481 xref: PMID:24173799 xref: PMID:24950970 xref: PMID:25356635 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:29291974 xref: PMID:29291981 xref: UBERON:0002606 xref: UMLS:C0228081 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000472 name: pharynx outer epithelium def: "Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are \"insunk\" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft." [ASIN:B000M4NK9M] synonym: "epithelial pharynx lining" EXACT [] synonym: "outer pharyngeal epidermis" EXACT [] synonym: "outer pharyngeal epithelium" EXACT [] synonym: "outer pharynx epidermis" EXACT [] synonym: "outer pharynx epithelium" EXACT [] xref: ASIN:B000M4NK9M xref: PMID:29674431 is_a: BFO:0000040 ! material entity is_a: PLANA:0002023 ! ciliated epithelium relationship: immediately_superficial_to PLANA:0000476 ! pharynx outer longitudinal muscle cell relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000473 name: pharynx outer circular muscle cell def: "Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles." [ASIN:B000M4NK9M] synonym: "outer circular muscle layer" EXACT [] synonym: "pharyneal outer circular muscle fiber" EXACT [] synonym: "pharyngeal outer circular muscle cell" EXACT [] synonym: "pharynx outer circular muscle fiber" EXACT [] xref: ASIN:B000M4NK9M xref: ISBN:9780070316607 is_a: PLANA:0007535 ! pharynx circular muscle cell relationship: immediately_deep_to PLANA:0000476 ! pharynx outer longitudinal muscle cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxoutercircularmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000474 name: pharynx inner circular muscle cell def: "Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers." [ASIN:B000M4NK9M] synonym: "inner circular muscle layer" EXACT [] synonym: "pharyngeal inner circular muscle cell" EXACT [] synonym: "pharyngeal inner circular muscle fiber" EXACT [] synonym: "pharynx inner circular muscle fiber" EXACT [] xref: ASIN:B000M4NK9M is_a: PLANA:0007535 ! pharynx circular muscle cell relationship: immediately_deep_to PLANA:0007534 ! pharynx inner epithelium relationship: immediately_superficial_to PLANA:0000475 ! pharynx inner longitudinal muscle cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxinnercircularmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000475 name: pharynx inner longitudinal muscle cell def: "Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface." [ASIN:B000M4NK9M] synonym: "inner longitudinal muscle layer" EXACT [] synonym: "pharyngeal inner longitudinal muscle cell" EXACT [] synonym: "pharyngeal inner longitudinal muscle fiber" EXACT [] synonym: "pharynx inner longitudinal muscle fiber" EXACT [] xref: ASIN:B000M4NK9M xref: ISBN:9780070316607 is_a: PLANA:0000241 ! pharynx longitudinal muscle cell relationship: immediately_deep_to PLANA:0000474 ! pharynx inner circular muscle cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxinnerlongitudinalmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000476 name: pharynx outer longitudinal muscle cell def: "Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium." [ASIN:B000M4NK9M] synonym: "pharyngeal outer longitudinal muscle cell" EXACT [] synonym: "pharyngeal outer longitudinal muscle fiber" EXACT [] synonym: "pharynx outer longitudinal muscle fiber" EXACT [] xref: ASIN:B000M4NK9M is_a: PLANA:0000241 ! pharynx longitudinal muscle cell relationship: immediately_deep_to PLANA:0000472 ! pharynx outer epithelium relationship: immediately_superficial_to PLANA:0000473 ! pharynx outer circular muscle cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxouterlongitudinalmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000477 name: pharynx radial muscle cell def: "Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts." [ASIN:B000M4NK9M] synonym: "pharyngeal radial muscle cell" EXACT [] synonym: "pharyngeal radial muscle fiber" EXACT [] synonym: "pharynx radial muscle fiber" EXACT [] synonym: "radial muscle cell" EXACT [] synonym: "radial muscle fiber" EXACT [] xref: ASIN:B000M4NK9M xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000478 ! pharynx musculature relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxradialmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000478 name: pharynx musculature def: "The total musculature within the pharynx." [PMID:26904543] synonym: "pharyngeal musculature" EXACT [] synonym: "pharynx muscle" EXACT [] synonym: "pharynx musculature" EXACT [] xref: ISBN:9780070316607 xref: PMID:26904543 xref: PMID:29674432 xref: UBERON:0004467 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000016 ! pharynx relationship: part_of PLANA:0000428 ! musculature system relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000479 name: pharynx inner nerve plexus def: "Ring of the pharynx nerve plexus that is proximal to the lumen." [ISBN:9780070316607] synonym: "inner pharyngeal nerve ring" EXACT [] synonym: "inner pharynx nerve ring" EXACT [] synonym: "pharynx inner nerve plexus" EXACT [] xref: ISBN:9780070316607 is_a: PLANA:0000465 ! pharynx nerve plexus relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxinnernerveplexus.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000480 name: pharynx outer nerve plexus def: "Ring of the pharynx nerve plexus that is proximal to the exterior surface." [ISBN:9780070316607] synonym: "outer pharyngeal nerve ring" EXACT [] synonym: "outer pharynx nerve plexus" EXACT [] synonym: "outer pharynx nerve ring" EXACT [] xref: doi:10.1002/jmor.1051550208 xref: ISBN:9780070316607 xref: PMID:27612384 is_a: PLANA:0000465 ! pharynx nerve plexus relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxouternerveplexus.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000481 name: serotonergic neuron def: "Neurons that express the neurotransmitter serotonin." [PMID:17624455] synonym: "serotonergic cell" EXACT [] xref: CL:0000850 xref: FBbt:00005133 xref: PMID:23903188 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24922054 xref: PMID:24950970 xref: PMID:25356635 xref: PMID:26525673 xref: PMID:27864883 xref: PMID:28137894 xref: PMID:29357350 xref: PMID:30194301 xref: WBbt:0006837 xref: ZFA:0009361 is_a: BFO:0000040 ! material entity is_a: PLANA:0000556 ! neurosecretory neuron relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: part_of PLANA:0000097 ! ventral nerve cord relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002202 PLANA:0007550 ! develops from serotonergic neural progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000482 name: dopaminergic neuron def: "A neuron that expresses the neurotransmitter dopamine." [PMID:17565705] xref: CL:0000700 xref: FBbt:00005131 xref: PMID:17565705 xref: PMID:21458439 xref: PMID:23250205 xref: PMID:23903188 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24950970 xref: PMID:25356635 xref: PMID:27864883 xref: PMID:30194301 xref: WBbt:0006746 xref: ZFA:0009301 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000556 ! neurosecretory neuron relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000483 name: octopaminergic neuron def: "Neurons that express the biogenic amine octopamine." [PMID:18926867] xref: FBbt:00007364 xref: PMID:18926867 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000556 ! neurosecretory neuron relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000484 name: secretory system def: "Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus." [PMID:20865784] xref: PMID:20865784 xref: WBbt:0006850 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000485 name: gland cell def: "Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly throughepithelial cells and form a secretory pore at the surface." [PMID:20865784] synonym: "secretory gland cell" EXACT [] xref: CLYH:1000090 xref: ISBN:9780070316607 xref: PMID:19247960 xref: PMID:20865784 xref: PMID:23318635 xref: PMID:24737865 xref: PMID:28807897 xref: PMID:29674431 xref: PMID:30962434 xref: WBbt:0003670 is_a: PLANA:0000100 ! epithelial cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/glandcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000486 name: secretory pore def: "The opening by which the gland cells secrete mucus to the exterior of the animal." [PMID:20865784] synonym: "pore" EXACT [] xref: ISBN:9780070316607 xref: PMID:20865784 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002079 ! pore relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/secretorypore.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000487 name: acidophilic gland cell def: "One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsoventral border of the animal." [PMID:20865784] synonym: "eosinophilic gland cell" EXACT [] synonym: "erythrophilous gland cell" EXACT [] xref: PMID:20865784 is_a: PLANA:0000485 ! gland cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000488 name: basophilic gland cell def: "One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells." [PMID:20865784] synonym: "cyanophilic gland cell" EXACT [] synonym: "cyanophilic secretory cell" EXACT [] synonym: "cyanophilous gland" EXACT [] xref: ISBN:9780070316607 xref: PMID:20865784 xref: PMID:23405188 is_a: PLANA:0000485 ! gland cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000489 name: obsolete anatomical line comment: replacing with CARO term is_obsolete: true replaced_by: CARO:0000008 [Term] id: PLANA:0000490 name: obsolete anatomical plane comment: replacing with BSPO term is_obsolete: true replaced_by: BSPO:0000400 [Term] id: PLANA:0000491 name: obsolete plane of autonomy name: obsolete plane of autotomy comment: let odk import from BSPO if needed comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0035086 [Term] id: PLANA:0000492 name: nerve plexus def: "Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]." [UBERON:0001810] synonym: "neural network" EXACT [] synonym: "neural plexus" EXACT [] synonym: "plexus" EXACT [] xref: AEO:0000138 xref: BTO:0000205 xref: C12929 xref: EHDAA2:0003138 xref: EHDAA:3780 xref: FMA:5901 xref: http://en.wikipedia.org/wiki/Nervous\:system\:plexus xref: http://linkedlifedata.com/resource/umls/id/C0501403 xref: http://www.snomedbrowser.com/Codes/Details/122455009 xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md xref: ISBN:9780070316607 xref: MA:0002407 xref: PMID:16311336 xref: PMID:21566185 xref: PMID:22899852 xref: UBERON:0001810 xref: UMLS:C0501403 is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000080 ! peripheral nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000493 name: obsolete nervous system commissure comment: we will just use commissural neuron moving forward is_obsolete: true replaced_by: PLANA:0000547 [Term] id: PLANA:0000494 name: brain commissure def: "any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain" [UBERON:0005970] xref: UBERON:0005970 is_a: BFO:0000040 ! material entity is_a: PLANA:0002025 ! commissure relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000495 name: blastema def: "A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise." [UBERON:0005306] synonym: "regeneration blastema" EXACT [] synonym: "regenerative blastema" EXACT [] xref: AEO:0000192 xref: BTO:0001638 xref: CARO:0000010 xref: EFO:0003658 xref: FMA:50705 xref: https://doi.org/10.1101/279364 xref: ncithesaurus:Blastemal_Cell xref: PMID:15866156 xref: PMID:15972844 xref: PMID:16033796 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17553481 xref: PMID:17670787 xref: PMID:17905225 xref: PMID:17942485 xref: PMID:18063755 xref: PMID:18202849 xref: PMID:18456843 xref: PMID:19048075 xref: PMID:19174194 xref: PMID:19247960 xref: PMID:19766622 xref: PMID:19852954 xref: PMID:20040488 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:20422023 xref: PMID:20599901 xref: PMID:21179478 xref: PMID:21295481 xref: PMID:21295483 xref: PMID:21356107 xref: PMID:21458439 xref: PMID:21566195 xref: PMID:21664348 xref: PMID:21806978 xref: PMID:21937596 xref: PMID:22125640 xref: PMID:22252539 xref: PMID:22318224 xref: PMID:22411224 xref: PMID:22439894 xref: PMID:22451003 xref: PMID:22479207 xref: PMID:22549959 xref: PMID:22884275 xref: PMID:22899852 xref: PMID:23235145 xref: PMID:23250205 xref: PMID:23318641 xref: PMID:23405188 xref: PMID:23629965 xref: PMID:23652002 xref: PMID:24040508 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24173799 xref: PMID:24415944 xref: PMID:24523458 xref: PMID:24704339 xref: PMID:24922054 xref: PMID:25254346 xref: PMID:25558068 xref: PMID:25725068 xref: PMID:25772472 xref: PMID:25956527 xref: PMID:26062938 xref: PMID:26459857 xref: PMID:26525673 xref: PMID:26711341 xref: PMID:26884331 xref: PMID:27013241 xref: PMID:27068018 xref: PMID:27240733 xref: PMID:27542689 xref: PMID:27551436 xref: PMID:27606067 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:28126842 xref: PMID:28137894 xref: PMID:28171748 xref: PMID:28216315 xref: PMID:28461239 xref: PMID:28757112 xref: PMID:28807897 xref: PMID:28893948 xref: PMID:29158443 xref: PMID:29273738 xref: PMID:29291974 xref: PMID:29291981 xref: PMID:29357350 xref: PMID:30194301 xref: PMID:30237141 xref: PMID:30282036 xref: PMID:30297872 xref: PMID:30471994 xref: PMID:30485821 xref: PMID:30729158 xref: TAO:0001270 xref: UBERON:0005306 xref: XAO:0004060 is_a: UBERON:0007567 ! regenerating anatomical structure relationship: part_of PLANA:0002133 ! regenerating fragment created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000496 name: obsolete anatomical boundary comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0000015 [Term] id: PLANA:0000497 name: obsolete anatomical junction comment: replacing with UBERON term is_obsolete: true replaced_by: UBERON:0007651 [Term] id: PLANA:0000498 name: obsolete main body axis comment: replacing duplicate PLANA term is_obsolete: true replaced_by: PLANA:0007519 [Term] id: PLANA:0000499 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CL:0000000] 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). xref: CALOHA:TS-2035 xref: CL:0000000 xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 is_a: UBERON:0000061 ! anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000500 name: obsolete cell part comment: PLANA:0000500 child terms moved to cellular component (GO:0005575) term and we think better serves interoperability and searchability is_obsolete: true replaced_by: GO:0005575 [Term] id: PLANA:0000501 name: cell projection def: "A prolongation or process extending from a cell." [GO:0042995] xref: GO:0042995 is_a: GO:0005575 ! cellular_component created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000502 name: actin-based cell projection def: "A cell projection supported by an assembly of actin filaments." [GO:0098858] xref: GO:0098858 is_a: PLANA:0000501 ! cell projection created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000503 name: obsolete cilium comment: inadvertently duplicated, going with ID that is best annotated is_obsolete: true replaced_by: PLANA:0002024 [Term] id: PLANA:0000504 name: microvillus def: "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments." [GO:0005902] xref: GO:0005902 is_a: PLANA:0000502 ! actin-based cell projection property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/microvillus.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000505 name: cell-cell contact zone def: "Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions." [GO:0044291] xref: GO:0044291 is_a: GO:0005575 ! cellular_component created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000506 name: cell junction def: "A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix." [GO:0030054] xref: GO:0030054 xref: PMID:20511647 xref: PMID:21458439 is_a: PLANA:0000505 ! cell-cell contact zone property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/celljunction.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000507 name: cell-cell junction def: "A cell junction that forms a connection between two or more cells in a multicellular organism; this excludes direct cytoplasmic junctions such as ring canals." [GO:0005911] xref: GO:0005911 is_a: PLANA:0000506 ! cell junction property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/cell-celljunction.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000508 name: cell-cell adhesion def: "The attachment of one cell to another cell via adhesion molecules." [GO:0098609] xref: GO:0098609 is_a: PLANA:0000505 ! cell-cell contact zone property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/cell-celladhesion.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000509 name: intracellular part def: "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [GO:0044424] xref: GO:0044424 is_a: GO:0005575 ! cellular_component created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000510 name: cytoplasm def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures" [GO:0005737] xref: GO:0005737 xref: PMID:16890156 xref: PMID:28976975 is_a: PLANA:0000509 ! intracellular part property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/cytoplasm.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000511 name: obsolete acidophilic cytoplasm comment: term is not needed. is_obsolete: true [Term] id: PLANA:0000512 name: obsolete basophilic cytoplasm comment: term is not needed. is_obsolete: true [Term] id: PLANA:0000513 name: cytoplasmic part def: "Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GO:0044444] xref: GO:0044444 is_a: PLANA:0000509 ! intracellular part relationship: part_of PLANA:0000510 ! cytoplasm created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000514 name: cytoplasmic vesicle part def: "Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell." [GO:0044433] xref: GO:0044433 is_a: PLANA:0000513 ! cytoplasmic part created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000515 name: vacuole def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GO:0005773] xref: GO:0005773 is_a: PLANA:0000526 ! membrane-bounded organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000516 name: obsolete cytoskeleton organization comment: term is not needed. is_obsolete: true [Term] id: PLANA:0000518 name: intracellular organelle def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GO:0043229] xref: GO:0043229 is_a: PLANA:0000509 ! intracellular part created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000519 name: intracellular non-membrane-bounded organelle def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes" [GO:0043232] xref: GO:0043232 is_a: PLANA:0000518 ! intracellular organelle is_a: PLANA:0000531 ! non-membrane-bounded organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000520 name: membrane def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GO:0016020] xref: GO:0016020 is_a: GO:0005575 ! cellular_component created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000521 name: bounding membrane of organelle def: "Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes." [GO:0098588] xref: GO:0098588 is_a: PLANA:0000520 ! membrane created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000522 name: membrane part def: "Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GO:0044425] xref: GO:0044425 is_a: GO:0005575 ! cellular_component relationship: part_of PLANA:0000520 ! membrane created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000523 name: plasma membrane part def: "Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [GO:0044459] xref: GO:0044459 is_a: PLANA:0000522 ! membrane part relationship: part_of PLANA:0007509 ! plasma membrane created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000524 name: organelle membrane def: "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle." [GO:0031090] xref: GO:0031090 is_a: PLANA:0000520 ! membrane relationship: part_of PLANA:0000526 ! membrane-bounded organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000525 name: organelle def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GO:0043226] xref: GO:0043226 is_a: GO:0005575 ! cellular_component created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000526 name: membrane-bounded organelle def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GO:0043227] xref: GO:0043227 is_a: PLANA:0000525 ! organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000527 name: intracellular membrane-bounded organelle def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GO:0043231] xref: GO:0043231 is_a: PLANA:0000518 ! intracellular organelle is_a: PLANA:0000526 ! membrane-bounded organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000528 name: Golgi apparatus def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [GO:0005794] xref: GO:0005794 is_a: PLANA:0000527 ! intracellular membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/golgiapparatus.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000529 name: nucleus def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GO:0005634] xref: GO:0005634 xref: ISBN:9780070316607 xref: PMID:23405188 xref: PMID:25404302 xref: PMID:26457503 xref: PMID:28976975 xref: PMID:29100657 xref: PMID:29357350 is_a: PLANA:0000527 ! intracellular membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nucleus.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000530 name: secretory vesicle def: "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space." [GO:0099503] xref: GO:0099503 is_a: PLANA:0000527 ! intracellular membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/secretoryvesicle.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000531 name: non-membrane-bounded organelle def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GO:0043228] xref: GO:0043228 is_a: PLANA:0000525 ! organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000532 name: nuclear part def: "Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated." [GO:0044428] xref: GO:0044428 is_a: PLANA:0000509 ! intracellular part relationship: part_of PLANA:0000529 ! nucleus created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000533 name: nucleolus def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [GO:0044428] xref: GO:0044428 is_a: PLANA:0000532 ! nuclear part property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nucleolus.png {comment="Image is an electron micrograph depicting a nucleus. Inside, the nucleolus has been labeled with arrowheads. Scale bar is 1 um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000534 name: chromatin def: "The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome." [GO:0000785] xref: GO:0000785 is_a: PLANA:0000532 ! nuclear part property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/chromatin.png {comment="Image is an electron micrograph showing a mitotic cell with condensed chromatin (arrowhead). Scale bar is 1um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000535 name: heterochromatin def: "A compact and highly condensed form of chromatin." [GO:0000792] xref: GO:0000792 is_a: PLANA:0000534 ! chromatin created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000536 name: euchromatin def: "A dispersed and relatively uncompacted form of chromatin." [GO:0000791] xref: GO:0000791 is_a: PLANA:0000534 ! chromatin created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000537 name: ribosome def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ https://www.worldcat.org/search?q=bn%3A0198506732 ]" [GO:0005840] xref: GO:0005840 is_a: PLANA:0000519 ! intracellular non-membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ribosome.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000538 name: axon tract def: "A group of axons linking two or more neuropils and having a common origin, termination" [UBERON:0001018] synonym: "axon bundle" EXACT [] synonym: "axon bundles" EXACT [] synonym: "axon tracts" EXACT [] xref: PMID:22884275 xref: PMID:24950970 xref: PMID:28137894 xref: UBERON:0001018 is_a: PLANA:0000113 ! tissue created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000539 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [CL:0000393] xref: CL:0000393 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000540 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [CL:0000404] xref: CL:0000404 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000541 name: nerve def: "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures." [UBERON:0001021] synonym: "nerve bundle" EXACT [] synonym: "nerves" EXACT [] synonym: "neural subtree" EXACT [] synonym: "peripheral nerve" EXACT [] xref: PMID:27612382 xref: PMID:27800171 xref: UBERON:0001021 is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000543 name: neuron projection bundle def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001] xref: CARO:0001001 xref: UBERON:0000122 is_a: PLANA:0000538 ! axon tract relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000545 name: afferent neuron def: "A neuron which conveys sensory information centrally from the periphery." [CL:0000526] synonym: "input neuron" EXACT [] xref: CL:0000526 xref: FMA:87653 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000546 name: bipolar neuron def: "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." [CL:0000103] synonym: "bipolar nerve cell" EXACT [] xref: CL:0000103 xref: FMA:67282 xref: ISBN:9780070316607 xref: PMID:16033796 xref: PMID:18202849 xref: PMID:21458439 xref: PMID:22445864 xref: PMID:24173799 xref: PMID:25493551 is_a: PLANA:0000550 ! interneuron relationship: part_of PLANA:0000466 ! subepidermal nerve plexus relationship: part_of PLANA:0000467 ! submuscular nerve plexus relationship: part_of PLANA:0007548 ! transverse commissure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000547 name: commissural neuron def: "A neuron that has an axon which crosses the midline." [CL:0000678] xref: CL:0000678 xref: PMID:22339734 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000548 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [CL:0000527] synonym: "output neuron" EXACT [] xref: CL:0000527 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000549 name: excitatory motor neuron def: "A motor neuron that is capable of directly inducing muscle contraction." [CL:0008014] comment: In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. synonym: "excitatory neuron" EXACT [] xref: CL:0008014 xref: PMID:25356635 is_a: PLANA:0000553 ! motor neuron is_a: PLANA:0000564 ! peripheral nervous system neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000550 name: interneuron def: "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [CL:0000099] xref: BTO:0003811 xref: CL:0000099 xref: FBbt:00005125 xref: FMA:67313 xref: WBbt:0005113 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000552 name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [CL:0000101] xref: BTO:0001037 xref: CL:0000101 xref: FBbt:00005124 xref: FMA:84649 xref: WBbt:0005759 is_a: PLANA:0000462 ! sensory cell is_a: PLANA:0000545 ! afferent neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000553 name: motor neuron def: "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." [CL:0000100] synonym: "motoneuron" EXACT [] xref: BTO:0000312 xref: CL:0000100 xref: FMA:83617 xref: WBbt:0005409 is_a: PLANA:0000548 ! efferent neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000556 name: neurosecretory neuron def: "Neuronal cells which synthesize, store and release neurohormones." [CL:0000381] synonym: "neurosecretory cell" EXACT [] xref: CL:0000381 xref: FBbt:00005130 xref: PMID:24173799 is_a: PLANA:0000099 ! neuron is_a: PLANA:0000105 ! secretory cell relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000558 name: sympathetic neuron def: "Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides." [CL:0011103] xref: CL:0011103 is_a: PLANA:0000099 ! neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000559 name: unipolar neuron def: "Neuron with one neurite that extends from the cell body." [CL:0000106] synonym: "unipolar nerve cell" EXACT [] xref: CL:0000106 xref: FMA:67278 xref: ISBN:9780070316607 xref: PMID:18499291 xref: PMID:24173799 is_a: PLANA:0000552 ! sensory neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000560 name: multipolar neuron def: "Neuron with an axon and two or more dendrites." [CL:0000104] synonym: "multipolar nerve cell" EXACT [] xref: CL:0000104 xref: FMA:67287 xref: ISBN:9780070316607 xref: PMID:18499291 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000103 ! central nervous system relationship: part_of PLANA:0000466 ! subepidermal nerve plexus created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000561 name: neuron associated cell (sensu Nematoda and Protostomia) def: "Cells that are in close proximity to neurons." [CL:0000130] xref: CL:0000130 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000562 name: central nervous system neuron def: "Any neuron that is part of a central nervous system." [CL:2000029] xref: CL:2000029 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000564 name: peripheral nervous system neuron def: "Any neuron that is part of a peripheral nervous system." [CL:2000032] synonym: "peripheral neuron" EXACT [] xref: CL:2000032 xref: PMID:23123964 xref: PMID:23954785 xref: PMID:25254346 xref: PMID:26711341 xref: PMID:29184198 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000565 name: autonomic neuron def: "A neruon whose cell body is within an autonomic ganglion." [CL:0000107] xref: CL:0000107 xref: FMA:80121 is_a: PLANA:0000564 ! peripheral nervous system neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0000566 name: enteric neuron def: "A neruon contained within with the enteric nervous system (gastrodermal plexus)." [CL:0007011] xref: CL:0007011 is_a: PLANA:0000565 ! autonomic neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0001005 name: basal lamina of epidermis def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [CARO:0000065] 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. synonym: "basal lamina" EXACT [] synonym: "basal lamina of epithelium" EXACT [] synonym: "basement membrane" EXACT [] xref: AAO:0010269 xref: AEO:0000065 xref: BILA:0000065 xref: C32186 xref: CARO:0000065 xref: EHDAA2:0003065 xref: FMA:62918 xref: HAO:0000065 xref: ISBN:9780070316607 xref: MESH:D001485 xref: NIF_Subcellular:sao1397492660 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:21664348 xref: PMID:21828097 xref: PMID:22479207 xref: PMID:23079596 xref: PMID:23405188 xref: PMID:23903188 xref: PMID:25017721 xref: PMID:26057828 xref: PMID:26457503 xref: PMID:27551436 xref: PMID:29100657 xref: PMID:30383829 xref: PMID:30962434 xref: TAO:0001485 xref: TGMA:0001850 xref: UMLS:C0085872 xref: VHOG:0001592 xref: WBbt:0005756 xref: XAO:0003163 xref: ZFA:0001485 is_a: UBERON:0000476 ! acellular anatomical structure relationship: immediately_deep_to PLANA:0000034 ! epidermis relationship: part_of PLANA:0004529 ! integumental system property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/basallamina.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002000 name: adenal rhabdite def: "Rhabdites that are located basally to the epidermis, in the mesenchyme. In Smed these are present in cells likely on their way to becoming part of the mature epidermis." [ISBN:9780070316607] 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. xref: ISBN:9780070316607 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000104 ! rhabdite relationship: part_of PLANA:0003501 ! dorsal epidermis progenitor cell relationship: part_of PLANA:0003503 ! ventral epidermis progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/adenalrhabdite.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002001 name: adherens junction def: "A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments." [GO:0005912] xref: GO:0005912 xref: PMID:26556349 is_a: PLANA:0000506 ! cell junction relationship: part_of PLANA:0000508 ! cell-cell adhesion property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/adherensjunction.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002002 name: adhesive papilla def: "Finger-like processes at the terminal pore of adhesive gland cells around the marginal adhesive zone. They protrude past the epidermis and are longer microvilli, and shorter than cilia." [ISBN:9780070316607] synonym: "adhesive papillae" EXACT [] xref: ISBN:9780070316607 is_a: BFO:0000040 ! material entity is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0007540 ! viscid gland cell relationship: part_of PLANA:0007541 ! releasing gland cell relationship: RO:0001018 PLANA:0000043 ! contained in dorsal ventral margin of the whole animal relationship: RO:0001018 PLANA:0002054 ! contained in marginal adhesive zone relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/adhesivepapilla.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002003 name: amputation def: "A wound resulting in two or more separate tissue fragments." [] is_a: PLANA:0002026 ! cut created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002004 name: anterior gut branch def: "A branch of the triclad gut located anterior to the pharynx." [PMID:21664348] synonym: "anterior branch" EXACT [] synonym: "anterior intestinal branch" EXACT [] xref: PMID:18063757 xref: PMID:18287199 xref: PMID:19174194 xref: PMID:20707997 xref: PMID:21458439 xref: PMID:21664348 xref: PMID:21806978 xref: PMID:22451003 xref: PMID:22479207 xref: PMID:23318635 xref: PMID:24063805 xref: PMID:28287248 xref: PMID:30194301 is_a: BFO:0000040 ! material entity is_a: PLANA:0002119 ! gut branch relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002005 name: anterior tip def: "The anterior-medial region of the head margin." [PMID:22479207] synonym: "head tip" EXACT [] xref: PMID:15866156 xref: PMID:18063755 xref: PMID:22479207 xref: PMID:24415944 xref: PMID:24992682 xref: PMID:27063937 xref: PMID:28126842 xref: PMID:28216315 xref: PMID:29547123 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriortip.png {comment="Illustration of the anterior tip in green."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002006 name: antrum def: "A chamber formation in an organ." [ISBN:9780070316607] xref: ISBN:9780070316607 xref: NCIT:C97102 is_a: UBERON:0002553 ! anatomical cavity created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002007 name: auricle def: "A sense organ located along the dorsolateral head margin. The auricular groove is highly innervtated by ciliated sensory neurons, and has an altered epidermis devoid of rhabdites and gland cells." [ISBN:9780070316607] xref: ISBN:9780070316607 xref: PMID:27800171 xref: PMID:28495872 xref: PMID:30399335 xref: PMID:30485821 is_a: BFO:0000040 ! material entity is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000125 ! sensory system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/auricles.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002008 name: axon def: "The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter." [GO:0030424] synonym: "nerve fiber" EXACT [] xref: GO:0030424 xref: PMID:16033796 xref: PMID:17251262 xref: PMID:17553481 xref: PMID:18202849 xref: PMID:20707997 xref: PMID:21566185 xref: PMID:22445864 xref: PMID:23318641 xref: PMID:23903188 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25493551 xref: PMID:25772472 xref: PMID:27800171 xref: PMID:28495872 is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0002061 ! neurite property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/axon.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002009 name: axoneme def: "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GO:0005930] xref: GO:0005930 xref: PMID:23144623 xref: PMID:26057828 xref: PMID:26912790 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000519 ! intracellular non-membrane-bounded organelle relationship: part_of PLANA:0002024 ! cilium relationship: part_of PLANA:0002040 ! flagellum property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/axoneme.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002010 name: basal body def: "A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport." [GO:0036064] xref: GO:0036064 xref: ISBN:9780070316607 xref: PMID:21282632 xref: PMID:21828097 xref: PMID:21937596 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000519 ! intracellular non-membrane-bounded organelle relationship: part_of PLANA:0002024 ! cilium relationship: part_of PLANA:0002040 ! flagellum property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/basalbody.png {comment="Image is an electron micrograph showing a cross-section of a cilium, revealing the basal body (arrowhead). Scale bar is 0.5um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002011 name: brain visual center def: "Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons)." [PMID:16033796] synonym: "visual center" EXACT [] xref: PMID:16033796 xref: PMID:26618653 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: part_of PLANA:0000124 ! visual system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002012 name: bulbar cavity def: "An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla." [ISBN:9780070316607] synonym: "bulbar lumen" EXACT [] xref: https://doi.org/10.1101/279364 xref: ISBN:9780070316607 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0002553 ! anatomical cavity relationship: part_of PLANA:0000234 ! seminal vesicle relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002013 name: Category 1 cell def: "Irradiation-sensitive, mesenchymal cells that are absent from the head region anterior to the eyes and the pharynx. The Category 1 designation encompasses the neoblast population." [PMID:18786419] synonym: "Category 1 gene expressing cell" EXACT [] xref: PMID:18786419 xref: PMID:21894189 xref: PMID:22439894 is_a: BFO:0000040 ! material entity is_a: PLANA:0002095 ! somatic cell is_a: PLANA:0003116 ! parenchymal cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002014 name: cell body def: "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." [GO:0044297] xref: GO:0044297 xref: PMID:15866156 xref: PMID:16033796 xref: PMID:20865784 xref: PMID:27612384 xref: PMID:28495872 is_a: GO:0005575 ! cellular_component created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002015 name: cephalic ganglia lobe def: "One of two bilaterally symmetric structures comprising the planarian brain." [PMID:17999079] synonym: "bi-lobed brain" EXACT [] synonym: "bi-lobed cephalic ganglia" EXACT [] synonym: "brain ganglia" EXACT [] synonym: "brain lobe" EXACT [] xref: ISBN:9780070316607 xref: PMID:15866156 xref: PMID:16033796 xref: PMID:16890156 xref: PMID:17251262 xref: PMID:17553481 xref: PMID:17670787 xref: PMID:17905225 xref: PMID:17999079 xref: PMID:18063757 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:19211673 xref: PMID:19247960 xref: PMID:19766622 xref: PMID:19852954 xref: PMID:20223763 xref: PMID:20422023 xref: PMID:20707997 xref: PMID:20967238 xref: PMID:21179478 xref: PMID:21282632 xref: PMID:21566185 xref: PMID:21806978 xref: PMID:21828097 xref: PMID:21852957 xref: PMID:22074376 xref: PMID:22125640 xref: PMID:22318224 xref: PMID:22371573 xref: PMID:22427692 xref: PMID:22439894 xref: PMID:22445864 xref: PMID:22451003 xref: PMID:22479207 xref: PMID:22884275 xref: PMID:23123964 xref: PMID:23250205 xref: PMID:23297191 xref: PMID:23318635 xref: PMID:23652002 xref: PMID:23903188 xref: PMID:24040508 xref: PMID:24063805 xref: PMID:24120894 xref: PMID:24131630 xref: PMID:24173799 xref: PMID:24238224 xref: PMID:24523458 xref: PMID:24704339 xref: PMID:24950970 xref: PMID:24992682 xref: PMID:25017721 xref: PMID:25254346 xref: PMID:25356635 xref: PMID:25493551 xref: PMID:25558068 xref: PMID:25772472 xref: PMID:26062938 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26525673 xref: PMID:26556349 xref: PMID:26618653 xref: PMID:27013241 xref: PMID:27034770 xref: PMID:27063937 xref: PMID:27074666 xref: PMID:27149082 xref: PMID:27150006 xref: PMID:27163480 xref: PMID:27523733 xref: PMID:27606067 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:27800171 xref: PMID:27864883 xref: PMID:28126842 xref: PMID:28137894 xref: PMID:28171748 xref: PMID:28245923 xref: PMID:28287248 xref: PMID:28434803 xref: PMID:28686611 xref: PMID:28807897 xref: PMID:28893948 xref: PMID:29100657 xref: PMID:29158443 xref: PMID:29291974 xref: PMID:29291981 xref: PMID:29357350 xref: PMID:29547123 xref: PMID:29557542 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:30143032 xref: PMID:30194301 xref: PMID:30282036 xref: PMID:30383829 xref: PMID:30399335 xref: PMID:30485821 xref: PMID:30729158 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000006 ! existence starts during or after Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002016 name: cephalic ganglia neuron def: "A central nervous system neuron located within the planarian brain." [PMID:17999079] synonym: "brain neuron" EXACT [] xref: PMID:17999079 xref: PMID:24173799 xref: PMID:27612382 is_a: BFO:0000040 ! material entity is_a: PLANA:0000562 ! central nervous system neuron relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002017 name: chemical amputation def: "Amputation carried out by application of chemicals." [PMID:24737865] xref: PMID:24737865 is_a: PLANA:0002108 ! wound created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002018 name: chemical pharynx amputation def: "Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide." [PMID:24737865] synonym: "chemical pharyngeal amputation" EXACT [] xref: PMID:24737865 is_a: PLANA:0002017 ! chemical amputation created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002019 name: chemosensory neuron def: "Any neuron that capable of some detection of chemical stimulus involved in sensory perception." [FBbt:00005922] synonym: "chemoreceptive neuron" EXACT [] synonym: "chemoreceptor neuron" EXACT [] xref: FBbt:00005922 xref: PMID:18202849 xref: PMID:26525673 xref: PMID:27612382 xref: PMID:28126842 xref: PMID:28686611 xref: PMID:29547123 is_a: PLANA:0000552 ! sensory neuron relationship: part_of PLANA:0000125 ! sensory system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002020 name: chromatoid body def: "A membrane-less, cytoplasmic ribonucleoprotein granule present in neoblasts and germ cells implicated in post-transcriptional regulation. The RNA helicase DHH1/RCK, Tudor, SmB, methylated substrates of PRMT5, PIWI-3 and Germinal Histone H4 localize to chromatoid bodies in neoblasts." [PMID:22318224, PMID:24903754] synonym: "nuage" EXACT [] xref: GO:0033391 xref: PMID:19247960 xref: PMID:20215344 xref: PMID:21356107 xref: PMID:22318224 xref: PMID:22385657 xref: PMID:22439894 xref: PMID:22543868 xref: PMID:24120894 xref: PMID:24367277 xref: PMID:24903754 xref: PMID:25017721 xref: PMID:27523733 is_a: PLANA:0000531 ! non-membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/chromatoidbody.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002021 name: chromosome def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [GO:0005694] xref: GO:0005694 xref: PMID:25404302 xref: PMID:28757112 xref: PMID:28812561 xref: PMID:29364871 xref: PMID:30143032 is_a: PLANA:0000531 ! non-membrane-bounded organelle is_a: PLANA:0000532 ! nuclear part property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/chromosome.png {comment="Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002022 name: chromosome arm def: "Under the microscope chromosomes appear as thin, thread-like structures. They all have a short arm and long arm separated by a primary constriction called the centromere. The short arm is designated as p and the long arm as q." [NCIT:C13355] xref: NCIT:C13355 xref: PMID:25404302 xref: SO:0000105 is_a: PLANA:0002121 ! chromosome part property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/chromosomearm.png {comment="Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002023 name: ciliated epithelium def: "Epithelium bearing vibratile cilia on the free surface." [UBERON:0007601] xref: PMID:26457503 xref: PMID:26711341 xref: PMID:28216315 xref: PMID:28292427 xref: UBERON:0007601 is_a: PLANA:0002118 ! epithelium property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ciliatedepithelialcell.png {comment="Image is an electron micrograph of an outer epidermal cell of the pharynx. These cells are heavily ciliated. Scale bar is 2um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002024 name: cilium def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. The longitudinal array of microtubules are almost always in a 9+2 array with 2 microtubles in the central cilia bundle and 9 sets of doublet microtubules around the perimeter. The exception to this arrangement is spermatazoa flagella, which have a 9+1 array in planarians." [GO:0005929] xref: GO:0005929 is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0000106 ! ciliated epithelial cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/cilium.png {comment="Image is an electron micrograph depicting several cilia (arrowheads) emerging from a ventral epidermis cell. Scale bar is 0.5um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002025 name: commissure def: "A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord." [NCIT:C32349] xref: NCIT:C32349 is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002026 name: cut def: "A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument." [NCIT:C50518] xref: NCIT:C50518 is_a: PLANA:0002099 ! surgical wound created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002027 name: dendrite def: "A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body." [GO:0030425] synonym: "cell dendrite" EXACT [] synonym: "dendritic process" EXACT [] synonym: "dendritic projection" EXACT [] xref: GO:0030425 xref: PMID:16033796 xref: PMID:17553481 xref: PMID:22445864 xref: PMID:25493551 xref: PMID:28495872 is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0002061 ! neurite created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002028 name: dorsal-ventral muscle cell def: "A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal." [PMID:30962434] synonym: "dorsal-ventral muscle" EXACT [] synonym: "dorsal-ventral muscle fibers" EXACT [] synonym: "dorsoventral muscle" EXACT [] synonym: "dorsoventralmuscle fibers" EXACT [] synonym: "DVM" EXACT [] xref: PMID:30471994 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000079 ! parenchymal musculature relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsal-ventralmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002029 name: early female germ cell def: "A premeiotic female germ cell (i.e., a diploid female germline stem cell or transit amplifying oogonial cell)." [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000229 ! female germ cell relationship: part_of PLANA:0000204 ! ovary relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002030 name: early male germ cell def: "A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell)." [PMID:27330085] xref: PMID:27330085 is_a: BFO:0000040 ! material entity is_a: PLANA:0000228 ! male germ cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002031 name: embryonic gut def: "A cryptic digestive cavity comprised of phagocytic embryonic gut cells." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0002120 ! extraembryonic organ relationship: part_of PLANA:0000058 ! embryonic digestive system relationship: RO:0001018 PLANA:0000041 ! contained in aboral hemisphere relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000004 ! existence starts during or after Stage 4 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002032 name: epidermal cell def: "An epithelial cell of the integument (the outer layer of an organism)." [CL:0000362] xref: CL:0000362 xref: PMID:21458439 xref: PMID:24922054 xref: PMID:25017721 xref: PMID:26457503 xref: PMID:28292427 xref: PMID:28686611 xref: PMID:28807897 xref: PMID:29100657 xref: PMID:29357350 xref: PMID:30399335 is_a: PLANA:0000100 ! epithelial cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/epidermalcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002033 name: epidermal rhabdite def: "Rhabdites located within epidermal cells." [ISBN:9780070316607] 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 xref: ISBN:9780070316607 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000104 ! rhabdite relationship: part_of PLANA:0003101 ! ventral epidermis cell relationship: part_of PLANA:0003105 ! dorsal epidermis cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/epidermalrhabdite.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002034 name: ER membrane def: "The lipid bilayer surrounding the endoplasmic reticulum." [GO:0005789] xref: GO:0005789 is_a: PLANA:0000521 ! bounding membrane of organelle relationship: part_of PLANA:0007513 ! endoplasmic reticulum property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ermembrane.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002035 name: eumelanin def: "The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color." [PMID:15760337, PMID:26017970, PMID:8812261] synonym: "eye cell pigment" EXACT [] synonym: "eye pigment" EXACT [] xref: CHEBI:24009 xref: PMID:25356635 xref: PMID:26017970 xref: PMID:27240733 is_a: BFO:0000004 ! independent continuant is_a: GO:0005575 ! cellular_component relationship: part_of PLANA:0002058 ! melanosome relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002036 name: excretory cell def: "A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids." [CL:0000424] xref: CL:0000424 xref: PMID:21566185 xref: PMID:24173799 is_a: PLANA:0000119 ! terminally differentiated cell relationship: part_of PLANA:0000088 ! renal system property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/excretorycell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002037 name: extracellular matrix def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GO:0031012] synonym: "ECM" EXACT [] xref: GO:0031012 xref: PMID:19048075 xref: PMID:28126842 xref: PMID:28137894 xref: PMID:28807897 xref: PMID:30962434 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0000476 ! acellular anatomical structure relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/extracellularmatrix.png {comment="Image is an electron micrograph showing the extracellular matrix (arrowheads) between two cells. Scale bar is 0.2um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002038 name: extracellular space def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [GO:0005615] xref: GO:0005615 xref: PMID:21828097 is_a: UBERON:0000476 ! acellular anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002039 name: fission def: "A form of asexual reproduction resulting in self-amputation of posterior tissue, generating an anterior fragment and a fission fragment." [] is_a: PLANA:0002108 ! wound created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002040 name: flagellum def: "Planarian undulipodia consisting of spermatazoa cell posterior protrusions. Planarian spermatozoa contain two flagella and are composed of 9 + 1 axonemal microtubule arrangements in their flagella (markedly different from the 9 + 2 structures generally observed in sperm of other animals)." [PMID:4190073] xref: PMID:29095551 xref: PMID:4190073 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0000090 ! sperm created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002041 name: gap junction def: "A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins." [GO:0005921] xref: GO:0005921 xref: PMID:17670787 xref: PMID:22125640 is_a: PLANA:0000507 ! cell-cell junction created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002042 name: genital atrium def: "A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the genital atrium; glands surrounding the genital atrium produce the egg capsule shell." [PMID:22074376] synonym: "atrium" EXACT [] synonym: "female antrum" EXACT [] xref: PMID: 22074376 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0002553 ! anatomical cavity relationship: part_of PLANA:0000126 ! reproductive system relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002043 name: germ cell cyst def: "A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells." [PMID:17376870] synonym: "germ cell cluster" EXACT [] xref: PMID:17376870 xref: PMID:22318224 is_a: PLANA:0002090 ! reproductive structure is_a: PLANA:0002136 ! syncytium relationship: part_of PLANA:0000217 ! gonad relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002044 name: germline stem cell def: "Stem cell that is the precursor of gametes." [FBbt:00004861] synonym: "germ cell" EXACT [] synonym: "germ stem cell" EXACT [] synonym: "germline cell" EXACT [] xref: CL:0000014 xref: FBbt:00004861 xref: https://doi.org/10.1101/279364 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:17390146 xref: PMID:18456843 xref: PMID:19247960 xref: PMID:20215344 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:22252538 xref: PMID:22318224 xref: PMID:22385657 xref: PMID:22543868 xref: PMID:23652002 xref: PMID:24173799 xref: PMID:24367277 xref: PMID:25278423 xref: PMID:27013241 xref: PMID:28434803 xref: PMID:28812561 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000121 ! stem cell relationship: part_of PLANA:0000217 ! gonad relationship: RO:0002202 PLANA:0000429 ! develops from neoblast relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002045 name: glycogen granule def: "Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface." [GO:0042587] xref: GO:0042587 xref: PMID:30608231 is_a: PLANA:0002137 ! intracellular granule property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/glycogengranule.png {comment="Image is an electron micrograph depicting glycogen granules (arrowheads) within the cytoplasm of a cell. Scale bar is 200 nm."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002046 name: incision def: "A surgical cut that breaches the epidermis, made with a defined edge." [] is_a: PLANA:0002026 ! cut created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002047 name: pharynx inner epidermal cell def: "Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated." [ISBN:9780070316607] synonym: "inner pharynx epidermal cell" EXACT [] xref: ISBN:9780070316607 xref: PMID:20511647 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell is_a: PLANA:0002032 ! epidermal cell relationship: part_of PLANA:0004528 ! pharynx epithelium relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxinnerepidermalcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002048 name: inner zone of gland cells def: "Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx." [ISBN:9780070316607] xref: ISBN:9780070316607 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/innerzoneofglandcells.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002049 name: intercellular junction def: "A cell junction that forms a connection between two or more cells in a multicellular organism." [GO:0005911] xref: GO:0005911 is_a: PLANA:0000507 ! cell-cell junction created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002050 name: linear amputation def: "An amputation performed with a transverse, oblique or longitudinal cut." [] is_a: PLANA:0002003 ! amputation created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002051 name: linear incision def: "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." [] synonym: "scratch" EXACT [] is_a: PLANA:0002046 ! incision created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002052 name: lipid droplet def: "An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins." [GO:0005811] xref: GO:0005811 xref: https://doi.org/10.1101/279364 xref: PMID:30608231 is_a: PLANA:0000519 ! intracellular non-membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/lipiddroplet.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002053 name: lumen def: "The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine." [NCIT:C94478] xref: NCIT:C94478 is_a: UBERON:0002553 ! anatomical cavity created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002054 name: marginal adhesive zone def: "Zone present along the lateral dorsoventral boundary that sits just underneath the animal, in contact with substrates. It is comprised of bunches of adhesion gland cells whose terminal pores form pore rosettes through the dorsal ventral boundary epidermis.This region of is devoid of rhabdites." [ISBN:9780070316607] xref: ISBN:9780070316607 xref: PMID:20865784 is_a: BSPO:0000086 ! anatomical compartment relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/marginaladhesivezone.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002055 name: mechanosensory neuron def: "Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception." [FBbt:00005919] synonym: "mechanosensory cell" EXACT [] xref: FBbt:00005919 xref: PMID:25725068 xref: PMID:28216315 xref: WBbt:0008431 is_a: PLANA:0000552 ! sensory neuron relationship: part_of PLANA:0000125 ! sensory system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002056 name: medial muscle cell def: "Subset of dorsal-ventral muscle cells located in the medial body region." [PMID:30962434] xref: PMID:29674431 xref: PMID:30962434 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000079 ! parenchymal musculature relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/medialmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002057 name: meiotic germ cell def: "A germ cell undergoing meiosis." [PMID:27330085] xref: PMID:27330085 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000227 ! germ cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002058 name: melanosome def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GO:0042470] xref: GO:0042470 is_a: BFO:0000040 ! material entity is_a: PLANA:0000527 ! intracellular membrane-bounded organelle relationship: part_of PLANA:0000031 ! pigment cup cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0002496 PLANA:0000007 ! existence starts during or after Stage 7 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002059 name: mucus def: "A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance." [PMID:22653920] xref: PMID:21282632 xref: PMID:22653920 xref: UBERON:0000912 is_a: BFO:0000040 ! material entity is_a: UBERON:0000476 ! acellular anatomical structure relationship: part_of PLANA:0000484 ! secretory system relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult relationship: RO:0003001 PLANA:0000105 ! produced by secretory cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/mucus.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002060 name: nephridiopore def: "The external opening and terminus of a protonephridium made by a terminal cell." [ISBN:9780070316607] xref: ISBN:9780070316607 xref: PMID:21828097 xref: UBERON:0006972 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002079 ! pore relationship: part_of PLANA:0000065 ! flame cell property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nephridiopore.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002061 name: neurite def: "Cell appendage of the neuron which includes the axon and the dendrite." [FMA:61814] synonym: "neuronal process" EXACT [] xref: FBbt:00005113 xref: FMA:61814 xref: ISBN:9780070316607 xref: PMID:27612382 xref: PMID:29547123 is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0000099 ! neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002062 name: neuropeptidergic neuron def: "A neuron that produces and releases neuropeptides at chemical synapses." [PMID:24173799] synonym: "cns peptidergic cell" EXACT [] synonym: "peptidergic neuron" EXACT [] xref: PMID:24173799 xref: PMID:25356635 xref: PMID:27163480 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002063 name: non-ciliated epidermis def: "Differentiating, immature epidermal cells lacking cilia." [PMID:26457503] xref: PMID:26457503 xref: PMID:28292427 is_a: PLANA:0000034 ! epidermis created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002064 name: nuclear envelope def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [GO:0005635] xref: GO:0005635 xref: https://doi.org/10.1101/279364 is_a: PLANA:0000520 ! membrane property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nuclearenvelope.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002065 name: nuclear inner membrane def: "The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope." [GO:0005637] synonym: "inner leaflet" EXACT [] xref: GO:0005637 is_a: PLANA:0000522 ! membrane part relationship: part_of PLANA:0002064 ! nuclear envelope property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nuclearinnermembrane.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002066 name: nuclear lumen def: "The volume enclosed by the nuclear inner membrane." [GO:0031981] xref: GO:0031981 is_a: PLANA:0000532 ! nuclear part created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002067 name: nuclear outer membrane def: "The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes." [GO:0005640] synonym: "outer leaflet" EXACT [] xref: GO:0005640 is_a: PLANA:0000522 ! membrane part relationship: part_of PLANA:0002064 ! nuclear envelope property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nuclearoutermembrane.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002068 name: nuclear periphery def: "The portion of the nuclear lumen proximal to the inner nuclear membrane." [GO:0034399] xref: GO:0034399 xref: PMID:25404302 is_a: PLANA:0000532 ! nuclear part created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002069 name: ommochrome pigment cell def: "Parenchymal cells that synthesize and contain brown ommonchrome pigment." [PMID:27240733] synonym: "non-melanin pigment cell" EXACT [] xref: PMID:27240733 is_a: BFO:0000040 ! material entity is_a: PLANA:0002075 ! pigment cell relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002070 name: optic nerve def: "A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila." [UBERON:0004904] xref: PMID:27800171 xref: UBERON:0004904 is_a: BFO:0000040 ! material entity is_a: PLANA:0000541 ! nerve relationship: part_of PLANA:0000124 ! visual system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002071 name: pharynx outer epidermal cell def: "Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature." [ISBN:9780070316607] synonym: "outer pharynx epidermal cell" EXACT [] xref: ISBN:9780070316607 xref: PMID:20511647 is_a: BFO:0000040 ! material entity is_a: PLANA:0000106 ! ciliated epithelial cell is_a: PLANA:0002032 ! epidermal cell relationship: part_of PLANA:0004528 ! pharynx epithelium relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxouterepidermalcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002073 name: phagocytic cell def: "A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome." [ISBN:9780070316607, PMID:30471994] synonym: "phagocyte" EXACT [] xref: CL:0000234 xref: ISBN:9780070316607 xref: PMID:25956527 xref: PMID:27501047 xref: PMID:30471994 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002074 name: pharynx tip def: "The distal-most end of the pharnyx containing an opening to the pharynx lumen." [] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxtip.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002075 name: pigment cell def: "A pigment cell is a cell that contains pigment granules." [CL:0000147] synonym: "pigment producing cell" EXACT [] synonym: "pigmented cell" EXACT [] xref: CL:0000147 xref: PMID:26618653 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002076 name: pigment granule def: "A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes." [GO:0048770] xref: GO:0048770 xref: ISBN:9780070316607 xref: PMID:27551436 is_a: PLANA:0000526 ! membrane-bounded organelle relationship: part_of PLANA:0002075 ! pigment cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002077 name: plug amputation def: "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." [] is_a: PLANA:0002003 ! amputation property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/plugamputation.png {comment="Illustration of an example of a plug amputation showing resultant fragment and donor wound."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002078 name: point incision def: "A breach of the epidermis made with a sharp pointed object, like a needle or an insect pin." [] synonym: "poke" EXACT [] is_a: PLANA:0002046 ! incision created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002079 name: pore def: "An anatomical space that is an opening, usually at the end of a canal or duct, on the surface of the integument or the lining of an internal anatomical space." [UBERON:0008915] xref: UBERON:0008915 is_a: UBERON:0002553 ! anatomical cavity created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002080 name: post-meiotic germ cell def: "A haploid gamete undergoing terminal differentiation." [] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000227 ! germ cell relationship: part_of PLANA:0000204 ! ovary relationship: part_of PLANA:0000208 ! testis relationship: RO:0002202 PLANA:0002082 ! develops from premeiotic germ cell relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002081 name: postsynaptic cell def: "A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane." [GO:0045211] synonym: "post-synaptic cell" EXACT [] xref: GO:0045211 xref: PMID:24950970 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000499 ! cell relationship: part_of PLANA:0000025 ! nervous system relationship: part_of PLANA:0007565 ! asexual organism relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002082 name: premeiotic germ cell def: "A diploid germline stem cell or transit amplifying germ cell that has not committed to undergoing meiotic DNA replication, reductive divisions or terminal differentiation." [] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000227 ! germ cell relationship: part_of PLANA:0000204 ! ovary relationship: part_of PLANA:0000208 ! testis relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002083 name: presynaptic cell def: "The part of a synapse that is part of the presynaptic cell." [GO:0098793] synonym: "pre-synaptic cell" EXACT [] xref: GO:0098793 xref: PMID:24950970 is_a: PLANA:0000099 ! neuron relationship: part_of PLANA:0000025 ! nervous system relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002084 name: presynaptic terminal def: "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it." [GO:0043195] synonym: "pre-synaptic terminal" EXACT [] xref: GO:0043195 xref: PMID:23903188 is_a: GO:0005575 ! cellular_component relationship: part_of PLANA:0002008 ! axon relationship: part_of PLANA:0002083 ! presynaptic cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002085 name: presynaptic vesicle def: "A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane." [GO:0008021] synonym: "pre-synaptic vesicle" EXACT [] xref: GO:0008021 xref: PMID:23903188 is_a: PLANA:0000526 ! membrane-bounded organelle relationship: part_of PLANA:0002083 ! presynaptic cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002086 name: primary gut branch def: "The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature." [PMID:21664348] synonym: "main gut branch" EXACT [] synonym: "primary intestine branch" EXACT [] xref: PMID:17553481 xref: PMID:20865784 xref: PMID:21664348 xref: PMID:27122174 xref: PMID:28137894 xref: PMID:29674431 is_a: PLANA:0002119 ! gut branch created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002087 name: primitive gut def: "Four large phagocytic cells associated with the embryonic pharynx." [PMID:28072387] synonym: "primitive endoderm" EXACT [] xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0002120 ! extraembryonic organ relationship: part_of PLANA:0000058 ! embryonic digestive system relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002088 name: quarternary gut branch def: "Gut branches originating from and connected to the tertiary gut branches." [PMID:21664348] xref: PMID:21664348 is_a: PLANA:0002119 ! gut branch created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002089 name: reproductive organ def: "An organ involved in reproduction" [UBERON:0003133] xref: https://doi.org/10.1101/279364 xref: PMID:16344473 xref: PMID:17376870 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:25278423 xref: PMID:27074666 xref: UBERON:0003133 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000126 ! reproductive system relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002090 name: reproductive structure def: "Any anatomical structure that is part of the reproductive system." [UBERON:0005156] xref: PMID:17376870 xref: UBERON:0005156 is_a: BFO:0000004 ! independent continuant is_a: UBERON:0000061 ! anatomical structure relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002091 name: rhabdome def: "The light sensing structure consisting of photoreceptor neuron dendrites that project into the optic lumen and show close associations with eumelanin-containing pigment cup cells." [PMID:15760337, PMID:16033796, PMID:21852957] xref: PMID:15760337 xref: PMID:16033796 xref: PMID:21852957 xref: PMID:26017970 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000036 ! eye relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002092 name: rhabdomere def: "The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light." [PMID:15760337, PMID:16033796, PMID:21852957] xref: GO:0016028 xref: PMID:15760337 xref: PMID:16033796 xref: PMID:18202849 xref: PMID:20865784 xref: PMID:21282632 xref: PMID:21852957 xref: PMID:22445864 xref: PMID:25772472 xref: PMID:26618653 xref: PMID:27800171 is_a: BFO:0000040 ! material entity is_a: PLANA:0000501 ! cell projection relationship: part_of PLANA:0000017 ! photoreceptor neuron relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002093 name: secretory duct def: "A tubular structure that transports secreted or excreted substances." [UBERON:0000058] synonym: "secretory canal" EXACT [] xref: PMID:30383829 xref: UBERON:0000058 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000484 ! secretory system relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/secretoryduct.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002094 name: secretory granule def: "A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules." [GO:0030141] xref: GO:0030141 xref: PMID:29100657 is_a: PLANA:0000526 ! membrane-bounded organelle relationship: part_of PLANA:0000105 ! secretory cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002095 name: somatic cell def: "One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells." [BTO:0001268] xref: BTO:0001268 xref: CL:0002371 xref: PMID:20599901 xref: PMID:21852957 xref: PMID:22074376 xref: PMID:22371573 xref: PMID:22385657 xref: PMID:25404302 xref: PMID:27606067 xref: PMID:28757112 is_a: PLANA:0000499 ! cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002096 name: somatic gonadal cell def: "A non-germline cell within the ovary or testis." [PMID:27163480, PMID:27330085] synonym: "gonadal niche cell" EXACT [] synonym: "somatic gonadal niche cell" EXACT [] synonym: "somatic gonadal support cell" EXACT [] xref: PMID:27163480 xref: PMID:27330085 xref: WBbt:0007815 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000119 ! terminally differentiated cell relationship: part_of PLANA:0000217 ! gonad created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002097 name: specialized neoblast def: "A presumptive progenitor cell that expresses both pan-neoblast markers and pro-differentiation gene(s), frequently developmental transcription factors, implicated in lineage commitment and tissue-specific differentiation programs." [PMID:23404104] xref: PMID:25254346 xref: PMID:26651295 xref: PMID:27542689 xref: PMID:29674432 xref: PMID:30962434 is_a: PLANA:0000429 ! neoblast created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002098 name: stalk def: "A thin, flexible rod that anchors an egg capsule to a solid substrate." [ISBN:9780070316607] xref: ISBN:9780070316607 is_a: BFO:0000040 ! material entity is_a: UBERON:0000476 ! acellular anatomical structure relationship: part_of PLANA:0000216 ! egg capsule relationship: RO:0003001 PLANA:0000224 ! produced by cement gland created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002099 name: surgical wound def: "A wound produced by non-autonomous physical means." [] is_a: PLANA:0002108 ! wound created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002100 name: synapse def: "The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [GO:0045202] synonym: "neural synapse" EXACT [] synonym: "neuronal synapse" EXACT [] xref: GO:0045202 xref: PMID:18202849 xref: PMID:18287199 xref: PMID:21282632 is_a: PLANA:0000507 ! cell-cell junction relationship: part_of PLANA:0000099 ! neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002101 name: synaptic cleft def: "The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released." [GO:0043083] xref: GO:0043083 xref: PMID:23903188 is_a: PLANA:0002038 ! extracellular space relationship: part_of PLANA:0000099 ! neuron relationship: part_of PLANA:0000539 ! electrically responsive cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002102 name: synaptic vesicle def: "Vesicles that store various neurotransmitters that are released at the synapse. The release is regulated by a voltage-dependent calcium channel. Vesicles are essential for propagating nerve impulses between neurons and are constantly recreated by the cell. [Wikipedia]" [GO:0008021] xref: GO:0008021 xref: PMID:24950970 is_a: PLANA:0000526 ! membrane-bounded organelle relationship: part_of PLANA:0000099 ! neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002103 name: synaptonemal complex def: "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." [] xref: GO:0000795 xref: PMID:25404302 is_a: PLANA:0002123 ! chromosomal_structural_element created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002104 name: tail tip def: "The posterior-medial region of the tail margin." [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/tailtip.png {comment="Illustration of the tail tip (in green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002105 name: telomere def: "The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins." [GO:0000781] xref: GO:0000781 xref: https://doi.org/10.1101/279364 xref: PMID:22371573 xref: PMID:25404302 is_a: PLANA:0002121 ! chromosome part relationship: part_of PLANA:0002022 ! chromosome arm created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002106 name: septate junction def: "A cell-cell junction in invertebrates that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other." [GO:0070160] xref: GO:0070160 is_a: PLANA:0000507 ! cell-cell junction relationship: part_of PLANA:0002118 ! epithelium property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/septatejunction.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002107 name: wedge amputation def: "A wound resulting from a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures." [] is_a: PLANA:0002003 ! amputation property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/wedgeamputation.png {comment="Illustration of a wedge amputation depicting the resultant donor wound and wedge fragment."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002108 name: wound def: "An injury that breaches the epidermis." [] synonym: "injury" EXACT [] is_a: PLANA:0002122 ! perturbation created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002109 name: X1 cell def: "A sorted cell population enriched for irradiation-sensitive, cycling cells (4n cells, with high levels of Hoescht 33342 staining) with scant cytoplasm (low levels of calcein-AM staining). X1 cells are enriched for cycling neoblasts." [PMID:16872450] synonym: "X1" EXACT [] synonym: "X1 cell population" EXACT [] synonym: "X1 neoblast" EXACT [] synonym: "X1 population" EXACT [] xref: PMID:16872450 xref: PMID:17670787 xref: PMID:18456843 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:21937596 xref: PMID:22385657 xref: PMID:22427692 xref: PMID:22543868 xref: PMID:22549959 xref: PMID:23235145 xref: PMID:23629965 xref: PMID:24120894 xref: PMID:24367277 xref: PMID:24992682 xref: PMID:25254346 xref: PMID:25558068 xref: PMID:25956527 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26711341 xref: PMID:27013241 xref: PMID:27068018 xref: PMID:27150006 xref: PMID:27502555 xref: PMID:27523733 xref: PMID:27551436 xref: PMID:28137894 xref: PMID:29100657 xref: PMID:29557542 xref: PMID:29674432 xref: PMID:29906446 xref: PMID:30194301 is_a: PLANA:0000499 ! cell is_a: PLANA:0002138 ! FACS sorted cell population created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002110 name: X1(FS) cell def: "A heterogeneous sorted cell population of unstained planarian cells with similar size and complexity to irradiation-sensitive, cycling cells contained in the X1 gate. Unlike X1 cells, X1(FS) cells are amenable to cell transplantation." [PMID:21566185] xref: PMID:21566185 is_a: PLANA:0000499 ! cell is_a: PLANA:0002138 ! FACS sorted cell population created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002111 name: X2 cell def: "A sorted cell population containing irradiation-sensitive and irradiation-insensitive cells, characterized by weak Hoescht 33342 and calcein-AM staining. X2 cell populations contain neoblasts as well as a variety of lineage-dedicated post-mitotic progenitor cells." [PMID:16872450] xref: PMID:16872450 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:22427692 xref: PMID:22543868 xref: PMID:23629965 xref: PMID:24367277 xref: PMID:25017721 xref: PMID:27013241 xref: PMID:27150006 xref: PMID:27502555 xref: PMID:27606067 xref: PMID:27864883 xref: PMID:28137894 xref: PMID:29674432 is_a: PLANA:0000499 ! cell is_a: PLANA:0002138 ! FACS sorted cell population created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002112 name: Xins cell def: "A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types." [PMID:16872450] synonym: "Xins" EXACT [] synonym: "Xins cell population" EXACT [] synonym: "Xins cells" EXACT [] xref: PMID:16872450 xref: PMID:17670787 xref: PMID:18456843 xref: PMID:18786419 xref: PMID:19048075 xref: PMID:20215344 xref: PMID:20223763 xref: PMID:22427692 xref: PMID:22479207 xref: PMID:22543868 xref: PMID:23629965 xref: PMID:24367277 xref: PMID:24992682 xref: PMID:25558068 xref: PMID:25956527 xref: PMID:26114597 xref: PMID:26457503 xref: PMID:26711341 xref: PMID:27013241 xref: PMID:27502555 xref: PMID:29100657 xref: PMID:29674432 xref: PMID:29906446 xref: PMID:30194301 is_a: PLANA:0000499 ! cell is_a: PLANA:0002138 ! FACS sorted cell population created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002113 name: postpharyngeal region def: "Posterior to the pharynx." [] synonym: "post pharyngeal" EXACT [] synonym: "post-pharyngeal" EXACT [] synonym: "post-pharyngeal region" EXACT [] synonym: "postpharyngeal region" EXACT [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/postpharyngealregion.png created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002114 name: post-blastema region def: "Adjacent to blastema, or proximal to blastema." [] synonym: "post-blastema" EXACT [] synonym: "postblastema" EXACT [] synonym: "postblastema region" EXACT [] is_a: BSPO:0000070 ! anatomical region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/post-blastemaregion.png {comment="Illustration of the post-blastema region(in green) in the anterior region of a regenerating tail fragment."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002116 name: fission fragment def: "A fragment derived from a spontaneous or induced fission event." [] is_a: PLANA:0002128 ! fragment created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002117 name: obsolete oblique comment: term is not needed. is_obsolete: true [Term] id: PLANA:0002118 name: epithelium def: "The avascular cellular layers that cover body surfaces and cavities and may form glands." [NCIT:C12710] xref: NCIT:C12710 xref: UBERON:0000483 is_a: PLANA:0000113 ! tissue property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/epithelium.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002119 name: gut branch def: "The triclad planarian gut is serially bifrucated into connected lumens where each bifrucation is a branch." [] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000026 ! gut relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002120 name: extraembryonic organ def: "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." [] is_a: PLANA:0000431 ! organ relationship: part_of PLANA:0000116 ! embryo created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002121 name: chromosome part def: "This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root." [SO:0000830] xref: SO:0000830 is_a: PLANA:0000532 ! nuclear part relationship: part_of PLANA:0002021 ! chromosome created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002122 name: perturbation def: "An event or occurrence that causes damage to a tissue or organ." [] synonym: "insult" EXACT [] created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002123 name: chromosomal_structural_element def: "structural element of a chromosome, for example, a telomere and a centromere" [SO:0000628] synonym: "chromosomal structural element" EXACT [] xref: SO:0000628 is_a: PLANA:0002121 ! chromosome part created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002125 name: thick fragment def: "A longitudinal fragment containing the preexisting midline and medial structures." [] is_a: PLANA:0003608 ! longitudinal fragment property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/thickfragment.png {comment="Illustration of a thick fragment (in green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002126 name: thin fragment def: "A longitudinal fragment lacking a midline and medial structures." [] is_a: PLANA:0003608 ! longitudinal fragment property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/thinfragment.png {comment="Illustration of a thin fragment (in green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002128 name: fragment def: "A piece of tissue isolated from the body." [] synonym: "piece" EXACT [] is_a: UBERON:0007567 ! regenerating anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002129 name: longitudinal region def: "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" [] is_a: BSPO:0000070 ! anatomical region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/longitudinalregion.png {comment="Illustration of a longitudinal region (green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002130 name: chemical wound def: "An intentional wound produced by non-autonomous chemical means." [] is_a: PLANA:0002108 ! wound created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002131 name: plug wound def: "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." [] is_a: PLANA:0002108 ! wound property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/plugwound.png {comment="Illustration of a wound left in a donor animal resulting from a plug amputation."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002132 name: wedge wound def: "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." [] is_a: PLANA:0002108 ! wound property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/wedgewound.png {comment="Illustration of a wedge wound."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002133 name: regenerating fragment def: "A fragment that has undergone wound healing and is undergoing tissue replacement and morphallaxis." [] is_a: PLANA:0002128 ! fragment created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002134 name: sagittal orientation def: "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." [] synonym: "longitudinal orientation" EXACT [] is_a: PATO:0005024 ! longitudinal orientation created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002135 name: parasagittal orientation def: "An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane, which runs longitudinally, and is never medial." [PATO:0005023] xref: PATO:0005023 is_a: PLANA:0002134 ! sagittal orientation created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002136 name: syncytium def: "An anatomical entity consisting of a single or a few multinucleated structures" [AEO:0000203] xref: AEO:0000203 xref: BTO:0005784 xref: PMID:27330085 is_a: UBERON:0000061 ! anatomical structure created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002137 name: intracellular granule def: "Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy." [MICRO:0000215] xref: MICRO:0000215 is_a: PLANA:0000519 ! intracellular non-membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/intracellulargranule.png {comment="Image is an electron micrograph depicting a cell with many intracellular granules (arrowheads) visible in the cytoplasm. The scale bar is 1um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002138 name: FACS sorted cell population def: "Any number of cells from dissociated planarian tissue sorted via a FACS sorter for any parameter." [] is_a: PLANA:0002139 ! derived cell population created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002139 name: derived cell population def: "Cells isolated from dissociated planarian tissue." [] is_a: UBERON:0000465 ! material anatomical entity created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002140 name: pharynx pouch epithelium def: "An epithelial monolayer lining the pharynx pouch cavity." [OCLC:16809160] xref: OCLC:16809160 is_a: BFO:0000040 ! material entity is_a: PLANA:0002118 ! epithelium relationship: part_of PLANA:0000081 ! pharynx pouch relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxpouchepithelium.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002141 name: sperm duct epithelial surface def: "Epithelial surface lining the sperm duct." [PMID:19022767, PMID:22074376] xref: PMID:19022767 xref: PMID:22074376 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0004533 ! sperm duct epithelium relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0002142 name: parenchyma def: "A loosely organized collection of connective tissue and cells, including neoblasts and their immediate progeny, located in the space outside of the organs between the body wall musculature and the gut." [OCLC:16809160] synonym: "mesenchyme" EXACT [] xref: OCLC:16809160 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0003000 name: dorsal region of tail def: "The dorsal region of the tail." [] synonym: "dorsal region of tail region" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0000421 ! contained in tail region relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionoftail.png {comment="Illustration of the dorsal region of the tail (in green)."} [Term] id: PLANA:0003001 name: lateral region of the whole animal def: "The lateral region of the medio-lateral axis of the whole animal." [] synonym: "lateral region of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000082 ! lateral region intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000082 ! lateral region relationship: RO:0001018 PLANA:0000136 ! contained in whole organism [Term] id: PLANA:0003002 name: anterior region of the eye def: "The anterior region of the eye." [] synonym: "anterior region of eye" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0000036 ! contained in eye relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0000036 ! contained in eye [Term] id: PLANA:0003003 name: posterior region of the eye def: "The posterior region of the eye." [] synonym: "posterior region of eye" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0000036 ! contained in eye relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0000036 ! contained in eye [Term] id: PLANA:0003004 name: prepharyngeal midline def: "The center-most region just anterior to the pharynx" [] synonym: "prepharyngeal region of midline" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps PLANA:0000419 ! prepharyngeal region intersection_of: RO:0001018 PLANA:0000030 ! contained in midline relationship: overlaps PLANA:0000419 ! prepharyngeal region relationship: RO:0001018 PLANA:0000030 ! contained in midline [Term] id: PLANA:0003100 name: testis cell def: "cell which is part of the testis" [PMID:29674431] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003101 name: ventral epidermis cell def: "cell which is part of the ventral epidermis" [PMID:22479207, PMID:23144623] synonym: "ventral ciliated cell" EXACT [] synonym: "ventral epithelial cell" EXACT [] synonym: "ventral motile ciliated cell" EXACT [] synonym: "ventral multiciliated cell" EXACT [] [Term] id: PLANA:0003102 name: visual system cell def: "cell which is part of the visual system" [PMID:17905225, PMID:24922054] synonym: "visual cell" EXACT [] [Term] id: PLANA:0003103 name: eye cell def: "cell which is part of the eye" [PMID:29357350] synonym: "photoreceptor cell" EXACT [] synonym: "photosensitive cell" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003104 name: enteric muscle cell def: "cell which is part of the enteric musculature" [PMID:23954785, PMID:25558068] synonym: "gut muscle cell" EXACT [] synonym: "intestinal muscle cell" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003105 name: dorsal epidermis cell def: "cell which is part of the dorsal region of the epidermis" [PMID:22479207] synonym: "dorsal epithelial cell" EXACT [] [Term] id: PLANA:0003106 name: adhesion gland cell def: "cell which is part of the adhesion gland" [PMID:16890156, PMID:28976975] [Term] id: PLANA:0003107 name: body wall muscle cell def: "cell which is part of the body wall musculature" [PMID:23954785, PMID:24992682, PMID:25254346, PMID:25725068, PMID:26525673] synonym: "body wall muscle fiber" EXACT [] synonym: "body-wall muscle cell" EXACT [] [Term] id: PLANA:0003108 name: gastrodermal cell def: "cell which is part of the gastrodermis" [PMID:19174194, PMID:22479207, PMID:27122174] synonym: "gut cell" EXACT [] synonym: "intestinal cell" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003109 name: anterior pole cell def: "cell which is part of the anterior pole" [PMID:24992682, PMID:29674431, PMID:30471994] [Term] id: PLANA:0003110 name: pharynx neuron def: "neuron which is part of the pharynx" [PMID:18202849, PMID:29674431, PMID:30485821] synonym: "pharyngeal neuron" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003111 name: pharynx epithelial cell def: "epithelial cell which is part of the pharynx" [PMID:20511647] synonym: "pharynx epithelial cell" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003112 name: pharynx muscle cell def: "muscle cell which is part of the pharynx" [PMID:27068018] synonym: "pharynx muscle fiber" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003113 name: pharynx pouch epithelial cell def: "epithelial cell which is part of the pharynx pouch" [] synonym: "pharyngeal cavity epithelial cell" EXACT [] synonym: "pharynx cavity epithelial cell" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003114 name: melanin pigment granule def: "pigment granule which is part of the eumelanin" [PMID:25356635, PMID:26017970, PMID:27551436] synonym: "melanin" EXACT [] synonym: "melanosome" EXACT [] synonym: "photoreceptor pigment" EXACT [] is_a: BFO:0000004 ! independent continuant [Term] id: PLANA:0003115 name: ommochrome pigment granule def: "pigment granule which is part of the ommochrome pigment cell" [] [Term] id: PLANA:0003116 name: parenchymal cell def: "cell which is part of the parenchyma" [PMID:19247960, PMID:29674431] [Term] id: PLANA:0003117 name: parapharyngeal cell def: "cell which is part of the parapharyngeal region" [] [Term] id: PLANA:0003118 name: prepharyngeal cell def: "cell which is part of the prepharyngeal region" [] [Term] id: PLANA:0003200 name: G1 phase neoblast def: "neoblast undergoing mitotic G1 phase" [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase relationship: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase [Term] id: PLANA:0003201 name: S phase neoblast def: "neoblast undergoing mitotic S phase" [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000084 ! contains process mitotic S phase relationship: BFO:0000067 GO:0000084 ! contains process mitotic S phase [Term] id: PLANA:0003202 name: G2 phase neoblast def: "neoblast undergoing mitotic G2 phase" [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase relationship: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase [Term] id: PLANA:0003203 name: prophase neoblast def: "neoblast undergoing mitotic prophase" [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000088 ! contains process mitotic prophase relationship: BFO:0000067 GO:0000088 ! contains process mitotic prophase property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/mitoticprophase.png {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."} [Term] id: PLANA:0003204 name: metaphase neoblast def: "neoblast undergoing mitotic metaphase" [] synonym: "M phase neoblast" EXACT [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000089 ! contains process mitotic metaphase relationship: BFO:0000067 GO:0000089 ! contains process mitotic metaphase property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/metaphaseneoblast.png {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."} [Term] id: PLANA:0003205 name: anaphase neoblast def: "neoblast undergoing mitotic anaphase" [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000090 ! contains process mitotic anaphase relationship: BFO:0000067 GO:0000090 ! contains process mitotic anaphase property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anaphaseneoblast.png {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."} [Term] id: PLANA:0003206 name: telophase neoblast def: "neoblast undergoing mitotic telophase" [] is_a: PLANA:0000429 ! neoblast intersection_of: PLANA:0000429 ! neoblast intersection_of: BFO:0000067 GO:0000093 ! contains process mitotic telophase relationship: BFO:0000067 GO:0000093 ! contains process mitotic telophase property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/mitotictelophase.png {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."} [Term] id: PLANA:0003207 name: G1 phase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic G1 phase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase relationship: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase [Term] id: PLANA:0003208 name: S phase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic S phase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000084 ! contains process mitotic S phase relationship: BFO:0000067 GO:0000084 ! contains process mitotic S phase [Term] id: PLANA:0003209 name: G2 phase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic G2 phase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase relationship: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase [Term] id: PLANA:0003210 name: prophase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic prophase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000088 ! contains process mitotic prophase relationship: BFO:0000067 GO:0000088 ! contains process mitotic prophase [Term] id: PLANA:0003211 name: metaphase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic metaphase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000089 ! contains process mitotic metaphase relationship: BFO:0000067 GO:0000089 ! contains process mitotic metaphase [Term] id: PLANA:0003212 name: anaphase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic anaphase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000090 ! contains process mitotic anaphase relationship: BFO:0000067 GO:0000090 ! contains process mitotic anaphase [Term] id: PLANA:0003213 name: telophase spermatogonial stem cell def: "spermatogonial stem cell undergoing mitotic telophase" [] is_a: PLANA:0000219 ! spermatogonial stem cell intersection_of: PLANA:0000219 ! spermatogonial stem cell intersection_of: BFO:0000067 GO:0000093 ! contains process mitotic telophase relationship: BFO:0000067 GO:0000093 ! contains process mitotic telophase [Term] id: PLANA:0003214 name: G1 phase oogonial stem cell def: "oogonial stem cell undergoing mitotic G1 phase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase relationship: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase [Term] id: PLANA:0003215 name: S phase oogonial stem cell def: "oogonial stem cell undergoing mitotic S phase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000084 ! contains process mitotic S phase relationship: BFO:0000067 GO:0000084 ! contains process mitotic S phase [Term] id: PLANA:0003216 name: G2 phase oogonial stem cell def: "oogonial stem cell undergoing mitotic G2 phase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase relationship: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase [Term] id: PLANA:0003217 name: prophase oogonial stem cell def: "oogonial stem cell undergoing mitotic prophase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000088 ! contains process mitotic prophase relationship: BFO:0000067 GO:0000088 ! contains process mitotic prophase [Term] id: PLANA:0003218 name: metaphase oogonial stem cell def: "oogonial stem cell undergoing mitotic metaphase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000089 ! contains process mitotic metaphase relationship: BFO:0000067 GO:0000089 ! contains process mitotic metaphase [Term] id: PLANA:0003219 name: anaphase oogonial stem cell def: "oogonial stem cell undergoing mitotic anaphase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000090 ! contains process mitotic anaphase relationship: BFO:0000067 GO:0000090 ! contains process mitotic anaphase [Term] id: PLANA:0003220 name: telophase oogonial stem cell def: "oogonial stem cell undergoing mitotic telophase" [] is_a: PLANA:0000223 ! oogonial stem cell intersection_of: PLANA:0000223 ! oogonial stem cell intersection_of: BFO:0000067 GO:0000093 ! contains process mitotic telophase relationship: BFO:0000067 GO:0000093 ! contains process mitotic telophase [Term] id: PLANA:0003221 name: G1 phase spermatogonium def: "spermatogonium undergoing mitotic G1 phase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase relationship: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase [Term] id: PLANA:0003222 name: S phase spermatogonium def: "spermatogonium undergoing mitotic S phase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000084 ! contains process mitotic S phase relationship: BFO:0000067 GO:0000084 ! contains process mitotic S phase [Term] id: PLANA:0003223 name: G2 phase spermatogonium def: "spermatogonium undergoing mitotic G2 phase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase relationship: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase [Term] id: PLANA:0003224 name: prophase spermatogonium def: "spermatogonium undergoing mitotic prophase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000088 ! contains process mitotic prophase relationship: BFO:0000067 GO:0000088 ! contains process mitotic prophase [Term] id: PLANA:0003225 name: metaphase spermatogonia def: "spermatogonium undergoing mitotic metaphase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000089 ! contains process mitotic metaphase relationship: BFO:0000067 GO:0000089 ! contains process mitotic metaphase [Term] id: PLANA:0003226 name: anaphase spermatogonia def: "spermatogonium undergoing mitotic anaphase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000090 ! contains process mitotic anaphase relationship: BFO:0000067 GO:0000090 ! contains process mitotic anaphase [Term] id: PLANA:0003227 name: telophase spermatogonium def: "spermatogonium undergoing mitotic telophase" [] is_a: PLANA:0000220 ! spermatogonium intersection_of: PLANA:0000220 ! spermatogonium intersection_of: BFO:0000067 GO:0000093 ! contains process mitotic telophase relationship: BFO:0000067 GO:0000093 ! contains process mitotic telophase [Term] id: PLANA:0003228 name: G1 phase oogonial cell def: "oogonial cell undergoing mitotic G1 phase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase relationship: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase [Term] id: PLANA:0003229 name: S phase oogonial cell def: "oogonial cell undergoing mitotic S phase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000084 ! contains process mitotic S phase relationship: BFO:0000067 GO:0000084 ! contains process mitotic S phase [Term] id: PLANA:0003230 name: G2 phase oogonial cell def: "oogonial cell undergoing mitotic G2 phase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase relationship: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase [Term] id: PLANA:0003231 name: prophase oogonial cell def: "oogonial cell undergoing mitotic prophase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000088 ! contains process mitotic prophase relationship: BFO:0000067 GO:0000088 ! contains process mitotic prophase [Term] id: PLANA:0003232 name: metaphase oogonial cell def: "oogonial cell undergoing mitotic metaphase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000089 ! contains process mitotic metaphase relationship: BFO:0000067 GO:0000089 ! contains process mitotic metaphase [Term] id: PLANA:0003233 name: anaphase oogonial cell def: "oogonial cell undergoing mitotic anaphase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000090 ! contains process mitotic anaphase relationship: BFO:0000067 GO:0000090 ! contains process mitotic anaphase [Term] id: PLANA:0003234 name: telophase oogonial cell def: "oogonial cell undergoing mitotic telophase" [] is_a: PLANA:0000239 ! oogonial cell intersection_of: PLANA:0000239 ! oogonial cell intersection_of: BFO:0000067 GO:0000093 ! contains process mitotic telophase relationship: BFO:0000067 GO:0000093 ! contains process mitotic telophase [Term] id: PLANA:0003235 name: G1 phase germ cell cyst def: "germ cell cyst undergoing mitotic G1 phase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase relationship: BFO:0000067 GO:0000080 ! contains process mitotic G1 phase [Term] id: PLANA:0003236 name: S phase germ cell cyst def: "germ cell cyst undergoing mitotic S phase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000084 ! contains process mitotic S phase relationship: BFO:0000067 GO:0000084 ! contains process mitotic S phase [Term] id: PLANA:0003237 name: G2 phase germ cell cyst def: "germ cell cyst undergoing mitotic G2 phase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase relationship: BFO:0000067 GO:0000085 ! contains process mitotic G2 phase [Term] id: PLANA:0003238 name: prophase germ cell cyst def: "germ cell cyst undergoing mitotic prophase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000088 ! contains process mitotic prophase relationship: BFO:0000067 GO:0000088 ! contains process mitotic prophase [Term] id: PLANA:0003239 name: metaphase germ cell cyst def: "germ cell cyst undergoing mitotic metaphase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000089 ! contains process mitotic metaphase relationship: BFO:0000067 GO:0000089 ! contains process mitotic metaphase [Term] id: PLANA:0003240 name: anaphase germ cell cyst def: "germ cell cyst undergoing mitotic anaphase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000090 ! contains process mitotic anaphase relationship: BFO:0000067 GO:0000090 ! contains process mitotic anaphase [Term] id: PLANA:0003241 name: telophase germ cell cyst def: "germ cell cyst undergoing mitotic telophase" [] is_a: PLANA:0002043 ! germ cell cyst intersection_of: PLANA:0002043 ! germ cell cyst intersection_of: BFO:0000067 GO:0000093 ! contains process mitotic telophase relationship: BFO:0000067 GO:0000093 ! contains process mitotic telophase [Term] id: PLANA:0003242 name: meiotic S phase spermatocyte def: "spermatocyte undergoing meiotic S phase" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0051332 ! contains process meiotic S phase relationship: BFO:0000067 GO:0051332 ! contains process meiotic S phase [Term] id: PLANA:0003243 name: meiotic G1 phase spermatocyte def: "spermatocyte undergoing meiotic G1 phase" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0051330 ! contains process meiotic G1 phase relationship: BFO:0000067 GO:0051330 ! contains process meiotic G1 phase [Term] id: PLANA:0003244 name: meiotic G2 phase spermatocyte def: "spermatocyte undergoing meiotic G2 phase" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0051331 ! contains process meiotic G2 phase relationship: BFO:0000067 GO:0051331 ! contains process meiotic G2 phase [Term] id: PLANA:0003245 name: meiotic prophase I spermatocyte def: "spermatocyte undergoing meiotic prophase I" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007128 ! contains process meiotic prophase I relationship: BFO:0000067 GO:0007128 ! contains process meiotic prophase I [Term] id: PLANA:0003246 name: leptotene stage spermatocyte def: "spermatocyte undergoing leptotene" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0000237 ! contains process leptotene relationship: BFO:0000067 GO:0000237 ! contains process leptotene [Term] id: PLANA:0003247 name: zygotene stage spermatocyte def: "spermatocyte undergoing zygotene" [https://doi.org/10.1101/279364] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0000238 ! contains process zygotene relationship: BFO:0000067 GO:0000238 ! contains process zygotene [Term] id: PLANA:0003248 name: pachytene stage spermatocyte def: "spermatocyte undergoing pachytene" [https://doi.org/10.1101/279364] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0000239 ! contains process pachytene relationship: BFO:0000067 GO:0000239 ! contains process pachytene [Term] id: PLANA:0003249 name: diplotene stage spermatocyte def: "spermatocyte undergoing diplotene" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0000240 ! contains process diplotene relationship: BFO:0000067 GO:0000240 ! contains process diplotene [Term] id: PLANA:0003250 name: diakinesis stage spermatocyte def: "spermatocyte undergoing diakinesis" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0000241 ! contains process diakinesis relationship: BFO:0000067 GO:0000241 ! contains process diakinesis [Term] id: PLANA:0003251 name: meiotic metaphase 1 stage spermatocyte def: "spermatocyte undergoing meiotic metaphase I" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007132 ! contains process meiotic metaphase I relationship: BFO:0000067 GO:0007132 ! contains process meiotic metaphase I [Term] id: PLANA:0003252 name: meiotic anaphase I stage spermatocyte def: "spermatocyte undergoing meiotic anaphase I" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007133 ! contains process meiotic anaphase I relationship: BFO:0000067 GO:0007133 ! contains process meiotic anaphase I [Term] id: PLANA:0003253 name: meiotic telophase I spermatocyte def: "spermatocyte undergoing meiotic telophase I" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007134 ! contains process meiotic telophase I relationship: BFO:0000067 GO:0007134 ! contains process meiotic telophase I [Term] id: PLANA:0003254 name: meiosis II stage spermatocyte def: "spermatocyte undergoing meiosis II cell cycle phase" [] is_a: PLANA:0000221 ! spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0098765 ! contains process meiosis II cell cycle phase relationship: BFO:0000067 GO:0098765 ! contains process meiosis II cell cycle phase [Term] id: PLANA:0003255 name: meiotic prophase II spermatocyte def: "spermatocyte undergoing meiotic prophase II" [] is_a: PLANA:0003254 ! meiosis II stage spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007136 ! contains process meiotic prophase II relationship: BFO:0000067 GO:0007136 ! contains process meiotic prophase II [Term] id: PLANA:0003256 name: meiotic metaphase 2 spermatocyte def: "spermatocyte undergoing meiotic metaphase II" [] is_a: PLANA:0003254 ! meiosis II stage spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007137 ! contains process meiotic metaphase II relationship: BFO:0000067 GO:0007137 ! contains process meiotic metaphase II [Term] id: PLANA:0003257 name: meiotic anaphase II spermatocyte def: "spermatocyte undergoing meiotic anaphase II" [] is_a: PLANA:0003254 ! meiosis II stage spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007138 ! contains process meiotic anaphase II relationship: BFO:0000067 GO:0007138 ! contains process meiotic anaphase II [Term] id: PLANA:0003258 name: meiotic telophase II spermatocyte def: "spermatocyte undergoing meiotic telophase II" [] is_a: PLANA:0003254 ! meiosis II stage spermatocyte intersection_of: PLANA:0000221 ! spermatocyte intersection_of: BFO:0000067 GO:0007139 ! contains process meiotic telophase II relationship: BFO:0000067 GO:0007139 ! contains process meiotic telophase II [Term] id: PLANA:0003300 name: cephalic ganglia primordium def: "This primordium develops into cephalic ganglia" [] synonym: "brain primordia" EXACT [] synonym: "brain primordium" EXACT [] synonym: "brain primoridia" EXACT [] synonym: "brain rudiment" EXACT [] synonym: "cephalic ganglia primordia" EXACT [] synonym: "cephalic ganglia primordium" EXACT [] xref: PMID:16033796 xref: PMID:17553481 xref: PMID:17905225 xref: PMID:19174194 xref: PMID:21806978 xref: PMID:22339734 xref: PMID:23318635 xref: PMID:25772472 xref: PMID:26525673 is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000131 ! primordium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000044 ! develops into cephalic ganglia relationship: RO:0002203 PLANA:0000044 ! develops into cephalic ganglia [Term] id: PLANA:0003301 name: eye primordium def: "This primordium develops into eye" [] synonym: "eye aggregate" EXACT [] xref: PMID:22884275 is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000131 ! primordium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000036 ! develops into eye relationship: RO:0002203 PLANA:0000036 ! develops into eye [Term] id: PLANA:0003302 name: pharynx primordium def: "This primordium develops into pharynx" [] xref: PMID:18202849 xref: PMID:21282632 xref: PMID:25254346 xref: PMID:26556349 xref: PMID:27074666 is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000131 ! primordium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000016 ! develops into pharynx relationship: RO:0002203 PLANA:0000016 ! develops into pharynx [Term] id: PLANA:0003303 name: pigment cup primordium def: "This primordium develops into optic cup" [] synonym: "optic cup primordium" EXACT [] xref: PMID:21852957 is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000131 ! primordium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000075 ! develops into optic cup relationship: RO:0002203 PLANA:0000075 ! develops into optic cup [Term] id: PLANA:0003304 name: testis primordium def: "This primordium develops into testis" [] xref: PMID:23652002 is_a: PLANA:0003305 ! gonad primoridium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000208 ! develops into testis relationship: RO:0002203 PLANA:0000208 ! develops into testis [Term] id: PLANA:0003305 name: gonad primoridium def: "This primordium develops into gonad" [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000131 ! primordium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000217 ! develops into gonad relationship: RO:0002203 PLANA:0000217 ! develops into gonad [Term] id: PLANA:0003306 name: ovary primordium def: "This primordium develops into ovary" [] is_a: PLANA:0003305 ! gonad primoridium intersection_of: PLANA:0000131 ! primordium intersection_of: RO:0002203 PLANA:0000204 ! develops into ovary relationship: RO:0002203 PLANA:0000204 ! develops into ovary [Term] id: PLANA:0003400 name: protonephridial lumen def: "lumen which is part of the protonephridia" [PMID:26057828] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002053 ! lumen intersection_of: PLANA:0002053 ! lumen intersection_of: part_of PLANA:0000020 ! protonephridia relationship: part_of PLANA:0000020 ! protonephridia [Term] id: PLANA:0003401 name: testis lumen def: "lumen which is part of the testis" [PMID:17390146] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002053 ! lumen intersection_of: PLANA:0002053 ! lumen intersection_of: part_of PLANA:0000208 ! testis relationship: part_of PLANA:0000208 ! testis [Term] id: PLANA:0003402 name: ovary lumen def: "lumen which is part of the ovary" [PMID:19247960] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002053 ! lumen intersection_of: PLANA:0002053 ! lumen intersection_of: part_of PLANA:0000204 ! ovary relationship: part_of PLANA:0000204 ! ovary [Term] id: PLANA:0003403 name: flame cell lumen def: "lumen which is part of the flame cell" [PMID:21828097] synonym: "flame cell barrel lumen" EXACT [] is_a: PLANA:0003400 ! protonephridial lumen intersection_of: PLANA:0002053 ! lumen intersection_of: part_of PLANA:0000065 ! flame cell relationship: part_of PLANA:0000065 ! flame cell [Term] id: PLANA:0003500 name: cephalic ganglia progenitor cell def: "A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system." [PMID:26525673] synonym: "brain progenitor" EXACT [] synonym: "brain progentitor cell" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000044 ! develops into cephalic ganglia relationship: RO:0002203 PLANA:0000044 ! develops into cephalic ganglia [Term] id: PLANA:0003501 name: dorsal epidermis progenitor cell def: "A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis." [PMID:28292427] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000054 ! develops into dorsal region of the epidermis relationship: RO:0002203 PLANA:0000054 ! develops into dorsal region of the epidermis [Term] id: PLANA:0003502 name: optic cup progenitor cell def: "A progenitor cell that gives rise to optic cup cells of the eye." [PMID:21852957] synonym: "optic cup trail cell" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000075 ! develops into optic cup relationship: RO:0002203 PLANA:0000075 ! develops into optic cup [Term] id: PLANA:0003503 name: ventral epidermis progenitor cell def: "A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis." [PMID:28292427] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0000096 ! develops into ventral epidermis relationship: RO:0002203 PLANA:0000096 ! develops into ventral epidermis [Term] id: PLANA:0003504 name: testis somatic gonadal cell progenitor cell def: "This progenitor cell develops into testis somatic gonadal cell" [PMID: 23652002] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000120 ! progenitor cell intersection_of: PLANA:0000120 ! progenitor cell intersection_of: RO:0002203 PLANA:0004506 ! develops into testis somatic gonadal cell relationship: RO:0002203 PLANA:0004506 ! develops into testis somatic gonadal cell [Term] id: PLANA:0003600 name: head fragment def: "A fragment derived from a prepharyngeal amputation encompassing the head." [] synonym: "head piece" EXACT [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PLANA:0000418 ! derives from head region relationship: RO:0001000 PLANA:0000418 ! derives from head region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/headfragment.png {comment="A fragment derived from a prepharyngeal amputation encompassing the head."} [Term] id: PLANA:0003601 name: trunk fragment def: "A fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region." [] synonym: "trunk piece" EXACT [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PLANA:0000420 ! derives from parapharyngeal region relationship: RO:0001000 PLANA:0000420 ! derives from parapharyngeal region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/trunkfragment.png {comment="Illustration of a trunk fragment (in green)."} [Term] id: PLANA:0003602 name: tail fragment def: "A fragment derived from a postpharyngeal amputation encompassing the tail." [] synonym: "tail piece" EXACT [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PLANA:0000421 ! derives from tail region relationship: RO:0001000 PLANA:0000421 ! derives from tail region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/tailfragment.png {comment="A fragment derived from a postpharyngeal amputation encompassing the tail."} [Term] id: PLANA:0003603 name: prepharyngeal fragment def: "A fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal." [] synonym: "neck fragment" EXACT [] synonym: "neck piece" EXACT [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PLANA:0000419 ! derives from prepharyngeal region relationship: RO:0001000 PLANA:0000419 ! derives from prepharyngeal region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/prepharyngealfragment.png {comment="Illustration of a prepharyngeal fragment (in green)."} [Term] id: PLANA:0003604 name: postpharyngeal fragment def: "A fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip." [] synonym: "post-pharyngeal fragment" EXACT [] synonym: "post-pharyngeal piece" EXACT [] synonym: "postpharyngeal piece" EXACT [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PLANA:0002113 ! derives from postpharyngeal region relationship: RO:0001000 PLANA:0002113 ! derives from postpharyngeal region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/postpharyngealfragment.png {comment="Illustration of a postpharyngeal fragment (in green)."} [Term] id: PLANA:0003605 name: anterior fragment def: "A fragment encompassing all or part of the anterior region of the animal." [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 BSPO:0000071 ! derives from anterior region relationship: RO:0001000 BSPO:0000071 ! derives from anterior region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorfragment.png {comment="A fragment encompassing all or part of the anterior region of the animal."} [Term] id: PLANA:0003606 name: posterior fragment def: "A fragment encompassing all or part of the posterior region of the animal." [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 BSPO:0000072 ! derives from posterior region relationship: RO:0001000 BSPO:0000072 ! derives from posterior region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorfragment.png {comment="Illustration of an example of a posterior fragment (in green)."} [Term] id: PLANA:0003607 name: lateral fragment def: "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]" [] synonym: "edge fragment" EXACT [] synonym: "longitudinal fragment" EXACT [] synonym: "sagittal fragment" EXACT [] synonym: "side fragment" EXACT [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 BSPO:0000066 ! derives from lateral side relationship: RO:0001000 BSPO:0000066 ! derives from lateral side property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/lateralfragment.png {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]"} [Term] id: PLANA:0003608 name: longitudinal fragment def: "a fragment derived from an amputation parallel to the midline." [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PLANA:0002129 ! derives from longitudinal region relationship: RO:0001000 PLANA:0002129 ! derives from longitudinal region property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/longitudinalfragment.png {comment="a fragment derived from an amputation parallel to the midline."} [Term] id: PLANA:0003609 name: plug fragment def: "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." [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PATO:0040012 ! derives from plug shaped relationship: RO:0001000 PATO:0040012 ! derives from plug shaped property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/plugfragment.png {comment="Illustration of an example plug fragment in green."} [Term] id: PLANA:0003610 name: wedge fragment def: "A piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures." [] is_a: PLANA:0002128 ! fragment intersection_of: PLANA:0002128 ! fragment intersection_of: RO:0001000 PATO:0001955 ! derives from cuneate relationship: RO:0001000 PATO:0001955 ! derives from cuneate property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/wedgefragment.png {comment="Illustration of an example wedge fragment in green."} [Term] id: PLANA:0003700 name: dorsal region of head fragment def: "The dorsal region of a fragment derived from a prepharyngeal amputation encompassing the head." [] synonym: "dorsal region of head fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003600 ! contained in head fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003600 ! contained in head fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofheadfragment.png {comment="Illustration of the dorsal region of a head fragment (green)."} [Term] id: PLANA:0003701 name: ventral region of head fragment def: "The ventral region of a fragment derived from a prepharyngeal amputation encompassing the head." [] synonym: "ventral region of head fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003600 ! contained in head fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003600 ! contained in head fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofheadfragment.png {comment="Illustration of the ventral region of a head fragment (green)."} [Term] id: PLANA:0003702 name: anterior region of head fragment def: "The anterior region of a fragment derived from a prepharyngeal amputation encompassing the head." [] synonym: "anterior region of head fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003600 ! contained in head fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003600 ! contained in head fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofheadfragment.png {comment="Illustration of the anterior region of a head fragment (green)."} [Term] id: PLANA:0003703 name: posterior region of head fragment def: "The posterior region of a fragment derived from a prepharyngeal amputation encompassing the head." [] synonym: "posterior region of head fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003600 ! contained in head fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003600 ! contained in head fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofheadfragment.png {comment="Illustration of the posterior region of a head fragment (green)."} [Term] id: PLANA:0003704 name: dorsal region of trunk fragment def: "The dorsal region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region." [] synonym: "dorsal region of trunk fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003601 ! contained in trunk fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003601 ! contained in trunk fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionoftrunkfragment.png {comment="Illustration of the dorsal region of a trunk fragment (green)."} [Term] id: PLANA:0003705 name: ventral region of trunk fragment def: "The ventral region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region." [] synonym: "ventral region of trunk fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003601 ! contained in trunk fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003601 ! contained in trunk fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionoftrunkfragment.png {comment="Illustration of the ventral region of a trunk fragment (green)."} [Term] id: PLANA:0003706 name: anterior region of trunk fragment def: "The anterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region." [] synonym: "anterior region of trunk fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003601 ! contained in trunk fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003601 ! contained in trunk fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionoftrunkfragment.png {comment="Illustration of the anterior region of a trunk fragment (green)."} [Term] id: PLANA:0003707 name: posterior region of trunk fragment def: "The posterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region." [] synonym: "posterior region of trunk fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003601 ! contained in trunk fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003601 ! contained in trunk fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionoftrunkfragment.png {comment="Illustration of the posterior region of a trunk fragment (green)."} [Term] id: PLANA:0003708 name: dorsal region of tail fragment def: "The dorsal region of a fragment derived from a postpharyngeal amputation encompassing the tail." [] synonym: "dorsal region of tail fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003602 ! contained in tail fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003602 ! contained in tail fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionoftailfragment.png {comment="Illustration of the dorsal region of a tail fragment (green)."} [Term] id: PLANA:0003709 name: ventral region of tail fragment def: "The ventral region of a fragment derived from a postpharyngeal amputation encompassing the tail." [] synonym: "ventral region of tail fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003602 ! contained in tail fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003602 ! contained in tail fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionoftailfragment.png {comment="Illustration of the ventral region of a tail fragment (green)."} [Term] id: PLANA:0003710 name: anterior region of tail fragment def: "The anterior region of a fragment derived from a postpharyngeal amputation encompassing the tail." [] synonym: "anterior region of tail fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003602 ! contained in tail fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003602 ! contained in tail fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionoftailfragment.png {comment="Illustration of the anterior region of a tail fragment (green)."} [Term] id: PLANA:0003711 name: posterior region of tail fragment def: "The posterior region of a fragment derived from a postpharyngeal amputation encompassing the tail." [] synonym: "posterior region of tail fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003602 ! contained in tail fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003602 ! contained in tail fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionoftailfragment.png {comment="Illustration of the posterior region of a tail fragment (green)."} [Term] id: PLANA:0003712 name: dorsal region of prepharyngeal fragment def: "The dorsal region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal." [] synonym: "dorsal region of prepharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofprepharyngealfragment.png {comment="Illustration of the dorsal region of a prepharyngeal fragment (green)."} [Term] id: PLANA:0003713 name: ventral region of prepharyngeal fragment def: "The ventral region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal." [] synonym: "ventral region of prepharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofprepharyngealfragment.png {comment="Illustration of the ventral region of a prepharyngeal fragment (green)."} [Term] id: PLANA:0003714 name: anterior region of prepharyngeal fragment def: "The anterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal." [] synonym: "anterior region of prepharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofprephayngealfragment.png {comment="Illustration of the anterior region of a prepharyngeal fragment (green)."} [Term] id: PLANA:0003715 name: posterior region of prepharyngeal fragment def: "The posterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal." [] synonym: "posterior region of prepharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003603 ! contained in prepharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofprepharyngealfragment.png {comment="Illustration of the posterior region of a prepharyngeal fragment (green)."} [Term] id: PLANA:0003716 name: dorsal region of postpharyngeal fragment def: "The dorsal region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip." [] synonym: "dorsal region of postpharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofpostpharyngealfragment.png {comment="Illustration of the dorsal region of a postpharyngeal fragment (green)."} [Term] id: PLANA:0003717 name: ventral region of postpharyngeal fragment def: "The ventral region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip." [] synonym: "ventral region of postpharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofpostpharyngealfragment.png {comment="Illustration of the ventral region of a postpharyngeal fragment (green)."} [Term] id: PLANA:0003718 name: anterior region of postpharyngeal fragment def: "The anterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip." [] synonym: "anterior region of postpharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofpostpharyngealfragment.png {comment="Illustration of the anterior region of a postpharyngeal fragment (green)."} [Term] id: PLANA:0003719 name: posterior region of postpharyngeal fragment def: "The posterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip." [] synonym: "posterior region of postpharyngeal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003604 ! contained in postpharyngeal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofpostpharyngealfragment.png {comment="Illustration of the posterior region of a postpharyngeal fragment (green)."} [Term] id: PLANA:0003720 name: dorsal region of anterior fragment def: "The dorsal region of a fragment encompassing all or part of the anterior region of the animal." [] synonym: "dorsal region of anterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003605 ! contained in anterior fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003605 ! contained in anterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofanteriorfragment.png {comment="Illustration of the dorsal region of an anterior fragment (green)."} [Term] id: PLANA:0003721 name: ventral region of anterior fragment def: "The ventral region of a fragment encompassing all or part of the anterior region of the animal." [] synonym: "ventral region of anterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003605 ! contained in anterior fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003605 ! contained in anterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofanteriorfragment.png {comment="Illustration of the ventral region of an anterior fragment (green)."} [Term] id: PLANA:0003722 name: anterior region of anterior fragment def: "The anterior region of a fragment encompassing all or part of the anterior region of the animal." [] synonym: "anterior region of anterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003605 ! contained in anterior fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003605 ! contained in anterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofanteriorfragment.png {comment="Illustration of the anterior region of an anterior fragment (green)."} [Term] id: PLANA:0003723 name: posterior region of anterior fragment def: "The posterior region of a fragment encompassing all or part of the anterior region of the animal." [] synonym: "posterior region of anterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003605 ! contained in anterior fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003605 ! contained in anterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofanteriorfragment.png {comment="Illustration of the posterior region of an anterior fragment (green)."} [Term] id: PLANA:0003724 name: dorsal region of posterior fragment def: "The dorsal region of a fragment encompassing all or part of the posterior region of the animal." [] synonym: "dorsal region of posterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003606 ! contained in posterior fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003606 ! contained in posterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofposteriorfragment.png {comment="Illustration of the dorsal region of a posterior fragment (green)."} [Term] id: PLANA:0003725 name: ventral region of posterior fragment def: "The ventral region of a fragment encompassing all or part of the posterior region of the animal." [] synonym: "ventral region of posterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003606 ! contained in posterior fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003606 ! contained in posterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofposteriorfragment.png {comment="Illustration of the ventral region of a posterior fragment (green)."} [Term] id: PLANA:0003726 name: anterior region of posterior fragment def: "The anterior region of a fragment encompassing all or part of the posterior region of the animal." [] synonym: "anterior region of posterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003606 ! contained in posterior fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003606 ! contained in posterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofposteriorfragment.png {comment="Illustration of the anterior region of a posterior fragment (green)."} [Term] id: PLANA:0003727 name: posterior region of posterior fragment def: "The posterior region of a fragment encompassing all or part of the posterior region of the animal." [] synonym: "posterior region of posterior fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003606 ! contained in posterior fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003606 ! contained in posterior fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofposteriorfragment.png {comment="Illustration of the posterior region of a posterior fragment (green)."} [Term] id: PLANA:0003728 name: dorsal region of lateral fragment def: "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." [] synonym: "dorsal region of lateral fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003607 ! contained in lateral fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003607 ! contained in lateral fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionoflateralfragment.png {comment="Illustration of the dorsal region of a lateral fragment (green)."} [Term] id: PLANA:0003729 name: ventral region of lateral fragment def: "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." [] synonym: "ventral region of lateral fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003607 ! contained in lateral fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003607 ! contained in lateral fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionoflateralfragment.png {comment="Illustration of the ventral region of a lateral fragment (green)."} [Term] id: PLANA:0003730 name: anterior region of lateral fragment def: "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." [] synonym: "anterior region of lateral fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003607 ! contained in lateral fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003607 ! contained in lateral fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionoflateralfragment.png {comment="Illustration of the anterior region of a lateral fragment (green)."} [Term] id: PLANA:0003731 name: posterior region of lateral fragment def: "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." [] synonym: "posterior region of lateral fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003607 ! contained in lateral fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003607 ! contained in lateral fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionoflateralfragment.png {comment="Illustration of the posterior region of a lateral fragment (green)."} [Term] id: PLANA:0003732 name: dorsal region of longitudinal fragment def: "The dorsal region of a fragment derived from an amputation parallel to the midline." [] synonym: "dorsal region of longitudinal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionoflongitudinalfragment.png {comment="Illustration of the dorsal region of a longitudinal fragment (green)."} [Term] id: PLANA:0003733 name: ventral region of longitudinal fragment def: "The ventral region of a fragment derived from an amputation parallel to the midline." [] synonym: "ventral region of longitudinal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionoflongitudinalfragment.png {comment="Illustration of the ventral region of a longitudinal fragment (green)."} [Term] id: PLANA:0003734 name: anterior region of longitudinal fragment def: "The anterior region of a fragment derived from an amputation parallel to the midline." [] synonym: "anterior region of longitudinal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionoflongitudinalfragment.png {comment="Illustration of the anterior region of a longitudinal fragment (green)."} [Term] id: PLANA:0003735 name: posterior region of longitudinal fragment def: "The posterior region of a fragment derived from an amputation parallel to the midline." [] synonym: "posterior region of longitudinal fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003608 ! contained in longitudinal fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionoflongitudinalfragment.png {comment="Illustration of the posterior region of a longitudinal fragment (green)."} [Term] id: PLANA:0003736 name: dorsal region of plug fragment def: "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." [] synonym: "dorsal region of plug fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003609 ! contained in plug fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003609 ! contained in plug fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofplugfragment.png {comment="Illustration of the dorsal region of a plug fragment (green)."} [Term] id: PLANA:0003737 name: ventral region of plug fragment def: "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." [] synonym: "ventral region of plug fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003609 ! contained in plug fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003609 ! contained in plug fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofplugfragment.png {comment="Illustration of the ventral region of a plug fragment (green)."} [Term] id: PLANA:0003738 name: anterior region of plug fragment def: "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." [] synonym: "anterior region of plug fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003609 ! contained in plug fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003609 ! contained in plug fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofplugfagment.png {comment="Illustration of the anterior region of a plug fragment (green)."} [Term] id: PLANA:0003739 name: posterior region of plug fragment def: "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." [] synonym: "posterior region of plug fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003609 ! contained in plug fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003609 ! contained in plug fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofplugfragment.png {comment="Illustration of the posterior region of a plug fragment (green)."} [Term] id: PLANA:0003740 name: dorsal region of wedge fragment def: "The dorsal region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures." [] synonym: "dorsal region of wedge fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000079 ! dorsal region intersection_of: RO:0001018 PLANA:0003610 ! contained in wedge fragment relationship: overlaps BSPO:0000079 ! dorsal region relationship: RO:0001018 PLANA:0003610 ! contained in wedge fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsalregionofplugfragment.png {comment="Illustration of the dorsal region of a plug fragment (green)."} [Term] id: PLANA:0003741 name: ventral region of wedge fragment def: "The ventral region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures." [] synonym: "ventral region of wedge fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000084 ! ventral region intersection_of: RO:0001018 PLANA:0003610 ! contained in wedge fragment relationship: overlaps BSPO:0000084 ! ventral region relationship: RO:0001018 PLANA:0003610 ! contained in wedge fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/ventralregionofplugfragment.png {comment="Illustration of the ventral region of a plug fragment (green)."} [Term] id: PLANA:0003742 name: anterior region of wedge fragment def: "The anterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures." [] synonym: "anterior region of wedge fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000071 ! anterior region intersection_of: RO:0001018 PLANA:0003610 ! contained in wedge fragment relationship: overlaps BSPO:0000071 ! anterior region relationship: RO:0001018 PLANA:0003610 ! contained in wedge fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorregionofwedgefragment.png {comment="Illustration of the anterior region of a wedge fragment (green)."} [Term] id: PLANA:0003743 name: posterior region of wedge fragment def: "The posterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures." [] synonym: "posterior region of wedge fragment" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000072 ! posterior region intersection_of: RO:0001018 PLANA:0003610 ! contained in wedge fragment relationship: overlaps BSPO:0000072 ! posterior region relationship: RO:0001018 PLANA:0003610 ! contained in wedge fragment property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorregionofwedgefragment.png {comment="Illustration of the posterior region of a wedge fragment (green)."} [Term] id: PLANA:0003800 name: anterior photoreceptor neuron def: "photoreceptor neuron is contained in the anterior region of the eye" [PMID: 20967238] synonym: "photoreceptor neuron contained in anterior region of the eye" EXACT [] is_a: PLANA:0000017 ! photoreceptor neuron intersection_of: PLANA:0000017 ! photoreceptor neuron intersection_of: RO:0001018 PLANA:0003002 ! contained in anterior region of the eye relationship: RO:0001018 PLANA:0003002 ! contained in anterior region of the eye [Term] id: PLANA:0003801 name: posterior photoreceptor neuron def: "photoreceptor neuron is contained in the posterior region of the eye" [PMID: 20967238] synonym: "photoreceptor neuron contained in posterior region of the eye" EXACT [] is_a: PLANA:0000017 ! photoreceptor neuron intersection_of: PLANA:0000017 ! photoreceptor neuron intersection_of: RO:0001018 PLANA:0003003 ! contained in posterior region of the eye relationship: RO:0001018 PLANA:0003003 ! contained in posterior region of the eye [Term] id: PLANA:0003802 name: lateral muscle cell def: "muscle cell is contained in the lateral region" [PMID: 29674431] synonym: "muscle cell contained in lateral region" EXACT [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell intersection_of: PLANA:0000101 ! muscle cell intersection_of: RO:0001018 BSPO:0000082 ! contained in lateral region relationship: RO:0001018 BSPO:0000082 ! contained in lateral region [Term] id: PLANA:0003803 name: anterior muscle cell def: "muscle cell is contained in the anterior region" [PMID: 29674432] synonym: "muscle cell contained in anterior region" EXACT [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell intersection_of: PLANA:0000101 ! muscle cell intersection_of: RO:0001018 BSPO:0000071 ! contained in anterior region relationship: RO:0001018 BSPO:0000071 ! contained in anterior region [Term] id: PLANA:0003804 name: posterior muscle cell def: "muscle cell is contained in the posterior region" [PMID: 29674433] synonym: "muscle cell contained in posterior region" EXACT [] is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell intersection_of: PLANA:0000101 ! muscle cell intersection_of: RO:0001018 BSPO:0000072 ! contained in posterior region relationship: RO:0001018 BSPO:0000072 ! contained in posterior region [Term] id: PLANA:0003900 name: head blastema def: "blastema which develops into head region" [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000495 ! blastema intersection_of: PLANA:0000495 ! blastema intersection_of: RO:0002203 PLANA:0000418 ! develops into head region relationship: RO:0002203 PLANA:0000418 ! develops into head region [Term] id: PLANA:0003901 name: tail blastema def: "blastema which develops into tail region" [] is_a: CARO:0000000 ! anatomical entity is_a: PLANA:0000495 ! blastema intersection_of: PLANA:0000495 ! blastema intersection_of: RO:0002203 PLANA:0000421 ! develops into tail region relationship: RO:0002203 PLANA:0000421 ! develops into tail region [Term] id: PLANA:0004000 name: regenerating head fragment def: "a head fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003600 ! head fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003600 ! head fragment [Term] id: PLANA:0004001 name: regenerating trunk fragment def: "a trunk fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003601 ! trunk fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003601 ! trunk fragment [Term] id: PLANA:0004002 name: regenerating tail fragment def: "a tail fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003602 ! tail fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003602 ! tail fragment [Term] id: PLANA:0004003 name: regenerating prepharyngeal fragment def: "a prepharyngeal fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003603 ! prepharyngeal fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003603 ! prepharyngeal fragment [Term] id: PLANA:0004004 name: regenerating postpharyngeal fragment def: "a postpharyngeal fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003604 ! postpharyngeal fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003604 ! postpharyngeal fragment [Term] id: PLANA:0004005 name: regenerating anterior fragment def: "a anterior fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003605 ! anterior fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003605 ! anterior fragment [Term] id: PLANA:0004006 name: regenerating posterior fragment def: "a posterior fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003606 ! posterior fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003606 ! posterior fragment [Term] id: PLANA:0004007 name: regenerating lateral fragment def: "a lateral fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003607 ! lateral fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003607 ! lateral fragment [Term] id: PLANA:0004008 name: regenerating longitudinal fragment def: "a longitudinal fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003608 ! longitudinal fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003608 ! longitudinal fragment [Term] id: PLANA:0004009 name: regenerating plug fragment def: "a plug fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003609 ! plug fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003609 ! plug fragment [Term] id: PLANA:0004010 name: regenerating wedge fragment def: "a wedge fragment that is regenerating" [] is_a: PLANA:0002133 ! regenerating fragment is_a: PLANA:0003610 ! wedge fragment intersection_of: PLANA:0002133 ! regenerating fragment intersection_of: PLANA:0003610 ! wedge fragment [Term] id: PLANA:0004503 name: adult hermaphrodite def: "A fully formed, sexually mature organism that reproduces through cross-fertilization." [PMID:11972158, PMID:19022767] synonym: "sexual adult" EXACT [] synonym: "sexually mature adult" EXACT [] xref: PMID:11972158 xref: PMID:19022767 is_a: UBERON:0000105 ! life cycle stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/sexuallymatureadult.png {comment="Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004504 name: asexual adult def: "Asexually reproducing Schmidtea mediterranea exist as constitutive adults, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system." [PMID:11972158, PMID:17376870] xref: PMID:11972158 xref: PMID:17376870 is_a: UBERON:0000105 ! life cycle stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/asexualadult.png {comment="Depicted by field shows an asexual adult with a scale bar of 500um"} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004506 name: testis somatic gonadal cell def: "dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation." [PMID:23652002, PMID:27163480] synonym: "somatic gonadal cell of the testis" EXACT [] synonym: "somatic niche cell of the testis" EXACT [] synonym: "somatic testis cell" EXACT [] xref: PMID:23652002 xref: PMID:27163480 is_a: BFO:0000040 ! material entity is_a: PLANA:0002096 ! somatic gonadal cell relationship: part_of PLANA:0000208 ! testis relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004507 name: ovarian somatic gonadal cell def: "ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia." [PMID:27163480] synonym: "somatic follicular cell of the ovary" EXACT [] synonym: "somatic ovarian cell" EXACT [] xref: PMID:27163480 is_a: BFO:0000040 ! material entity is_a: PLANA:0000119 ! terminally differentiated cell relationship: part_of PLANA:0000204 ! ovary relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004511 name: oral-aboral axis of the embryo def: "Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the embryonic pharynx; the aboral pole is located opposite the embryonic pharynx." [PMID:28072387] synonym: "oral-aboral axis of embryo" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000198 ! oral-aboral axis intersection_of: RO:0001018 PLANA:0000116 ! contained in embryo relationship: overlaps BSPO:0000198 ! oral-aboral axis relationship: RO:0001018 PLANA:0000116 ! contained in embryo property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/oralaboralaxis.png {comment="Illustration noting the oral-aboral axis in cyan double headed arrow. It starts at the embryonic pharynx and extends to opposite pole."} [Term] id: PLANA:0004512 name: primitive ectoderm surface def: "The apical surface of the single layered primitive ectoderm that is in contact with the environment." [https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md, OCLC:20423827, OCLC:464776945, OCLC:82522822, PMID:28072387] xref: https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md xref: OCLC:20423827 xref: OCLC:464776945 xref: OCLC:82522822 xref: PMID:28072387 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0000029 ! primitive ectoderm relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004513 name: primtive gut cell surface def: "The surface of the primitive gut cells in contact with the embryonic wall." [PMID:28072387] xref: PMID:28072387 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0000085 ! primitive gut cell relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000005 ! existence ends during or before Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004514 name: embryonic gut cell surface def: "The surface of phagocytic embryonic gut cells in contact with ingested yolk cells." [PMID:28072387] xref: PMID:28072387 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0000059 ! embryonic gut cell relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000004 ! existence starts during or after Stage 4 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004516 name: embryonic pharynx lumen epithelial surface def: "The epithelial cell surface lining the embryonic pharynx lumen." [PMID:28072387] xref: PMID:20100474 xref: PMID:28072387 is_a: BSPO:0000005 ! anatomical surface relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004517 name: blastomere def: "An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Blastomeres give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5." [PMID:28072387] xref: CL:0000353 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000123 ! embryonic cell relationship: part_of PLANA:0000056 ! ectolecithal embryo relationship: RO:0001018 PLANA:0000041 ! contained in aboral hemisphere relationship: RO:0001018 PLANA:0000060 ! contained in embryonic wall relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0000098 ! develops from zygote relationship: RO:0002490 PLANA:0000001 ! existence overlaps Stage 1 relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002496 PLANA:0000001 ! existence starts during or after Stage 1 relationship: RO:0002497 PLANA:0000005 ! existence ends during or before Stage 5 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004518 name: extraembryonic cell def: "Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues." [PMID:28072387] xref: CL:0000349 xref: PMID:28072387 is_a: PLANA:0000119 ! terminally differentiated cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004519 name: embryonic pharynx neuron def: "A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000099 ! neuron is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004520 name: embryonic pharynx radial muscle cell def: "Differentiated radial muscle cell present in the embryonic pharynx." [PMID:16932928] synonym: "embryonic pharynx radial muscle fiber" EXACT [] xref: PMID:16932928 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004521 name: embryonic pharynx epithelial cell def: "foxA1+ epithelial cell contained in the embryonic pharynx." [PMID:28072387] xref: PMID:20100474 xref: PMID:28072387 is_a: BFO:0000040 ! material entity is_a: PLANA:0000100 ! epithelial cell is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004524 name: embryonic pharynx circular muscle cell def: "Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx." [PMID:16932928] synonym: "embryonic pharynx circular muscle fiber" EXACT [] xref: PMID:16932928 is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell is_a: PLANA:0004518 ! extraembryonic cell relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: RO:0001018 PLANA:0000076 ! contained in oral hemisphere relationship: RO:0002202 PLANA:0004517 ! develops from blastomere relationship: RO:0002490 PLANA:0000002 ! existence overlaps Stage 2 relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000002 ! existence starts during or after Stage 2 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004527 name: copulatory region def: "Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus." [PMID:22074376] xref: PMID:22074376 is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: posterior_to PLANA:0000420 ! parapharyngeal region relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/copulatoryregion.png {comment="Depicted by field contains diagram representation of body region."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004528 name: pharynx epithelium def: "Epithelia associated with the pharynx organ." [] synonym: "pharnyx epidermis" EXACT [] synonym: "pharyngeal epidermis" EXACT [] synonym: "pharyngeal epithelium" EXACT [] xref: UBERON:0003351 is_a: BFO:0000040 ! material entity is_a: PLANA:0002118 ! epithelium relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxepithelium.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004529 name: integumental system def: "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle." [UBERON:0002416] xref: UBERON:0002416 is_a: PLANA:0000114 ! anatomical system relationship: part_of PLANA:0007564 ! sexual organism relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004530 name: oviduct lumen def: "Anatomical space enclosed by the oviduct epithelium." [PMID:22074376] xref: PMID:22074376 xref: TADS:0000435 is_a: BFO:0000141 ! immaterial entity is_a: PLANA:0002053 ! lumen relationship: part_of PLANA:0000205 ! oviduct relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0002572 PLANA:0000205 ! luminal space of oviduct created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004531 name: sperm duct lumen def: "Anatomical space enclosed by the sperm duct epithelium." [PMID:19022767, PMID:22074376] xref: PMID:19022767 xref: PMID:22074376 is_a: BFO:0000141 ! immaterial entity is_a: PLANA:0002053 ! lumen relationship: part_of PLANA:0000207 ! sperm duct relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0002572 PLANA:0000207 ! luminal space of sperm duct created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004532 name: oviduct epithelium def: "Ciliated epithelium lining the oviduct." [PMID:22074376] xref: CL:2000064 xref: PMID:22074376 xref: UBERON:0004804 is_a: BFO:0000040 ! material entity is_a: PLANA:0002023 ! ciliated epithelium relationship: part_of PLANA:0000205 ! oviduct relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004533 name: sperm duct epithelium def: "Ciliated epithelium lining the sperm duct." [PMID:19022767, PMID:22074376] xref: PMID:19022767 xref: PMID:22074376 is_a: BFO:0000040 ! material entity is_a: PLANA:0002023 ! ciliated epithelium relationship: part_of PLANA:0000207 ! sperm duct relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0004534 name: tuba lumen def: "Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct." [PMID:19022767, PMID:20844018, PMID:22074376, PMID:27149082] xref: PMID:19022767 xref: PMID:20844018 xref: PMID:22074376 xref: PMID:27149082 is_a: BFO:0000141 ! immaterial entity is_a: PLANA:0002053 ! lumen relationship: part_of PLANA:0000230 ! tuba relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0002572 PLANA:0000230 ! luminal space of tuba created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007502 name: obsolete coronal plane comment: let odk import from BSPO if needed is_obsolete: true [Term] id: PLANA:0007503 name: sagittal plane of the whole animal def: "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." [] synonym: "sagittal plane of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000417 ! sagittal plane intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000417 ! sagittal plane relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/sagittalplaneofthewholeanimal.png {comment="Illustration of a sagittal plane of the whole animal (in green)."} [Term] id: PLANA:0007504 name: obsolete dorsal compartment comment: replaced by dorsal region PLANA:0000141 is_obsolete: true replaced_by: PLANA:0000141 [Term] id: PLANA:0007505 name: obsolete ventral compartment comment: now using patterned term ventral region PLANA:0000143 is_obsolete: true [Term] id: PLANA:0007506 name: obsolete anterior compartment comment: now using patterned term anterior region is_obsolete: true replaced_by: PLANA:0000140 [Term] id: PLANA:0007507 name: obsolete posterior compartment comment: replaced comment: replacing duplicate PLANA term is_obsolete: true replaced_by: PLANA:0000142 [Term] id: PLANA:0007508 name: obsolete extracellular component comment: choosing to use UBERON:0000476, acellular anatomical structure instead is_obsolete: true replaced_by: UBERON:0000476 [Term] id: PLANA:0007509 name: plasma membrane def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [GO:0005886] synonym: "cell membrane" EXACT [] synonym: "cytoplasmic membrane" EXACT [] xref: GO:0005886 xref: PMID:20511647 xref: PMID:27523733 is_a: PLANA:0000520 ! membrane property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/plasmamembrane.png {comment="Image is an electron micrograph showing several cells. Arrowheads label the plasma membrane, the boundary between cells. Scale bar is 1um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007511 name: extracellular organelle def: "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." [GO:0043230] xref: GO:0043230 is_a: PLANA:0000525 ! organelle created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007512 name: mitochondrion def: "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." [] synonym: "mitochondria" EXACT [] xref: GO:0005739 xref: PMID:21828097 xref: PMID:22318224 xref: PMID:26516985 xref: PMID:29100657 is_a: PLANA:0000527 ! intracellular membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/mitochondrion.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007513 name: endoplasmic reticulum def: "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." [] xref: GO:0005783 xref: PMID:30143032 is_a: PLANA:0000527 ! intracellular membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/endoplasmiceeticulum.png {comment="Image is an electron micrograph depicting endoplasmic reticulum (magenta) in multiple cells. Scale bar is 0.5um."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007514 name: rough endoplasmic reticulum def: "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." [] xref: GO:0005791 xref: PMID:30143032 is_a: PLANA:0007513 ! endoplasmic reticulum property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/roughendoplasmicreticulum.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007515 name: smooth endoplasmic reticulum def: "Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids." [] xref: GO:0005790 is_a: PLANA:0007513 ! endoplasmic reticulum property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/smoothendoplasmicreticulum.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007516 name: nuclear pore def: "Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined." [GO:0005643] xref: GO:0005643 is_a: PLANA:0000532 ! nuclear part is_a: PLANA:0002079 ! pore property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/nuclearpore.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007518 name: lysosome def: "The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers." [] xref: GO:0005764 xref: ISBN:0-71677033-4 xref: PMID:4853064 is_a: PLANA:0000527 ! intracellular membrane-bounded organelle property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/lysosome.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007519 name: anterior-posterior axis of the whole animal def: "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." [] synonym: "anterior-posterior axis" EXACT [] synonym: "anterior-posterior axis of whole organism" EXACT [] synonym: "body axis" EXACT [] synonym: "longitudinal axis" EXACT [] synonym: "main body axis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000013 ! anterior-posterior axis intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000013 ! anterior-posterior axis relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteroposterioraxis.png {comment="Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um"} [Term] id: PLANA:0007520 name: dorsal-ventral axis of the whole animal def: "Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side." [PMID:18287199, PMID:18786419, PMID:19174194, PMID:21295481, PMID:21295483, PMID:21664348, PMID:21806978, PMID:22445864, PMID:23318641, PMID:23954785, PMID:24415944, PMID:24523458, PMID:25017721, PMID:27063937, PMID:27523733, PMID:27612382, PMID:28137894, PMID:28292427, PMID:28686611, PMID:29100657, PMID:29547123, PMID:29674431, PMID:30471994] synonym: "D/V axis" EXACT [] synonym: "dorsal-ventral axis" EXACT [] synonym: "dorsal-ventral axis of whole organism" EXACT [] synonym: "DV axis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000016 ! dorsal-ventral axis intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000016 ! dorsal-ventral axis relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dorsal-ventralaxisofthewholeanimal.png [Term] id: PLANA:0007521 name: left-right axis of the whole animal def: "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." [] synonym: "dextro-sinister axis" EXACT [] synonym: "left-right axis" EXACT [] synonym: "left-right axis of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000017 ! left-right axis intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000017 ! left-right axis relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/dextro-sinisteraxis.png {comment="Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um"} [Term] id: PLANA:0007522 name: medial-lateral axis of the whole animal def: "Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal." [PMID:20707997, PMID:21282632, PMID:21295483, PMID:21664348, PMID:21806978, PMID:23250205, PMID:23318641, PMID:23903188, PMID:23954785, PMID:25017721, PMID:26062938, PMID:26525673, PMID:27523733, PMID:28287248, PMID:29291981, PMID:29547123, PMID:30471994, PMID:30962434] synonym: "medial-lateral axis" EXACT [] synonym: "medial-lateral axis of whole organism" EXACT [] synonym: "mediolateral" EXACT [] synonym: "mediolateral axis" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0001001 ! medial-lateral axis intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0001001 ! medial-lateral axis relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/mediolateralaxis.png {comment="Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um"} [Term] id: PLANA:0007523 name: proximal-distal axis of the whole animal def: "Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body." [PMID:21828097] synonym: "proximal-distal axis" EXACT [] synonym: "proximal-distal axis of whole organism" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: overlaps BSPO:0000015 ! proximal-distal axis intersection_of: RO:0001018 PLANA:0000136 ! contained in whole organism relationship: overlaps BSPO:0000015 ! proximal-distal axis relationship: RO:0001018 PLANA:0000136 ! contained in whole organism property_value: foaf:depiction https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/proximodistalaxis.png {comment="Pharynx of an asexual adult exposed by tricaine treatment. The proximodistal axis is denoted with the double headed magenta arrow."} [Term] id: PLANA:0007524 name: anterior pole def: "Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD." [PMID:21566195, PMID:23297191, PMID:24040508, PMID:24415944, PMID:24704339, PMID:24992682] synonym: "anterior signaling center" EXACT [] xref: PMID:18063755 xref: PMID:21566195 xref: PMID:23297191 xref: PMID:23318641 xref: PMID:23903188 xref: PMID:23954785 xref: PMID:24040508 xref: PMID:24415944 xref: PMID:24523458 xref: PMID:24704339 xref: PMID:24992682 xref: PMID:25254346 xref: PMID:25725068 xref: PMID:26062938 xref: PMID:26525673 xref: PMID:27074666 xref: PMID:27800171 xref: PMID:28216315 xref: PMID:28292427 xref: PMID:28893948 xref: PMID:29547123 xref: PMID:29906446 xref: PMID:30485821 is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: RO:0001018 PLANA:0000030 ! contained in midline relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anteriorpole.png {comment="Illustration of the anterior pole (green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007525 name: posterior pole def: "Distinct posterior cluster of muscle cells located at the midline which express wnt1." [PMID:18063755, PMID:21680047] synonym: "posterior regeneration pole" EXACT [] xref: PMID:18063755 xref: PMID:19805089 xref: PMID:21566195 xref: PMID:23318641 xref: PMID:23903188 xref: PMID:24415944 xref: PMID:25725068 xref: PMID:26062938 xref: PMID:27074666 xref: PMID:30485821 is_a: BFO:0000040 ! material entity is_a: PLANA:0000102 ! anatomical region relationship: RO:0001018 PLANA:0000030 ! contained in midline relationship: RO:0001018 PLANA:0002104 ! contained in tail tip relationship: RO:0002490 PLANA:0000007 ! existence overlaps Stage 7 relationship: RO:0002490 PLANA:0000008 ! existence overlaps Stage 8 relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/posteriorpole.png {comment="Illustration of the posterior pole (in green)."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007528 name: glial cell def: "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons." [PMID:27612384] synonym: "glia" EXACT [] synonym: "glia cell" EXACT [] xref: CL:0000125 xref: PMID:27612382 xref: PMID:27612384 xref: PMID:28137894 xref: PMID:29674431 xref: PMID:29674432 xref: PMID:30471994 is_a: BFO:0000040 ! material entity is_a: PLANA:0000561 ! neuron associated cell (sensu Nematoda and Protostomia) relationship: part_of PLANA:0000470 ! neuropil relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/glialcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007529 name: ganglion def: "A biological tissue mass of nerve cell bodies." [UBERON:0000045] synonym: "ganglia" EXACT [] xref: UBERON:0000045 is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007534 name: pharynx inner epithelium def: "Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft." [doi:10.1002/jmor.1051550208, OCLC:16809160] synonym: "epithelial pharynx lining" EXACT [] synonym: "epithelium lining the lumen of the pharynx" EXACT [] synonym: "inner epithelium" EXACT [] synonym: "inner pharyngeal epidermis" EXACT [] synonym: "inner pharyngeal epithelium" EXACT [] synonym: "inner pharynx epidermis" EXACT [] synonym: "inner pharynx epithelium" EXACT [] xref: doi:10.1002/jmor.1051550208 xref: OCLC:16809160 xref: PMID:24120894 is_a: BFO:0000040 ! material entity is_a: PLANA:0002023 ! ciliated epithelium relationship: immediately_superficial_to PLANA:0000474 ! pharynx inner circular muscle cell relationship: part_of PLANA:0000016 ! pharynx relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxinnerepithelium.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007535 name: pharynx circular muscle cell def: "Pharynx muscle fibers running circumferentially about the pharynx." [ASIN:B000M4NK9M] synonym: "pharyngeal circular muscle cell" EXACT [] synonym: "pharynx circular muscle cell" EXACT [] synonym: "pharynx circular muscle fiber" EXACT [] xref: ASIN:B000M4NK9M is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0000478 ! pharynx musculature relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/pharynxcircularmusclecell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007536 name: obsolete specific_to comment: using part of instead is_obsolete: true [Term] id: PLANA:0007537 name: obsolete brain comment: replacing duplicate PLANA term is_obsolete: true replaced_by: PLANA:0000044 [Term] id: PLANA:0007538 name: adhesion gland def: "Groupings of specialized epithelial cells located along the dorsal ventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epidermal surface." [OCLC:16809160, PMID:20865784] synonym: "marginal adhesive gland" EXACT [] xref: ISBN:9780070316607 xref: OCLC:16809160 xref: PMID:20865784 is_a: BFO:0000040 ! material entity is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000484 ! secretory system relationship: RO:0001018 PLANA:0000043 ! contained in dorsal ventral margin of the whole animal relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/adhesiongland.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007539 name: anchor cell def: "Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells." [OCLC:16809160, PMID:20865784] xref: OCLC:16809160 xref: PMID:20865784 is_a: BFO:0000040 ! material entity is_a: PLANA:0000487 ! acidophilic gland cell relationship: part_of PLANA:0007538 ! adhesion gland relationship: RO:0001018 PLANA:0000043 ! contained in dorsal ventral margin of the whole animal relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/anchorcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007540 name: viscid gland cell def: "A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate." [OCLC:16809160, PMID:20865784] xref: OCLC:16809160 xref: PMID:20865784 is_a: BFO:0000040 ! material entity is_a: PLANA:0000487 ! acidophilic gland cell relationship: part_of PLANA:0007538 ! adhesion gland relationship: RO:0001018 PLANA:0000043 ! contained in dorsal ventral margin of the whole animal relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/viscidglandcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007541 name: releasing gland cell def: "Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance." [OCLC:16809160, PMID:20865784] xref: OCLC:16809160 xref: PMID:20865784 is_a: BFO:0000040 ! material entity is_a: PLANA:0000487 ! acidophilic gland cell relationship: part_of PLANA:0007538 ! adhesion gland relationship: RO:0001018 PLANA:0000043 ! contained in dorsal ventral margin of the whole animal relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/releasingglandcell.png {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."} created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007543 name: TrpA+ central nervous system neuron def: "A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2." [PMID:25254346] synonym: "TrpA+ neuron" EXACT [] xref: PMID:25254346 is_a: BFO:0000040 ! material entity is_a: PLANA:0000562 ! central nervous system neuron relationship: part_of PLANA:0000044 ! cephalic ganglia relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002202 PLANA:0007546 ! develops from TrpA+ neural progenitor cell relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007544 name: cintillo+ sensory neuron def: "A subset of sensory neurons located along the dorsal head margin." [PMID:12557210, PMID:25254346, PMID:29674431] synonym: "cintillo+ neuron" EXACT [] xref: PMID:12557210 xref: PMID:25254346 xref: PMID:29674431 is_a: BFO:0000040 ! material entity is_a: PLANA:0000552 ! sensory neuron relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000418 ! contained in head region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007545 name: obsolete epidermal compartment comment: no longer designating mediolateral regions using the contained_in object property is_obsolete: true [Term] id: PLANA:0007546 name: TrpA+ neural progenitor cell def: "piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons." [PMID:25254346] xref: PMID:25254346 is_a: PLANA:0000012 ! neural progenitor cell is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007547 name: anterior pole progenitor cell def: "piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole." [PMID:24415944] xref: PMID:24415944 is_a: PLANA:0000429 ! neoblast created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007548 name: transverse commissure def: "Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords." [PMID:17999079] xref: PMID:17999079 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0002025 ! commissure relationship: part_of PLANA:0000097 ! ventral nerve cord relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007549 name: obsolete body wall musculature compartment comment: no longer designating mediolateral regions using the contained_in object property is_obsolete: true [Term] id: PLANA:0007550 name: serotonergic neural progenitor cell def: "piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons." [PMID:23903188, PMID:24131630, PMID:25254346] xref: PMID:23903188 xref: PMID:24131630 xref: PMID:25254346 is_a: PLANA:0000012 ! neural progenitor cell is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007551 name: klf+ sensory neuron progenitor cell def: "piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons." [PMID:25254346] xref: PMID:25254346 is_a: PLANA:0000012 ! neural progenitor cell is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0007565 ! asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007552 name: nu neoblast def: "A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages." [PMID:27150006] synonym: "vNeoblast" EXACT [] xref: PMID:27150006 is_a: PLANA:0000012 ! neural progenitor cell is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000025 ! nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007553 name: lateral nerve def: "A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus." [PMID:17999079] xref: PMID:17999079 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000113 ! tissue relationship: part_of PLANA:0000080 ! peripheral nervous system relationship: part_of PLANA:0007565 ! asexual organism relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007554 name: obsolete parenchymal compartment comment: no longer designating mediolateral regions using the contained_in object property is_obsolete: true [Term] id: PLANA:0007555 name: pax3/7+ neural progenitor cell def: "piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons." [PMID:25254346] xref: PMID:25254346 is_a: PLANA:0000012 ! neural progenitor cell is_a: PLANA:0000429 ! neoblast relationship: part_of PLANA:0000103 ! central nervous system created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007556 name: embryonic pharynx lumen def: "A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity." [PMID:28072387] xref: PMID:28072387 is_a: BFO:0000141 ! immaterial entity is_a: PLANA:0002053 ! lumen relationship: part_of PLANA:0000023 ! embryonic pharynx relationship: RO:0002490 PLANA:0000003 ! existence overlaps Stage 3 relationship: RO:0002490 PLANA:0000004 ! existence overlaps Stage 4 relationship: RO:0002490 PLANA:0000005 ! existence overlaps Stage 5 relationship: RO:0002490 PLANA:0000006 ! existence overlaps Stage 6 relationship: RO:0002496 PLANA:0000003 ! existence starts during or after Stage 3 relationship: RO:0002497 PLANA:0000006 ! existence ends during or before Stage 6 relationship: RO:0002572 PLANA:0000023 ! luminal space of embryonic pharynx created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007557 name: testis nerve plexus def: "Nerve plexus surrounding the testis." [PMID:17999079, PMID:7833618] xref: PMID:17999079 xref: PMID:7833618 is_a: BFO:0000040 ! material entity is_a: PLANA:0000492 ! nerve plexus relationship: part_of PLANA:0000126 ! reproductive system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000141 ! contained in dorsal region of the whole animal relationship: RO:0001018 PLANA:0000142 ! contained in posterior region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0001018 PLANA:0000420 ! contained in parapharyngeal region relationship: RO:0001018 PLANA:0000421 ! contained in tail region relationship: RO:0001018 PLANA:0004527 ! contained in copulatory region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007558 name: fission plane def: "Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs." [OCLC:16809160, PMID:11972158] xref: OCLC:16809160 xref: PMID:11972158 is_a: BSPO:0000400 ! anatomical plane created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007559 name: ovary nerve plexus def: "Nerve plexus surrounding the ovary." [PMID:17999079, PMID:7833618] xref: PMID:17999079 xref: PMID:7833618 is_a: BFO:0000040 ! material entity is_a: PLANA:0000492 ! nerve plexus relationship: part_of PLANA:0000126 ! reproductive system relationship: RO:0001018 PLANA:0000140 ! contained in anterior region of the whole animal relationship: RO:0001018 PLANA:0000143 ! contained in ventral region of the whole animal relationship: RO:0001018 PLANA:0000419 ! contained in prepharyngeal region relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007560 name: obsolete gastrovascular compartment comment: no longer designating mediolateral regions using the contained_in object property is_obsolete: true [Term] id: PLANA:0007561 name: head margin def: "Peripheral region of the head." [] is_a: PLANA:0000043 ! dorsal ventral margin of the whole animal property_value: http://purl.obolibrary.org/obo/foaf_depicted_by https://raw.githubusercontent.com/obophenotype/planaria-ontology/master/metadata/images/headmargin.png created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007563 name: glutamatergic neuron def: "Neurons that express the biogenic amine glutamate." [PMID:24131630] xref: CL:0000679 xref: PMID:24131630 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000556 ! neurosecretory neuron relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002490 PLANA:0004503 ! existence overlaps adult hermaphrodite relationship: RO:0002490 PLANA:0004504 ! existence overlaps asexual adult created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007564 name: sexual organism def: "An individual member of the sexual biotype of Schmidtea mediterranea." [] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000136 ! whole organism relationship: RO:0002202 PLANA:0000116 ! develops from embryo created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007565 name: asexual organism def: "An individual member of the asexual biotype of Schmidtea mediterranea." [] xref: CARO:0000030 is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000136 ! whole organism relationship: RO:0002202 PLANA:0007565 ! develops from asexual organism created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007566 name: non-ciliated neuron def: "A neuron cell that does not have cilia." [PMID:29674431] synonym: "non cilated neuron" EXACT [] synonym: "uncilated neuon" EXACT [] is_a: PLANA:0000099 ! neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007567 name: cilated neuron def: "A neuron that has cilia." [PMID:29674431] xref: WBbt:0006816 is_a: PLANA:0000099 ! neuron created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007568 name: guidepost cell def: "A cell present near the brain and eye where photoreceptor axons form a bundle projecting out from the eye that are near axon choice points. Guidepost cells are positive for Arrestin, notum, fz5/8-4+, 6G10, and low levels of troponin, tropomyosin, colF-2 and mp-1." [PMID:32586989] is_a: BFO:0000040 ! material entity is_a: PLANA:0000101 ! muscle cell relationship: part_of PLANA:0003102 ! visual system cell relationship: RO:0001018 PLANA:0000418 ! contained in head region created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007569 name: NME cell def: "Guidepost cell associated with the visual circuit that are present near the eye, located along axons just anterior and ventral to the eye. Name acronym stands for notum+ muscle cell near eye." [PMID:32586989] is_a: PLANA:0007568 ! guidepost cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007570 name: NMC cell def: "Guidepost cell assocaited with the visual circuit, present at the axon choice point ventral, posterior to and slightly medial to the eye. Name acronym stands for notum+ muscle cells at the choice point." [PMID:32586989] is_a: PLANA:0007569 ! NME cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007571 name: NBC cell def: "Guidepost cell present at the medial brain, ventral to the optic chiasm. Closely associated with photoreceptor axons during regneration. Name acronym stands for notum+ brain cells." [PMID:32586989] is_a: PLANA:0007570 ! NMC cell created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: PLANA:0007572 name: juvenile organism def: "A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype" [] synonym: "juvenile" EXACT [] is_a: BFO:0000004 ! independent continuant is_a: PLANA:0000136 ! whole organism relationship: RO:0002490 PLANA:0000214 ! existence overlaps juvenile stage relationship: RO:0002496 PLANA:0000214 ! existence starts during or after juvenile stage relationship: RO:0002497 PLANA:0000214 ! existence ends during or before juvenile stage created_by: https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 [Term] id: UBERON:0000061 name: anatomical structure namespace: uberon def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] subset: common_anatomy subset: upper_level synonym: "biological structure" EXACT [] synonym: "connected biological structure" EXACT [CARO:0000003] xref: AAO:0010825 xref: AEO:0000003 xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 xref: FBbt:00007001 xref: FMA:305751 xref: FMA:67135 xref: GAID:781 xref: HAO:0000003 xref: http://dbpedia.org/ontology/AnatomicalStructure xref: MA:0003000 xref: MESH:D000825 xref: SCTID:362889002 xref: TAO:0000037 xref: TGMA:0001823 xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000068 name: embryo stage namespace: uberon def: "A life cycle stage that starts with fertilization and ends with the fully formed embryo." [http://orcid.org/0000-0002-6601-2165] synonym: "embryogenesis" RELATED [] synonym: "embryonic stage" EXACT [] xref: BilaDO:0000002 xref: EV:0300001 xref: FBdv:00005289 xref: FMA:72652 xref: HsapDv:0000002 xref: MmusDv:0000002 xref: OGES:000000 xref: OGES:000022 xref: SCTID:296280003 xref: WBls:0000003 xref: WBls:0000092 xref: WBls:0000102 xref: XAO:1000012 is_a: UBERON:0000105 ! life cycle stage [Term] id: UBERON:0000105 name: life cycle stage namespace: uberon def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] subset: common_anatomy subset: efo_slim subset: upper_level synonym: "developmental stage" NARROW [] synonym: "stage" NARROW [] xref: BILS:0000105 xref: EFO:0000399 xref: FBdv:00007012 xref: FMA:24120 xref: HsapDv:0000000 xref: MESH:D008018 xref: MmusDv:0000000 xref: ncithesaurus:Developmental_Stage xref: OlatDv:0000010 xref: PdumDv:0000090 xref: WBls:0000002 xref: XAO:1000000 xref: ZFS:0000000 xref: ZFS:0100000 property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string [Term] id: UBERON:0000465 name: material anatomical entity namespace: uberon def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] subset: common_anatomy subset: upper_level xref: AAO:0010264 xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 xref: TGMA:0001826 xref: VHOG:0001721 is_a: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000475 name: organism subdivision namespace: uberon def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [CARO:0000032, CARO:DOS, http://orcid.org/0000-0001-9114-8737] subset: common_anatomy subset: efo_slim subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "anatomic region" EXACT [MA:0002433] synonym: "body part" RELATED [] synonym: "body region" RELATED [FMA:7153] synonym: "cardinal body part" RELATED [FMA:7153] xref: AAO:0010053 xref: AEO:0000032 xref: BILA:0000032 xref: BIRNLEX:7 xref: CALOHA:TS-2084 xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 xref: FBbt:00007009 xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 xref: MA:0002433 xref: MAT:0000293 xref: MESH:D001829 xref: MIAA:0000293 xref: NCIT:C32221 xref: TAO:0001308 xref: TGMA:0001840 xref: VHOG:0001758 xref: Wikipedia:Body_part xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string [Term] id: UBERON:0000476 name: acellular anatomical structure namespace: uberon def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [http://orcid.org/0000-0001-9114-8737] subset: common_anatomy subset: vertebrate_core synonym: "acellular anatomical structures" RELATED PLURAL [ZFA:0000382] xref: AAO:0010268 xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 xref: FBbt:00007013 xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 xref: TGMA:0001841 xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure [Term] id: UBERON:0001062 name: anatomical entity namespace: uberon def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 xref: FBbt:10000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 xref: NCIT:C12219 xref: TAO:0100000 xref: TGMA:0001822 xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 [Term] id: UBERON:0002553 name: anatomical cavity namespace: uberon def: "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina." [FMA:67552] subset: upper_level synonym: "cavity" BROAD [] xref: BIRNLEX:1011 xref: FMA:67552 xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0005423 name: developing anatomical structure namespace: uberon subset: common_anatomy synonym: "developing structure" RELATED [] synonym: "developmental structure" RELATED [] synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 xref: FBbt:00007006 xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0007567 name: regenerating anatomical structure namespace: uberon def: "An anatomical structure that is undergoing regeneration." [http://orcid.org/0000-0002-6601-2165] synonym: "regenerating tissue" RELATED [ZFA:0005147] synonym: "regenerating tissues" RELATED PLURAL [ZFA:0005147] synonym: "regenerative tissue" RELATED [] xref: AEO:0000200 xref: EHDAA2:0003233 xref: TAO:0005147 xref: XAO:0004059 xref: ZFA:0005147 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000116 "we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure." xsd:string [Typedef] id: BFO:0000062 name: preceded by def: "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." [] subset: ro-eco property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes [Typedef] id: BFO:0000063 name: precedes def: "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." [] subset: ro-eco property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to [Typedef] id: BFO:0000066 name: occurs in def: "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 a process and an independent continuant, in which the process takes place entirely within the independent continuant subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of BFO:0000066 inverse_of: BFO:0000067 ! contains process transitive_over: part_of ! part_of [Typedef] id: BFO:0000067 name: contains process def: "[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 property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Typedef] id: BSPO:0001102 name: parallel to namespace: spatial def: "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross." [BSPO:curators] [Typedef] id: IAO:0000136 name: is about def: "A (currently) primitive relation that relates an information artifact to an entity." [] property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome 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." xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string domain: IAO:0000030 ! information content entity [Typedef] id: IAO:0000219 name: denotes def: "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" [] property_value: 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." xsd:string property_value: IAO:0000116 "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.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string domain: IAO:0000030 ! information content entity range: BFO:0000001 ! entity is_a: IAO:0000136 ! is about inverse_of: IAO:0000235 ! denoted by [Typedef] id: IAO:0000235 name: denoted by def: "inverse of the relation 'denotes'" [] property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206 domain: BFO:0000001 ! entity range: IAO:0000030 ! information content entity [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000312 name: is_specified_output_of def: "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." [] property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: RO:0000052 name: characteristic of def: "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." [] 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. property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: RO:0000053 ! has characteristic [Typedef] id: RO:0000053 name: has characteristic def: "Inverse of characteristic_of" [] property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true [Typedef] id: RO:0000056 name: participates in def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] property_value: IAO:0000111 "participates in" xsd:string property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant [Typedef] id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: has_part RO:0000057 [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] 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. property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function [Typedef] id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] 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. property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] 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. property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of def: "inverse of has disposition" [] 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. subset: RO:0002259 is_a: RO:0000052 ! characteristic of [Typedef] id: RO:0001000 name: derives from def: "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" [] subset: ro-eco property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string property_value: IAO:0000118 "derives_from" xsd:string property_value: IAO:0000232 "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." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] id: RO:0001001 name: derives into def: "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" [] subset: ro-eco property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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'." xsd:string property_value: IAO:0000118 "derives_into" xsd:string [Typedef] id: RO:0001018 name: contained in subset: ro-eco property_value: IAO:0000111 "contained in" xsd:string property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string property_value: IAO:0000116 "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):" xsd:string property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000004 ! independent continuant inverse_of: RO:0001019 ! contains [Typedef] id: RO:0001019 name: contains subset: ro-eco property_value: IAO:0000111 "contains" xsd:string property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002013 name: has regulatory component activity def: "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." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z [Typedef] id: RO:0002014 name: has negative regulatory component activity def: "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." [] 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'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by created_by: dos creation_date: 2017-05-24T09:31:01Z [Typedef] id: RO:0002015 name: has positive regulatory component activity def: "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." [] 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'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by created_by: dos creation_date: 2017-05-24T09:31:17Z [Typedef] id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process created_by: dos creation_date: 2017-05-24T09:44:33Z [Typedef] id: RO:0002018 name: has component process def: "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." [] domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component created_by: dos creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by 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. {xref="GOC:dos"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates created_by: dos creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates created_by: dos creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates created_by: dos creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity created_by: dos creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002087 name: immediately preceded by comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string is_a: BFO:0000062 ! preceded by inverse_of: RO:0002090 ! immediately precedes [Typedef] id: RO:0002090 name: immediately precedes comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 is_a: BFO:0000063 ! precedes [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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. " xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "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" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002180 name: has component def: "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." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: IAO:0000232 "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." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part [Typedef] id: RO:0002202 name: develops from def: "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" [] comment: This is the transitive form of the develops from relation property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into [Typedef] id: RO:0002203 name: develops into def: "inverse of develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into is_a: RO:0002388 ! has potential to directly develop into [Typedef] id: RO:0002211 name: regulates def: "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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: RO:0002578 RO:0002578 is_transitive: true is_a: RO:0002411 ! causally upstream of inverse_of: RO:0002334 ! regulated by transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 is_a: RO:0002211 ! regulates is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 holds_over_chain: RO:0002212 RO:0002212 is_transitive: true is_a: RO:0002211 ! regulates is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] id: RO:0002215 name: capable of def: "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. " [] subset: ro-eco property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 property_value: IAO:0000232 "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)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: RO:0002216 ! capable of part of [Typedef] id: RO:0002216 name: capable of part of def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "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." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent [Typedef] id: RO:0002233 name: has input def: "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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 ! process is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of [Typedef] id: RO:0002254 name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity holds_over_chain: has_part RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to [Typedef] id: RO:0002258 name: developmentally preceded by def: "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" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by [Typedef] id: RO:0002263 name: acts upstream of def: "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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: 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." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 RO:0002411 is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 name: acts upstream of or within def: "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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002304 name: causally upstream of, positive effect def: "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." [] 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002305 name: causally upstream of, negative effect def: "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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect [Typedef] id: RO:0002314 name: characteristic of part of def: "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." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0000052 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002502 ! depends on transitive_over: part_of ! part_of [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "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." xsd:string is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in holds_over_chain: RO:0002327 part_of is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of transitive_over: part_of ! part_of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002334 name: regulated by def: "inverse of regulates" [] subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true is_a: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002335 name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002336 name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002352 name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002384 name: has developmental potential involving def: "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)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of [Typedef] id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates is_a: RO:0012012 ! indirectly regulates transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates is_a: RO:0012012 ! indirectly regulates transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 name: causally upstream of def: "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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002418 name: causally upstream of or within def: "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." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 is_a: RO:0002428 ! involved in regulation of [Typedef] id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 is_a: RO:0002428 ! involved in regulation of [Typedef] id: RO:0002431 name: involved in or involved in regulation of def: "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" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: overlaps ! overlaps is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002434 name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "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." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true [Typedef] id: RO:0002436 name: molecularly interacts with def: "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." [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002448 name: directly regulates activity of def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000117 "Vasundra Touré" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with is_a: RO:0011002 ! regulates activity of [Typedef] id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000117 "Vasundra Touré" xsd:string property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000117 "Vasundra Touré" xsd:string property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002479 name: has part that occurs in def: "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." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "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." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent [Typedef] id: RO:0002490 name: existence overlaps def: "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))" [] 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. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage [Typedef] id: RO:0002496 name: existence starts during or after def: "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)." [] 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. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002496 holds_over_chain: RO:0002258 RO:0002496 is_a: RO:0002487 ! relation between physical entity and a process or stage transitive_over: BFO:0000062 ! preceded by transitive_over: part_of ! part_of [Typedef] id: RO:0002497 name: existence ends during or before def: "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." [] 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. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002497 holds_over_chain: RO:0002286 RO:0002497 is_a: RO:0002487 ! relation between physical entity and a process or stage transitive_over: BFO:0000063 ! precedes transitive_over: part_of ! part_of [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002559 name: causally influenced by property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "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)." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000117 "Vasundra Touré" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002571 name: lumen of def: "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." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 ! material entity is_a: part_of ! part_of [Typedef] id: RO:0002572 name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 ! immaterial entity is_a: RO:0002571 ! lumen of [Typedef] id: RO:0002578 name: directly regulates def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "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" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] id: RO:0002595 name: causal relation between material entity and a process def: "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." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: RO:0002215 RO:0002211 is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: RO:0002215 RO:0002212 is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: RO:0002215 RO:0002213 is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0002608 name: process has causal agent def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002629 name: directly positively regulates def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0003000 name: produces def: "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." [] 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. subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: RO:0003001 ! produced by [Typedef] id: RO:0003001 name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part is_a: RO:0002328 ! functionally related to created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] id: RO:0004034 name: acts upstream of, positive effect def: "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" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] id: RO:0004035 name: acts upstream of, negative effect def: "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" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 is_a: RO:0002418 ! causally upstream of or within created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 is_a: RO:0002418 ! causally upstream of or within created_by: cjm created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] id: RO:0011002 name: regulates activity of def: "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." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000117 "Vasundra Touré" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences [Typedef] id: RO:0012011 name: indirectly causally upstream of def: "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." [] is_a: RO:0002411 ! causally upstream of created_by: pg creation_date: 2022-09-26T06:07:17Z [Typedef] id: RO:0012012 name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of created_by: pg creation_date: 2022-09-26T06:08:01Z [Typedef] id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000117 "https://orcid.org/0000-0003-2620-0345" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "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." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z [Typedef] id: RO:0019000 name: regulates characteristic def: "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." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: RO:0002211 RO:0019000 is_a: RO:0002410 ! causally related to [Typedef] id: RO:0019001 name: positively regulates characteristic def: "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." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: RO:0002213 RO:0019001 is_a: RO:0019000 ! regulates characteristic [Typedef] id: RO:0019002 name: negatively regulates characteristic def: "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." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: RO:0002212 RO:0019001 holds_over_chain: RO:0002213 RO:0019002 is_a: RO:0019000 ! regulates characteristic [Typedef] id: adjacent_to name: adjacent to namespace: spatial def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 property_value: 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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: 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." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_symmetric: true is_a: RO:0002163 ! spatially disjoint from [Typedef] id: anterior_to name: anterior to namespace: spatial def: "x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail." [BSPO:cjm] synonym: "rostral_to" EXACT [] xref: BSPO:0000096 property_value: seeAlso FBcv:0000039 property_value: seeAlso FBql:00005863 is_transitive: true inverse_of: posterior_to ! posterior to [Typedef] id: approximately_perpendicular_to name: approximately perpendicular to namespace: spatial def: "Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole." [BSPO:cjm] xref: BSPO:0000104 domain: BSPO:0000010 ! anatomical axis range: BSPO:0000010 ! anatomical axis [Typedef] id: dc-creator name: creator namespace: uberon xref: http://purl.org/dc/elements/1.1/creator is_metadata_tag: true [Typedef] id: dc-description name: description namespace: uberon xref: http://purl.org/dc/elements/1.1/description is_metadata_tag: true [Typedef] id: dc-title name: title namespace: uberon xref: http://purl.org/dc/elements/1.1/title is_metadata_tag: true [Typedef] id: dcterms-license name: license namespace: uberon xref: http://purl.org/dc/terms/license is_metadata_tag: true [Typedef] id: deep_to name: deep to namespace: spatial def: "Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines." [BSPO:cjm] xref: BSPO:0000107 is_transitive: true inverse_of: superficial_to ! superficial to [Typedef] id: dorsal_to name: dorsal to namespace: spatial def: "x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly)." [BSPO:cjm] xref: BSPO:0000098 property_value: seeAlso FBcv:0000041 property_value: seeAlso FBql:00005865 is_transitive: true inverse_of: ventral_to ! ventral to [Typedef] id: ends_during name: ends during namespace: external xref: RO:0002093 [Typedef] id: finishes_axis name: finishes axis namespace: spatial 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 xref: BSPO:0015001 domain: BSPO:0000054 ! anatomical side range: BSPO:0000010 ! anatomical axis [Typedef] id: happens_during name: happens during namespace: external xref: RO:0002092 is_transitive: true is_a: ends_during ! ends during [Typedef] id: has_part name: has part name: has_part namespace: external namespace: quality namespace: spatial namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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/" xsd:string property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true is_a: overlaps ! overlaps [Typedef] id: immediately_deep_to name: immediately deep to namespace: spatial def: "x immediately deep to y iff x deep_to y and x is contiguous with y." [BSPO:curators] xref: BSPO:0001107 is_a: deep_to ! deep to inverse_of: immediately_superficial_to ! immediately superficial to [Typedef] id: immediately_superficial_to name: immediately superficial to namespace: spatial def: "x immediately superficial to y iff x superficial to y and x is contiguous with y." [BSPO:curators] xref: BSPO:0015014 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2453 is_a: adjacent_to ! adjacent to is_a: superficial_to ! superficial to [Typedef] id: in_lateral_side_of name: in lateral side of namespace: spatial def: "X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure" [UBERON:cjm] xref: BSPO:0000126 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2453 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI is_a: part_of ! part_of [Typedef] id: in_left_side_of name: in left side of namespace: spatial def: "X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion." [BSPO:PATO_mtg_2009] xref: BSPO:0000120 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI is_a: in_lateral_side_of ! in lateral side of disjoint_from: in_right_side_of ! in right side of [Typedef] id: in_right_side_of name: in right side of namespace: spatial def: "X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion." [BSPO:PATO_mtg_2009] xref: BSPO:0000121 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI is_a: in_lateral_side_of ! in lateral side of [Typedef] id: opposite_to name: opposite to namespace: spatial def: "Direcly opposite to. i.e. on the opposite side through the axis." [BSPO:cjm] xref: BSPO:0000113 [Typedef] id: orthogonal_to name: orthogonal to namespace: spatial def: "crossing at right angles" [BSPO:cjm] xref: BSPO:0015005 domain: BSPO:0000010 ! anatomical axis range: BSPO:0000400 ! anatomical plane [Typedef] id: overlaps name: overlaps namespace: spatial def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] def: "x overlaps y iff they have some part in common." [BSPO:cjm] comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] id: part_of name: part of name: part_of namespace: external namespace: quality namespace: spatial namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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/" xsd:string property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 property_value: RO:0040042 BFO:0000017 property_value: RO:0040042 BFO:0000019 property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part [Typedef] id: passes_through name: passes through namespace: spatial def: "Intersects at two points." [BSPO:cjm] xref: BSPO:0015006 domain: BSPO:0000010 ! anatomical axis [Typedef] id: posterior_to name: posterior to namespace: spatial def: "x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail." [BSPO:cjm] synonym: "caudal to" NARROW vertebrate [] xref: BSPO:0000099 property_value: seeAlso FBcv:0000045 property_value: seeAlso FBql:00005864 is_transitive: true [Typedef] id: starts_axis name: starts axis namespace: spatial 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 xref: BSPO:0015007 domain: BSPO:0000054 ! anatomical side range: BSPO:0000010 ! anatomical axis [Typedef] id: superficial_to name: superficial to namespace: spatial def: "Near the outer surface of the organism. Thus, skin is superficial to the muscle layer." [BSPO:cjm] xref: BSPO:0000108 is_transitive: true [Typedef] id: surface_of name: surface of namespace: spatial comment: placeholder. used for relation between anatomical surface and an anatomical side. xref: BSPO:0015008 domain: BSPO:0000005 ! anatomical surface [Typedef] id: ventral_to name: ventral to namespace: spatial def: "x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly)." [BSPO:cjm] xref: BSPO:0000102 property_value: seeAlso FBcv:0000049 property_value: seeAlso FBql:00005866 is_transitive: true