format-version: 1.2 data-version: releases/2021-08-30 subsetdef: added_for_HCA "" subsetdef: attribute_slim "" subsetdef: cumbo "" subsetdef: developmental_classification "" subsetdef: early_development "" subsetdef: efo_slim "" subsetdef: emapa_ehdaa2 "" subsetdef: EnvO-Lite-GSC "" subsetdef: functional_classification "" subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_manually_annotate "" subsetdef: goslim_agr "" subsetdef: goslim_aspergillus "" 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: grouping_class "" subsetdef: homology_grouping "" subsetdef: hpo_slim "" 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: inconsistent_with_fma "" subsetdef: major_organ "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" subsetdef: pheno_slim "" subsetdef: phenotype_rcn "" subsetdef: reference "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: TraitNet "" subsetdef: uberon_slim "" subsetdef: ubprop:upper_level "" subsetdef: upper_level "" subsetdef: value_slim "" subsetdef: vertebrate_core "" ontology: rbo property_value: dc-description "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments." xsd:string property_value: dc-title "Radiation Biology Ontology" xsd:string property_value: dcterms-license http://creativecommons.org/licenses/by/3.0/ property_value: owl:versionInfo "2021-08-30" xsd:string [Term] id: APOLLO_SV:00000008 name: software development def: "A planned process that has specified output a software product and that involves the creation of source code." [] is_a: OBI:0000011 ! planned process property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Software_development xsd:string property_value: IAO:0000600 "A planned process resulting in a software product involving the creation of source code." xsd:string [Term] id: APOLLO_SV:00000796 name: dataset creating def: "A planned process that has a data set as its specified output." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000299 IAO:0000100 ! has_specified_output data set relationship: OBI:0000299 IAO:0000100 ! has_specified_output data set property_value: IAO:0000111 "creating a data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data set creation" xsd:string property_value: IAO:0000118 "dataset creation" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string property_value: editor_note "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string property_value: editor_note "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" 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: example_of_usage "Julius Caesar" xsd:string property_value: example_of_usage "the Second World War" xsd:string property_value: example_of_usage "Verdi’s Requiem" xsd:string property_value: example_of_usage "your body mass index" xsd:string 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 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000111 "continuant" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl 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 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." 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: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." 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:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: example_of_usage "a chair" xsd:string property_value: example_of_usage "a heart" xsd:string property_value: example_of_usage "a leg" xsd:string property_value: example_of_usage "a molecule" xsd:string property_value: example_of_usage "a spatial region" xsd:string property_value: example_of_usage "an atom" xsd:string property_value: example_of_usage "an orchestra." xsd:string property_value: example_of_usage "an organism" xsd:string property_value: example_of_usage "the bottom right portion of a human torso" xsd:string property_value: example_of_usage "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:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: editor_note "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string property_value: editor_note "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} 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: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: example_of_usage "a process of cell-division, \\ a beating of the heart" xsd:string property_value: example_of_usage "a process of meiosis" xsd:string property_value: example_of_usage "a process of sleeping" xsd:string property_value: example_of_usage "the course of a disease" xsd:string property_value: example_of_usage "the flight of a bird" xsd:string property_value: example_of_usage "the life of an organism" xsd:string property_value: example_of_usage "your process of aging." 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: editor_note "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string property_value: example_of_usage "an atom of element X has the disposition to decay to an atom of element Y" xsd:string property_value: example_of_usage "certain people have a predisposition to colon cancer" xsd:string property_value: example_of_usage "children are innately disposed to categorize objects in certain ways." xsd:string property_value: example_of_usage "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" 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 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 ! realizable entity property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: example_of_usage "the disposition of this piece of metal to conduct electricity." xsd:string property_value: example_of_usage "the disposition of your blood to coagulate" xsd:string property_value: example_of_usage "the function of your reproductive organs" xsd:string property_value: example_of_usage "the role of being a doctor" xsd:string property_value: example_of_usage "the role of this boundary to delineate where Utah and Colorado meet" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 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 ! quality property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string property_value: example_of_usage "the ambient temperature of this portion of air" xsd:string property_value: example_of_usage "the color of a tomato" xsd:string property_value: example_of_usage "the length of the circumference of your waist" xsd:string property_value: example_of_usage "the mass of this piece of gold." xsd:string property_value: example_of_usage "the shape of your nose" xsd:string property_value: example_of_usage "the shape of your nostril" xsd:string property_value: IAO:0000111 "quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl 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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} 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 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." 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: example_of_usage "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: example_of_usage "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: example_of_usage "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: example_of_usage "the disposition of this fish to decay" xsd:string property_value: example_of_usage "the function of this heart: to pump blood" xsd:string property_value: example_of_usage "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string property_value: example_of_usage "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string property_value: example_of_usage "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string property_value: example_of_usage "the role of being a doctor" xsd:string property_value: example_of_usage "the shape of this hole." xsd:string property_value: example_of_usage "the smell of this portion of mozzarella" xsd:string property_value: IAO:0000111 "specifically dependent continuant" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} 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: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: example_of_usage "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: example_of_usage "the priest role" xsd:string property_value: example_of_usage "the role of a boundary to demarcate two neighboring administrative territories" xsd:string property_value: example_of_usage "the role of a building in serving as a military target" xsd:string property_value: example_of_usage "the role of a stone in marking a property boundary" xsd:string property_value: example_of_usage "the role of subject in a clinical trial" xsd:string property_value: example_of_usage "the student role" 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:0000024 name: fiat object name: fiat object part is_a: BFO:0000040 ! material entity [Term] id: BFO:0000027 name: object aggregate is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object-aggregate" xsd:string property_value: BFO:0000180 "ObjectAggregate" xsd:string property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} property_value: editor_note "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: example_of_usage "a collection of cells in a blood biobank." xsd:string property_value: example_of_usage "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string property_value: example_of_usage "a symphony orchestra" xsd:string property_value: example_of_usage "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string property_value: example_of_usage "defined by fiat: the aggregate of members of an organization" xsd:string property_value: example_of_usage "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string property_value: example_of_usage "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string property_value: example_of_usage "defined via attributive delimitations such as: the patients in this hospital" xsd:string property_value: example_of_usage "the aggregate of bearings in a constant velocity axle joint" xsd:string property_value: example_of_usage "the aggregate of blood cells in your body" xsd:string property_value: example_of_usage "the nitrogen atoms in the atmosphere" xsd:string property_value: example_of_usage "the restaurants in Palo Alto" xsd:string property_value: example_of_usage "your collection of Meissen ceramic plates." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000029 name: site is_a: BFO:0000141 ! immaterial entity [Term] id: BFO:0000030 name: object is_a: BFO:0000040 ! material entity [Term] id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] 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: example_of_usage "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: example_of_usage "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: example_of_usage "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: editor_note "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string property_value: example_of_usage "the function of a hammer to drive in nails" xsd:string property_value: example_of_usage "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: example_of_usage "the function of amylase in saliva to break down starch into sugar" 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: editor_note "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string property_value: editor_note "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string property_value: editor_note "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: example_of_usage "a flame" xsd:string property_value: example_of_usage "a forest fire" xsd:string property_value: example_of_usage "a human being" xsd:string property_value: example_of_usage "a hurricane" xsd:string property_value: example_of_usage "a photon" xsd:string property_value: example_of_usage "a puff of smoke" xsd:string property_value: example_of_usage "a sea wave" xsd:string property_value: example_of_usage "a tornado" xsd:string property_value: example_of_usage "an aggregate of human beings." xsd:string property_value: example_of_usage "an energy wave" xsd:string property_value: example_of_usage "an epidemic" xsd:string property_value: example_of_usage "the undetached arm of a human being" xsd:string property_value: IAO:0000111 "material entity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl 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 property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string property_value: editor_note "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000182 name: history is_a: BFO:0000015 ! process property_value: BFO:0000179 "history" xsd:string property_value: BFO:0000180 "History" xsd:string property_value: IAO:0000600 "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: CARO:0000000 name: anatomical entity is_a: CARO:0030000 ! biological entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000003 name: connected anatomical structure is_a: CARO:0000006 ! material anatomical entity [Term] id: CARO:0000006 name: material anatomical entity is_a: BFO:0000040 ! material entity is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0001010 name: organism or virus or viroid def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] is_a: PCO:0000031 ! organismal entity property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string property_value: IAO:0000589 "organism or virus" xsd:string [Term] id: CARO:0030000 name: biological entity is_a: BFO:0000004 ! independent continuant [Term] id: CHEBI:10545 name: electron is_a: CHEBI:36338 ! lepton [Term] id: CHEBI:138675 name: gas molecular entity is_a: CHEBI:33579 ! main group molecular entity [Term] id: CHEBI:15022 name: electron donor is_a: CHEBI:17891 ! donor [Term] id: CHEBI:15377 name: water is_a: CHEBI:33693 ! oxygen hydride is_a: CHEBI:37176 ! mononuclear parent hydride is_a: CHEBI:52625 ! inorganic hydroxy compound [Term] id: CHEBI:15379 name: dioxygen is_a: CHEBI:138675 ! gas molecular entity is_a: CHEBI:25362 ! elemental molecule is_a: CHEBI:33263 ! diatomic oxygen [Term] id: CHEBI:16336 name: hyaluronic acid is_a: CHEBI:37395 ! mucopolysaccharide is_a: CHEBI:72813 ! exopolysaccharide [Term] id: CHEBI:16526 name: carbon dioxide is_a: CHEBI:138675 ! gas molecular entity is_a: CHEBI:23014 ! carbon oxide is_a: CHEBI:64708 ! one-carbon compound [Term] id: CHEBI:167559 name: glycan is_a: CHEBI:78616 ! carbohydrates and carbohydrate derivatives [Term] id: CHEBI:17891 name: donor is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:17997 name: dinitrogen is_a: CHEBI:138675 ! gas molecular entity is_a: CHEBI:25362 ! elemental molecule is_a: CHEBI:33266 ! diatomic nitrogen [Term] id: CHEBI:18085 name: glycosaminoglycan is_a: CHEBI:22506 ! aminoglycan [Term] id: CHEBI:22506 name: aminoglycan is_a: CHEBI:35352 ! organonitrogen compound is_a: CHEBI:65212 ! polysaccharide derivative [Term] id: CHEBI:23014 name: carbon oxide is_a: CHEBI:25701 ! organic oxide is_a: CHEBI:36963 ! organooxygen compound [Term] id: CHEBI:23114 name: chloride salt is_a: CHEBI:23117 ! chlorine molecular entity is_a: CHEBI:33958 ! halide salt [Term] id: CHEBI:23117 name: chlorine molecular entity is_a: CHEBI:24471 ! halogen molecular entity [Term] id: CHEBI:23367 name: molecular entity is_a: CHEBI:24431 ! chemical entity [Term] id: CHEBI:24431 name: chemical entity is_a: BFO:0000030 ! object [Term] id: CHEBI:24432 name: biological role is_a: CHEBI:50906 ! role [Term] id: CHEBI:24433 name: group is_a: CHEBI:24431 ! chemical entity relationship: has_part CHEBI:33250 ! atom [Term] id: CHEBI:24471 name: halogen molecular entity is_a: CHEBI:33675 ! p-block molecular entity [Term] id: CHEBI:24651 name: hydroxides is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:33608 ! hydrogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:24835 name: inorganic molecular entity is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:24839 name: inorganic salt is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:24866 ! salt [Term] id: CHEBI:24866 name: salt is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:25362 name: elemental molecule is_a: CHEBI:25367 ! molecule is_a: CHEBI:33259 ! elemental molecular entity [Term] id: CHEBI:25367 name: molecule is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:25555 name: nitrogen atom is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33300 ! pnictogen [Term] id: CHEBI:25585 name: nonmetal atom is_a: CHEBI:33250 ! atom [Term] id: CHEBI:25701 name: organic oxide is_a: CHEBI:25741 ! oxide is_a: CHEBI:72695 ! organic molecule [Term] id: CHEBI:25704 name: organic sulfate is_a: CHEBI:26820 ! sulfates [Term] id: CHEBI:25741 name: oxide is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:25805 name: oxygen atom is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33303 ! chalcogen [Term] id: CHEBI:25806 name: oxygen molecular entity is_a: CHEBI:33304 ! chalcogen molecular entity relationship: has_part CHEBI:25805 ! oxygen atom [Term] id: CHEBI:26710 name: sodium chloride is_a: CHEBI:36093 ! inorganic chloride is_a: CHEBI:38702 ! inorganic sodium salt [Term] id: CHEBI:26712 name: sodium molecular entity is_a: CHEBI:33296 ! alkali metal molecular entity [Term] id: CHEBI:26714 name: sodium salt is_a: CHEBI:26712 ! sodium molecular entity is_a: CHEBI:35479 ! alkali metal salt [Term] id: CHEBI:26819 name: sulfuric ester is_a: CHEBI:35701 ! ester is_a: CHEBI:37826 ! sulfuric acid derivative [Term] id: CHEBI:26820 name: sulfates is_a: CHEBI:37826 ! sulfuric acid derivative [Term] id: CHEBI:26833 name: sulfur atom is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33303 ! chalcogen [Term] id: CHEBI:26835 name: sulfur molecular entity is_a: CHEBI:33304 ! chalcogen molecular entity relationship: has_part CHEBI:26833 ! sulfur atom [Term] id: CHEBI:27594 name: carbon atom is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33306 ! carbon group element atom [Term] id: CHEBI:33233 name: fundamental particle is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:33241 name: oxoacid derivative is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:33242 name: inorganic hydride is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:33692 ! hydrides [Term] id: CHEBI:33250 name: atom def: "A chemical entity constituting the smallest component of an element having the chemical properties of the element." [] is_a: CHEBI:24431 ! chemical entity relationship: has_part CHEBI:10545 ! electron relationship: has_part CHEBI:33252 ! atomic nucleus property_value: IAO:0000111 "atom" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33252 name: atomic nucleus is_a: CHEBI:36347 ! nuclear particle relationship: has_part CHEBI:33253 ! nucleon [Term] id: CHEBI:33253 name: nucleon is_a: CHEBI:36339 ! baryon is_a: CHEBI:36347 ! nuclear particle [Term] id: CHEBI:33259 name: elemental molecular entity is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33262 name: elemental oxygen is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:33259 ! elemental molecular entity [Term] id: CHEBI:33263 name: diatomic oxygen is_a: CHEBI:33262 ! elemental oxygen [Term] id: CHEBI:33266 name: diatomic nitrogen is_a: CHEBI:33267 ! elemental nitrogen [Term] id: CHEBI:33267 name: elemental nitrogen is_a: CHEBI:33465 ! elemental pnictogen is_a: CHEBI:51143 ! nitrogen molecular entity [Term] id: CHEBI:33284 name: nutrient is_a: CHEBI:78295 ! food component [Term] id: CHEBI:33285 name: heteroorganic entity is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33296 name: alkali metal molecular entity is_a: CHEBI:33674 ! s-block molecular entity [Term] id: CHEBI:33300 name: pnictogen is_a: CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33302 name: pnictogen molecular entity is_a: CHEBI:33675 ! p-block molecular entity relationship: has_part CHEBI:33300 ! pnictogen [Term] id: CHEBI:33303 name: chalcogen is_a: CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33304 name: chalcogen molecular entity is_a: CHEBI:33675 ! p-block molecular entity relationship: has_part CHEBI:33303 ! chalcogen [Term] id: CHEBI:33306 name: carbon group element atom is_a: CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33318 name: main group element atom is_a: CHEBI:33250 ! atom [Term] id: CHEBI:33424 name: sulfur oxoacid derivative is_a: CHEBI:26835 ! sulfur molecular entity is_a: CHEBI:33241 ! oxoacid derivative [Term] id: CHEBI:33465 name: elemental pnictogen is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:33259 ! elemental molecular entity is_a: CHEBI:33302 ! pnictogen molecular entity [Term] id: CHEBI:33521 name: metal atom is_a: CHEBI:33250 ! atom [Term] id: CHEBI:33560 name: p-block element atom is_a: CHEBI:33318 ! main group element atom [Term] id: CHEBI:33579 name: main group molecular entity is_a: CHEBI:23367 ! molecular entity relationship: has_part CHEBI:33318 ! main group element atom [Term] id: CHEBI:33582 name: carbon group molecular entity is_a: CHEBI:33675 ! p-block molecular entity relationship: has_part CHEBI:33306 ! carbon group element atom [Term] id: CHEBI:33583 name: noble gas molecular entity is_a: CHEBI:33579 ! main group molecular entity [Term] id: CHEBI:33608 name: hydrogen molecular entity is_a: CHEBI:33674 ! s-block molecular entity [Term] id: CHEBI:33674 name: s-block molecular entity is_a: CHEBI:33579 ! main group molecular entity [Term] id: CHEBI:33675 name: p-block molecular entity is_a: CHEBI:33579 ! main group molecular entity relationship: has_part CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33679 name: helium molecular entity is_a: CHEBI:33583 ! noble gas molecular entity is_a: CHEBI:33674 ! s-block molecular entity [Term] id: CHEBI:33692 name: hydrides is_a: CHEBI:33608 ! hydrogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:33693 name: oxygen hydride is_a: CHEBI:36902 ! chalcogen hydride [Term] id: CHEBI:33694 name: biomacromolecule is_a: CHEBI:33839 ! macromolecule is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33839 name: macromolecule is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:33958 name: halide salt is_a: CHEBI:24866 ! salt is_a: CHEBI:37578 ! halide [Term] id: CHEBI:35352 name: organonitrogen compound is_a: CHEBI:33285 ! heteroorganic entity is_a: CHEBI:51143 ! nitrogen molecular entity [Term] id: CHEBI:35479 name: alkali metal salt is_a: CHEBI:24866 ! salt is_a: CHEBI:33296 ! alkali metal molecular entity [Term] id: CHEBI:35701 name: ester is_a: CHEBI:36963 ! organooxygen compound [Term] id: CHEBI:35722 name: sulfated glycosaminoglycan is_a: CHEBI:18085 ! glycosaminoglycan is_a: CHEBI:35724 ! carbohydrate sulfate [Term] id: CHEBI:35724 name: carbohydrate sulfate is_a: CHEBI:25704 ! organic sulfate is_a: CHEBI:26819 ! sulfuric ester is_a: CHEBI:63299 ! carbohydrate derivative [Term] id: CHEBI:36093 name: inorganic chloride is_a: CHEBI:23114 ! chloride salt is_a: CHEBI:24839 ! inorganic salt [Term] id: CHEBI:36338 name: lepton is_a: CHEBI:33233 ! fundamental particle is_a: CHEBI:36340 ! fermion [Term] id: CHEBI:36339 name: baryon is_a: CHEBI:36340 ! fermion is_a: CHEBI:36344 ! hadron [Term] id: CHEBI:36340 name: fermion is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:36342 name: subatomic particle is_a: BFO:0000040 ! material entity [Term] id: CHEBI:36343 name: composite particle is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:36344 name: hadron is_a: CHEBI:36343 ! composite particle [Term] id: CHEBI:36347 name: nuclear particle is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:36357 name: polyatomic entity is_a: CHEBI:23367 ! molecular entity relationship: has_part CHEBI:24433 ! group [Term] id: CHEBI:36902 name: chalcogen hydride is_a: CHEBI:33242 ! inorganic hydride is_a: CHEBI:33304 ! chalcogen molecular entity [Term] id: CHEBI:36908 name: argon molecular entity is_a: CHEBI:33583 ! noble gas molecular entity [Term] id: CHEBI:36962 name: organochalcogen compound is_a: CHEBI:33285 ! heteroorganic entity is_a: CHEBI:33304 ! chalcogen molecular entity [Term] id: CHEBI:36963 name: organooxygen compound is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:36962 ! organochalcogen compound [Term] id: CHEBI:37176 name: mononuclear parent hydride is_a: CHEBI:33692 ! hydrides [Term] id: CHEBI:37395 name: mucopolysaccharide is_a: CHEBI:18085 ! glycosaminoglycan [Term] id: CHEBI:37577 name: heteroatomic molecular entity is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:37578 name: halide is_a: CHEBI:24471 ! halogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:37826 name: sulfuric acid derivative is_a: CHEBI:33424 ! sulfur oxoacid derivative [Term] id: CHEBI:38702 name: inorganic sodium salt is_a: CHEBI:24839 ! inorganic salt is_a: CHEBI:26714 ! sodium salt [Term] id: CHEBI:46662 name: mineral is_a: CHEBI:59999 ! chemical substance [Term] id: CHEBI:50047 name: organic amino compound is_a: CHEBI:35352 ! organonitrogen compound [Term] id: CHEBI:50860 name: organic molecular entity is_a: CHEBI:33582 ! carbon group molecular entity relationship: has_part CHEBI:27594 ! carbon atom [Term] id: CHEBI:50906 name: role [Term] id: CHEBI:51086 name: chemical role is_a: CHEBI:50906 ! role [Term] id: CHEBI:51143 name: nitrogen molecular entity is_a: CHEBI:33302 ! pnictogen molecular entity relationship: has_part CHEBI:25555 ! nitrogen atom [Term] id: CHEBI:52211 name: physiological role is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:52625 name: inorganic hydroxy compound is_a: CHEBI:24651 ! hydroxides is_a: CHEBI:24835 ! inorganic molecular entity [Term] id: CHEBI:59999 name: chemical substance is_a: CHEBI:24431 ! chemical entity [Term] id: CHEBI:63299 name: carbohydrate derivative is_a: CHEBI:78616 ! carbohydrates and carbohydrate derivatives [Term] id: CHEBI:64708 name: one-carbon compound is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:65212 name: polysaccharide derivative is_a: CHEBI:167559 ! glycan is_a: CHEBI:33694 ! biomacromolecule is_a: CHEBI:63299 ! carbohydrate derivative [Term] id: CHEBI:72695 name: organic molecule is_a: CHEBI:25367 ! molecule is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:72813 name: exopolysaccharide is_a: CHEBI:33694 ! biomacromolecule [Term] id: CHEBI:76413 name: greenhouse gas subset: envoPolar is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:78295 name: food component is_a: CHEBI:52211 ! physiological role [Term] id: CHEBI:78616 name: carbohydrates and carbohydrate derivatives is_a: CHEBI:36963 ! organooxygen compound [Term] id: CHMO:0000993 name: portion of material def: "An independent material continuant that is self-connected and retains its identity over time." [https://orcid.org/0000-0001-5985-7429] is_a: BFO:0000002 ! continuant [Term] id: CHMO:0002793 name: sensor def: "A piece of apparatus that is used to measure a physical quantity." [https://orcid.org/0000-0001-5985-7429] is_a: OBI:0000968 ! device [Term] id: CHMO:0002796 name: dosimetry def: "Measurement of the dose of a substance taken up by an object." [https://doi.org/10.1039/9781847559753-00013] is_a: OBI:0000070 ! assay relationship: BFO:0000057 CHMO:0002797 ! has participant dosimeter [Term] id: CHMO:0002797 name: dosimeter def: "A sensor that is used to measure the dose of a substance taken by up an object." [https://doi.org/10.1039/9781847559753-00013] is_a: CHMO:0002793 ! sensor [Term] id: CL:0000000 name: cell namespace: 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." [] 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). subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: CL:0000003 name: native cell namespace: cell def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [] comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). subset: ubprop:upper_level synonym: "cell in vivo" NARROW [] xref: CARO:0000013 is_a: CL:0000000 ! cell [Term] id: CL:0000005 name: fibroblast neural crest derived namespace: cell def: "Any fibroblast that is deriived from the neural crest." [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell [Term] id: CL:0000006 name: neuronal receptor cell namespace: cell synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] is_a: CL:0000101 ! sensory neuron is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception [Term] id: CL:0000007 name: early embryonic cell (metazoa) namespace: cell def: "A cell found in the embryo before the formation of all the gem layers is complete." [] is_a: CL:0002321 ! embryonic cell (metazoa) [Term] id: CL:0000008 name: migratory cranial neural crest cell namespace: cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [] is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000014 name: germ line stem cell namespace: cell synonym: "germline stem cell" EXACT [] is_a: CL:0000034 ! stem cell is_a: CL:0000039 ! germ line cell intersection_of: CL:0000039 ! germ line cell intersection_of: capable_of GO:0017145 ! stem cell division [Term] id: CL:0000027 name: smooth muscle cell neural crest derived namespace: cell def: "A smooth muscle cell derived from the neural crest." [] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell [Term] id: CL:0000029 name: neuron neural crest derived namespace: cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0002676 ! neural crest derived neuroblast [Term] id: CL:0000030 name: glioblast namespace: cell xref: FBbt:00005145 is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000031 name: neuroblast (sensu Vertebrata) namespace: cell alt_id: CL:0000337 def: "A cell that will develop into a neuron often after a migration phase." [] synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000548 ! animal cell [Term] id: CL:0000034 name: stem cell namespace: 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." [] xref: CALOHA:TS-2086 xref: FMA:63368 is_a: CL:0011115 ! precursor cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division [Term] id: CL:0000037 name: hematopoietic stem cell namespace: cell def: "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." [] comment: Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] synonym: "HSC" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: FMA:70337 xref: FMA:86475 xref: VHOG:0001485 is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell relationship: capable_of GO:0002244 ! hematopoietic progenitor cell differentiation relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell [Term] id: CL:0000038 name: erythroid progenitor cell namespace: cell def: "A progenitor cell committed to the erythroid lineage." [] synonym: "BFU-E" RELATED [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] synonym: "CFU-E" RELATED [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 ! myeloid lineage restricted progenitor cell relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell [Term] id: CL:0000039 name: germ line cell namespace: cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [] comment: Originally this term had some plant germ line cell children. subset: ubprop:upper_level is_a: CL:0000003 ! native cell disjoint_from: CL:0002371 ! somatic cell relationship: capable_of GO:0022414 ! reproductive process [Term] id: CL:0000047 name: neuronal stem cell namespace: cell def: "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors." [] synonym: "neural stem cell" EXACT [] synonym: "NSC" EXACT [] xref: BTO:0002881 xref: CALOHA:TS-2360 xref: FMA:86684 is_a: CL:0000048 ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0001017 ! central nervous system relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000048 name: multi fate stem cell namespace: cell def: "A stem cell that can give rise to multiple lineages of cells." [] synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 is_a: CL:0000034 ! stem cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000049 name: common myeloid progenitor namespace: cell def: "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages." [] comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). synonym: "CFU-GEMM" RELATED [] synonym: "CFU-S" RELATED [] synonym: "CMP" EXACT [] synonym: "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte" RELATED [] synonym: "common myeloid precursor" EXACT [] synonym: "multipotential myeloid stem cell" RELATED [] synonym: "myeloid stem cell" RELATED [] synonym: "pluripotent stem cell (bone marrow)" RELATED [] xref: BTO:0004730 is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell [Term] id: CL:0000050 name: megakaryocyte-erythroid progenitor cell namespace: cell def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." [] comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation [Term] id: CL:0000052 name: totipotent stem cell namespace: cell def: "A stem cell from which all cells of the body can form." [] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 is_a: CL:0000723 ! somatic stem cell [Term] id: CL:0000055 name: non-terminally differentiated cell namespace: cell def: "A precursor cell with a limited number of potential fates." [] comment: define using PATO mulit-potent or oligopotent? synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 is_a: CL:0011115 ! precursor cell [Term] id: CL:0000056 name: myoblast namespace: cell def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [] xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 xref: FMA:70335 xref: VHOG:0001529 is_a: CL:0000680 ! muscle precursor cell [Term] id: CL:0000057 name: fibroblast namespace: cell def: "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." [] comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal stem cell [Term] id: CL:0000058 name: chondroblast namespace: cell def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [] synonym: "chrondoplast" EXACT [] xref: BTO:0003607 xref: FMA:66783 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0007009 ! prechondroblast [Term] id: CL:0000064 name: ciliated cell namespace: cell def: "A cell that has a filiform extrusion of the cell surface." [] xref: VHOG:0001532 xref: XAO:0000031 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_part GO:0005929 ! cilium relationship: has_part GO:0005929 ! cilium [Term] id: CL:0000066 name: epithelial cell namespace: 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 apical part is directed towards the lumen and the basal part to the basal lamina." [] synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 xref: FBbt:00000124 xref: FMA:66768 xref: WBbt:0003672 is_a: CL:0000548 ! animal cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0000483 ! epithelium relationship: part_of UBERON:0000483 ! epithelium [Term] id: CL:0000067 name: ciliated epithelial cell namespace: cell def: "An epithelial cell that has a cilia." [] xref: FMA:70605 is_a: CL:0000064 ! ciliated cell is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: has_part GO:0005929 ! cilium [Term] id: CL:0000068 name: duct epithelial cell namespace: cell def: "An epithelial cell that is part of a duct." [] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000058 ! duct relationship: part_of UBERON:0000058 ! duct [Term] id: CL:0000071 name: blood vessel endothelial cell namespace: cell def: "An endothelial cell that lines the vasculature." [] synonym: "cuboidal endothelial cell of vascular tree" EXACT [] is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium [Term] id: CL:0000075 name: columnar/cuboidal epithelial cell namespace: cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000076 name: squamous epithelial cell namespace: cell xref: CALOHA:TS-1249 is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000077 name: mesothelial cell namespace: cell def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [] synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell [Term] id: CL:0000080 name: circulating cell namespace: cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0000179 ! haemolymphatic fluid [Term] id: CL:0000081 name: blood cell namespace: cell def: "A cell found predominately in the blood." [] xref: FMA:62844 is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation relationship: capable_of GO:0008015 ! blood circulation [Term] id: CL:0000082 name: epithelial cell of lung namespace: cell def: "An epithelial cell of the lung." [] synonym: "lung epithelial cell" EXACT [] xref: BTO:0004299 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0000115 ! lung epithelium [Term] id: CL:0000095 name: neuron associated cell namespace: cell is_a: CL:0002319 ! neural cell relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000098 name: sensory epithelial cell namespace: cell def: "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells." [] comment: The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 is_a: CL:0000066 ! epithelial cell is_a: CL:0000197 ! sensory receptor cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception [Term] id: CL:0000099 name: interneuron namespace: cell 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." [] xref: BTO:0003811 xref: FBbt:00005125 xref: FMA:67313 xref: WBbt:0005113 is_a: CL:0000540 ! neuron [Term] id: CL:0000100 name: motor neuron namespace: cell 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." [] synonym: "motoneuron" EXACT [] xref: BTO:0000312 xref: FMA:83617 xref: WBbt:0005409 is_a: CL:0000527 ! efferent neuron [Term] id: CL:0000101 name: sensory neuron namespace: cell def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [] xref: BTO:0001037 xref: FBbt:00005124 xref: FMA:84649 xref: WBbt:0005759 is_a: CL:0000526 ! afferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception [Term] id: CL:0000115 name: endothelial cell namespace: cell def: "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm." [] comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) namespace: cell is_a: CL:0000540 ! neuron relationship: develops_from CL:0000031 ! neuroblast (sensu Vertebrata) relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000125 name: glial cell namespace: 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." [] synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: CALOHA:TS-0415 xref: FMA:54536 is_a: CL:0000095 ! neuron associated cell relationship: develops_from CL:0000030 ! glioblast [Term] id: CL:0000133 name: neurectodermal cell namespace: cell def: "Ectoderm destined to be nervous tissue." [] synonym: "neurectoderm cell" EXACT [] is_a: CL:0000221 ! ectodermal cell [Term] id: CL:0000134 name: mesenchymal stem cell namespace: cell alt_id: CL:0002452 def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. synonym: "BMSC" NARROW [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED [] synonym: "colony-forming unit-fibroblast" NARROW [] synonym: "marrow stromal cells" NARROW [] synonym: "mesenchymal precursor cell" RELATED [] synonym: "mesenchymal progenitor cells" RELATED [] synonym: "mesenchymal stem cell" RELATED [] synonym: "mesenchymal stromal cell" RELATED [] synonym: "mesenchymal stromal cells" RELATED [] synonym: "MSC" RELATED [] synonym: "stem cells, mesenchymal" RELATED [] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 ! connective tissue cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/474 xsd:string [Term] id: CL:0000136 name: fat cell namespace: cell alt_id: CL:0000450 def: "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides." [] synonym: "adipocyte" EXACT [] synonym: "adipose cell" EXACT [] xref: BTO:0000443 xref: CALOHA:TS-0012 xref: FMA:63880 is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal stem cell [Term] id: CL:0000138 name: chondrocyte namespace: cell def: "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [] synonym: "cartilage cell" EXACT [] xref: BTO:0000249 xref: CALOHA:TS-0138 xref: FMA:66782 is_a: CL:0000153 ! glycosaminoglycan secreting cell is_a: CL:0000667 ! collagen secreting cell relationship: develops_from CL:0000058 ! chondroblast [Term] id: CL:0000147 name: pigment cell namespace: cell def: "A pigment cell is a cell that contains pigment granules." [] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000149 name: visual pigment cell namespace: cell synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell [Term] id: CL:0000151 name: secretory cell namespace: cell def: "A cell that specializes in controlled release of one or more substances." [] xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0032940 ! secretion by cell relationship: capable_of GO:0032940 ! secretion by cell [Term] id: CL:0000152 name: exocrine cell namespace: cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [] xref: FMA:16014 is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland relationship: part_of UBERON:0002365 ! exocrine gland [Term] id: CL:0000153 name: glycosaminoglycan secreting cell namespace: cell def: "A cell that secretes glycosaminoglycans." [] synonym: "GAG secreting cell" EXACT [] synonym: "hyaluronic acid secreting cell" NARROW [] is_a: CL:0000327 ! extracellular matrix secreting cell is_a: CL:0000447 ! carbohydrate secreting cell [Term] id: CL:0000159 name: seromucus secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000163 name: endocrine cell namespace: cell def: "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions." [] synonym: "endocrinocyte" EXACT [] xref: FMA:83809 is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0060986 ! endocrine hormone secretion relationship: capable_of GO:0060986 ! endocrine hormone secretion relationship: part_of UBERON:0002368 ! endocrine gland [Term] id: CL:0000165 name: neuroendocrine cell namespace: cell def: "An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals." [] synonym: "neurosecretory cell" EXACT [] xref: BTO:0002691 xref: FMA:83810 is_a: CL:0000163 ! endocrine cell is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000710 ! neurecto-epithelial cell [Term] id: CL:0000174 name: steroid hormone secreting cell namespace: cell is_a: CL:0000163 ! endocrine cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035929 ! steroid hormone secretion relationship: capable_of GO:0035929 ! steroid hormone secretion [Term] id: CL:0000183 name: contractile cell namespace: cell def: "A cell whose primary function is to shorten." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000187 name: muscle cell namespace: cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [] synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 xref: FBbt:00005074 xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000056 ! myoblast [Term] id: CL:0000188 name: cell of skeletal muscle namespace: cell def: "A somatic cell located in skeletal muscle." [] synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 is_a: CL:0002371 ! somatic cell intersection_of: CL:0002371 ! somatic cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue [Term] id: CL:0000192 name: smooth muscle cell namespace: cell alt_id: CL:0000191 def: "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." [] synonym: "myocytes, smooth muscle" EXACT [] synonym: "non-striated muscle cell" NARROW [] synonym: "SMCs" EXACT [] synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: develops_from CL:0000514 ! smooth muscle myoblast [Term] id: CL:0000197 name: sensory receptor cell namespace: cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] synonym: "receptor cell" EXACT [] is_a: CL:0000003 ! native cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception intersection_of: part_of UBERON:0001032 ! sensory system relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system [Term] id: CL:0000210 name: photoreceptor cell namespace: cell def: "A cell specialized to detect and transduce light." [] xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 xref: FMA:86740 is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception [Term] id: CL:0000211 name: electrically active cell namespace: cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000213 name: lining cell namespace: cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [] synonym: "boundary cell" EXACT [] is_a: CL:0000215 ! barrier cell [Term] id: CL:0000214 name: synovial cell namespace: cell def: "A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid." [] synonym: "hyaluronic acid secreting cell" NARROW [] synonym: "synoviocyte" EXACT [] xref: BTO:0003652 xref: CALOHA:TS-0995 xref: FMA:66786 is_a: CL:0000153 ! glycosaminoglycan secreting cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell intersection_of: CL:0002078 ! meso-epithelial cell intersection_of: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint [Term] id: CL:0000215 name: barrier cell namespace: cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000219 name: motile cell namespace: cell def: "A cell that moves by its own activities." [] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0048870 ! cell motility relationship: capable_of GO:0048870 ! cell motility [Term] id: CL:0000221 name: ectodermal cell namespace: cell def: "A cell of the outer of the three germ layers of the embryo." [] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm [Term] id: CL:0000222 name: mesodermal cell namespace: cell def: "A cell of the middle germ layer of the embryo." [] synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm [Term] id: CL:0000223 name: endodermal cell namespace: cell def: "A cell of the inner of the three germ layers of the embryo." [] synonym: "endoderm cell" EXACT [] xref: FMA:72555 is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm [Term] id: CL:0000228 name: multinucleate cell namespace: cell def: "A cell with more than one nucleus." [] synonym: "syncitium" EXACT [] synonym: "syncytial cell" EXACT [] synonym: "syncytium" EXACT [] xref: AEO:0000203 xref: WBbt:0008074 is_a: CL:0002242 ! nucleate cell [Term] id: CL:0000232 name: erythrocyte namespace: cell def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." [] synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 xref: CALOHA:TS-0290 xref: FMA:81100 is_a: CL:0000081 ! blood cell is_a: CL:0000329 ! oxygen accumulating cell is_a: CL:0000764 ! erythroid lineage cell relationship: develops_from CL:0000558 ! reticulocyte [Term] id: CL:0000255 name: eukaryotic cell namespace: cell is_a: CL:0000003 ! native cell [Term] id: CL:0000287 name: eye photoreceptor cell namespace: cell is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0000970 ! eye [Term] id: CL:0000293 name: structural cell namespace: cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000306 name: crystallin accumulating cell namespace: cell synonym: "lens cell" EXACT [] xref: FBbt:00004193 is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000313 name: serous secreting cell namespace: cell def: "Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid." [] synonym: "serous cell" EXACT [] xref: BTO:0003687 xref: FMA:62511 is_a: CL:0000159 ! seromucus secreting cell [Term] id: CL:0000325 name: stuff accumulating cell namespace: cell def: "A cell that is specialised to accumulate a particular substance(s)." [] subset: ubprop:upper_level is_a: CL:0000003 ! native cell [Term] id: CL:0000327 name: extracellular matrix secreting cell namespace: cell is_a: CL:0000151 ! secretory cell is_a: CL:0000499 ! stromal cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070278 ! extracellular matrix constituent secretion relationship: capable_of GO:0070278 ! extracellular matrix constituent secretion [Term] id: CL:0000329 name: oxygen accumulating cell namespace: cell is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0015671 ! oxygen transport relationship: capable_of GO:0015671 ! oxygen transport [Term] id: CL:0000333 name: migratory neural crest cell namespace: cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [] xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell relationship: develops_from CL:0007004 ! premigratory neural crest cell [Term] id: CL:0000335 name: mesenchyme condensation cell namespace: cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [] is_a: CL:0008019 ! mesenchymal cell [Term] id: CL:0000347 name: scleral cell namespace: cell def: "A cell of the sclera of the eye." [] is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001773 ! sclera [Term] id: CL:0000348 name: choroidal cell of the eye namespace: cell def: "A cell of the choroid of the eye." [] is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001776 ! optic choroid [Term] id: CL:0000349 name: extraembryonic cell namespace: cell is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0000478 ! extraembryonic structure [Term] id: CL:0000352 name: epiblast cell namespace: cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [] is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000355 name: multi-potent skeletal muscle stem cell namespace: cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. xref: FMA:86767 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000188 ! cell of skeletal muscle intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue [Term] id: CL:0000359 name: vascular associated smooth muscle cell namespace: cell def: "A smooth muscle cell assocatiated with the vasculature." [] synonym: "vascular smooth muscle cell" EXACT [] synonym: "VSMC" EXACT [] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002049 ! vasculature relationship: part_of UBERON:0002049 ! vasculature [Term] id: CL:0000362 name: epidermal cell namespace: cell alt_id: CL:1000396 def: "An epithelial cell of the integument (the outer layer of an organism)." [] synonym: "cell of epidermis" EXACT [] synonym: "epithelial cell of skin" NARROW [] xref: BTO:0001470 xref: CALOHA:TS-0283 xref: FMA:62411 is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0007376 ! outer epithelium relationship: part_of UBERON:0007376 ! outer epithelium [Term] id: CL:0000365 name: animal zygote namespace: cell def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [] synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 xref: FMA:72395 is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0010017 ! zygote [Term] id: CL:0000381 name: neurosecretory neuron namespace: cell xref: FBbt:00005130 is_a: CL:0000151 ! secretory cell is_a: CL:0000527 ! efferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0046879 ! hormone secretion relationship: capable_of GO:0046879 ! hormone secretion [Term] id: CL:0000393 name: electrically responsive cell namespace: cell def: "A cell whose function is determined by its response to an electric signal." [] is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000402 name: CNS interneuron namespace: cell is_a: CL:0000099 ! interneuron is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron [Term] id: CL:0000404 name: electrically signaling cell namespace: cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [] is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000447 name: carbohydrate secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000488 name: visible light photoreceptor cell namespace: cell def: "A photoreceptor cell that detects visible light." [] is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: capable_of GO:0009584 ! detection of visible light relationship: capable_of GO:0009584 ! detection of visible light [Term] id: CL:0000499 name: stromal cell namespace: cell def: "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [] xref: BTO:0002064 xref: FMA:83624 is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal stem cell [Term] id: CL:0000513 name: cardiac muscle myoblast namespace: cell alt_id: CL:0000714 def: "A precursor cell destined to differentiate into cardiac muscle cell." [] synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast relationship: part_of UBERON:0001133 ! cardiac muscle tissue [Term] id: CL:0000514 name: smooth muscle myoblast namespace: cell def: "A precursor cell destined to differentiate into smooth muscle myocytes." [] synonym: "myoblast, smooth muscle" EXACT [] synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast [Term] id: CL:0000515 name: skeletal muscle myoblast namespace: cell def: "A myoblast that differentiates into skeletal muscle fibers." [] synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell relationship: develops_from CL:0000355 ! multi-potent skeletal muscle stem cell [Term] id: CL:0000526 name: afferent neuron namespace: cell def: "A neuron which conveys sensory information centrally from the periphery." [] synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron [Term] id: CL:0000527 name: efferent neuron namespace: cell def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [] synonym: "output neuron" EXACT [] is_a: CL:0000540 ! neuron [Term] id: CL:0000530 name: primary neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000531 name: primary sensory neuron namespace: cell is_a: CL:0000101 ! sensory neuron is_a: CL:0000530 ! primary neuron intersection_of: CL:0000101 ! sensory neuron intersection_of: CL:0000530 ! primary neuron [Term] id: CL:0000540 name: neuron namespace: cell 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." [] comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 xref: FBbt:00005106 xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: CL:0000547 name: proerythroblast namespace: cell def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [] synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [] xref: FMA:83518 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CP:0000028 relationship: has_part CP:0000037 relationship: has_part GO:0005730 ! nucleolus relationship: has_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000548 name: animal cell namespace: cell subset: ubprop:upper_level is_a: CL:0000255 ! eukaryotic cell [Term] id: CL:0000549 name: basophilic erythroblast namespace: cell def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [] synonym: "basophilic normoblast" EXACT [] synonym: "early erythroblast" EXACT [] synonym: "early normoblast" EXACT [] synonym: "prorubricyte" EXACT [] xref: FMA:83505 is_a: CL:0000765 ! erythroblast relationship: has_part CP:0000028 relationship: has_part GO:0000792 ! heterochromatin relationship: has_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000550 name: polychromatophilic erythroblast namespace: cell def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [] synonym: "intermediate erythroblast" EXACT [] synonym: "intermediate normoblast" EXACT [] synonym: "polychromatic erythroblast" EXACT [] synonym: "polychromatic normoblast" EXACT [] synonym: "polychromatophilic normoblast" EXACT [] synonym: "rubricyte" EXACT [] xref: FMA:83506 is_a: CL:0000765 ! erythroblast relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CP:0000035 relationship: has_part GO:0000792 ! heterochromatin relationship: has_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000552 name: orthochromatic erythroblast namespace: cell def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [] synonym: "acidophilic erythroblast" EXACT [] synonym: "eosinophilic erythroblast" EXACT [] synonym: "late erythoblast" EXACT [] synonym: "orthochromatic normoblast" EXACT [] synonym: "pyknotic eto enrythroblast" EXACT [] xref: FMA:84646 is_a: CL:0000765 ! erythroblast relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CP:0000027 [Term] id: CL:0000558 name: reticulocyte namespace: cell def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [] xref: BTO:0001173 xref: CALOHA:TS-0864 is_a: CL:0000764 ! erythroid lineage cell relationship: capable_of GO:0071971 ! extracellular exosome assembly relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: has_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000566 name: angioblastic mesenchymal cell namespace: cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: has_part PR:000001444 ! cadherin-5 relationship: has_part PR:000002112 ! vascular endothelial growth factor receptor 2 relationship: has_part PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 [Term] id: CL:0000573 name: retinal cone cell namespace: cell def: "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." [] xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: develops_from CL:0002672 ! retinal progenitor cell [Term] id: CL:0000575 name: corneal epithelial cell namespace: cell alt_id: CL:1000431 def: "An epithelial cell of the cornea." [] synonym: "epithelial cell of cornea" EXACT [] xref: BTO:0004298 xref: CALOHA:TS-0173 xref: FMA:70551 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea [Term] id: CL:0000586 name: germ cell namespace: cell def: "The reproductive cell in multicellular organisms." [] xref: BTO:0000535 xref: VHOG:0001534 xref: WBbt:0006796 is_a: CL:0000039 ! germ line cell relationship: capable_of GO:0048609 ! multicellular organismal reproductive process [Term] id: CL:0000593 name: androgen secreting cell namespace: cell def: "A steroid hormone secreting cell that secretes androgen." [] is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035935 ! androgen secretion relationship: capable_of GO:0035935 ! androgen secretion [Term] id: CL:0000604 name: retinal rod cell namespace: cell def: "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." [] xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: develops_from CL:0002672 ! retinal progenitor cell [Term] id: CL:0000630 name: supportive cell namespace: cell def: "A cell whose primary function is to support other cell types." [] xref: BTO:0002315 is_a: CL:0000003 ! native cell [Term] id: CL:0000667 name: collagen secreting cell namespace: cell def: "An extracellular matrix secreting cell that secretes collagen." [] is_a: CL:0000327 ! extracellular matrix secreting cell [Term] id: CL:0000670 name: primordial germ cell namespace: cell def: "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells." [] synonym: "gonocyte" EXACT [] synonym: "primitive germ cell" EXACT [] xref: FMA:70567 is_a: CL:0000039 ! germ line cell is_a: CL:0000219 ! motile cell intersection_of: CL:0000039 ! germ line cell intersection_of: capable_of GO:0048870 ! cell motility intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo [Term] id: CL:0000680 name: muscle precursor cell namespace: cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [] is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000222 ! mesodermal cell [Term] id: CL:0000710 name: neurecto-epithelial cell namespace: cell def: "Epithelial cells derived from neural plate and neural crest." [] comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 xref: FMA:70557 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002077 ! ecto-epithelial cell intersection_of: CL:0002077 ! ecto-epithelial cell intersection_of: develops_from CL:0000133 ! neurectodermal cell relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000723 name: somatic stem cell namespace: cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [] xref: CALOHA:TS-2086 xref: FMA:63368 is_a: CL:0000034 ! stem cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division relationship: capable_of GO:0048103 ! somatic stem cell division [Term] id: CL:0000737 name: striated muscle cell namespace: cell def: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [] xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 is_a: CL:0000187 ! muscle cell disjoint_from: CL:0008000 ! non-striated muscle cell relationship: has_part GO:0030017 ! sarcomere [Term] id: CL:0000740 name: retinal ganglion cell namespace: cell def: "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve." [] synonym: "gangliocyte" EXACT [] synonym: "ganglion cell of retina" EXACT [] synonym: "RGC" EXACT [] xref: BTO:0001800 xref: FMA:67765 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000746 name: cardiac muscle cell namespace: cell alt_id: FMA:83808 def: "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." [] comment: This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. synonym: "cardiac muscle fiber" EXACT [] synonym: "cardiac myocyte" EXACT [] synonym: "cardiocyte" BROAD [] synonym: "cardiomyocyte" EXACT [] synonym: "heart muscle cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 is_a: CL:0000737 ! striated muscle cell is_a: CL:0002494 ! cardiocyte relationship: develops_from CL:0000513 ! cardiac muscle myoblast [Term] id: CL:0000763 name: myeloid cell namespace: cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [] xref: BTO:0001441 xref: CALOHA:TS-0647 is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: develops_from CL:0000049 ! common myeloid progenitor relationship: develops_from CL:0000049 ! common myeloid progenitor [Term] id: CL:0000764 name: erythroid lineage cell namespace: cell alt_id: CL:0002156 def: "A immature or mature cell in the lineage leading to and including erythrocytes." [] comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell [Term] id: CL:0000765 name: erythroblast namespace: cell def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [] synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus [Term] id: CL:0000837 name: hematopoietic multipotent progenitor cell namespace: cell def: "A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans." [] comment: Markers differ between mouse and human. synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 is_a: CL:0008001 ! hematopoietic precursor cell disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: develops_from CL:0000037 ! hematopoietic stem cell relationship: has_part PR:000001003 ! CD34 molecule [Term] id: CL:0000839 name: myeloid lineage restricted progenitor cell namespace: cell def: "A progenitor cell restricted to the myeloid lineage." [] comment: Note that this is a class of cell types, not an identified single cell type. synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation [Term] id: CL:0000988 name: hematopoietic cell namespace: cell def: "A cell of a hematopoietic lineage." [] synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0001035 name: bone cell namespace: cell def: "A connective tissue cell found in bone." [] is_a: CL:0000548 ! animal cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element created_by: adiehl creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0002031 name: hematopoietic lineage restricted progenitor cell namespace: cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [] is_a: CL:0008001 ! hematopoietic precursor cell disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell created_by: tmeehan creation_date: 2010-01-06T03:43:20Z [Term] id: CL:0002032 name: hematopoietic oligopotent progenitor cell namespace: cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). is_a: CL:0008001 ! hematopoietic precursor cell relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell created_by: tmeehan creation_date: 2010-01-06T03:43:27Z [Term] id: CL:0002068 name: Purkinje myocyte namespace: cell def: "Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter." [] synonym: "myocytus conducens cardiacus" EXACT [] synonym: "Purkinje cell fiber" EXACT [] synonym: "Purkinje muscle cell" EXACT [] xref: BTO:0001032 xref: FMA:14146 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-28T08:36:15Z [Term] id: CL:0002072 name: nodal myocyte namespace: cell def: "A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." [] synonym: "cardiac pacemaker cell" EXACT [] synonym: "myocytus nodalis" EXACT [] synonym: "P cell" EXACT [] synonym: "pacemaker cell" BROAD [] xref: BTO:0004190 xref: FMA:67101 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-29T11:41:37Z [Term] id: CL:0002073 name: transitional myocyte namespace: cell def: "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." [] xref: FMA:67142 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-29T02:39:32Z [Term] id: CL:0002074 name: myocardial endocrine cell namespace: cell def: "The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides)." [] xref: FMA:67111 is_a: CL:0000163 ! endocrine cell is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-29T11:50:47Z [Term] id: CL:0002076 name: endo-epithelial cell namespace: cell def: "An epithelial cell derived from endoderm." [] xref: FMA:69075 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000223 ! endodermal cell created_by: tmeehan creation_date: 2010-06-29T03:38:14Z [Term] id: CL:0002077 name: ecto-epithelial cell namespace: cell def: "An epithelial cell derived from ectoderm." [] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: develops_from CL:0000221 ! ectodermal cell relationship: develops_from CL:0000221 ! ectodermal cell created_by: tmeehan creation_date: 2010-06-29T03:38:22Z [Term] id: CL:0002078 name: meso-epithelial cell namespace: cell def: "Epithelial cell derived from mesoderm or mesenchyme." [] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: develops_from CL:0000222 ! mesodermal cell relationship: develops_from CL:0000222 ! mesodermal cell created_by: tmeehan creation_date: 2010-06-29T03:49:14Z [Term] id: CL:0002086 name: specialized cardiac myocyte namespace: cell def: "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." [] xref: FMA:67968 is_a: CL:0000746 ! cardiac muscle cell created_by: tmeehan creation_date: 2010-07-21T01:33:38Z [Term] id: CL:0002092 name: bone marrow cell namespace: cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. xref: BTO:0004850 xref: FMA:83621 is_a: CL:0001035 ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow created_by: tmeehan creation_date: 2010-07-22T04:48:15Z [Term] id: CL:0002095 name: hilus cell of ovary namespace: cell def: "A cell in the hilum of the ovary that produces androgens." [] synonym: "hilar cell of ovary" EXACT [] xref: FMA:18710 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary created_by: tmeehan creation_date: 2010-08-23T11:18:18Z [Term] id: CL:0002132 name: stromal cell of ovary namespace: cell def: "A stomal cell of the ovary" [] synonym: "ovarian stromal cell" EXACT [] xref: FMA:72299 is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary created_by: tmeehan creation_date: 2010-08-23T12:10:31Z [Term] id: CL:0002139 name: endothelial cell of vascular tree namespace: cell def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell created_by: tmeehan creation_date: 2010-08-24T02:06:40Z [Term] id: CL:0002144 name: capillary endothelial cell namespace: cell def: "An endothelial cell found in capillaries." [] xref: BTO:0004956 xref: CALOHA:TS-0112 xref: FMA:67756 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001915 ! endothelium of capillary relationship: part_of UBERON:0001915 ! endothelium of capillary created_by: tmeehan creation_date: 2010-08-24T10:15:00Z [Term] id: CL:0002159 name: general ecto-epithelial cell namespace: cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell created_by: tmeehan creation_date: 2010-08-26T08:31:08Z [Term] id: CL:0002222 name: vertebrate lens cell namespace: cell def: "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." [] xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell is_a: CL:0002371 ! somatic cell relationship: part_of UBERON:0000965 ! lens of camera-type eye created_by: tmeehan creation_date: 2010-09-07T10:38:03Z [Term] id: CL:0002224 name: lens epithelial cell namespace: cell def: "A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth." [] xref: FMA:67559 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002222 ! vertebrate lens cell intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell intersection_of: part_of UBERON:0001803 ! epithelium of lens relationship: part_of UBERON:0001803 ! epithelium of lens created_by: tmeehan creation_date: 2010-09-07T10:45:47Z [Term] id: CL:0002240 name: marrow fibroblast namespace: cell def: "A fibroblast in the bone marrow." [] xref: FMA:84377 is_a: CL:0000057 ! fibroblast is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002371 ! bone marrow created_by: tmeehan creation_date: 2010-09-07T02:25:18Z [Term] id: CL:0002242 name: nucleate cell namespace: cell def: "A cell containing at least one nucleus." [] xref: FMA:67513 is_a: CL:0000003 ! native cell created_by: tmeehan creation_date: 2010-09-07T03:32:33Z [Term] id: CL:0002246 name: peripheral blood stem cell namespace: cell def: "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells)." [] synonym: "PBSC" EXACT [] xref: BTO:0002669 xref: FMA:86711 is_a: CL:0000037 ! hematopoietic stem cell is_a: CL:0000080 ! circulating cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000178 ! blood relationship: part_of UBERON:0000178 ! blood created_by: tmeehan creation_date: 2010-09-07T03:57:09Z [Term] id: CL:0002251 name: epithelial cell of alimentary canal namespace: cell def: "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." [] is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract created_by: tmeehan creation_date: 2010-09-08T09:26:53Z [Term] id: CL:0002252 name: epithelial cell of esophagus namespace: cell alt_id: CL:1000402 def: "An epithelial cell of the esophagus." [] xref: FMA:63071 is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus created_by: tmeehan creation_date: 2010-09-08T09:28:20Z [Term] id: CL:0002262 name: endothelial cell of sinusoid namespace: cell alt_id: CL:1000403 def: "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver." [] xref: FMA:63134 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003909 ! sinusoid relationship: part_of UBERON:0003909 ! sinusoid created_by: tmeehan creation_date: 2010-09-14T10:57:26Z [Term] id: CL:0002308 name: epithelial cell of skin gland namespace: cell def: "An epithelial cell of a skin gland." [] synonym: "epithelial cell of gland of skin" EXACT [] xref: FMA:70657 is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002419 ! skin gland relationship: part_of UBERON:0002419 ! skin gland created_by: tmeehan creation_date: 2010-09-14T12:00:07Z [Term] id: CL:0002319 name: neural cell namespace: cell def: "A cell that is part of the nervous system." [] xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system created_by: tmeehan creation_date: 2010-09-15T01:34:57Z [Term] id: CL:0002320 name: connective tissue cell namespace: cell alt_id: CL:1000406 def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [] xref: CALOHA:TS-2096 xref: FMA:63875 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0002371 ! somatic cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue created_by: tmeehan creation_date: 2010-09-15T03:01:54Z [Term] id: CL:0002321 name: embryonic cell (metazoa) namespace: cell def: "A cell of the embryo." [] xref: CALOHA:TS-0263 xref: FMA:82840 xref: FMA:82841 xref: WBbt:0007028 is_a: CL:0000548 ! animal cell created_by: tmeehan creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0002333 name: neural crest derived fat cell namespace: cell def: "A fat cell derived from a neural crest cell." [] is_a: CL:0000136 ! fat cell intersection_of: CL:0000136 ! fat cell intersection_of: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0000005 ! fibroblast neural crest derived created_by: tmeehan creation_date: 2010-09-20T02:25:25Z [Term] id: CL:0002350 name: endocardial cell namespace: cell alt_id: CL:1000475 def: "An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin." [] synonym: "endocardial endothelial cell" EXACT [] synonym: "endothelial cell of endocardium" EXACT [] xref: FMA:75621 is_a: CL:0010008 ! cardiac endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002165 ! endocardium relationship: part_of UBERON:0002165 ! endocardium created_by: tmeehan creation_date: 2010-09-21T04:33:05Z [Term] id: CL:0002352 name: gestational hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell that exists during embryogenesis." [] is_a: CL:0000037 ! hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo created_by: tmeehan creation_date: 2010-09-22T09:05:13Z [Term] id: CL:0002363 name: keratocyte namespace: cell def: "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate." [] synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] is_a: CL:0000005 ! fibroblast neural crest derived intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea created_by: tmeehan creation_date: 2010-09-22T01:57:40Z [Term] id: CL:0002368 name: respiratory epithelial cell namespace: cell def: "An endo-epithelial cell of the respiratory tract." [] synonym: "airway epithelial cell" EXACT [] xref: BTO:0004533 is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000065 ! respiratory tract created_by: tmeehan creation_date: 2010-09-23T04:38:49Z [Term] id: CL:0002371 name: somatic cell namespace: cell def: "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." [] subset: ubprop:upper_level xref: BTO:0001268 xref: FMA:72300 xref: WBbt:0008378 is_a: CL:0000003 ! native cell created_by: tmeehan creation_date: 2010-09-24T09:44:42Z [Term] id: CL:0002372 name: myotube namespace: cell alt_id: CL:0000369 def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [] synonym: "myotubule" EXACT [] synonym: "single cell sarcomere" EXACT [] is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell created_by: tmeehan creation_date: 2010-09-24T01:13:01Z [Term] id: CL:0002494 name: cardiocyte namespace: cell def: "A cell located in the heart, including both muscle and non muscle cells." [] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0002371 ! somatic cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ created_by: tmeehan creation_date: 2010-12-07T09:37:22Z [Term] id: CL:0002503 name: adventitial cell namespace: cell def: "A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc" [] xref: BTO:0002441 xref: FMA:84639 is_a: CL:0000630 ! supportive cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0005742 ! adventitia relationship: part_of UBERON:0005742 ! adventitia created_by: tmeehan creation_date: 2010-12-07T04:03:56Z [Term] id: CL:0002521 name: subcutaneous fat cell namespace: cell def: "A fat cell that is part of subcutaneous adipose tissue." [] synonym: "subcutaneous adipocyte" EXACT [] is_a: CL:0000136 ! fat cell intersection_of: CL:0000136 ! fat cell intersection_of: part_of UBERON:0002190 ! subcutaneous adipose tissue relationship: part_of UBERON:0002190 ! subcutaneous adipose tissue created_by: tmeehan creation_date: 2011-02-21T02:51:22Z [Term] id: CL:0002539 name: aortic smooth muscle cell namespace: cell def: "A smooth muscle cell of the aorta." [] xref: BTO:0004577 is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0004178 ! aorta smooth muscle tissue relationship: part_of UBERON:0004178 ! aorta smooth muscle tissue created_by: tmeehan creation_date: 2011-02-28T01:42:12Z [Term] id: CL:0002540 name: mesenchymal stem cell of the bone marrow namespace: cell def: "A mesenchymal stem cell that is part of the bone marrow." [] is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002371 ! bone marrow created_by: tmeehan creation_date: 2011-02-28T01:47:47Z [Term] id: CL:0002543 name: vein endothelial cell namespace: cell alt_id: CL:1000393 def: "An endothelial cell that is part of the vein." [] synonym: "endothelial cell of vein" EXACT [] synonym: "venous endothelial cell" EXACT [] xref: FMA:62104 xref: KUPO:0001099 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein created_by: tmeehan creation_date: 2011-02-28T03:48:11Z [Term] id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell namespace: cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell is_a: CL:0002371 ! somatic cell created_by: tmeehan creation_date: 2011-02-28T04:20:39Z [Term] id: CL:0002547 name: fibroblast of the aortic adventitia namespace: cell def: "A fibroblast of the aortic adventitia." [] is_a: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia relationship: part_of UBERON:0004664 ! aorta tunica adventitia created_by: tmeehan creation_date: 2011-02-28T04:43:41Z [Term] id: CL:0002548 name: fibroblast of cardiac tissue namespace: cell def: "A fibroblast that is part of the heart." [] synonym: "cardiac fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart created_by: tmeehan creation_date: 2011-02-28T04:57:44Z [Term] id: CL:0002551 name: fibroblast of dermis namespace: cell is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis created_by: tmeehan creation_date: 2011-02-28T05:05:33Z [Term] id: CL:0002553 name: fibroblast of lung namespace: cell def: "A fibroblast that is part of lung." [] xref: BTO:0000764 xref: CALOHA:TS-0575 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung created_by: tmeehan creation_date: 2011-02-28T05:11:03Z [Term] id: CL:0002557 name: fibroblast of pulmonary artery namespace: cell def: "A fibroblast of pulmonary artery." [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery created_by: tmeehan creation_date: 2011-02-28T05:22:27Z [Term] id: CL:0002570 name: mesenchymal stem cell of adipose namespace: cell def: "A mesenchymal stem cell of adipose tissue." [] is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: part_of UBERON:0001013 ! adipose tissue created_by: tmeehan creation_date: 2011-03-01T09:57:17Z [Term] id: CL:0002573 name: Schwann cell namespace: cell def: "A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function." [] xref: BTO:0001220 xref: CALOHA:TS-0898 is_a: CL:0000125 ! glial cell intersection_of: CL:0000125 ! glial cell intersection_of: part_of UBERON:0000010 ! peripheral nervous system relationship: part_of UBERON:0000010 ! peripheral nervous system created_by: tmeehan creation_date: 2011-03-02T01:19:27Z [Term] id: CL:0002585 name: retinal blood vessel endothelial cell namespace: cell def: "A blood vessel endothelial cell that is part of the retina." [] is_a: CL:0000071 ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina created_by: tmeehan creation_date: 2011-03-06T03:28:27Z [Term] id: CL:0002590 name: smooth muscle cell of the brain vasculature namespace: cell def: "A vascular associated smooth muscle cell of the brain vasculature." [] is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:0002319 ! neural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain created_by: tmeehan creation_date: 2011-03-06T05:01:20Z [Term] id: CL:0002591 name: smooth muscle cell of the pulmonary artery namespace: cell def: "A smooth muscle of the pulmonary artery." [] xref: BTO:0003336 is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery created_by: tmeehan creation_date: 2011-03-06T05:01:28Z [Term] id: CL:0002596 name: smooth muscle cell of the carotid artery namespace: cell def: "Smooth muscle cell of the carotid artery." [] is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0005396 ! carotid artery segment relationship: part_of UBERON:0005396 ! carotid artery segment created_by: tmeehan creation_date: 2011-03-06T05:01:56Z [Term] id: CL:0002599 name: smooth muscle cell of the esophagus namespace: cell def: "A smooth muscle cell of the esophagus." [] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus created_by: tmeehan creation_date: 2011-03-06T05:48:17Z [Term] id: CL:0002620 name: skin fibroblast namespace: cell def: "A fibroblast of skin." [] xref: BTO:0001255 xref: CALOHA:TS-0935 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body created_by: tmeehan creation_date: 2011-03-14T12:31:49Z [Term] id: CL:0002632 name: epithelial cell of lower respiratory tract namespace: cell is_a: CL:0002368 ! respiratory epithelial cell intersection_of: CL:0002368 ! respiratory epithelial cell intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract created_by: tmeehan creation_date: 2011-06-21T12:29:31Z [Term] id: CL:0002663 name: myocardial endocrine cell of atrium namespace: cell def: "A myocardial endocrine cell that is part of the atrium." [] xref: FMA:83389 is_a: CL:0002074 ! myocardial endocrine cell intersection_of: CL:0002074 ! myocardial endocrine cell intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium created_by: tmeehan creation_date: 2011-07-11T02:45:39Z [Term] id: CL:0002672 name: retinal progenitor cell namespace: cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [] is_a: CL:0000048 ! multi fate stem cell relationship: develops_from CL:0000133 ! neurectodermal cell created_by: tmeehan creation_date: 2011-08-16T02:38:01Z [Term] id: CL:0002676 name: neural crest derived neuroblast namespace: cell def: "A neuroblast derived from a neural crest cell." [] is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell relationship: develops_from CL:0000333 ! migratory neural crest cell created_by: tmeehan creation_date: 2011-08-22T09:24:15Z [Term] id: CL:0005000 name: spinal cord interneuron namespace: cell def: "A CNS interneuron located in the spinal cord." [] comment: Is_a interneuron, part_of UBERON:0002240. is_a: CL:0000402 ! CNS interneuron [Term] id: CL:0007001 name: skeletogenic cell namespace: cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [] is_a: CL:0000003 ! native cell created_by: haendel creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007004 name: premigratory neural crest cell namespace: cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [] is_a: CL:0011012 ! neural crest cell relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest created_by: haendel creation_date: 2012-06-27T08:27:35Z [Term] id: CL:0007009 name: prechondroblast namespace: cell def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [] is_a: CL:0000055 ! non-terminally differentiated cell created_by: haendel creation_date: 2012-06-27T10:44:01Z [Term] id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [] is_a: CL:0000187 ! muscle cell [Term] id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [] is_a: CL:0000988 ! hematopoietic cell [Term] id: CL:0008002 name: skeletal muscle fiber def: "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [] is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0002372 ! myotube relationship: develops_from CL:0000515 ! skeletal muscle myoblast [Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle" [] is_a: CL:0000187 ! muscle cell [Term] id: CL:0008019 name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0002371 ! somatic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme [Term] id: CL:0008034 name: mural cell def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation." [] subset: added_for_HCA is_a: CL:0002371 ! somatic cell created_by: dos creation_date: 2020-02-29T17:33:55Z [Term] id: CL:0008035 name: microcirculation associated smooth muscle cell is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:0008034 ! mural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0010523 ! microcirculatory vessel relationship: part_of UBERON:0010523 ! microcirculatory vessel created_by: dos creation_date: 2020-02-29T17:37:00Z [Term] id: CL:0009004 name: retinal cell namespace: cell def: "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [] xref: PMID:10702418 is_a: CL:0002319 ! neural cell intersection_of: CL:0002319 ! neural cell intersection_of: part_of UBERON:0005388 ! photoreceptor array relationship: part_of UBERON:0005388 ! photoreceptor array [Term] id: CL:0010001 name: stromal cell of bone marrow def: "A stromal cell that is part_of a bone marrow." [] synonym: "bone marrow stromal cell" EXACT [] is_a: CL:0000499 ! stromal cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002371 ! bone marrow created_by: GOC:cjm [Term] id: CL:0010006 name: cardiac blood vessel endothelial cell is_a: CL:0000071 ! blood vessel endothelial cell is_a: CL:0010008 ! cardiac endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000948 ! heart [Term] id: CL:0010008 name: cardiac endothelial cell is_a: CL:0000115 ! endothelial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart [Term] id: CL:0010009 name: camera-type eye photoreceptor cell synonym: "camera type eye photoreceptor cell" EXACT [] is_a: CL:0000287 ! eye photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye [Term] id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] is_a: CL:0000003 ! native cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0010020 name: cardiac glial cell is_a: CL:0000125 ! glial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000125 ! glial cell intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart [Term] id: CL:0010021 name: cardiac myoblast namespace: cell is_a: CL:0000056 ! myoblast [Term] id: CL:0010022 name: cardiac neuron is_a: CL:0000540 ! neuron is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000540 ! neuron intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart [Term] id: CL:0011007 name: paraxial cell def: "A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites." [] synonym: "paraxial mesoderm cell" EXACT [] synonym: "presomitic mesoderm cell" NARROW [] synonym: "somitic mesoderm cell" EXACT [] is_a: CL:0000222 ! mesodermal cell intersection_of: CL:0000222 ! mesodermal cell intersection_of: part_of UBERON:0003059 ! presomitic mesoderm relationship: part_of UBERON:0003059 ! presomitic mesoderm [Term] id: CL:0011012 name: neural crest cell namespace: cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) [Term] id: CL:0011019 name: mesothelial cell of epicardium def: "A mesothelial cell that is part of the epicardium." [] is_a: CL:0000077 ! mesothelial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002348 ! epicardium relationship: part_of UBERON:0002348 ! epicardium created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011022 name: fibroblast of skin of back def: "A fibroblast that is part of skin of back." [] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001068 ! skin of back relationship: part_of UBERON:0001068 ! skin of back created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [] is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: develops_from CL:0000034 ! stem cell relationship: develops_from CL:0000034 ! stem cell created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011027 name: skeletal muscle fibroblast def: "Any fibroblast that is part of skeletal muscle tissue." [] synonym: "skeleton muscle fibroblast" EXACT [] is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:1001609 ! muscle fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0030154 ! cell differentiation relationship: capable_of GO:0030154 ! cell differentiation [Term] id: CL:0019018 name: blood vessel smooth muscle cell def: "A smooth muscle cell that is part of any blood vessel." [] synonym: "smooth muscle cell of blood vessel" EXACT [] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: dc-creator http://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0001981 ! blood vessel property_value: http://purl.org/dc/elements/1.1/date 2020-07-21T12:42:48Z xsd:dateTime [Term] id: CL:1000223 name: lung neuroendocrine cell is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0000165 ! neuroendocrine cell is_a: CL:1000272 ! lung secretory cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0002048 ! lung [Term] id: CL:1000271 name: lung ciliated cell is_a: CL:0000064 ! ciliated cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: CL:1000272 name: lung secretory cell is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: CL:1000303 name: fibroblast of areolar connective tissue namespace: cell def: "A fibroblast that is part of the areolar connective tissue." [] xref: FMA:261279 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0006815 ! areolar connective tissue relationship: part_of UBERON:0006815 ! areolar connective tissue [Term] id: CL:1000306 name: fibroblast of tunica adventitia of artery namespace: cell def: "A fibroblast that is part of the tunica adventitia of artery." [] xref: FMA:261285 is_a: CL:0000057 ! fibroblast is_a: CL:0002503 ! adventitial cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005734 ! tunica adventitia of blood vessel relationship: part_of UBERON:0005734 ! tunica adventitia of blood vessel [Term] id: CL:1000307 name: fibroblast of dense regular elastic tissue namespace: cell def: "A fibroblast that is part of the dense regular elastic tissue." [] xref: FMA:261287 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0007846 ! dense regular connective tissue relationship: part_of UBERON:0002521 ! elastic tissue relationship: part_of UBERON:0007846 ! dense regular connective tissue [Term] id: CL:1000309 name: epicardial adipocyte namespace: cell def: "A fat cell that is part of the epicardial fat." [] synonym: "adipocyte of epicardial fat" EXACT [] synonym: "epicardial fat cell" EXACT [] xref: FMA:261293 is_a: CL:0000136 ! fat cell is_a: CL:0002494 ! cardiocyte relationship: part_of UBERON:0002348 ! epicardium [Term] id: CL:1000310 name: adipocyte of epicardial fat of right ventricle namespace: cell def: "A fat cell that is part of the epicardial fat of right ventricle." [] synonym: "epicardial adipocyte of right ventricle" EXACT [] synonym: "epicardial fat cell of right ventricle" EXACT [] xref: FMA:261297 is_a: CL:1000309 ! epicardial adipocyte intersection_of: CL:1000309 ! epicardial adipocyte intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: part_of UBERON:0002080 ! heart right ventricle [Term] id: CL:1000311 name: adipocyte of epicardial fat of left ventricle namespace: cell def: "A fat cell that is part of the epicardial fat of left ventricle." [] synonym: "epicardial adipocyte of left ventricle" EXACT [] synonym: "epicardial fat cell of left ventricle" EXACT [] xref: FMA:261300 is_a: CL:1000309 ! epicardial adipocyte intersection_of: CL:1000309 ! epicardial adipocyte intersection_of: part_of UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0002084 ! heart left ventricle [Term] id: CL:1000361 name: transitional myocyte of interatrial septum namespace: cell def: "A transitional myocyte that is part of the interatrial septum." [] xref: FMA:263152 is_a: CL:0002073 ! transitional myocyte is_a: CL:2000022 ! cardiac septum cell intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002085 ! interatrial septum relationship: part_of UBERON:0002085 ! interatrial septum [Term] id: CL:1000362 name: transitional myocyte of interventricular septum namespace: cell def: "A transitional myocyte that is part of the interventricular septum." [] xref: FMA:263154 is_a: CL:0002073 ! transitional myocyte is_a: CL:2000022 ! cardiac septum cell intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum [Term] id: CL:1000376 name: Purkinje myocyte of interventricular septum namespace: cell def: "A Purkinje myocyte that is part of the interventricular septum." [] xref: FMA:263182 is_a: CL:0002068 ! Purkinje myocyte is_a: CL:2000022 ! cardiac septum cell intersection_of: CL:0002068 ! Purkinje myocyte intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum [Term] id: CL:1000409 name: myocyte of sinoatrial node namespace: cell def: "A muscle cell that is part of the sinoatrial node." [] synonym: "myocyte of sinoatrial node" EXACT [] synonym: "SA nodal myocyte" EXACT [] synonym: "SA node cardiac muscle cell" EXACT [] synonym: "sinoatrial node cell" EXACT [] synonym: "sinoatrial node myocyte" EXACT [] synonym: "sinuatrial node myocyte" EXACT [] xref: FMA:67102 is_a: CL:0002072 ! nodal myocyte intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0002351 ! sinoatrial node relationship: part_of UBERON:0002351 ! sinoatrial node [Term] id: CL:1000410 name: myocyte of atrioventricular node namespace: cell def: "A muscle cell that is part of the atrioventricular node." [] synonym: "atrioventricular node cell" EXACT [] synonym: "atrioventricular node myocyte" EXACT [] synonym: "AV nodal myocyte" EXACT [] synonym: "AV node cardiac muscle cell" EXACT [] synonym: "AV node cell" EXACT [] xref: FMA:67106 is_a: CL:0002072 ! nodal myocyte is_a: CL:2000022 ! cardiac septum cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0002352 ! atrioventricular node relationship: part_of UBERON:0002352 ! atrioventricular node [Term] id: CL:1000412 name: endothelial cell of arteriole namespace: cell def: "An endothelial cell that is part of the arteriole." [] xref: FMA:67760 xref: KUPO:0001097 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001980 ! arteriole relationship: part_of UBERON:0001980 ! arteriole [Term] id: CL:1000413 name: endothelial cell of artery namespace: cell alt_id: CL:0002542 def: "A blood vessel endothelial cell that is part of an arterial endothelium." [] synonym: "arterial endothelial cell" EXACT [] xref: BTO:0004758 xref: FMA:67761 xref: KUPO:0001095 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001917 ! endothelium of artery [Term] id: CL:1000414 name: endothelial cell of venule namespace: cell def: "An endothelial cell that is part of the venule." [] xref: FMA:67762 is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0001979 ! venule relationship: part_of UBERON:0001979 ! venule [Term] id: CL:1000428 name: stem cell of epidermis namespace: cell def: "A somatic stem cell that is part of the epidermis." [] synonym: "epidermal stem cell" EXACT [] xref: FMA:70541 is_a: CL:0000723 ! somatic stem cell intersection_of: CL:0000723 ! somatic stem cell intersection_of: part_of UBERON:0001003 ! skin epidermis relationship: part_of UBERON:0001003 ! skin epidermis [Term] id: CL:1000443 name: ciliary muscle cell namespace: cell def: "A smooth muscle cell that is part of the ciliary body." [] synonym: "smooth muscle cell of ciliary body" EXACT [] xref: FMA:70610 is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001775 ! ciliary body [Term] id: CL:1000444 name: mesothelial cell of anterior chamber of eye namespace: cell def: "A mesothelial cell that is part of the anterior chamber of eyeball." [] xref: FMA:70615 is_a: CL:0000077 ! mesothelial cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0001766 ! anterior chamber of eyeball [Term] id: CL:1000478 name: transitional myocyte of sinoatrial node namespace: cell def: "A transitional myocyte that is part of the sinoatrial node." [] synonym: "transitinal myocyte of sinuatrial node" EXACT [] xref: FMA:83384 is_a: CL:0002073 ! transitional myocyte is_a: CL:1000409 ! myocyte of sinoatrial node intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002351 ! sinoatrial node [Term] id: CL:1000479 name: Purkinje myocyte of atrioventricular node namespace: cell def: "A Purkinje myocyte that is part of the atrioventricular node." [] xref: FMA:83386 is_a: CL:0002068 ! Purkinje myocyte is_a: CL:1000410 ! myocyte of atrioventricular node intersection_of: CL:0002068 ! Purkinje myocyte intersection_of: part_of UBERON:0002352 ! atrioventricular node [Term] id: CL:1000482 name: myocardial endocrine cell of interventricular septum namespace: cell def: "A myocardial endocrine cell that is part of the interventricular septum." [] xref: FMA:83390 is_a: CL:0002074 ! myocardial endocrine cell is_a: CL:2000022 ! cardiac septum cell intersection_of: CL:0002074 ! myocardial endocrine cell intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum [Term] id: CL:1001567 name: lung endothelial cell namespace: cl synonym: "endothelial cell of lung" RELATED [] synonym: "pulmonary vessel endothelial cell" RELATED [] is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0000102 ! lung vasculature [Term] id: CL:1001568 name: pulmonary artery endothelial cell namespace: cl synonym: "PAEC cell" RELATED [] xref: BTO:0001141 is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0005317 ! pulmonary artery endothelium [Term] id: CL:1001576 name: oral mucosa squamous cell def: "Squamous cell of oral epithelium." [] synonym: "oral cavity mucosa squamous cell" RELATED [] synonym: "oral cavity mucosa squamous epithelial cell" RELATED [] synonym: "oral mucosa squamous epithelial cell" RELATED [] synonym: "oral mucosa squamous epithelial cells" RELATED [] xref: CALOHA:TS-1252 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0002424 ! oral epithelium relationship: part_of UBERON:0002424 ! oral epithelium [Term] id: CL:1001609 name: muscle fibroblast def: "Fibroblast from muscle organ." [] xref: CALOHA:TS-0643 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0001630 ! muscle organ [Term] id: CL:1001610 name: bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [] synonym: "bone marrow hematopoietic cells" RELATED [] synonym: "bone marrow poietic cells" RELATED [] xref: CALOHA:TS-2109 is_a: CL:0000988 ! hematopoietic cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0012429 ! hematopoietic tissue [Term] id: CL:2000010 name: dermis blood vessel endothelial cell namespace: cell def: "Any blood vessel endothelial cell that is part of a dermis." [] is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis created_by: TermGenie creation_date: 2014-06-04T15:12:06Z [Term] id: CL:2000013 name: fibroblast of skin of abdomen namespace: cell def: "Any skin fibroblast that is part of a skin of abdomen." [] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001416 ! skin of abdomen relationship: part_of UBERON:0001416 ! skin of abdomen created_by: TermGenie creation_date: 2014-06-04T15:18:16Z [Term] id: CL:2000022 name: cardiac septum cell namespace: cell def: "Any native cell that is part of a cardiac septum." [] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: part_of UBERON:0002099 ! cardiac septum relationship: part_of UBERON:0002099 ! cardiac septum created_by: TermGenie creation_date: 2014-06-24T23:17:07Z [Term] id: CL:2000029 name: central nervous system neuron namespace: cell def: "Any neuron that is part of a central nervous system." [] is_a: CL:0000540 ! neuron created_by: TermGenie creation_date: 2014-06-25T01:17:43Z [Term] id: CL:2000042 name: embryonic fibroblast namespace: cell def: "Any fibroblast that is part of a embryo." [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo created_by: TermGenie creation_date: 2014-07-09T00:12:00Z [Term] id: CL:2000046 name: ventricular cardiac muscle cell namespace: cell def: "Any cardiac muscle cell that is part of a cardiac ventricle." [] is_a: CL:0000746 ! cardiac muscle cell intersection_of: CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle created_by: TermGenie creation_date: 2014-08-12T20:50:28Z [Term] id: CL:2000063 name: ovarian fibroblast namespace: cell def: "Any fibroblast that is part of a female gonad." [] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7330 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary created_by: TermGenie creation_date: 2014-10-07T17:57:42Z [Term] id: CL:2000064 name: ovarian surface epithelial cell namespace: cell def: "Any epithelial cell that is part of a female gonad." [] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7310 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary created_by: TermGenie creation_date: 2014-10-07T17:59:13Z [Term] id: CL:2000066 name: cardiac ventricle fibroblast namespace: cell def: "Any fibroblast that is part of a cardiac ventricle." [] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6310 is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle created_by: TermGenie creation_date: 2014-10-07T18:35:38Z [Term] id: CL:2000067 name: cardiac atrium fibroblast namespace: cell def: "Any fibroblast that is part of a cardiac atrium." [] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6320 is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium created_by: TermGenie creation_date: 2014-10-07T18:36:54Z [Term] id: CL:2000068 name: pericardium fibroblast namespace: cell def: "Any fibroblast that is part of a pericardium." [] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6430 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002407 ! pericardium relationship: part_of UBERON:0002407 ! pericardium created_by: TermGenie creation_date: 2014-10-07T18:38:06Z [Term] id: CL:2000070 name: optic choroid fibroblast namespace: cell def: "Any fibroblast that is part of a optic choroid." [] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6620 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001776 ! optic choroid created_by: TermGenie creation_date: 2014-10-07T18:50:43Z [Term] id: CL:2000073 name: migratory cardiac neural crest cell namespace: cell def: "Any migratory neural crest cell that is part of a cardiac neural crest." [] is_a: CL:0000333 ! migratory neural crest cell intersection_of: CL:0000333 ! migratory neural crest cell intersection_of: part_of UBERON:0000095 ! cardiac neural crest relationship: part_of UBERON:0000095 ! cardiac neural crest created_by: TermGenie creation_date: 2014-11-05T01:18:43Z [Term] id: CL:2000080 name: mesenchymal stem cell of abdominal adipose namespace: cell def: "Any mesenchymal stem cell of adipose that is part of a abdomen." [] is_a: CL:0002570 ! mesenchymal stem cell of adipose intersection_of: CL:0002570 ! mesenchymal stem cell of adipose intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen created_by: TermGenie creation_date: 2014-12-02T19:10:34Z [Term] id: CL:3000000 name: ciliated epithelial cell of esophagus namespace: cell def: "A ciliated epithelial cell of the esophagus." [] is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus intersection_of: CL:0000067 ! ciliated epithelial cell intersection_of: part_of UBERON:0001976 ! epithelium of esophagus relationship: part_of UBERON:0001976 ! epithelium of esophagus created_by: CellBLAST creation_date: 2019-02-09T16:40:30Z [Term] id: COB:0000001 name: quality is_a: COB:0000502 ! characteristic [Term] id: COB:0000003 name: mass is_a: COB:0000001 ! quality [Term] id: COB:0000004 name: charge is_a: COB:0000001 ! quality [Term] id: COB:0000006 name: material entity relationship: COB:0000041 COB:0000003 ! has quality mass [Term] id: COB:0000007 name: subatomic particle is_a: COB:0000006 ! material entity [Term] id: COB:0000011 name: atom def: "A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it." [] comment: This atom is closely related to ChEBI's atom, but not exactly equivalent to. is_a: COB:0000006 ! material entity relationship: COB:0000047 COB:0000012 ! has part atomic nucleus [Term] id: COB:0000012 name: atomic nucleus comment: Some people may be uncomfortable calling every proton an atomic nucleus comment: This is equivalent to CHEBI:33252 is_a: COB:0000007 ! subatomic particle [Term] id: COB:0000042 name: monoatomic ion is_a: COB:0000011 ! atom intersection_of: COB:0000011 ! atom intersection_of: COB:0000041 COB:0000004 ! has quality charge disjoint_from: COB:0000043 ! uncharged atom relationship: COB:0000041 COB:0000004 ! has quality charge [Term] id: COB:0000043 name: uncharged atom is_a: COB:0000011 ! atom [Term] id: COB:0000502 name: characteristic relationship: COB:0000047 COB:0000502 ! has part characteristic property_value: seeAlso https://github.com/OBOFoundry/COB/issues/65 xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/pull/284 xsd:string [Term] id: DOID:0050161 name: lower respiratory tract disease namespace: disease_ontology def: "A respiratory system disease which involves the lower respiratory tract." [url:http\://en.wikipedia.org/wiki/lower_respiratory_tract] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim xref: ICD9CM:478.19 xref: SNOMEDCT_US_2020_09_01:195823002 xref: UMLS_CUI:C0029581 is_a: DOID:1579 ! respiratory system disease [Term] id: DOID:0050700 name: cardiomyopathy namespace: disease_ontology def: "A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle." [url:http\://en.wikipedia.org/wiki/Cardiomyopathy, url:http\://www.nhlbi.nih.gov/health/health-topics/topics/cm/] {http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: MESH:D009202 added from NeuroDevNet [WAK]. subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "Cardiomyopathies" EXACT [] xref: ICD10CM:I42 xref: ICD9CM:425 xref: ICD9CM:425.9 xref: MESH:D009202 xref: NCI:C34830 xref: NCI:C53654 xref: SNOMEDCT_US_2020_09_01:266301006 xref: SNOMEDCT_US_2020_09_01:89461002 xref: SNOMEDCT_US_2020_09_01:89600009 xref: UMLS_CUI:C0033141 xref: UMLS_CUI:C0036529 xref: UMLS_CUI:C0878544 is_a: DOID:114 ! heart disease created_by: lschriml creation_date: 2012-01-03T02:54:11Z [Term] id: DOID:0050851 name: glomerulosclerosis namespace: disease_ontology def: "A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney." [url:http\://en.wikipedia.org/wiki/Glomerulosclerosis] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim is_a: DOID:2921 ! glomerulonephritis created_by: lschriml creation_date: 2014-04-15T03:40:31Z [Term] id: DOID:0050902 name: medulloblastoma namespace: disease_ontology alt_id: DOID:0060105 alt_id: DOID:168 alt_id: DOID:3858 alt_id: DOID:4981 def: "An infratentorial cancer that is located_in the lower part of the brain and is a type of primitive neuroectodermal tumor." [url:http\://en.wikipedia.org/wiki/Medulloblastoma, url:http\://www.cancer.gov/dictionary?CdrID=45780, url:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306779/] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: OMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "brain medulloblastoma" EXACT [] synonym: "CNS PNET" EXACT [] synonym: "CPNET" EXACT [] synonym: "infratentorial primitive neuroectodermal tumor" EXACT [] synonym: "localized primitive neuroectodermal tumor" EXACT [] xref: GARD:7005 xref: MESH:D008527 xref: MESH:D018242 xref: NCI:C27294 xref: NCI:C3222 xref: NCI:C3716 xref: OMIM:155255 xref: SNOMEDCT_US_2020_09_01:189925001 xref: SNOMEDCT_US_2020_09_01:443333004 xref: UMLS_CUI:C0025149 xref: UMLS_CUI:C0206663 xref: UMLS_CUI:C1334410 is_a: DOID:1319 ! brain cancer created_by: lschriml creation_date: 2014-10-06T14:36:37Z [Term] id: DOID:0060037 name: developmental disorder of mental health namespace: disease_ontology def: "A disease of mental health that occur during a child's developmental period between birth and age 18 resulting in retarding of the child's psychological or physical development." [url:http\://en.wikipedia.org/wiki/Developmental_disorders] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim is_a: DOID:150 ! disease of mental health [Term] id: DOID:0060058 name: lymphoma namespace: disease_ontology alt_id: DOID:1033 alt_id: DOID:353 def: "A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs." [url:http\://en.wikipedia.org/wiki/Lymphoma, url:http\://www.lymphoma.org/site/pp.asp?c=bkLTKaOQLmK8E&b=6300161, url:http\://www.nlm.nih.gov/medlineplus/lymphoma.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "lymphoid cancer" EXACT [] xref: ICD10CM:C85.9 xref: MESH:D008223 xref: NCI:C3208 xref: NCI:C7065 xref: SNOMEDCT_US_2020_09_01:118600007 xref: SNOMEDCT_US_2020_09_01:414628006 xref: UMLS_CUI:C0024299 xref: UMLS_CUI:C0598798 is_a: DOID:2531 ! hematologic cancer [Term] id: DOID:0060071 name: pre-malignant neoplasm namespace: disease_ontology def: "A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer." [url:http\://en.wikipedia.org/wiki/Neoplasm] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_AGR_slim subset: DO_GXD_slim subset: DO_MGI_slim subset: DO_RAD_slim is_a: DOID:14566 ! disease of cellular proliferation created_by: lschriml creation_date: 2011-05-11T12:18:41Z [Term] id: DOID:0060072 name: benign neoplasm namespace: disease_ontology def: "A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize." [url:http\://en.wikipedia.org/wiki/Benign_neoplasm, url:http\://www.nlm.nih.gov/medlineplus/benigntumors.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_AGR_slim subset: DO_GXD_slim subset: DO_MGI_slim subset: DO_RAD_slim is_a: DOID:14566 ! disease of cellular proliferation disjoint_from: DOID:162 ! cancer created_by: lschriml creation_date: 2011-05-11T12:18:41Z [Term] id: DOID:10124 name: corneal disease namespace: disease_ontology alt_id: DOID:2284 def: "An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction." [url:https\://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C26731] {http://purl.org/dc/elements/1.1/type="ECO:0007636"} subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:H18.9 xref: ICD9CM:371.9 xref: MESH:D003316 xref: NCI:C26731 xref: SNOMEDCT_US_2020_09_01:15250008 xref: UMLS_CUI:C0010034 is_a: DOID:5614 ! eye disease [Term] id: DOID:10273 name: heart conduction disease namespace: disease_ontology def: "A cardiovascular system disease that involves the heart's electrical conduction system." [url:http\://en.wikipedia.org/wiki/Conduction_system_of_the_heart] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim synonym: "heart rhythm disease" EXACT [] xref: ICD9CM:426.6 xref: SNOMEDCT_US_2020_09_01:195053008 xref: UMLS_CUI:C0029630 is_a: DOID:114 ! heart disease [Term] id: DOID:10286 name: prostate carcinoma namespace: disease_ontology def: "A prostate cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells." [url:http\://en.wikipedia.org/wiki/Carcinoma] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "cancer of prostate" EXACT [] synonym: "carcinoma of prostate" EXACT [] xref: EFO:0001663 xref: KEGG:05215 xref: NCI:C4863 xref: SNOMEDCT_US_2020_09_01:254900004 xref: UMLS_CUI:C0600139 is_a: DOID:162 ! cancer [Term] id: DOID:1037 name: lymphoid leukemia namespace: disease_ontology alt_id: DOID:10747 def: "A leukemia that has_material_basis_in a B-cell or T-cell lineage involving primarily the bone marrow and the peripheral blood." [url:http\://www.cancer.gov/dictionary?CdrID=616067] {http://purl.org/dc/elements/1.1/type="ECO:0007641"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "lymphoblastic leukaemia" EXACT [] synonym: "lymphoblastic leukemia" EXACT [] synonym: "lymphocytic leukaemia" EXACT [] synonym: "lymphoid leukemia" EXACT [] xref: ICD10CM:C91 xref: ICD9CM:204 xref: MESH:D007945 xref: NCI:C7539 xref: SNOMEDCT_US_2020_09_01:93170002 xref: UMLS_CUI:C0023448 is_a: DOID:1240 ! leukemia [Term] id: DOID:1040 name: chronic lymphocytic leukemia namespace: disease_ontology def: "A lymphocytic leukemia characterized by over production of B-cells and their accumulation in bone marrow and blood." [url:http\://en.wikipedia.org/wiki/B-cell_chronic_lymphocytic_leukemia, url:http\://www.cancer.gov/dictionary?cdrid=346545] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Xref MGI. subset: DO_cancer_slim subset: DO_RAD_slim subset: DO_rare_slim subset: NCIthesaurus synonym: "B-cell chronic lymphocytic leukaemia" EXACT [] synonym: "B-cell chronic lymphocytic leukemia" EXACT [] synonym: "B-cell chronic lymphoid leukemia" RELATED [] synonym: "chronic lymphatic leukaemia" EXACT [] synonym: "chronic lymphatic leukemia" EXACT [] synonym: "chronic lymphocytic leukaemia" EXACT [] synonym: "CLL" EXACT [] synonym: "lymphoplasmacytic leukaemia" EXACT [] synonym: "lymphoplasmacytic leukemia" EXACT [] xref: EFO:0000095 xref: GARD:6104 xref: ICD10CM:C91.10 xref: ICD9CM:204.1 xref: MESH:D015451 xref: NCI:C3163 xref: OMIM:109543 xref: OMIM:151400 xref: OMIM:609630 xref: OMIM:612557 xref: OMIM:612558 xref: OMIM:612559 xref: ORDO:67038 xref: SNOMEDCT_US_2020_09_01:51092000 xref: UMLS_CUI:C0023434 is_a: DOID:1037 ! lymphoid leukemia [Term] id: DOID:10534 name: stomach cancer namespace: disease_ontology alt_id: DOID:10539 alt_id: DOID:10542 alt_id: DOID:10543 alt_id: DOID:4713 def: "A gastrointestinal system cancer that is located_in the stomach." [url:http\://cancergenome.nih.gov/cancersselected/stomach-esophagealcancer, url:http\://en.wikipedia.org/wiki/Stomach] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} comment: OMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "gastric cancer" EXACT [] synonym: "gastric neoplasm" EXACT [] xref: GARD:7704 xref: ICD10CM:C16 xref: ICD10CM:C16.2 xref: ICD10CM:C16.5 xref: ICD10CM:C16.6 xref: ICD9CM:151 xref: ICD9CM:151.4 xref: ICD9CM:151.5 xref: ICD9CM:151.6 xref: MESH:D013274 xref: NCI:C3387 xref: NCI:C9331 xref: OMIM:613659 xref: SNOMEDCT_US_2020_09_01:126824007 xref: SNOMEDCT_US_2020_09_01:269459004 xref: SNOMEDCT_US_2020_09_01:269460009 xref: SNOMEDCT_US_2020_09_01:93717002 xref: SNOMEDCT_US_2020_09_01:94074003 xref: UMLS_CUI:C0024623 xref: UMLS_CUI:C0038356 xref: UMLS_CUI:C0153421 xref: UMLS_CUI:C0153422 xref: UMLS_CUI:C0153423 is_a: DOID:162 ! cancer [Term] id: DOID:10652 name: Alzheimer's disease namespace: disease_ontology def: "A tauopathy that is characterized by memory lapses, confusion, emotional instability and progressive loss of mental ability and results in progressive memory loss, impaired thinking, disorientation, and changes in personality and mood starting and leads in advanced cases to a profound decline in cognitive and physical functioning and is marked histologically by the degeneration of brain neurons especially in the cerebral cortex and by the presence of neurofibrillary tangles and plaques containing beta-amyloid." [url:http\://en.wikipedia.org/wiki/Alzheimer%27s_disease, url:http\://www.merriam-webster.com/medical/alzheimer%27s%20disease, url:http\://www.nia.nih.gov/alzheimers/publication/alzheimers-disease-fact-sheet] {comment="ls:IEDB", http://purl.org/dc/elements/1.1/type="ECO:0007643", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Xref MGI.\nOMIM mapping confirmed by DO. [SN]. subset: DO_RAD_slim subset: NCIthesaurus synonym: "Alzheimer disease" EXACT [] synonym: "Alzheimers dementia" EXACT [] xref: EFO:0000249 xref: GARD:10254 xref: ICD10CM:G30 xref: ICD9CM:331.0 xref: KEGG:05010 xref: MESH:D000544 xref: NCI:C2866 xref: SNOMEDCT_US_2020_09_01:73768007 xref: UMLS_CUI:C0002395 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:11054 name: urinary bladder cancer namespace: disease_ontology alt_id: DOID:5428 def: "An urinary system cancer that results_in malignant growth located_in the urinary bladder." [url:http\://en.wikipedia.org/wiki/Bladder_cancer] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} comment: OMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "bladder cancer" EXACT [] synonym: "tumor of the bladder" EXACT [] xref: GARD:12210 xref: ICD10CM:C67 xref: ICD9CM:188 xref: KEGG:05219 xref: MESH:D001749 xref: NCI:C2901 xref: NCI:C9334 xref: OMIM:109800 xref: SNOMEDCT_US_2020_09_01:126885006 xref: SNOMEDCT_US_2020_09_01:363455001 xref: UMLS_CUI:C0005684 xref: UMLS_CUI:C0005695 is_a: DOID:162 ! cancer [Term] id: DOID:1115 name: sarcoma namespace: disease_ontology alt_id: DOID:3936 def: "A cell type cancer that has_material_basis_in abnormally proliferating cells derives from embryonic mesoderm." [url:http\://cancergenome.nih.gov/cancersselected/Sarcoma, url:http\://en.wikipedia.org/wiki/Sarcoma, url:http\://www.cancer.gov/dictionary?CdrID=45562] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_cancer_slim subset: DO_RAD_slim subset: TopNodes_DOcancerslim synonym: "connective and soft tissue neoplasm" EXACT [] synonym: "tumor of soft tissue and skeleton" EXACT [] xref: ICD10CM:C49 xref: ICD9CM:171.9 xref: SNOMEDCT_US_2020_09_01:93765001 xref: UMLS_CUI:C0153519 is_a: DOID:162 ! cancer [Term] id: DOID:114 name: heart disease namespace: disease_ontology def: "A cardiovascular system disease that involves the heart." [url:http\://en.wikipedia.org/wiki/Heart_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:I51.9 xref: ICD9CM:429.9 xref: MESH:D006331 xref: NCI:C3079 xref: SNOMEDCT_US_2020_09_01:194707003 xref: UMLS_CUI:C0018799 is_a: DOID:1287 ! cardiovascular system disease [Term] id: DOID:1176 name: bronchial disease namespace: disease_ontology alt_id: DOID:1175 alt_id: DOID:12322 def: "A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage." [url:https\://www.ncbi.nlm.nih.gov/pubmed/11685087] {http://purl.org/dc/elements/1.1/type="ECO:0007645"} subset: DO_RAD_slim synonym: "Bronchospasm" EXACT [] xref: MESH:D001982 xref: SNOMEDCT_US_2020_09_01:41427001 xref: UMLS_CUI:C0006261 is_a: DOID:0050161 ! lower respiratory tract disease [Term] id: DOID:1240 name: leukemia namespace: disease_ontology alt_id: DOID:9145 def: "A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells." [url:http\://en.wikipedia.org/wiki/Leukemia, url:http\://www.cancer.gov/dictionary?CdrID=45343] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:C95.90 xref: ICD9CM:208 xref: MESH:D007938 xref: NCI:C3161 xref: SNOMEDCT_US_2020_09_01:255049003 xref: UMLS_CUI:C0023418 is_a: DOID:2531 ! hematologic cancer [Term] id: DOID:1247 name: blood coagulation disease namespace: disease_ontology alt_id: DOID:13997 alt_id: DOID:2212 alt_id: DOID:9474 def: "A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding." [url:https\://www.cedars-sinai.edu/Patients/Health-Conditions/Coagulation-System-Disorders.aspx] subset: DO_RAD_slim subset: NCIthesaurus synonym: "coagulation protein disease" EXACT [] synonym: "inherited blood coagulation disease" NARROW [] synonym: "postpartum coagulation defect" EXACT [] synonym: "postpartum coagulation defect with delivery" EXACT [] xref: ICD10CM:D68.9 xref: ICD9CM:286 xref: MESH:D001778 xref: NCI:C2902 xref: SNOMEDCT_US_2020_09_01:64779008 xref: UMLS_CUI:C0005779 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:1287 name: cardiovascular system disease namespace: disease_ontology alt_id: DOID:73 def: "A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." [url:http\://en.wikipedia.org/wiki/Circulatory_system] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_AGR_slim subset: DO_GXD_slim subset: DO_MGI_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "disease of subdivision of hemolymphoid system" EXACT [] xref: ICD9CM:429.2 xref: MESH:D002318 xref: NCI:C2931 xref: SNOMEDCT_US_2020_09_01:266275004 xref: UMLS_CUI:C0007222 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:1307 name: dementia namespace: disease_ontology def: "A cognitive disorder resulting from a loss of brain function affecting memory, thinking, language, judgement and behavior." [url:http\://www.nlm.nih.gov/medlineplus/ency/article/000739.htm] {http://purl.org/dc/elements/1.1/type="ECO:0007640"} subset: DO_RAD_slim xref: ICD9CM:290.8 xref: UMLS_CUI:C0154319 is_a: DOID:1561 ! cognitive disorder [Term] id: DOID:1319 name: brain cancer namespace: disease_ontology alt_id: DOID:2125 alt_id: DOID:2126 alt_id: DOID:3543 alt_id: DOID:6649 alt_id: DOID:911 def: "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." [url:http\://www.cancer.gov/dictionary?CdrID=387264] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "adult brain tumor" EXACT [] synonym: "adult malignant brain neoplasm" EXACT [] synonym: "brain neoplasm" EXACT [] synonym: "brain neoplasm, adult" EXACT [] synonym: "BT - Brain tumour" EXACT [] synonym: "malignant brain tumour" EXACT [] synonym: "malignant primary brain neoplasm" EXACT [] synonym: "malignant primary brain tumor" EXACT [] synonym: "malignant tumor of adult brain" EXACT [] synonym: "malignant tumor of Brain" EXACT [] synonym: "neoplasm of brain" EXACT [] synonym: "primary brain neoplasm" EXACT [] synonym: "primary brain tumor" EXACT [] synonym: "primary malignant neoplasm of brain" EXACT [] synonym: "tumor of the Brain" EXACT [] xref: ICD10CM:C71 xref: ICD9CM:191 xref: ICD9CM:239.6 xref: MESH:D001932 xref: NCI:C2907 xref: NCI:C3568 xref: NCI:C5115 xref: NCI:C7710 xref: SNOMEDCT_US_2020_09_01:126952004 xref: SNOMEDCT_US_2020_09_01:428061005 xref: SNOMEDCT_US_2020_09_01:93727008 xref: UMLS_CUI:C0006118 xref: UMLS_CUI:C0153633 xref: UMLS_CUI:C0220624 xref: UMLS_CUI:C0750974 xref: UMLS_CUI:C0750979 xref: UMLS_CUI:C1334557 is_a: DOID:162 ! cancer [Term] id: DOID:1443 name: cerebral degeneration namespace: disease_ontology def: "A brain disease that is characterized by loss of structure or function of neurons, including death of neurons and loss of brain tissue." [url:https\://en.wikipedia.org/wiki/Neurodegeneration] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim synonym: "Brain degeneration" EXACT [] xref: GARD:6019 xref: ICD9CM:331.9 xref: SNOMEDCT_US_2020_09_01:52522001 xref: UMLS_CUI:C0154671 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:14566 name: disease of cellular proliferation namespace: disease_ontology alt_id: DOID:0000818 def: "A disease that is characterized by abnormally rapid cell division." [url:http\://en.wikipedia.org/w/index.php?title=Cell_proliferation] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_FlyBase_slim subset: DO_RAD_slim synonym: "cell process disease" EXACT [] synonym: "neoplasm" EXACT [] is_a: DOID:4 ! disease property_value: OBI:9991118 "neoplasm" xsd:string [Term] id: DOID:150 name: disease of mental health namespace: disease_ontology def: "A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture." [url:http\://en.wikipedia.org/wiki/Mental_disorder] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_AGR_slim subset: DO_GXD_slim subset: DO_MGI_slim subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:F99 xref: MESH:D001523 xref: NCI:C2893 xref: SNOMEDCT_US_2020_09_01:74732009 xref: UMLS_CUI:C0004936 is_a: DOID:4 ! disease [Term] id: DOID:1510 name: personality disorder namespace: disease_ontology def: "A disease of mental health that involve long-term patterns of thoughts and behaviors that cause serious problems with relationships and work." [url:http\://www.nlm.nih.gov/medlineplus/personalitydisorders.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644"} subset: DO_RAD_slim synonym: "character disorder" EXACT [] xref: ICD9CM:301.8 xref: SNOMEDCT_US_2020_09_01:191770003 xref: UMLS_CUI:C0029707 is_a: DOID:150 ! disease of mental health [Term] id: DOID:1532 name: pleural disease namespace: disease_ontology alt_id: DOID:1531 def: "A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism." [url:http\://en.wikipedia.org/wiki/Pleural_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "disorder of pleura" EXACT [] synonym: "non-neoplastic pleural disease" EXACT [] xref: MESH:D010995 xref: NCI:C26859 xref: SNOMEDCT_US_2020_09_01:88075009 xref: UMLS_CUI:C0032226 is_a: DOID:0050161 ! lower respiratory tract disease [Term] id: DOID:1561 name: cognitive disorder namespace: disease_ontology def: "A disease of mental health that affects cognitive functions including memory processing, perception and problem solving." [url:http\://en.wikipedia.org/wiki/Cognitive_disorder] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "cognitive disease" EXACT [] synonym: "Organic Mental disorder" RELATED [] xref: ICD10CM:F09 xref: MESH:D019965 xref: NCI:C34870 xref: SNOMEDCT_US_2020_09_01:111479008 xref: UMLS_CUI:C0029227 is_a: DOID:150 ! disease of mental health [Term] id: DOID:1579 name: respiratory system disease namespace: disease_ontology alt_id: DOID:3226 def: "A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm." [url:http\://en.wikipedia.org/wiki/File\:Respiratory_system_complete_en.svg, url:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=respiratory%20system] {http://purl.org/dc/elements/1.1/type="ECO:0007643", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_AGR_slim subset: DO_GXD_slim subset: DO_MGI_slim subset: DO_RAD_slim xref: ICD10CM:J98 xref: ICD9CM:519 xref: SNOMEDCT_US_2020_09_01:155603009 xref: UMLS_CUI:C0029582 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:1612 name: breast cancer namespace: disease_ontology alt_id: DOID:1648 alt_id: DOID:4241 def: "A thoracic cancer that originates in the mammary gland." [url:http\://en.wikipedia.org/wiki/Breast_cancer, url:http\://en.wikipedia.org/wiki/Mammary, url:http\://www.cancer.gov/cancertopics/types/breast, url:http\://www.nlm.nih.gov/medlineplus/breastcancer.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Xref MGI.\nOMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "breast tumor" EXACT [] synonym: "malignant neoplasm of breast" EXACT [] synonym: "malignant tumor of the breast" EXACT [] synonym: "mammary cancer" EXACT [] synonym: "mammary neoplasm" RELATED [] synonym: "mammary tumor" EXACT [] synonym: "primary breast cancer" EXACT [] xref: ICD10CM:C50 xref: MESH:D001943 xref: NCI:C9335 xref: OMIM:114480 xref: SNOMEDCT_US_2020_09_01:254837009 xref: UMLS_CUI:C0006142 is_a: DOID:162 ! cancer [Term] id: DOID:162 name: cancer namespace: disease_ontology def: "A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis." [url:http\://en.wikipedia.org/wiki/cancer, url:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer] {http://purl.org/dc/elements/1.1/type="ECO:0007643", http://purl.org/dc/elements/1.1/type="ECO:0007638"} comment: Updating out dated UMLS CUI. subset: DO_AGR_slim subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_GXD_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "malignant neoplasm" EXACT [] synonym: "malignant tumor" EXACT [] synonym: "primary cancer" EXACT [] xref: ICD10CM:C80.1 xref: ICD9CM:199 xref: ICDO:M8000/3 xref: MESH:D009369 xref: NCI:C9305 xref: SNOMEDCT_US_2020_09_01:269513004 xref: UMLS_CUI:C0006826 is_a: DOID:14566 ! disease of cellular proliferation [Term] id: DOID:178 name: vascular disease namespace: disease_ontology alt_id: DOID:0000405 alt_id: DOID:2403 alt_id: DOID:2869 alt_id: DOID:324 alt_id: DOID:325 alt_id: DOID:45 def: "A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart." [url:http\://en.wikipedia.org/wiki/Vascular_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "vascular tissue disease" EXACT [] xref: ICD10CM:I72.9 xref: ICD9CM:442.9 xref: MESH:D000783 xref: MESH:D014652 xref: MESH:D020758 xref: MESH:D020760 xref: NCI:C26693 xref: NCI:C35117 xref: SNOMEDCT_US_2020_09_01:27550009 xref: SNOMEDCT_US_2020_09_01:371029002 xref: SNOMEDCT_US_2020_09_01:432119003 xref: UMLS_CUI:C0002940 xref: UMLS_CUI:C0042373 xref: UMLS_CUI:C0752127 xref: UMLS_CUI:C0752130 is_a: DOID:1287 ! cardiovascular system disease [Term] id: DOID:1787 name: pericarditis namespace: disease_ontology def: "A pericardium disease that is characterized by an inflammation of the pericardium and has_symptom chest pain." [url:http\://en.wikipedia.org/wiki/Pericarditis] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus xref: MESH:D010493 xref: NCI:C34915 xref: SNOMEDCT_US_2020_09_01:3238004 xref: UMLS_CUI:C0031046 is_a: DOID:1287 ! cardiovascular system disease [Term] id: DOID:1909 name: melanoma namespace: disease_ontology def: "A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye." [url:http\://en.wikipedia.org/wiki/Melanoma, url:https\://www.ncbi.nlm.nih.gov/pubmed/22123420] {http://purl.org/dc/elements/1.1/type="ECO:0007645", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "malignant melanoma" EXACT [] synonym: "Naevocarcinoma" EXACT [] xref: EFO:0000756 xref: KEGG:05218 xref: MESH:D008545 xref: NCI:C3224 xref: SNOMEDCT_US_2020_09_01:2092003 xref: UMLS_CUI:C0025202 is_a: DOID:162 ! cancer property_value: exactMatch MESH:D008545 xsd:string [Term] id: DOID:1936 name: atherosclerosis namespace: disease_ontology subset: DO_RAD_slim subset: NCIthesaurus xref: EFO:0003914 xref: ICD10CM:I70 xref: ICD9CM:440 xref: MESH:D050197 xref: NCI:C35768 xref: SNOMEDCT_US_2020_09_01:155414001 xref: UMLS_CUI:C0004153 is_a: DOID:178 ! vascular disease property_value: exactMatch MESH:D050197 xsd:string [Term] id: DOID:2030 name: anxiety disorder namespace: disease_ontology alt_id: DOID:12884 def: "A cognitive disorder that involves an excessive, irrational dread of everyday situations." [url:http\://www.nimh.nih.gov/health/topics/anxiety-disorders/index.shtml] {http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "anxiety" EXACT [] synonym: "anxiety state" EXACT [] xref: ICD10CM:F41.9 xref: MESH:D001008 xref: NCI:C2878 xref: OMIM:607834 xref: SNOMEDCT_US_2020_09_01:65673007 xref: UMLS_CUI:C0003469 is_a: DOID:1561 ! cognitive disorder [Term] id: DOID:2394 name: ovarian cancer namespace: disease_ontology alt_id: DOID:0060070 alt_id: DOID:2144 alt_id: DOID:9595 def: "A female reproductive organ cancer that is located_in the ovary." [url:http\://www.cancer.gov/dictionary?CdrID=445074] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Xref MGI.\nOMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_RAD_slim subset: DO_rare_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "malignant Ovarian tumor" EXACT [] synonym: "malignant tumour of ovary" EXACT [] synonym: "ovarian neoplasm" EXACT [] synonym: "ovary neoplasm" EXACT [] synonym: "primary ovarian cancer" EXACT [] synonym: "tumor of the Ovary" EXACT [] xref: GARD:7295 xref: ICD10CM:C56 xref: ICD9CM:183.0 xref: MESH:D010051 xref: NCI:C4984 xref: NCI:C7431 xref: OMIM:167000 xref: OMIM:607893 xref: ORDO:213500 xref: ORDO:213517 xref: SNOMEDCT_US_2020_09_01:123843001 xref: SNOMEDCT_US_2020_09_01:372117006 xref: SNOMEDCT_US_2020_09_01:93934004 xref: UMLS_CUI:C0919267 xref: UMLS_CUI:C1140680 xref: UMLS_CUI:C1299247 is_a: DOID:162 ! cancer [Term] id: DOID:240 name: iris disease namespace: disease_ontology subset: DO_RAD_slim subset: NCIthesaurus xref: MESH:D007499 xref: NCI:C34737 xref: SNOMEDCT_US_2020_09_01:85478004 xref: UMLS_CUI:C0022078 is_a: DOID:5614 ! eye disease [Term] id: DOID:2468 name: psychotic disorder namespace: disease_ontology def: "A cognitive disorder that involves abnormal thinking and perceptions resulting in a disconnection with reality." [url:http\://www.nlm.nih.gov/medlineplus/psychoticdisorders.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644"} subset: DO_RAD_slim synonym: "mental or behavioural disorder" EXACT [] xref: EFO:0000677 xref: ICD9CM:298.8 xref: UMLS_CUI:C0029516 is_a: DOID:1561 ! cognitive disorder [Term] id: DOID:2513 name: basal cell carcinoma namespace: disease_ontology alt_id: DOID:4275 alt_id: DOID:4276 def: "A skin carcinoma affecting basal cells." [url:http\://en.wikipedia.org/wiki/Basal-cell_carcinoma] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} comment: Xref MGI. subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "Basal cell cancer" EXACT [] synonym: "Basal cell carcinoma of skin" EXACT [] synonym: "Basal cell neoplasm" EXACT [] synonym: "Basal cell tumor" EXACT [] synonym: "Epithelioma basal cell" EXACT [] synonym: "malignant Basal cell neoplasm" EXACT [] synonym: "malignant basal cell tumor" EXACT [] synonym: "Rodent ulcer" EXACT [] xref: EFO:0004193 xref: KEGG:05217 xref: MESH:D018295 xref: NCI:C156767 xref: NCI:C3784 xref: NCI:C7586 xref: SNOMEDCT_US_2020_09_01:127570002 xref: SNOMEDCT_US_2020_09_01:154507009 xref: SNOMEDCT_US_2020_09_01:252995000 xref: UMLS_CUI:C0007117 xref: UMLS_CUI:C0206710 xref: UMLS_CUI:C1368295 is_a: DOID:3451 ! skin carcinoma [Term] id: DOID:2531 name: hematologic cancer namespace: disease_ontology alt_id: DOID:1034 alt_id: DOID:2532 def: "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." [url:http\://en.wikipedia.org/wiki/Blood_cancer, url:http\://www.cancer.gov/dictionary/?CdrID=45708] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "blood cancer" EXACT [] synonym: "Hematologic malignancy" EXACT [] synonym: "Hematologic neoplasm" EXACT [] synonym: "Hematological tumors" EXACT [] synonym: "hematopoietic and lymphoid system tumor" EXACT [] synonym: "hematopoietic cancer" EXACT [] synonym: "hematopoietic neoplasm" EXACT [] synonym: "hematopoietic tumors" EXACT [] synonym: "malignant hematopoietic neoplasm" EXACT [] xref: MESH:D019337 xref: NCI:C27134 xref: SNOMEDCT_US_2020_09_01:414388001 xref: UMLS_CUI:C0376544 is_a: DOID:162 ! cancer [Term] id: DOID:2786 name: cerebellar disease namespace: disease_ontology def: "A brain disease that is characterized by damage to brain substance located_in cerebellum; has_symptom ataxia, has_symptom dysarthria, and has_symptom cerebellar cognitive affective syndrome." [url:https\://en.wikipedia.org/wiki/Cerebellum, url:https\://www.ncbi.nlm.nih.gov/pubmed/15377747] {http://purl.org/dc/elements/1.1/type="ECO:0007645", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim xref: MESH:D002526 xref: SNOMEDCT_US_2020_09_01:267691001 xref: UMLS_CUI:C0007760 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:28 name: endocrine system disease namespace: disease_ontology def: "A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body." [url:http\://en.wikipedia.org/wiki/Endocrine_system] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_AGR_slim subset: DO_GXD_slim subset: DO_MGI_slim subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:E34.9 xref: ICD9CM:259.9 xref: MESH:D004700 xref: NCI:C3009 xref: SNOMEDCT_US_2020_09_01:67432001 xref: UMLS_CUI:C0014130 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:2921 name: glomerulonephritis namespace: disease_ontology def: "A nephritis that causes inflammation of the glomeruli located_in kidney." [url:http\://en.wikipedia.org/wiki/Glomerulonephritis] {comment="sn:IEDB", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus xref: GARD:6516 xref: ICD10CM:N08 xref: MESH:D005921 xref: NCI:C26784 xref: SNOMEDCT_US_2020_09_01:36171008 xref: UMLS_CUI:C0017658 is_a: DOID:557 ! kidney disease [Term] id: DOID:2994 name: germ cell cancer namespace: disease_ontology alt_id: DOID:2157 def: "A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from germ cells." [url:http\://en.wikipedia.org/wiki/Germ_cell_tumor] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "germ cell neoplasm" RELATED [] synonym: "germ cell tumour" RELATED [] synonym: "malignant tumor of the germ cell" EXACT [] xref: MESH:D009373 xref: NCI:C3708 xref: SNOMEDCT_US_2020_09_01:302853003 xref: UMLS_CUI:C0205851 is_a: DOID:162 ! cancer [Term] id: DOID:303 name: substance-related disorder namespace: disease_ontology def: "A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning." [url:https\://www.psychologytoday.com/us/conditions/substance-related-disorders] subset: DO_RAD_slim subset: NCIthesaurus xref: MESH:D019966 xref: NCI:C92203 xref: UMLS_CUI:C0236969 is_a: DOID:150 ! disease of mental health [Term] id: DOID:3083 name: chronic obstructive pulmonary disease namespace: disease_ontology alt_id: DOID:11500 alt_id: DOID:6144 def: "An obstructive lung disease that is characterized by irreversible airflow obstruction due to chronic bronchitis, emphysema, and/or small airways disease." [url:https\://pubmed.ncbi.nlm.nih.gov/28513453/, url:https\://www.nhlbi.nih.gov/health-topics/copd] subset: DO_RAD_slim subset: NCIthesaurus synonym: "chronic obstructive airway disease" EXACT [] synonym: "chronic obstructive lung disease" EXACT [] synonym: "COLD" EXACT [] synonym: "COPD" EXACT [] xref: EFO:0000341 xref: ICD10CM:J44.9 xref: MESH:D029424 xref: NCI:C3199 xref: OMIM:606963 xref: SNOMEDCT_US_2020_09_01:13645005 xref: UMLS_CUI:C0024117 is_a: DOID:850 ! lung disease [Term] id: DOID:3393 name: coronary artery disease namespace: disease_ontology alt_id: DOID:10506 alt_id: DOID:3363 alt_id: DOID:3394 alt_id: DOID:9420 def: "An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles." [url:http\://en.wikipedia.org/wiki/Coronary_heart_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} comment: Xref MGI. subset: DO_RAD_slim subset: NCIthesaurus synonym: "CHD" EXACT [] synonym: "coronary arteriosclerosis" EXACT [] synonym: "Coronary disease" EXACT [] synonym: "coronary heart disease" EXACT [] xref: EFO:0001645 xref: ICD10CM:I20-I25 xref: ICD10CM:I25 xref: ICD10CM:I25.10 xref: ICD9CM:410-414.99 xref: ICD9CM:414.0 xref: ICD9CM:414.9 xref: MESH:D003324 xref: MESH:D003327 xref: MESH:D017202 xref: NCI:C35505 xref: NCI:C50625 xref: OMIM:300464 xref: OMIM:607339 xref: OMIM:608316 xref: OMIM:608318 xref: OMIM:608320 xref: OMIM:610947 xref: OMIM:611139 xref: OMIM:612030 xref: OMIM:614293 xref: SNOMEDCT_US_2020_09_01:194852007 xref: SNOMEDCT_US_2020_09_01:233822007 xref: SNOMEDCT_US_2020_09_01:41702007 xref: SNOMEDCT_US_2020_09_01:53741008 xref: UMLS_CUI:C0010054 xref: UMLS_CUI:C0010068 xref: UMLS_CUI:C0151744 xref: UMLS_CUI:C0264694 is_a: DOID:178 ! vascular disease [Term] id: DOID:3451 name: skin carcinoma namespace: disease_ontology def: "A skin cancer that is located_in tissues of the skin and develops from epithelial cells." [url:http\://www.cancer.gov/cancertopics/types/skin] {http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "carcinoma of skin" EXACT [] xref: NCI:C4914 xref: UMLS_CUI:C0699893 is_a: DOID:162 ! cancer [Term] id: DOID:3571 name: liver cancer namespace: disease_ontology alt_id: DOID:12300 alt_id: DOID:269 alt_id: DOID:7330 alt_id: DOID:915 alt_id: DOID:919 def: "A hepatobiliary system cancer that is located_in the liver." [url:http\://en.wikipedia.org/wiki/Liver] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "Ca liver - primary" EXACT [] synonym: "ca liver - primary" EXACT [] synonym: "hepatic cancer" EXACT [] synonym: "hepatic neoplasm" EXACT [] synonym: "malignant hepato-biliary neoplasm" EXACT [] synonym: "malignant neoplasm of liver" EXACT [] synonym: "malignant neoplasm of liver, not specified as primary or secondary" EXACT [] synonym: "malignant neoplasm of liver, primary" EXACT [] synonym: "malignant tumor of liver" EXACT [] synonym: "neoplasm of liver" EXACT [] synonym: "non-resectable primary hepatic malignant neoplasm" EXACT [] synonym: "primary liver cancer" EXACT [] synonym: "primary malignant neoplasm of Liver" EXACT [] synonym: "primary malignant neoplasm of liver" EXACT [] synonym: "Resectable malignant neoplasm of Liver" EXACT [] synonym: "resectable malignant neoplasm of the liver" EXACT [] xref: ICD10CM:C22.0 xref: ICD10CM:C22.9 xref: ICD9CM:155.0 xref: ICD9CM:155.2 xref: MESH:D008113 xref: NCI:C34803 xref: NCI:C7692 xref: SNOMEDCT_US_2020_09_01:126851005 xref: SNOMEDCT_US_2020_09_01:187771009 xref: SNOMEDCT_US_2020_09_01:93870000 xref: UMLS_CUI:C0023903 xref: UMLS_CUI:C0024620 xref: UMLS_CUI:C0345904 xref: UMLS_CUI:C0854795 is_a: DOID:162 ! cancer [Term] id: DOID:37 name: skin disease namespace: disease_ontology alt_id: DOID:1576 alt_id: DOID:1698 alt_id: DOID:187 alt_id: DOID:6486 alt_id: DOID:8948 def: "An integumentary system disease that is located_in skin." [url:http\://en.wikipedia.org/wiki/Skin_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "Genodermatosis" EXACT [] synonym: "skin and subcutaneous tissue disease" EXACT [] xref: ICD9CM:702 xref: MESH:D012871 xref: MESH:D012873 xref: NCI:C156032 xref: NCI:C3371 xref: SNOMEDCT_US_2020_09_01:201095006 xref: SNOMEDCT_US_2020_09_01:5613003 xref: SNOMEDCT_US_2020_09_01:95320005 xref: UMLS_CUI:C0029574 xref: UMLS_CUI:C0037274 xref: UMLS_CUI:C0037277 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:4 name: disease namespace: disease_ontology def: "A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [url:http\://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf] {http://purl.org/dc/elements/1.1/type="ECO:0007645"} subset: DO_RAD_slim subset: NCIthesaurus xref: MESH:D004194 xref: NCI:C2991 xref: SNOMEDCT_US_2020_09_01:64572001 xref: UMLS_CUI:C0012634 is_a: BFO:0000016 ! disposition [Term] id: DOID:403 name: mouth disease namespace: disease_ontology def: "A gastrointestinal system disease that is located_in the mouth." [url:http\://en.wikipedia.org/wiki/Oral_and_maxillofacial_pathology] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus xref: MESH:D009059 xref: NCI:C27641 xref: SNOMEDCT_US_2020_09_01:118938008 xref: UMLS_CUI:C0026636 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:4079 name: heart valve disease namespace: disease_ontology alt_id: DOID:989 def: "A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right)." [url:http\://en.wikipedia.org/wiki/Heart_valve_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "Valvular heart disease" EXACT [] xref: MESH:D006349 xref: MESH:D016127 xref: NCI:C45525 xref: SNOMEDCT_US_2020_09_01:368009 xref: SNOMEDCT_US_2020_09_01:398995000 xref: UMLS_CUI:C0018824 xref: UMLS_CUI:C0079485 is_a: DOID:114 ! heart disease [Term] id: DOID:409 name: liver disease namespace: disease_ontology alt_id: DOID:2164 alt_id: DOID:2165 alt_id: DOID:46 subset: DO_RAD_slim subset: NCIthesaurus synonym: "disorder of liver" EXACT [] synonym: "hepatic disorder" EXACT [] xref: ICD10CM:K76.9 xref: ICD9CM:573.9 xref: MESH:D008107 xref: NCI:C3196 xref: SNOMEDCT_US_2020_09_01:62857009 xref: UMLS_CUI:C0023895 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:4737 name: somatoform disorder namespace: disease_ontology alt_id: DOID:10133 alt_id: DOID:144 def: "A disease of mental health that involves physical symptoms suggesting a physical illness where the biological or medical cause of the symptoms is indeterminate." [url:http\://allpsych.com/disorders/somatoform/index.html, url:http\://en.wikipedia.org/wiki/Somatoform_disorder] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "physiological malfunction arising from mental factor" EXACT [] synonym: "psychophysiologic disorder" EXACT [] synonym: "psychosomatic disorder" EXACT [] xref: ICD10CM:F45 xref: ICD10CM:F45.0 xref: ICD9CM:300.8 xref: ICD9CM:300.81 xref: MESH:D013001 xref: NCI:C34956 xref: SNOMEDCT_US_2020_09_01:192430009 xref: SNOMEDCT_US_2020_09_01:60368009 xref: UMLS_CUI:C0037650 xref: UMLS_CUI:C0520482 is_a: DOID:150 ! disease of mental health [Term] id: DOID:4961 name: bone marrow disease namespace: disease_ontology subset: DO_RAD_slim subset: NCIthesaurus synonym: "bone marrow disorder" EXACT [] xref: MESH:D001855 xref: NCI:C34433 xref: SNOMEDCT_US_2020_09_01:127035006 xref: UMLS_CUI:C0005956 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:5041 name: esophageal cancer namespace: disease_ontology alt_id: DOID:10291 alt_id: DOID:10292 alt_id: DOID:10448 alt_id: DOID:1102 alt_id: DOID:1104 def: "A gastrointestinal system cancer that is located_in the esophagus." [url:http\://cancergenome.nih.gov/cancersselected/stomach-esophagealcancer, url:http\://en.wikipedia.org/wiki/Esophagus] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus subset: TopNodes_DOcancerslim synonym: "Ca lower third oesophagus" EXACT [] synonym: "Ca middle third oesophagus" EXACT [] synonym: "esophagus cancer" EXACT [] synonym: "malignant neoplasm of distal third of esophagus" EXACT [] synonym: "malignant neoplasm of lower third of oesophagus" EXACT [] synonym: "malignant neoplasm of middle third of oesophagus" EXACT [] synonym: "malignant neoplasm of proximal third of esophagus" EXACT [] synonym: "malignant neoplasm of upper third esophagus" EXACT [] synonym: "malignant tumor of abdominal esophagus" EXACT [] synonym: "malignant tumor of Distal Third of esophagus" EXACT [] synonym: "malignant tumor of Proximal Third of esophagus" EXACT [] synonym: "malignant tumor of the middle Third of the esophagus" EXACT [] xref: GARD:6383 xref: ICD10CM:C15.3 xref: ICD10CM:C15.4 xref: ICD10CM:C15.5 xref: ICD9CM:150.2 xref: ICD9CM:150.3 xref: ICD9CM:150.4 xref: ICD9CM:150.5 xref: ICD9CM:150.8 xref: MESH:D004938 xref: NCI:C3028 xref: NCI:C3533 xref: NCI:C3534 xref: NCI:C3535 xref: NCI:C4764 xref: OMIM:133239 xref: SNOMEDCT_US_2020_09_01:126817006 xref: SNOMEDCT_US_2020_09_01:187729008 xref: SNOMEDCT_US_2020_09_01:93656003 xref: SNOMEDCT_US_2020_09_01:93877002 xref: SNOMEDCT_US_2020_09_01:93895004 xref: SNOMEDCT_US_2020_09_01:94119000 xref: UMLS_CUI:C0014859 xref: UMLS_CUI:C0153413 xref: UMLS_CUI:C0153414 xref: UMLS_CUI:C0153415 xref: UMLS_CUI:C0153416 xref: UMLS_CUI:C0496775 is_a: DOID:162 ! cancer [Term] id: DOID:535 name: sleep disorder namespace: disease_ontology alt_id: DOID:9028 def: "A disease of mental health that involves disruption of sleep patterns." [url:http\://en.wikipedia.org/wiki/Sleep_disorder] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_FlyBase_slim subset: DO_RAD_slim synonym: "Non-organic sleep disorder" EXACT [] xref: ICD9CM:307.4 xref: UMLS_CUI:C0154564 is_a: DOID:150 ! disease of mental health [Term] id: DOID:5353 name: colonic disease namespace: disease_ontology alt_id: DOID:10758 def: "A intestinal disease located in the colon." [url:https\://www.nature.com/subjects/colonic-diseases] subset: DO_RAD_slim synonym: "colon disorder" EXACT [] xref: MESH:D003108 xref: SNOMEDCT_US_2020_09_01:128524007 xref: UMLS_CUI:C0009373 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:557 name: kidney disease namespace: disease_ontology alt_id: DOID:11705 def: "A urinary system disease that is located_in the kidney." [url:http\://www.nlm.nih.gov/medlineplus/kidneydiseases.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644"} subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "impaired renal function disease" EXACT [] synonym: "nephropathy" EXACT [] xref: EFO:0003086 xref: ICD10CM:N08 xref: MESH:D007674 xref: NCI:C3149 xref: SNOMEDCT_US_2020_09_01:266612003 xref: UMLS_CUI:C0022658 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:5614 name: eye disease namespace: disease_ontology alt_id: DOID:2933 def: "An eye and adnexa disease that is located_in the eye." [url:http\://en.wikipedia.org/wiki/Eye_disease] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:H44 xref: ICD9CM:379.90 xref: MESH:D005128 xref: NCI:C26767 xref: SNOMEDCT_US_2020_09_01:371409005 xref: UMLS_CUI:C0015397 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:5621 name: histiocytic and dendritic cell cancer namespace: disease_ontology def: "A sarcoma and hematologic cancer that derives_from follicular lymphoma." [url:http\://www.springerlink.com/content/h9wrn7p72x26q035/] {http://purl.org/dc/elements/1.1/type="ECO:0007645"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "histiocytic and dendritic cell" EXACT [] xref: NCI:C9294 xref: UMLS_CUI:C1334030 is_a: DOID:2531 ! hematologic cancer [Term] id: DOID:6199 name: cornea cancer namespace: disease_ontology alt_id: DOID:12757 subset: DO_RAD_slim subset: NCIthesaurus synonym: "Corneal tumor" EXACT [] synonym: "malignant Corneal tumor" EXACT [] synonym: "malignant neoplasm of cornea" EXACT [] synonym: "malignant tumor of cornea" EXACT [] synonym: "neoplasm of cornea" EXACT [] xref: ICD10CM:C69.1 xref: ICD9CM:190.4 xref: NCI:C3565 xref: NCI:C4361 xref: SNOMEDCT_US_2020_09_01:126997008 xref: SNOMEDCT_US_2020_09_01:93766000 xref: UMLS_CUI:C0153629 xref: UMLS_CUI:C0339304 is_a: DOID:162 ! cancer [Term] id: DOID:630 name: genetic disease namespace: disease_ontology def: "A disease that has_material_basis_in genetic variations in the human genome." [url:http\://ghr.nlm.nih.gov/] {http://purl.org/dc/elements/1.1/type="ECO:0007637"} subset: DO_RAD_slim subset: NCIthesaurus xref: MESH:D030342 xref: NCI:C3101 xref: SNOMEDCT_US_2020_09_01:32895009 xref: UMLS_CUI:C0019247 is_a: DOID:4 ! disease [Term] id: DOID:657 name: adenoma namespace: disease_ontology alt_id: DOID:2655 def: "A cell type benign neoplasm that is composed_of epithelial tissue in which tumor cells form glands or glandlike structures." [url:http\://coloncancer.about.com/od/glossaries/g/Adenoma.htm, url:http\://en.wikipedia.org/wiki/Adenoma] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "acinar cell adenoma" EXACT [] synonym: "acinic cell adenoma" EXACT [] synonym: "adenomas" EXACT [] xref: MESH:D000236 xref: NCI:C2855 xref: NCI:C4196 xref: SNOMEDCT_US_2020_09_01:443416007 xref: SNOMEDCT_US_2020_09_01:79041005 xref: UMLS_CUI:C0001430 xref: UMLS_CUI:C0334389 is_a: DOID:0060072 ! benign neoplasm property_value: exactMatch MESH:D000236 xsd:string [Term] id: DOID:7 name: disease of anatomical entity namespace: disease_ontology alt_id: DOID:1 alt_id: DOID:2 alt_id: DOID:5 alt_id: DOID:71 alt_id: DOID:72 alt_id: DOID:8 def: "A disease that manifests in a defined anatomical structure." [url:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic] {http://purl.org/dc/elements/1.1/type="ECO:0007643"} subset: DO_RAD_slim is_a: DOID:4 ! disease [Term] id: DOID:75 name: lymphatic system disease namespace: disease_ontology def: "An immune system disease that is located_in the lymphatic system." [url:http\://en.wikipedia.org/wiki/Lymphatic_disease, url:http\://www.nlm.nih.gov/medlineplus/lymphaticdiseases.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644", http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim synonym: "Adenopathy" EXACT [] synonym: "disease of lympoid system" EXACT [] synonym: "disorder of lymph node and lymphatics" EXACT [] synonym: "disorder of lymphatic system" EXACT [] synonym: "disorder of lymphoid system" EXACT [] synonym: "Lymphangiopathy" EXACT [] synonym: "Lymphatic disease" EXACT [] synonym: "Lymphatic disorder" EXACT [] synonym: "lymphatic disorder" EXACT [] synonym: "lympoid system disease" EXACT [] xref: MESH:D008206 xref: SNOMEDCT_US_2020_09_01:266326002 xref: UMLS_CUI:C0024228 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:7757 name: childhood leukemia namespace: disease_ontology def: "A leukemia that occurs in children." [url:http\://www.nlm.nih.gov/medlineplus/leukemiachildhood.html] {http://purl.org/dc/elements/1.1/type="ECO:0007644"} subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus xref: NCI:C4989 xref: UMLS_CUI:C1332977 is_a: DOID:1240 ! leukemia [Term] id: DOID:83 name: cataract namespace: disease_ontology def: "A lens disease characterized by clouding of the lens inside the eye which leads to a decrease in vision." [url:http\://en.wikipedia.org/wiki/Cataract, url:https\://www.ncbi.nlm.nih.gov/pubmed/10414631] {http://purl.org/dc/elements/1.1/type="ECO:0007645", http://purl.org/dc/elements/1.1/type="ECO:0007638"} comment: Xref MGI. subset: DO_RAD_slim xref: ICD10CM:H26 xref: ICD9CM:366.8 xref: OMIM:601371 xref: OMIM:PS116200 xref: SNOMEDCT_US_2020_09_01:193620000 xref: UMLS_CUI:C0029531 is_a: DOID:5614 ! eye disease property_value: exactMatch MESH:D002386 xsd:string [Term] id: DOID:850 name: lung disease namespace: disease_ontology alt_id: DOID:11894 alt_id: DOID:11895 alt_id: DOID:29 alt_id: DOID:766 def: "A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide." [url:http\://www.niehs.nih.gov/health/topics/conditions/lung-disease/index.cfm, url:http\://www.nlm.nih.gov/medlineplus/ency/article/000066.htm] {http://purl.org/dc/elements/1.1/type="ECO:0007640", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Updating out dated CUI and removing lung abscess as a synonym. subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:J98.4 xref: MESH:D008171 xref: NCI:C3198 xref: SNOMEDCT_US_2020_09_01:266374002 xref: UMLS_CUI:C0024115 is_a: DOID:0050161 ! lower respiratory tract disease [Term] id: DOID:8552 name: chronic myeloid leukemia namespace: disease_ontology alt_id: DOID:8551 alt_id: DOID:8606 def: "A myeloid leukemia that is characterized by over production of white blood cells." [url:http\://www.cancer.gov/dictionary?CdrID=46755] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: OMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "chronic granulocytic leukaemia" EXACT [] synonym: "chronic granulocytic leukemia" EXACT [] synonym: "chronic myelogenous leukaemia" EXACT [] synonym: "chronic myelogenous leukemia" EXACT [] synonym: "chronic myeloid leukaemia" EXACT [] synonym: "CML" EXACT [] synonym: "CML - chronic Myelogenous Leukemia" EXACT [] synonym: "Myeloid Leukemia, chronic" EXACT [] xref: EFO:0000339 xref: GARD:6105 xref: ICD9CM:205.1 xref: KEGG:05220 xref: OMIM:608232 xref: ORDO:521 xref: SNOMEDCT_US_2020_09_01:154592009 xref: UMLS_CUI:C0023473 is_a: DOID:8692 ! myeloid leukemia [Term] id: DOID:8692 name: myeloid leukemia namespace: disease_ontology alt_id: DOID:8878 alt_id: DOID:8879 alt_id: DOID:8910 alt_id: DOID:9066 alt_id: DOID:9126 def: "A leukemia that is located_in myeloid tissue." [url:http\://en.wikipedia.org/wiki/Myeloid_leukemia] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus synonym: "leukaemia myelogenous" EXACT [] synonym: "leukemia myelogenous" EXACT [] synonym: "myeloid granulocytic leukaemia" EXACT [] synonym: "myeloid granulocytic leukemia" EXACT [] synonym: "myeloid leukaemia" EXACT [] synonym: "Non-Lymphocytic Leukemia" EXACT [] xref: GARD:8226 xref: ICD10CM:C92 xref: ICD9CM:205 xref: MESH:D007951 xref: NCI:C3172 xref: SNOMEDCT_US_2020_09_01:269631008 xref: UMLS_CUI:C0023470 is_a: DOID:1240 ! leukemia [Term] id: DOID:8719 name: in situ carcinoma namespace: disease_ontology alt_id: DOID:8793 alt_id: DOID:8821 def: "A carcinoma that is an early development defined by the absence of invasion of surrounding tissues." [url:http\://en.wikipedia.org/wiki/Carcinoma_in_situ] {http://purl.org/dc/elements/1.1/type="ECO:0007638"} subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:D09.9 xref: ICD9CM:230-234.99 xref: MESH:D002278 xref: NCI:C2917 xref: SNOMEDCT_US_2020_09_01:109355002 xref: UMLS_CUI:C0007099 is_a: DOID:0060071 ! pre-malignant neoplasm [Term] id: DOID:8761 name: acute megakaryocytic leukemia namespace: disease_ontology alt_id: DOID:9009 def: "An acute myeloid leukemia that derives from blood-forming tissue in which megakaryocytes proliferate in the bone marrow and circulate in the blood in large numbers." [url:https\://en.wikipedia.org/wiki/Acute_megakaryoblastic_leukemia, url:https\://pubmed.ncbi.nlm.nih.gov/26228843/, url:https\://www.orpha.net/data/patho/GB/uk-AMLM7.pdf] subset: DO_RAD_slim subset: NCIthesaurus synonym: "Megakaryocytic myelosis" EXACT [] synonym: "Thrombocytic leukaemia" EXACT [] xref: GARD:524 xref: ICD10CM:C94.2 xref: ICD9CM:207.2 xref: MESH:D007947 xref: NCI:C3170 xref: SNOMEDCT_US_2020_09_01:52220008 xref: UMLS_CUI:C0023462 is_a: DOID:9119 ! acute myeloid leukemia [Term] id: DOID:9119 name: acute myeloid leukemia namespace: disease_ontology alt_id: DOID:9118 alt_id: DOID:9171 def: "A myeloid leukemia that is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells." [url:http\://cancergenome.nih.gov/cancersselected/acutemyeloidleukemia, url:http\://en.wikipedia.org/wiki/Acute_myeloid_leukemia, url:http\://www.cancer.gov/dictionary?cdrid=44363, url:https\://www.cancer.org/cancer/acute-myeloid-leukemia/detection-diagnosis-staging/how-classified.html] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007638", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: OMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_RAD_slim subset: NCIthesaurus synonym: "acute myeloblastic leukaemia" EXACT [] synonym: "acute myeloblastic leukemia" EXACT [] synonym: "acute myelogenous leukaemia" EXACT [] synonym: "acute myelogenous leukemia" EXACT [] synonym: "acute myeloid leukaemia" EXACT [] synonym: "AML - acute Myeloid Leukemia" EXACT [] synonym: "Leukemia, Myelocytic, acute" EXACT [] xref: GARD:12757 xref: ICD10CM:C92.0 xref: ICD9CM:205.0 xref: KEGG:05221 xref: MESH:D015470 xref: NCI:C3171 xref: OMIM:601626 xref: SNOMEDCT_US_2020_09_01:91861009 xref: UMLS_CUI:C0023467 is_a: DOID:8692 ! myeloid leukemia [Term] id: DOID:9256 name: colorectal cancer namespace: disease_ontology def: "A large intestine cancer that is located_in the colon and/or located_in the rectum." [url:http\://www.cancer.gov/dictionary?CdrID=444983] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Xref MGI.\nOMIM mapping confirmed by DO. [SN]. subset: DO_cancer_slim subset: DO_FlyBase_slim subset: DO_RAD_slim xref: ICD10CM:C18.9 xref: KEGG:05210 xref: MESH:D015179 xref: NCI:C2956 xref: NCI:C4978 xref: OMIM:114500 xref: SNOMEDCT_US_2020_09_01:126837005 xref: SNOMEDCT_US_2020_09_01:93854002 xref: UMLS_CUI:C0009404 xref: UMLS_CUI:C0346629 is_a: DOID:162 ! cancer [Term] id: DOID:9637 name: stomatitis namespace: disease_ontology def: "A mouth disease that is characterized by inflammation of the mouth and lips." [url:https\://en.wikipedia.org/wiki/Stomatitis] subset: DO_RAD_slim subset: NCIthesaurus xref: ICD10CM:K12.1 xref: MESH:D013280 xref: NCI:C26887 xref: SNOMEDCT_US_2020_09_01:95361005 xref: UMLS_CUI:C0038362 is_a: DOID:403 ! mouth disease [Term] id: DOID:9952 name: acute lymphoblastic leukemia namespace: disease_ontology alt_id: DOID:5600 def: "A acute leukemia that is characterized by over production of lymphoblasts." [url:http\://www.cancer.gov/dictionary?CdrID=46332] {http://purl.org/dc/elements/1.1/type="ECO:0007641", http://purl.org/dc/elements/1.1/type="ECO:0007637"} comment: Xref MGI. subset: DO_cancer_slim subset: DO_RAD_slim subset: DO_rare_slim subset: NCIthesaurus synonym: "acute lymphoblastic leukaemia" EXACT [] synonym: "acute lymphoblastic leukemia" EXACT [] synonym: "acute lymphocytic leukaemia" EXACT [] synonym: "ALL" EXACT [] synonym: "precursor lymphoblastic lymphoma/leukemia" EXACT [] xref: EFO:0000220 xref: GARD:522 xref: ICD10CM:C91.00 xref: ICD9CM:204.0 xref: NCI:C3167 xref: NCI:C7055 xref: OMIM:247640 xref: OMIM:613065 xref: ORDO:513 xref: SNOMEDCT_US_2020_09_01:128822004 xref: UMLS_CUI:C0023449 xref: UMLS_CUI:C1335469 is_a: DOID:1037 ! lymphoid leukemia [Term] id: ENVO:00000000 name: geographic feature comment: This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass. subset: envoPolar synonym: "macroscopic spatial feature" EXACT [] xref: https://en.wikipedia.org/wiki/Geographic_feature is_a: ENVO:01000813 ! astronomical body part [Term] id: ENVO:00000002 name: anthropogenic geographic feature def: "An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature." [ORCID:0000-0002-4366-3088] synonym: "man-made feature" RELATED [] synonym: "manmade feature" RELATED [] xref: FTT:78 xref: TGN:50001 is_a: ENVO:00000000 ! geographic feature intersection_of: ENVO:00000000 ! geographic feature intersection_of: RO:0002354 ENVO:01000952 ! formed as result of anthropisation relationship: RO:0002354 ENVO:01000952 ! formed as result of anthropisation [Term] id: ENVO:00000012 name: hydrographic feature def: "A geographical feature associated with water." [MA:ma] subset: envoPolar synonym: "fluvial feature" RELATED [ADL:FTT] xref: FTT:131 xref: FTT:280 xref: FTT:711 xref: FTT:761 xref: FTT:824 xref: FTT:825 xref: FTT:826 xref: FTT:827 xref: FTT:828 xref: FTT:829 xref: Geonames:H.OVF is_a: ENVO:00000000 ! geographic feature [Term] id: ENVO:00000015 name: ocean alt_id: LTER:695 {xref="https://vocab.lternet.edu/vocab/vocab/index.php?tema=695&/oceans"} def: "A marine water body which is constitutes the majority of an astronomical body's hydrosphere." [] subset: envoMarine subset: envoPolar synonym: "Ocean" EXACT [NASA:earthrealm] synonym: "ocean" EXACT [Geonames:feature] synonym: "ocean region" RELATED [ADL:FTT] xref: EcoLexicon:ocean xref: FTT:1019 xref: FTT:943 xref: Geonames:H.OCN xref: https://en.wikipedia.org/wiki/Ocean xref: SWEETRealm:Ocean xref: TGN:21102 is_a: ENVO:00001999 ! marine water body is_a: ENVO:01001319 ! saline water body relationship: composed_primarily_of ENVO:00002149 ! sea water [Term] id: ENVO:00000016 name: sea def: "A large expanse of saline water usually connected with an ocean." [https://en.wikipedia.org/wiki/Sea] subset: envoMarine subset: envoPolar synonym: "channel" NARROW [] synonym: "closed sea" NARROW [USGS:SDTS] synonym: "marginal sea" NARROW [USGS:SDTS] synonym: "open sea" NARROW [USGS:SDTS] synonym: "open sound" NARROW [USGS:SDTS] synonym: "open water" NARROW [USGS:SDTS] synonym: "Sea" EXACT [NASA:earthrealm] synonym: "sea" EXACT [Geonames:feature] synonym: "sea" EXACT [ADL:FTT] xref: EcoLexicon:sea xref: FTT:233 xref: FTT:830 xref: Geonames:H.SEA xref: https://en.wikipedia.org/wiki/Sea xref: TGN:21103 is_a: ENVO:00001999 ! marine water body is_a: ENVO:01001319 ! saline water body relationship: composed_primarily_of ENVO:00002149 ! sea water [Term] id: ENVO:00000017 name: saline hydrographic feature namespace: ENVO def: "A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L)." [https://en.wikipedia.org/wiki/Salinity] is_a: ENVO:00000012 ! hydrographic feature [Term] id: ENVO:00000019 name: saline lake def: "A lake whose water contains a considerable concentration of dissolved salts." [MA:ma] synonym: "salina" RELATED [USGS:SDTS] synonym: "salt lake" EXACT [USGS:SDTS] synonym: "soda lake" RELATED [] xref: FTT:221 xref: FTT:907 xref: Geonames:H.LKN xref: Geonames:H.LKSN xref: https://en.wikipedia.org/wiki/Saline_lake xref: TGN:21116 is_a: ENVO:00000020 ! lake is_a: ENVO:01001319 ! saline water body intersection_of: ENVO:00000020 ! lake intersection_of: composed_primarily_of ENVO:00002010 ! saline water [Term] id: ENVO:00000020 name: lake alt_id: LTER:278 {xref="https://vocab.lternet.edu/vocab/vocab/index.php?tema=278&/lakes"} def: "A body of water or other liquid of considerable size contained in a depression on a landmass." [https://en.wikipedia.org/wiki/Lake] subset: envoPolar synonym: "broad" RELATED [] synonym: "catch basin" NARROW [USGS:SDTS] synonym: "llyn" RELATED [] synonym: "loch" RELATED [] synonym: "lochan" RELATED [ADL:FTT] synonym: "lough" RELATED [] synonym: "mere" RELATED [] synonym: "mortlake" RELATED [USGS:SDTS] synonym: "open water" NARROW [USGS:SDTS] synonym: "pasteuer lake" RELATED [USGS:SDTS] synonym: "tarn" NARROW [ADL:FTT] xref: EcoLexicon:lake xref: FTT:221 xref: FTT:704 xref: FTT:909 xref: Geonames:H.LK xref: Geonames:H.LKS xref: SPIRE:Lake_or_pond xref: SWEETRealm:Lake xref: TGN:21114 xref: TGN:21115 is_a: ENVO:01000617 ! lentic water body relationship: ENVO:01001307 ENVO:01000635 ! partially_surrounded_by planetary landmass [Term] id: ENVO:00000063 name: water body def: "An accumulation of water of varying size." [https://en.wikipedia.org/wiki/Body_of_water] comment: https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water. synonym: "aquatic feature" EXACT [] synonym: "bodies of water" EXACT [Getty:TGN] synonym: "body of water" EXACT [ADL:FTT] synonym: "body of water" EXACT [Getty:TGN] synonym: "hydrographic feature" BROAD [ADL:FTT] synonym: "waterbody" EXACT [] xref: EcoLexicon:waterbody xref: FTT:131 xref: FTT:280 xref: FTT:827 xref: https://en.wikipedia.org/wiki/Water_body xref: SWEETRealm:BodyOfWater xref: TGN:21100 xref: TGN:21101 is_a: ENVO:01000685 ! water mass relationship: composed_primarily_of CHEBI:15377 ! water relationship: part_of ENVO:01000819 ! hydrosphere [Term] id: ENVO:00000097 name: desert area def: "A region rendered barren or partially barren by environmental extremes, especially by low rainfall." [USGS:SDTS] subset: envoPolar synonym: "arid region" RELATED [ADL:FTT] xref: EcoLexicon:desert xref: FTT:1 xref: FTT:188 xref: Geonames:T.DSRT xref: https://en.wikipedia.org/wiki/Desert xref: LTER:147 xref: SWEETRealm:Desert xref: TGN:21201 is_a: ENVO:01000752 ! area of barren land intersection_of: ENVO:01000752 ! area of barren land intersection_of: has_quality ENVO:01000230 ! arid relationship: has_quality ENVO:01000230 ! arid [Term] id: ENVO:00000100 name: valley def: "A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate." [ADL:FTT, https://en.wikipedia.org/wiki/Valley] comment: Valleys are typically located between hills our mountains. synonym: "chasm" NARROW [USGS:SDTS] synonym: "coulee" NARROW [USGS:SDTS] synonym: "dale" NARROW [USGS:SDTS] synonym: "glacial gorge" NARROW [USGS:SDTS] synonym: "glacial trough" NARROW [USGS:SDTS] synonym: "glen" RELATED [ADL:FTT] synonym: "glen" RELATED [USGS:SDTS] synonym: "goe" RELATED [USGS:SDTS] synonym: "gorge" RELATED [USGS:SDTS] synonym: "gorge" RELATED [Geonames:feature] synonym: "graben" RELATED [USGS:SDTS] synonym: "gulch" NARROW [USGS:SDTS] synonym: "gully" NARROW [USGS:SDTS] synonym: "gully" NARROW [Getty:TGN] synonym: "hollow" RELATED [Getty:TGN] synonym: "hollow" RELATED [ADL:FTT] synonym: "hollow" RELATED [USGS:SDTS] synonym: "lavaka" RELATED [] synonym: "median valley" NARROW [Geonames:feature] synonym: "median valley" NARROW [ADL:FTT] synonym: "moat" RELATED [USGS:SDTS] synonym: "ravine" RELATED [USGS:SDTS] synonym: "re-entrant" RELATED [USGS:SDTS] synonym: "seachannel" RELATED [USGS:SDTS] synonym: "shelf valley" NARROW [Geonames:feature] synonym: "strath" RELATED [USGS:SDTS] synonym: "trench" RELATED [USGS:SDTS] synonym: "vale" RELATED [] synonym: "water gap" RELATED [USGS:SDTS] xref: EcoLexicon:valley xref: FTT:158 xref: FTT:166 xref: FTT:418 xref: FTT:761 xref: FTT:811 xref: FTT:949 xref: Geonames:T.GRGE xref: Geonames:T.VAL xref: Geonames:T.VALS xref: SWEETRealm:Valley xref: TGN:21425 xref: TGN:21451 xref: TGN:21452 xref: TGN:21453 is_a: ENVO:03000015 ! geographic basin relationship: has_quality PATO:0001154 ! elongated relationship: RO:0002354 ENVO:02500028 ! formed as result of planetary erosion [Term] id: ENVO:00000131 name: glacial feature def: "A hydrographic feature characterized by the dominance of snow or ice." [MA:ma] comment: Likely to be depopulated and "glacial" made into a quality or similar. subset: envoPolar synonym: "glacer" NARROW [ADL:FTT] synonym: "glacial landform" RELATED [Getty:TGN] synonym: "glacier feature" RELATED [ADL:FTT] synonym: "Ice" RELATED [NASA:earthrealm] synonym: "LandIce" RELATED [NASA:earthrealm] xref: EcoLexicon:ice xref: FTT:648 xref: SWEETRealm:LandIce xref: TGN:21410 is_a: BFO:0000040 ! material entity [Term] id: ENVO:00000134 name: permafrost def: "Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years." [https://en.wikipedia.org/wiki/Permafrost, https://orcid.org/0000-0003-4808-4736] comment: Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material. subset: envoPolar synonym: "Permafrost" EXACT [NASA:earthrealm] xref: EcoLexicon:permafrost xref: http://sweetontology.net/realmSoil/Permafrost xref: https://en.wikipedia.org/wiki/Permafrost xref: LTER:408 is_a: ENVO:00010483 ! environmental material relationship: has_quality PATO:0001306 ! decreased temperature [Term] id: ENVO:00000191 name: solid astronomical body part def: "A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes." [https://en.wikipedia.org/wiki/Landform] synonym: "geological feature" RELATED [ADL:FTT] synonym: "physiographic feature" RELATED [] xref: EcoLexicon:landform xref: EcoLexicon:landforms xref: FTT:754 xref: FTT:96 xref: SWEETRealm:Landform xref: TGN:21400 xref: TGN:21401 is_a: ENVO:01000813 ! astronomical body part intersection_of: ENVO:01000813 ! astronomical body part intersection_of: composed_primarily_of ENVO:01000814 ! solid environmental material relationship: composed_primarily_of ENVO:01000814 ! solid environmental material [Term] id: ENVO:00000194 name: scree namespace: ENVO def: "Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders." [https://en.wikipedia.org/wiki/Scree] synonym: "TALUS" RELATED [USGS:SDTS] synonym: "talus slope" RELATED [Geonames:feature] synonym: "talus slope" RELATED [Getty:TGN] xref: EcoLexicon:scree xref: FTT:1078 xref: FTT:96 xref: Geonames:T.TAL xref: https://en.wikipedia.org/wiki/Scree xref: SWEETRealm:Talus xref: TGN:21508 is_a: ENVO:00010483 ! environmental material intersection_of: ENVO:00010483 ! environmental material intersection_of: has_part ENVO:00000339 ! piece of rock intersection_of: RO:0001000 ENVO:00001995 ! derives from rock relationship: has_part ENVO:00000339 ! piece of rock relationship: RO:0001000 ENVO:00001995 ! derives from rock [Term] id: ENVO:00000248 name: glacial valley namespace: ENVO def: "A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section." [MA:ma] subset: envoPolar synonym: "valley" RELATED [USGS:SDTS] xref: https://en.wikipedia.org/wiki/Glacial_valley is_a: ENVO:00000100 ! valley [Term] id: ENVO:00000309 name: depression def: "A landform sunken or depressed below the surrounding area." [https://en.wikipedia.org/wiki/Depression_%28geology%29] synonym: "barrier basin" RELATED [USGS:SDTS] synonym: "depression" RELATED [Geonames:feature] synonym: "non tidal basin" RELATED [USGS:SDTS] synonym: "pan" RELATED [Geonames:feature] synonym: "pan" RELATED [Getty:TGN] synonym: "pan (geologic)" RELATED [ADL:FTT] synonym: "pans" RELATED [Geonames:feature] synonym: "tidal basin" RELATED [USGS:SDTS] xref: EcoLexicon:depression xref: FTT:175 xref: FTT:215 xref: FTT:216 xref: Geonames:T.DPR xref: Geonames:T.PAN xref: Geonames:T.PANS xref: SWEETRealm:Depression xref: TGN:21454 xref: TGN:21497 xref: TGN:21521 is_a: ENVO:00000191 ! solid astronomical body part relationship: has_part ENVO:00002000 ! slope relationship: has_quality PATO:0001689 ! decreased elevation relationship: has_quality PATO:0002143 ! sloped downward property_value: editor_note "Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486" xsd:string [Term] id: ENVO:00000339 name: piece of rock def: "An abiotic mesoscopic feature made of the mineral material of the crust of the Earth." [MA:ma] xref: FTT:1010 xref: FTT:145 xref: Geonames:T.RK xref: Geonames:T.RKS xref: TGN:21444 is_a: ENVO:01001687 ! mass of solid material intersection_of: ENVO:01001687 ! mass of solid material intersection_of: composed_primarily_of ENVO:00001995 ! rock relationship: composed_primarily_of ENVO:00001995 ! rock [Term] id: ENVO:00000428 name: biome alt_id: LTER:809 {xref="https://vocab.lternet.edu/vocab/vocab/index.php?tema=809&/biomes"} def: "A biome is an ecosystem to which resident ecological communities have evolved adaptations." [DOI:10.1186/2041-1480-4-43, https://en.wikipedia.org/wiki/Biome] comment: There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. synonym: "EcosytemType" RELATED [NASA:earthrealm] synonym: "major habitat type" EXACT [WWF:Biome] xref: EcoLexicon:biome is_a: ENVO:01001110 ! ecosystem disjoint_from: ENVO:01000276 ! ecoregion disjoint_from: ENVO:01000280 ! ecozone relationship: has_component ENVO:01000739 {minCardinality="2"} ! habitat relationship: has_part ENVO:01000739 ! habitat relationship: part_of ENVO:01000817 ! biosphere relationship: RO:0002507 PCO:0000002 ! determined by ecological community [Term] id: ENVO:00000446 name: terrestrial biome def: "A biome which is primarily or completely situated on a landmass." [https://en.wikipedia.org/wiki/Biome#Terrestrial_biomes] synonym: "terrestrial realm" RELATED [] xref: LTER:798 xref: SPIRE:Terrestrial is_a: ENVO:00000428 ! biome [Term] id: ENVO:00000447 name: marine biome def: "An aquatic biome which is determined by a marine water body." [https://en.wikipedia.org/wiki/Ocean, https://orcid.org/0000-0002-4366-3088, ISBN:978-0-618-45504-1, MA:ma] comment: This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. subset: envoPolar synonym: "marine realm" RELATED [] xref: SPIRE:Marine is_a: ENVO:00002030 ! aquatic biome is_a: ENVO:01001788 ! marine ecosystem intersection_of: ENVO:00002030 ! aquatic biome intersection_of: RO:0002507 ENVO:00001999 ! determined by marine water body [Term] id: ENVO:00001995 name: rock def: "A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids." [https://en.wikipedia.org/wiki/Rock_(geology), MA:ma] comment: From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. xref: EcoLexicon:rock xref: FTT:1010 xref: FTT:145 xref: Geonames:T.RK xref: Geonames:T.RKS xref: https://en.wikipedia.org/wiki/Rock xref: SWEETRealm:Rock xref: TGN:21444 is_a: ENVO:01000814 ! solid environmental material disjoint_from: ENVO:01000256 ! mineral material relationship: has_quality PATO:0000386 ! hard [Term] id: ENVO:00001998 name: soil def: "Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms." [https://en.wikipedia.org/wiki/Soil] comment: 'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil\n\n" The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants.\n\nThe lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280 subset: EnvO-Lite-GSC synonym: "regolith" BROAD [] xref: https://en.wikipedia.org/wiki/Soil xref: LTER:535 xref: SPIRE:Soil xref: SWEETRealm:Soil is_a: ENVO:00010483 ! environmental material relationship: has_part ENVO:00002982 ! clay relationship: has_part ENVO:01000016 ! silt relationship: has_part ENVO:01000017 ! sand relationship: has_part ENVO:01000155 ! organic material relationship: has_part ENVO:01000256 ! mineral material relationship: has_quality PATO:0000984 ! porous relationship: part_of ENVO:01000820 ! pedosphere property_value: editor_note "The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]" xsd:string [Term] id: ENVO:00001999 name: marine water body def: "A significant accumulation of water which is part of a marine biome." [] comment: Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review. synonym: "body of marine water" EXACT [] synonym: "marine waterbody" EXACT [] is_a: ENVO:01000044 ! marine pelagic feature is_a: ENVO:01000617 ! lentic water body is_a: ENVO:01001308 ! hydroform relationship: part_of ENVO:00000447 ! marine biome [Term] id: ENVO:00002000 name: slope def: "A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land." [MA:ma] synonym: "flank" RELATED [] synonym: "side" RELATED [] xref: EcoLexicon:slope xref: https://en.wikipedia.org/wiki/Slope xref: SWEETRealm:Slope is_a: ENVO:00000191 ! solid astronomical body part relationship: has_quality PATO:0001481 ! sloped [Term] id: ENVO:00002005 name: air def: "The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth." [https://en.wikipedia.org/wiki/Air] subset: EnvO-Lite-GSC subset: envoPolar xref: EcoLexicon:air xref: https://en.wikipedia.org/wiki/Air xref: LTER:18 xref: SWEETRealm:Air is_a: ENVO:01000797 ! gaseous environmental material relationship: composed_primarily_of CHEBI:17997 ! dinitrogen relationship: has_part CHEBI:15379 ! dioxygen relationship: has_part CHEBI:16526 ! carbon dioxide relationship: has_part CHEBI:36908 ! argon molecular entity relationship: has_part ENVO:01000266 ! water vapour [Term] id: ENVO:00002006 name: liquid water def: "An environmental material primarily composed of dihydrogen oxide in its liquid form." [MA:ma] synonym: "water" BROAD [] xref: EcoLexicon:water xref: https://en.wikipedia.org/wiki/Water xref: LTER:617 is_a: ENVO:01000815 ! liquid environmental material relationship: composed_primarily_of CHEBI:15377 ! water [Term] id: ENVO:00002007 name: sediment def: "Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid." [https://en.wikipedia.org/wiki/Sediment] comment: It is recommended to use a combination of sediment terms to describe a more specific sediment type. subset: EnvO-Lite-GSC subset: envoPolar xref: EcoLexicon:sediment xref: EcoLexicon:sedimentation xref: https://en.wikipedia.org/wiki/Sediment xref: LTER:492 xref: LTER:493 xref: SWEETRealm:Sediment is_a: ENVO:00010483 ! environmental material relationship: has_quality PATO:0000984 ! porous relationship: has_quality PATO:0001759 ! granular [Term] id: ENVO:00002010 name: saline water def: "Water which contains a significant concentration of dissolved salts." [] comment: The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight. synonym: "salt water" EXACT [] xref: EcoLexicon:saltwater xref: https://en.wikipedia.org/wiki/Saline_water xref: SWEETRealm:SalineWater xref: SWEETRealm:SaltWater is_a: ENVO:00002006 ! liquid water relationship: has_increased_levels_of CHEBI:26710 ! sodium chloride relationship: has_quality PATO:0001657 ! increased osmolarity [Term] id: ENVO:00002030 name: aquatic biome def: "A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water." [] xref: LTER:41 is_a: ENVO:00000428 ! biome is_a: ENVO:01001787 ! aquatic ecosystem intersection_of: ENVO:00000428 ! biome intersection_of: RO:0002507 ENVO:00000063 ! determined by water body [Term] id: ENVO:00002114 name: chemically enriched sediment def: "Sediment which has increased levels of one or more chemical compounds." [] is_a: ENVO:00002007 ! sediment intersection_of: ENVO:00002007 ! sediment intersection_of: has_increased_levels_of CHEBI:24431 ! chemical entity relationship: has_increased_levels_of CHEBI:24431 ! chemical entity [Term] id: ENVO:00002149 name: sea water def: "Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean." [] comment: This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels. synonym: "ocean water" EXACT [] synonym: "seawater" EXACT [] xref: EcoLexicon:sea_water xref: https://en.wikipedia.org/wiki/Sea_water xref: LTER:701 xref: SWEETRealm:SeaWater is_a: ENVO:00002010 ! saline water property_value: editor_note "When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class." xsd:string [Term] id: ENVO:00002202 name: organically enriched sediment def: "Chemically-enriched sediment which has increased levels of organic compounds." [] is_a: ENVO:00002114 ! chemically enriched sediment intersection_of: ENVO:00002114 ! chemically enriched sediment intersection_of: has_increased_levels_of CHEBI:50860 ! organic molecular entity relationship: has_increased_levels_of CHEBI:50860 ! organic molecular entity [Term] id: ENVO:00002203 name: inorganically enriched sediment def: "Chemically-enriched sediment which has increased levels of inorganic compounds." [] is_a: ENVO:00002114 ! chemically enriched sediment intersection_of: ENVO:00002114 ! chemically enriched sediment intersection_of: has_increased_levels_of CHEBI:24835 ! inorganic molecular entity relationship: has_increased_levels_of CHEBI:24835 ! inorganic molecular entity [Term] id: ENVO:00002982 name: clay def: "A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water." [https://en.wikipedia.org/wiki/Clay] xref: EcoLexicon:clay xref: https://en.wikipedia.org/wiki/Clay xref: SWEETRealm:Clay is_a: ENVO:00010483 ! environmental material disjoint_from: ENVO:01000016 ! silt relationship: has_quality PATO:0000984 ! porous [Term] id: ENVO:00003074 name: manufactured product def: "A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products." [] {comment="https://en.wikipedia.org/wiki/Manufactured_product"} synonym: "manufactured good" EXACT [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: output_of ENVO:01000993 ! manufacturing process relationship: output_of ENVO:01000993 ! manufacturing process [Term] id: ENVO:00003082 name: enriched soil namespace: ENVO def: "A portion of enriched soil is a portion of soil with elevated levels of some material entity." [] comment: This could be demoted to an inferred class if issues with double inheritance arise. is_a: ENVO:00001998 ! soil intersection_of: ENVO:00001998 ! soil intersection_of: has_increased_levels_of BFO:0000040 ! material entity relationship: has_increased_levels_of BFO:0000040 ! material entity [Term] id: ENVO:00005800 name: desert sand def: "Sand which is part of a desert." [] is_a: ENVO:01000017 ! sand intersection_of: ENVO:01000017 ! sand intersection_of: part_of ENVO:01001357 ! desert relationship: part_of ENVO:01001357 ! desert [Term] id: ENVO:00010483 name: environmental material def: "A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system." [DOI:10.1186/2041-1480-4-43, MA:ma, ORCID:0000-0002-4366-3088, URL:http\://ontology.buffalo.edu/smith/articles/niches.html] comment: Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. synonym: "portion of environmental material" EXACT [] is_a: BFO:0000024 ! fiat object part [Term] id: ENVO:00010504 name: surface layer def: "A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings." [URL:http\://www.merriam-webster.com/dictionary/surface] comment: This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here. xref: EcoLexicon:surface xref: http://sweetontology.net/reprSpaceGeometry/Surface xref: https://en.wikipedia.org/wiki/Surface is_a: ENVO:01001684 ! interface layer [Term] id: ENVO:00010505 name: aerosol def: "Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets." [https://en.wikipedia.org/wiki/Aerosol] comment: Should connect to PATO as "quality of an aerosol" subset: envoAtmo xref: EcoLexicon:aerosol xref: SWEETRealm:Aerosol is_a: ENVO:00010483 ! environmental material relationship: has_part ENVO:01000797 ! gaseous environmental material relationship: has_quality PATO:0001332 ! amorphous [Term] id: ENVO:0010001 name: anthropogenic environmental material namespace: ENVO def: "Anthropogenic material in or on which organisms may live." [MA:ma] is_a: ENVO:00010483 ! environmental material [Term] id: ENVO:01000016 name: silt def: "Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar." [https://en.wikipedia.org/wiki/Silt] comment: https://en.wikipedia.org/wiki/ In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity. xref: EcoLexicon:silt xref: https://en.wikipedia.org/wiki/Silt xref: SWEETRealm:Silt is_a: ENVO:00010483 ! environmental material disjoint_from: ENVO:01000017 ! sand relationship: has_quality PATO:0000984 ! porous relationship: has_quality PATO:0001759 ! granular [Term] id: ENVO:01000017 name: sand namespace: ENVO def: "A naturally occurring granular material composed of finely divided rock and mineral particles." [https://en.wikipedia.org/wiki/Sand] xref: EcoLexicon:sand xref: https://en.wikipedia.org/wiki/Sand xref: LTER:484 xref: SWEETRealm:Sand is_a: ENVO:00010483 ! environmental material relationship: RO:0001000 ENVO:00001995 ! derives from rock [Term] id: ENVO:01000023 name: marine pelagic biome namespace: ENVO def: "The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths." [ISBN:978-0-7506-3384-0] subset: envoPolar is_a: ENVO:00000447 ! marine biome relationship: has_part ENVO:00001999 ! marine water body created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-15T11:17:06Z [Term] id: ENVO:01000032 name: neritic pelagic zone biome namespace: ENVO def: "The neritic epipelagic zone biome comprises the marine water column above a continental shelf." [ISBN:978-0-444-82619-0, ISBN:978-0-7506-3384-0, ORCID:0000-0002-4366-3088] is_a: ENVO:01000023 ! marine pelagic biome disjoint_from: ENVO:01000033 ! oceanic pelagic zone biome created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-15T11:19:19Z [Term] id: ENVO:01000033 name: oceanic pelagic zone biome namespace: ENVO def: "The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf." [ISBN:978-0-444-82619-0, ISBN:978-0-7506-3384-0, ORCID:0000-0002-4366-3088] is_a: ENVO:01000023 ! marine pelagic biome created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-15T11:19:19Z [Term] id: ENVO:01000034 name: oceanic sea surface microlayer biome namespace: ENVO def: "The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath." [https://en.wikipedia.org/wiki/Sea_surface_microlayer, ORCID:0000-0002-4366-3088] is_a: ENVO:01000033 ! oceanic pelagic zone biome created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-15T11:21:03Z [Term] id: ENVO:01000041 name: neritic sea surface microlayer biome namespace: ENVO def: "The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath." [https://en.wikipedia.org/wiki/Sea_surface_microlayer, ORCID:0000-0002-4366-3088] is_a: ENVO:01000032 ! neritic pelagic zone biome created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-15T11:22:09Z [Term] id: ENVO:01000044 name: marine pelagic feature def: "A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column." [ISBN:978-0-618-45504-1, ORCID:0000-0002-4366-3088] subset: envoPolar is_a: ENVO:00000012 ! hydrographic feature created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-16T12:10:50Z [Term] id: ENVO:01000048 name: ocean biome def: "A marine biome which is determined by an ocean." [https://en.wikipedia.org/wiki/Ocean, ORCID:0000-0002-4366-3088] comment: Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt. subset: envoPolar is_a: ENVO:00000447 ! marine biome intersection_of: ENVO:00000428 ! biome intersection_of: RO:0002507 ENVO:00000015 ! determined by ocean relationship: RO:0002507 ENVO:00000015 ! determined by ocean created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-15T11:23:23Z [Term] id: ENVO:01000060 name: particulate matter def: "Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material." [] subset: envoAtmo subset: envoPolar is_a: ENVO:00010483 ! environmental material property_value: editor_note "Subclasses should be assigned by inference." xsd:string [Term] id: ENVO:01000155 name: organic material def: "Environmental material derived from living organisms and composed primarily of one or more biomacromolecules." [ISBN:978-0-618-45504-1, ORCID:0000-0002-4366-3088] synonym: "biomass" EXACT [] xref: EcoLexicon:organic_material is_a: ENVO:00010483 ! environmental material intersection_of: ENVO:00010483 ! environmental material intersection_of: composed_primarily_of CHEBI:33694 ! biomacromolecule relationship: composed_primarily_of CHEBI:33694 ! biomacromolecule created_by: ORCID:0000-0002-4366-3088 creation_date: 2010-03-20T08:40:04Z [Term] id: ENVO:01000176 name: shrubland biome def: "A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs." [] comment: Preliminary definition. is_a: ENVO:00000446 ! terrestrial biome created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-04-07T14:26:46Z [Term] id: ENVO:01000179 name: desert biome def: "A desert biome is a terrestrial biome which loses more liquid water by evapotranspiration than is supplied by precipitation and includes communities adapted to these conditions." [] comment: Preliminary definition. subset: wwfBiome xref: SPIRE:Desert_or_dune is_a: ENVO:01001780 ! desert ecosystem intersection_of: ENVO:01001780 ! desert ecosystem intersection_of: RO:0002507 PCO:0000002 ! determined by ecological community relationship: overlaps ENVO:00000097 ! desert area relationship: RO:0002507 PCO:0000002 ! determined by ecological community created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-04-07T14:26:46Z [Term] id: ENVO:01000203 name: environmental condition def: "An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system." [DOI:10.1186/2041-1480-4-43] comment: A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. subset: envoPolar is_a: PATO:0001018 ! physical quality property_value: IAO:0000114 IAO:0000121 created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-04-07T14:35:18Z [Term] id: ENVO:01000216 name: montane shrubland biome def: "A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions." [] comment: Preliminary definition. subset: wwfBiome is_a: ENVO:01000176 ! shrubland biome is_a: ENVO:01001836 ! montane biome created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-04-07T14:40:32Z [Term] id: ENVO:01000219 name: anthropogenic terrestrial biome def: "An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity." [http://www.eoearth.org/view/article/150128/] comment: Preliminary definition. synonym: "anthrome" EXACT [] synonym: "human biome" EXACT [] is_a: ENVO:00000446 ! terrestrial biome intersection_of: ENVO:00000446 ! terrestrial biome intersection_of: RO:0002354 ENVO:01000952 ! formed as result of anthropisation relationship: RO:0002354 ENVO:01000952 ! formed as result of anthropisation created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-04-07T14:45:22Z [Term] id: ENVO:01000230 name: arid def: "An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration." [] subset: envoPolar xref: EcoLexicon:aridity is_a: ENVO:01000203 ! environmental condition created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-04-24T13:28:18Z [Term] id: ENVO:01000254 name: environmental system def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. synonym: "environment" EXACT [] xref: EcoLexicon:environment is_a: RO:0002577 ! system creation_date: 2013-09-23T16:04:08Z [Term] id: ENVO:01000256 name: mineral material def: "A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure." [https://en.wikipedia.org/wiki/Mineral] xref: LTER:341 is_a: ENVO:01000814 ! solid environmental material intersection_of: ENVO:00010483 ! environmental material intersection_of: composed_primarily_of CHEBI:46662 ! mineral relationship: composed_primarily_of CHEBI:46662 ! mineral property_value: editor_note "Look for \"mineral\" in a chemical or geochemical ontology to formalise the composed primarily of link.\nFrom https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure." xsd:string created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-05T12:37:41Z [Term] id: ENVO:01000266 name: water vapour def: "Water vapour is a vapour which is the gas phase of water." [https://en.wikipedia.org/wiki/Water_vapor] comment: Perhaps a better relation between water vapour and water can be found in or added to RO? synonym: "aqueous vapor" EXACT [https://en.wikipedia.org/wiki/Water_vapor] synonym: "aqueous vapour" EXACT [https://en.wikipedia.org/wiki/Water_vapor] synonym: "water vapor" EXACT [https://en.wikipedia.org/wiki/Water_vapor] is_a: ENVO:01000797 ! gaseous environmental material relationship: composed_primarily_of CHEBI:15377 ! water created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-10T07:58:18Z [Term] id: ENVO:01000267 name: atmosphere def: "An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body." [https://en.wikipedia.org/wiki/Atmosphere, https://en.wikipedia.org/wiki/Physical_geography] xref: LTER:48 is_a: ENVO:01001678 ! fluid layer relationship: adjacent_to ENVO:01000799 ! astronomical body created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-10T08:14:50Z [Term] id: ENVO:01000268 name: atmospheric water vapour namespace: ENVO def: "Atmospheric water vapour is water vapour that is part of an atmosphere." [https://en.wikipedia.org/wiki/Water_vapor] subset: envoPolar synonym: "atmospheric water vapor" EXACT [https://en.wikipedia.org/wiki/Water_vapor] is_a: ENVO:01000266 ! water vapour intersection_of: ENVO:01000266 ! water vapour intersection_of: part_of ENVO:01000267 ! atmosphere relationship: part_of ENVO:01000267 ! atmosphere relationship: RO:0000087 CHEBI:76413 ! has role greenhouse gas created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-10T08:22:07Z [Term] id: ENVO:01000276 name: ecoregion def: "A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions." [DOI:10.1641/0006-3568(2001)051[0933\:TEOTWA\]2.0.CO;2, URL:http\://worldwildlife.org/biomes] comment: Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO. subset: envoPolar is_a: ENVO:01001110 ! ecosystem relationship: part_of ENVO:01000280 ! ecozone created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-12T17:21:09Z [Term] id: ENVO:01000277 name: water ice def: "Ice which is formed from water." [https://en.wikipedia.org/wiki/Ice] comment: Water ice can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance.\n\nWhen speaking about ice on Earth, usually water ice is meant - the solid, crystalline form of water found in the atmosphere as snow crystals, hail, ice pellets, etc., and on the earth's surface in forms such as hoarfrost, rime, glaze, sea ice, glacier ice, ground ice, frazil, anchor ice, etc. \n\nThis form of water is, strictly speaking, called ice Ih, the Roman numeral I distinguishing it from more than a dozen other phases and the letter h distinguishing it from the metastable cubic phase ice Ic. Ice Ih is the only one of the several known phases of water ice that is stable at commonly occurring temperatures and pressures. (Some of the other forms have very unusual properties, ice VII, for example, being stable only at pressures above 22 400 kg/cm^2, but then existing at temperatures up to about 100C.) \n\nIt has an open structure with a specific gravity of 0.9166 which is slightly less than water; because the water molecules bond to their neighbors covalently only in four directions; it therefore floats on higher density water, where broken molecular bonds permit closer packing. All commonly occurring forms of ice are crystalline, although large single crystals are relatively rare except in glaciers. The ice crystal lattice possesses hexagonal symmetry that manifests itself in the gross forms of such single crystals as are sometimes found in snow. At an air pressure of one atmosphere, ice melts at 0 C by definition of the Celsius temperature scale. (Strictly speaking the equilibrium point among water, ice, and vapor occurs at +0.01C, the triple point.) On the other hand, ice does not invariably form in liquid water cooled below this temperature; it has a tendency to supercool, more so in the absence of ice nuclei. \n\nIn permafrost regions, ice may occupy voids in soils and rocks and may develop in a variety of forms. Ice may be colourless to pale blue or greenish-blue. It may appear white due to included gas bubbles; in exposures, ground ice may also appear black.\n\nIn nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze. subset: envoPolar synonym: "ice" RELATED [http://www.eionet.europa.eu/gemet/concept/4131] xref: http://sweetontology.net/matrWater/Ice xref: LTER:262 is_a: ENVO:01000814 ! solid environmental material is_a: ENVO:01001125 ! ice intersection_of: ENVO:01001125 ! ice intersection_of: composed_primarily_of ENVO:00002006 ! liquid water relationship: composed_primarily_of ENVO:00002006 ! liquid water created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2013-10-13T12:01:28Z [Term] id: ENVO:01000280 name: ecozone def: "Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration." [https://en.wikipedia.org/wiki/ecozone] comment: ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO.\nhttps://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories. subset: envoPolar is_a: ENVO:01001110 ! ecosystem relationship: part_of ENVO:01000817 ! biosphere created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-13T18:32:46Z [Term] id: ENVO:01000281 name: layer def: "A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface." [Wiktionary:layer] comment: Preliminary definition. subset: envoPolar is_a: BFO:0000040 ! material entity relationship: has_quality PATO:0002124 ! laminar created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-15T16:42:02Z [Term] id: ENVO:01000283 name: lake layer namespace: ENVO def: "A layer which is part of a lake." [] comment: Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline. subset: envoPolar is_a: ENVO:01000325 ! aquatic layer intersection_of: ENVO:01000325 ! aquatic layer intersection_of: part_of ENVO:00000020 ! lake relationship: part_of ENVO:00000020 ! lake created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-15T16:57:43Z [Term] id: ENVO:01000293 name: ice mass def: "A mass of water ice." [] subset: envoPolar synonym: "accumulation of ice" BROAD [] synonym: "ice accumulation" BROAD [] xref: http://sweetontology.net/phenCryo/Accumulation is_a: ENVO:00000131 ! glacial feature is_a: ENVO:01001687 ! mass of solid material intersection_of: ENVO:01001687 ! mass of solid material intersection_of: composed_primarily_of ENVO:01000277 ! water ice relationship: composed_primarily_of ENVO:01000277 ! water ice relationship: part_of ENVO:01000818 ! cryosphere property_value: editor_note "Class should be populated by inference and asserted subclasses redistributed." xsd:string created_by: ORCID:0000-0002-4366-3088 creation_date: 2013-10-15T19:49:11Z [Term] id: ENVO:01000295 name: marine layer def: "A layer that is part of a marine water body." [ORCID:0000-0002-4366-3088] subset: envoMarine subset: envoPolar is_a: ENVO:01000325 ! aquatic layer relationship: composed_primarily_of ENVO:00002149 ! sea water relationship: part_of ENVO:00001999 ! marine water body created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000303 name: endolithic environment def: "An endolithic environment is an environment that exists within solid rock." [] is_a: ENVO:01000254 ! environmental system intersection_of: ENVO:01000254 ! environmental system intersection_of: surrounded_by ENVO:00001995 ! rock relationship: surrounded_by ENVO:00001995 ! rock [Term] id: ENVO:01000307 name: saline water environment def: "An environmental system which has its properties and dynamics determined by saline water." [] subset: envoEmpo subset: envoOmics subset: envoPolar is_a: ENVO:01000317 ! aquatic environment is_a: ENVO:01001040 ! saline environment intersection_of: ENVO:01000317 ! aquatic environment intersection_of: RO:0002507 ENVO:00002010 ! determined by saline water relationship: RO:0002507 ENVO:00002010 ! determined by saline water property_value: IAO:0000118 "Water (saline)" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/"} [Term] id: ENVO:01000309 name: cold environment def: "An environment which has a lower temperature than some local or global average." [] comment: The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'. subset: envoPolar is_a: ENVO:01000254 ! environmental system intersection_of: ENVO:01000254 ! environmental system intersection_of: has_quality PATO:0001306 ! decreased temperature relationship: has_quality PATO:0001306 ! decreased temperature [Term] id: ENVO:01000313 name: anthropogenic environment def: "An anthropogenic environment is an environmental system which is the product of human activity." [] comment: Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. is_a: ENVO:01000254 ! environmental system [Term] id: ENVO:01000314 name: high osmolarity environment def: "A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes." [] is_a: ENVO:01000997 ! environmental system determined by a quality intersection_of: ENVO:01000997 ! environmental system determined by a quality intersection_of: has_quality PATO:0001657 ! increased osmolarity relationship: has_quality PATO:0001657 ! increased osmolarity [Term] id: ENVO:01000317 name: aquatic environment def: "An environment whose dynamics are strongly influenced by water." [] is_a: ENVO:01000997 ! environmental system determined by a quality is_a: ENVO:01000998 ! environmental system determined by a material intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 ENVO:00002006 ! determined by liquid water relationship: RO:0002507 ENVO:00002006 ! determined by liquid water [Term] id: ENVO:01000319 name: rocky slope def: "A rocky slope is a slope which has a surface primarily composed of rock." [] is_a: ENVO:00002000 ! slope [Term] id: ENVO:01000320 name: marine environment def: "A marine environment and enviroment which is determined by a marine water body." [NM:nm] subset: envoPolar is_a: ENVO:01000254 ! environmental system intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 ENVO:00001999 ! determined by marine water body relationship: RO:0002507 ENVO:00001999 ! determined by marine water body [Term] id: ENVO:01000321 name: sea water environment def: "An environmental system determined by seawater." [] subset: envoPolar synonym: "ocean water environment" EXACT [] is_a: ENVO:01000307 ! saline water environment intersection_of: ENVO:01000307 ! saline water environment intersection_of: RO:0002507 ENVO:00002149 ! determined by sea water relationship: RO:0002507 ENVO:00002149 ! determined by sea water [Term] id: ENVO:01000323 name: atmospheric boundary layer def: "The atmospheric boundary layer is the lowest layer of an atmosphere which is strongly influenced by its contact with a planetary surface with strong vertical mixing and in which physical quantities such as flow velocity, temperature, and moisture display rapid fluctuations (turbulence)." [] subset: envoPolar synonym: "planetary boundary layer" EXACT [] is_a: ENVO:01000543 ! atmospheric layer is_a: ENVO:01000544 ! boundary layer relationship: adjacent_to ENVO:01000324 ! planetary surface relationship: bounding_layer_of ENVO:01000267 ! atmosphere [Term] id: ENVO:01000324 name: planetary surface def: "A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space." [] comment: a useful class: this can be used to define sub-terrestrial and sub-marine entities is_a: ENVO:01001483 ! surface of an astronomical body intersection_of: ENVO:01001483 ! surface of an astronomical body intersection_of: part_of ENVO:01000800 ! planet relationship: part_of ENVO:01000800 ! planet [Term] id: ENVO:01000325 name: aquatic layer def: "A layer in a water mass, itself composed primarily of water." [] comment: This class will eventually be populated by inference, and its asserted subclasses removed. subset: envoPolar is_a: ENVO:01001273 ! liquid layer intersection_of: ENVO:01001273 ! liquid layer intersection_of: composed_primarily_of ENVO:00002006 ! liquid water relationship: composed_primarily_of ENVO:00002006 ! liquid water [Term] id: ENVO:01000334 name: talus slope def: "A talus slope is a slope which has a surface layer composed of scree." [] synonym: "scree slope" EXACT [] is_a: ENVO:00002000 ! slope [Term] id: ENVO:01000342 name: montane def: "An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line." [https://en.wikipedia.org/wiki/Altitudinal_zonation] comment: The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. {xref="https://en.wikipedia.org/wiki/Altitudinal_zonation"} subset: envoPolar xref: LTER:350 is_a: ENVO:01000343 ! altitudinal condition created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000343 name: altitudinal condition def: "An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude." [https://en.wikipedia.org/wiki/Altitudinal_zonation] comment: Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change. subset: envoPolar is_a: ENVO:01000203 ! environmental condition created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000355 name: vegetation layer def: "A layer which is determined by a form of vegetation." [] comment: Usually found in woodlands and forests. synonym: "forest layer" RELATED [] synonym: "forest stratum" RELATED [] synonym: "woodland layer" RELATED [] synonym: "woodland stratum" RELATED [] is_a: ENVO:01000281 ! layer intersection_of: ENVO:01000281 ! layer intersection_of: composed_primarily_of NCBITaxon:33090 ! Viridiplantae relationship: composed_primarily_of NCBITaxon:33090 ! Viridiplantae [Term] id: ENVO:01000406 name: snow def: "Snow is an environmental material which is primarily composed of flakes of crystalline water ice." [http://www.eionet.europa.eu/gemet/concept/7769, https://en.wikipedia.org/wiki/Snow] subset: envoPolar is_a: ENVO:00000131 ! glacial feature is_a: ENVO:00010483 ! environmental material relationship: composed_primarily_of ENVO:01000277 ! water ice relationship: has_part ENVO:00002005 ! air relationship: output_of ENVO:01000895 ! snowfall [Term] id: ENVO:01000408 name: environmental zone def: "A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein." [] comment: Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. subset: envoPolar synonym: "environmental area" RELATED [] is_a: BFO:0000029 ! site relationship: part_of ENVO:01000254 ! environmental system [Term] id: ENVO:01000538 name: stratosphere def: "The layer of the atmosphere which is sandwiched between the troposphere and mesosphere. Of the energy that reaches the Earth from the sun, only 3% is absorbed in the stratosphere, but that includes the vitally important process of absorption of ultraviolet radiation by the stratospheric ozone layer. The stratosphere is cloudless and dust free, and almost unaffected by the turbulent conditions of the underlying level of the atmosphere. (Source: WRIGHT)" [GEMET:http\://www.eionet.europa.eu/gemet/concept/8128] comment: Definition from GEMET - will be refined. is_a: ENVO:01000543 ! atmospheric layer created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000539 name: mesosphere def: "The mesosphere is part of the earth's atmosphere which is between the stratosphere and the thermosphere in which temperature decreases with altitude to the atmosphere's absolute minimum" [http://www.merriam-webster.com/dictionary/mesosphere] is_a: ENVO:01000543 ! atmospheric layer created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000540 name: troposphere def: "The lowest of the concentric layers of the atmosphere, occurring between the Earth's surface and the tropopause. It is the zone where atmospheric turbulence is at its greatest and where the bulk of the Earth's weather is generated. It contains almost all the water vapour and aerosols and three-quarters of the total gaseous mass of the atmosphere. Throughout the troposphere temperature decreases with height at a mean rate of 6.5°C/km and the whole zone is capped by either an inversion of temperature or an isothermal layer at the tropopause. (Source: WHIT)" [GEMET:http\://www.eionet.europa.eu/gemet/concept/8695] comment: Definition from GEMET - will be refined. is_a: ENVO:01000543 ! atmospheric layer created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000541 name: thermosphere def: "The thermosphere is a part of the earth's atmosphere that begins at about 50 miles (80 kilometers) above the earth's surface, extends to outer space, and is characterized by steadily increasing temperature with height" [http://www.merriam-webster.com/dictionary/thermosphere] is_a: ENVO:01000543 ! atmospheric layer relationship: adjacent_to ENVO:01000539 ! mesosphere relationship: part_of ENVO:01000267 ! atmosphere [Term] id: ENVO:01000543 name: atmospheric layer def: "A layer that is part of the atmosphere." [] comment: This could be made into an inferred class, rather than having asserted subclasses. subset: envoPolar synonym: "atmospheric layering" RELATED [GEMET:http\://www.eionet.europa.eu/gemet/concept/627] is_a: ENVO:01001678 ! fluid layer intersection_of: ENVO:01001678 ! fluid layer intersection_of: part_of ENVO:01000267 ! atmosphere relationship: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: part_of ENVO:01000267 ! atmosphere created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000544 name: boundary layer def: "A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow." [https://en.wikipedia.org/wiki/Boundary_layer] synonym: "boundary layer" EXACT [http://www.eionet.europa.eu/gemet/concept/976] is_a: ENVO:01001677 ! fluid interface layer relationship: adjacent_to ENVO:00010504 ! surface layer created_by: ORCID:0000-0002-4366-3088 [Term] id: ENVO:01000604 name: vehicle def: "A vehicle is a mobile machine which transports people or cargo." [https://en.wikipedia.org/wiki/Vehicle] is_a: ENVO:00003074 ! manufactured product [Term] id: ENVO:01000617 name: lentic water body def: "A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow." [] is_a: ENVO:00000063 ! water body [Term] id: ENVO:01000624 name: hydrological condensation process def: "Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase." [https://en.wikipedia.org/wiki/Condensation] comment: "process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog) subset: envoAtmo subset: envoPolar synonym: "condensation" BROAD [] is_a: ENVO:01000724 ! condensation process is_a: ENVO:02500031 ! hydrological process relationship: RO:0002233 ENVO:01000268 ! has input atmospheric water vapour relationship: RO:0002234 ENVO:00002006 ! has output liquid water [Term] id: ENVO:01000635 name: planetary landmass def: "A landmass which is part of a planet." [Adpated from https://en.wikipedia.org/wiki/Planetary_surface] synonym: "ground" RELATED [] synonym: "land" BROAD [] is_a: ENVO:01000324 ! planetary surface is_a: ENVO:01001782 ! landmass [Term] id: ENVO:01000637 name: outer space def: "Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies." [https://en.wikipedia.org/wiki/Outer_space] subset: envoAstro synonym: "space" BROAD [] is_a: ENVO:00010483 ! environmental material [Term] id: ENVO:01000638 name: planetary crust def: "A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle." [https://en.wikipedia.org/wiki/Crust_(geology)] comment: This class is meant to be applicable accross planets. Earth's crust would be an instance. synonym: "crust" BROAD [] is_a: ENVO:01000639 ! planetary structural layer relationship: has_quality PATO:0001546 ! quality of a solid [Term] id: ENVO:01000639 name: planetary structural layer def: "A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition." [] is_a: ENVO:01000281 ! layer relationship: part_of ENVO:01000800 ! planet property_value: editor_note "Label should be improved to match definition." xsd:string [Term] id: ENVO:01000640 name: planetary mantle def: "A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density." [https://en.wikipedia.org/wiki/Mantle_(geology)] comment: This class is meant to be applicable accross planets. Earth's mantle would be an instance. synonym: "mantle" BROAD [] is_a: ENVO:01000639 ! planetary structural layer relationship: adjacent_to ENVO:01000638 ! planetary crust [Term] id: ENVO:01000646 name: lithosphere def: "A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties." [https://en.wikipedia.org/wiki/Lithosphere] comment: Earth's lithosphere includes the crust and uppermost mantle. is_a: ENVO:01000639 ! planetary structural layer is_a: ENVO:01001275 ! solid layer relationship: has_part ENVO:01000638 ! planetary crust relationship: has_quality PATO:0001545 ! inflexible [Term] id: ENVO:01000685 name: water mass def: "A mass of water." [] is_a: ENVO:01001476 ! body of liquid relationship: composed_primarily_of ENVO:00002006 ! liquid water [Term] id: ENVO:01000687 name: coast def: "A coast is the area where land meets the sea, ocean, or lake." [https://en.wikipedia.org/wiki/Coast] comment: Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore' is_a: ENVO:01001479 ! fluid astronomical body part is_a: ENVO:01001784 ! compound astronomical body part relationship: overlaps ENVO:01000635 ! planetary landmass [Term] id: ENVO:01000703 name: hydrological precipitation process def: "Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity." [https://en.wikipedia.org/wiki/Precipitation] comment: "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) synonym: "precipitation" BROAD [] is_a: ENVO:01000875 ! precipitation process [Term] id: ENVO:01000724 name: condensation process def: "Condensation is a process during which a gas undergoes a phase transition into a liquid." [https://en.wikipedia.org/wiki/Condensation] is_a: ENVO:01001510 ! material congelation process [Term] id: ENVO:01000726 name: desublimation process def: "Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid." [https://en.wikipedia.org/wiki/Deposition_(phase_transition)] synonym: "deposition" BROAD [] is_a: ENVO:01001510 ! material congelation process [Term] id: ENVO:01000739 name: habitat def: "An environmental system which can sustain and allow the growth of an ecological population." [EnvO:EnvO] comment: A habitat's specificity to an ecological population differentiates it from other environment classes. xref: EcoLexicon:habitat xref: https://en.wikipedia.org/wiki/Habitat xref: LTER:238 xref: SWEETRealm:Habitat is_a: ENVO:01001110 ! ecosystem relationship: part_of ENVO:01000817 ! biosphere relationship: RO:0002507 PCO:0000001 ! determined by population of organisms [Term] id: ENVO:01000752 name: area of barren land alt_id: NLCD:31 def: "An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction." [https://en.wikipedia.org/wiki/Exosphere, https://en.wikipedia.org/wiki/Planetary_surface, https://www.mrlc.gov/nlcd11_leg.php] comment: According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition. subset: envoPolar subset: nlcd2011 is_a: ENVO:01001199 ! terrestrial environmental zone relationship: adjacent_to ENVO:01000323 ! atmospheric boundary layer property_value: editor_note "The range of entities that are considered \"barren land\" are not exhaustive, making axiomatisation risky at this stage." xsd:string property_value: IAO:0000118 "Barren Land (Rock/Sand/Clay)" xsd:string [Term] id: ENVO:01000755 name: aeroform def: "A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes." [] comment: Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas. subset: envoAtmo is_a: ENVO:01001478 ! gaseous astronomical body part relationship: located_in ENVO:01000267 ! atmosphere property_value: editor_note "This may not need to be in the atmosphere, also note that \"meteor\" will do much of the same work." xsd:string [Term] id: ENVO:01000797 name: gaseous environmental material def: "A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely." [http://www.merriam-webster.com/dictionary/gas] synonym: "gas" NARROW [] is_a: ENVO:02000140 ! fluid environmental material intersection_of: ENVO:00010483 ! environmental material intersection_of: has_quality PATO:0001547 ! quality of a gas relationship: has_quality PATO:0001547 ! quality of a gas property_value: editor_note "This class is to be populated by inference." xsd:string [Term] id: ENVO:01000798 name: plasma def: "A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields." [http://www.merriam-webster.com/dictionary/plasma, https://en.wikipedia.org/wiki/Plasma_%28physics%29] is_a: ENVO:02000140 ! fluid environmental material property_value: editor_note "An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88" xsd:string [Term] id: ENVO:01000799 name: astronomical body def: "An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space." [https://en.wikipedia.org/wiki/Astronomical_object] comment: Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'. subset: envoAstro synonym: "celestial body" RELATED [] is_a: ENVO:01000804 ! astronomical object [Term] id: ENVO:01000800 name: planet def: "A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals." [http://solarsystem.nasa.gov/planets/whatisaplanet, https://en.wikipedia.org/wiki/Planet] comment: Considerable debate on the definition of planet exists. subset: envoAstro subset: envoPolar is_a: ENVO:01000799 ! astronomical body [Term] id: ENVO:01000801 name: star def: "An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces." [https://en.wikipedia.org/wiki/Star] subset: envoAstro subset: envoPolar is_a: ENVO:01000799 ! astronomical body is_a: ENVO:01001686 ! mass of environmental material relationship: composed_primarily_of ENVO:01000798 ! plasma property_value: editor_note "Add qualities such as spherical. Request NTRs if not available in PATO." xsd:string [Term] id: ENVO:01000804 name: astronomical object def: "An object which is composed of one or more gravitationally bound structures that are associated with a position in space." [https://en.wikipedia.org/wiki/Astronomical_object] comment: If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far. subset: envoAstro synonym: "celestial object" RELATED [] is_a: BFO:0000030 ! object relationship: has_part ENVO:01000799 ! astronomical body relationship: has_quality ENVO:01001164 ! geodiversity relationship: surrounded_by ENVO:01000637 ! outer space [Term] id: ENVO:01000813 name: astronomical body part def: "A material part of an astronomical body." [] subset: envoAstro subset: envoPolar is_a: BFO:0000024 ! fiat object part relationship: part_of ENVO:01000799 ! astronomical body [Term] id: ENVO:01000814 name: solid environmental material def: "An environmental material which is in a solid state." [] comment: This is a defined class: its subclasses will not be asserted, but filled by inference. is_a: ENVO:00010483 ! environmental material intersection_of: ENVO:00010483 ! environmental material intersection_of: has_quality PATO:0001546 ! quality of a solid relationship: has_quality PATO:0001546 ! quality of a solid [Term] id: ENVO:01000815 name: liquid environmental material def: "An environmental material which is in a liquid state." [] comment: This is a defined class: most of its subclasses will not be asserted, but filled by inference. subset: envoPolar is_a: ENVO:02000140 ! fluid environmental material intersection_of: ENVO:00010483 ! environmental material intersection_of: has_quality PATO:0001548 ! quality of a liquid relationship: has_quality PATO:0001548 ! quality of a liquid [Term] id: ENVO:01000817 name: biosphere def: "A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact." [http://www.biology-online.org/dictionary/Biosphere, https://en.wikipedia.org/wiki/Biosphere] comment: The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. subset: envoAstro subset: envoPolar is_a: ENVO:01001479 ! fluid astronomical body part is_a: ENVO:01001784 ! compound astronomical body part relationship: has_part PCO:0000000 ! collection of organisms property_value: editor_note "Whether this class should be grouped with classes such as \"hydrosphere\" and \"cryosphere\" requires some discussion." xsd:string [Term] id: ENVO:01000818 name: cryosphere def: "A cryosphere is that part of a planet which is primarily composed of water is in solid form." [https://en.wikipedia.org/wiki/Cryosphere] comment: This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. subset: envoAstro subset: envoPolar is_a: ENVO:00000131 ! glacial feature is_a: ENVO:03000110 ! cryoform relationship: composed_primarily_of ENVO:01000277 ! water ice [Term] id: ENVO:01000819 name: hydrosphere def: "An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet." [https://en.wikipedia.org/wiki/Hydrosphere] comment: This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. subset: envoAstro subset: envoPolar is_a: ENVO:01001477 ! liquid astronomical body part relationship: composed_primarily_of ENVO:00002006 ! liquid water [Term] id: ENVO:01000820 name: pedosphere def: "An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere." [https://en.wikipedia.org/wiki/Pedosphere] comment: This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. subset: envoAstro is_a: ENVO:01001479 ! fluid astronomical body part is_a: ENVO:01001784 ! compound astronomical body part relationship: composed_primarily_of ENVO:00001998 ! soil relationship: overlaps ENVO:01000267 ! atmosphere relationship: overlaps ENVO:01000646 ! lithosphere relationship: overlaps ENVO:01000817 ! biosphere relationship: overlaps ENVO:01000819 ! hydrosphere [Term] id: ENVO:01000845 name: crystal def: "A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions." [https://en.wikipedia.org/wiki/Crystal] comment: This class refers to a portion of crystal and not an individual crystal. is_a: ENVO:01000814 ! solid environmental material relationship: has_quality PATO:0001411 ! structured [Term] id: ENVO:01000846 name: water ice crystal def: "A crystal which is primarily composed of water ice." [] comment: Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions. {xref="https://orcid.org/0000-0003-4808-4736"} subset: envoPolar synonym: "ice crystal" BROAD [] xref: http://sweetontology.net/matrWater/Ice is_a: ENVO:00000131 ! glacial feature is_a: ENVO:01000845 ! crystal relationship: composed_primarily_of ENVO:01000277 ! water ice [Term] id: ENVO:01000875 name: precipitation process def: "A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force." [https://en.wikipedia.org/wiki/Precipitation_%28chemistry%29] {comment="https://en.wikipedia.org/wiki/Precipitation"} is_a: ENVO:03000010 ! material transport process [Term] id: ENVO:01000895 name: snowfall def: "A hydrological process in which irregular aggregates of snow fall to a planetary surface." [] subset: environmental_hazards subset: envoPolar synonym: "snow fall" EXACT [] is_a: ENVO:01000703 ! hydrological precipitation process relationship: RO:0000057 ENVO:01000406 ! has participant snow [Term] id: ENVO:01000951 name: natural environment def: "An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition." [https://en.wikipedia.org/wiki/Anthropization, https://en.wikipedia.org/wiki/Natural_environment] comment: In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised. is_a: ENVO:01000254 ! environmental system property_value: IAO:0000118 "non-anthropised environment" xsd:string property_value: IAO:0000118 "non-anthropized environment" xsd:string [Term] id: ENVO:01000952 name: anthropisation def: "A process during which a natural environmental system is altered by human action." [https://en.wikipedia.org/wiki/Anthropization] comment: An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. {xref="https://en.wikipedia.org/wiki/Anthropization"} synonym: "anthropization" EXACT [] is_a: ENVO:01001434 ! anthropogenic ecosystem conversion process intersection_of: ENVO:01001434 ! anthropogenic ecosystem conversion process intersection_of: RO:0002233 ENVO:01000951 ! has input natural environment intersection_of: RO:0002234 ENVO:01000313 ! has output anthropogenic environment relationship: RO:0002233 ENVO:01000951 ! has input natural environment relationship: RO:0002234 ENVO:01000313 ! has output anthropogenic environment [Term] id: ENVO:01000958 name: terrestrial planet def: "A planet that is composed primarily of silicate rocks or metals." [https://en.wikipedia.org/wiki/Terrestrial_planet] subset: envoAstro synonym: "Earth-like planet" RELATED [] synonym: "rocky planet" EXACT [] synonym: "telluric planet" EXACT [] is_a: ENVO:01000800 ! planet [Term] id: ENVO:01000981 name: mass liquid flow def: "A process whereby a volume of liquid moves due to a disequilibrium of physical forces." [https://en.wikipedia.org/wiki/Wind] comment: This class can refer to the flow of any material in a liquid phase. subset: envoPolar is_a: ENVO:01001747 ! mass fluid flow relationship: RO:0000057 ENVO:01000815 ! has participant liquid environmental material [Term] id: ENVO:01000982 name: water flow process def: "A process during which a volume of water is transported due to a disequilibria in physical forces." [] subset: environmental_hazards is_a: ENVO:01000981 ! mass liquid flow is_a: ENVO:02500031 ! hydrological process relationship: RO:0000057 ENVO:00002006 ! has participant liquid water [Term] id: ENVO:01000993 name: manufacturing process def: "A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation." [https://en.wikipedia.org/wiki/Manufacturing] comment: The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale. {xref="https://en.wikipedia.org/wiki/Manufacturing"} is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: RO:0002234 ENVO:00003074 ! has output manufactured product relationship: RO:0002234 ENVO:00003074 ! has output manufactured product relationship: RO:0002608 NCBITaxon:9606 ! process has causal agent Homo sapiens [Term] id: ENVO:01000997 name: environmental system determined by a quality def: "An environmental system which is determined by materials bearing roughly homogeneous qualities." [] comment: Organisational class. Not intended for annotation. is_a: ENVO:01000254 ! environmental system [Term] id: ENVO:01000998 name: environmental system determined by a material def: "An environmental system within which an environmental material strongly influences the system's composition and properties." [] comment: Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump). is_a: ENVO:01000254 ! environmental system intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 ENVO:00010483 ! determined by environmental material relationship: RO:0002507 ENVO:00010483 ! determined by environmental material [Term] id: ENVO:01001000 name: environmental system determined by an organism def: "An environmental system which is determined by a living organism." [] subset: envoEmpo subset: envoOmics synonym: "host-associated environment" RELATED [] is_a: ENVO:01001110 ! ecosystem intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 NCBITaxon:131567 ! determined by cellular organisms relationship: RO:0002507 NCBITaxon:131567 ! determined by cellular organisms [Term] id: ENVO:01001001 name: plant-associated environment def: "An environmental system determined by a green plant." [] subset: envoEmpo subset: envoOmics synonym: "plant environment" BROAD [] synonym: "Viridiplantae-associated environment" EXACT [] is_a: ENVO:01001000 ! environmental system determined by an organism intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 NCBITaxon:33090 ! determined by Viridiplantae relationship: RO:0002507 NCBITaxon:33090 ! determined by Viridiplantae property_value: IAO:0000118 "Plant" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/"} [Term] id: ENVO:01001002 name: animal-associated environment def: "An environmental system determined by an animal." [] subset: envoEmpo subset: envoMeo subset: envoOmics synonym: "animal environment" BROAD [] synonym: "Metazoan-associated environment" EXACT [] is_a: ENVO:01001000 ! environmental system determined by an organism intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 NCBITaxon:33208 ! determined by Metazoa relationship: RO:0002507 NCBITaxon:33208 ! determined by Metazoa property_value: IAO:0000118 "Animal" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/"} [Term] id: ENVO:01001008 name: meteor def: "A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body." [https://cloudatlas.wmo.int/other-meteors.html] subset: envoAtmo is_a: BFO:0000030 ! object intersection_of: BFO:0000030 ! object intersection_of: located_in ENVO:01000267 ! atmosphere relationship: located_in ENVO:01000267 ! atmosphere [Term] id: ENVO:01001010 name: hydrometeor def: "A meteor which is primarily composed of water." [https://cloudatlas.wmo.int/other-meteors.html] subset: envoAtmo is_a: ENVO:01001008 ! meteor [Term] id: ENVO:01001012 name: lithometeor def: "A meteor which is primarily composed of rock." [] subset: envoAtmo is_a: ENVO:00000339 ! piece of rock is_a: ENVO:01001008 ! meteor intersection_of: ENVO:01001008 ! meteor intersection_of: composed_primarily_of ENVO:00001995 ! rock relationship: RO:0001000 ENVO:01001068 ! derives from meteoroid [Term] id: ENVO:01001022 name: natural lake def: "A lake which has formed as the result of processes that are not or are only minimally driven by human activity." [] is_a: ENVO:00000020 ! lake property_value: editor_note "This class is to be filled by inference." xsd:string [Term] id: ENVO:01001023 name: radiation def: "A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium." [https://en.wikipedia.org/wiki/Radiation] subset: environmental_hazards subset: envoAstro is_a: ENVO:01001852 ! energy transfer process relationship: RO:0000057 CHEBI:36342 ! has participant subatomic particle relationship: RO:0000057 ENVO:00010483 ! has participant environmental material property_value: editor_note "Requires addition of waves for full axiomatisation. This should be linked to \"subatomic particle\" with an \"or\". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions)." xsd:string [Term] id: ENVO:01001024 name: particle radiation def: "A radiation process during which energy is transmitted or emitted by means of fast-moving subatomic particles." [https://en.wikipedia.org/wiki/Particle_radiation] subset: environmental_hazards subset: envoAstro is_a: ENVO:01001023 ! radiation [Term] id: ENVO:01001026 name: electromagnetic radiation def: "A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy." [https://en.wikipedia.org/wiki/Electromagnetic_radiation] comment: Note that this class is concerned only with active radiative processes: static electric and magnetic fields are not inlcuded. All electromagnetic radiation carries radiant energy. subset: environmental_hazards subset: envoAstro synonym: "EM radiation" EXACT [] is_a: ENVO:01001023 ! radiation [Term] id: ENVO:01001040 name: saline environment def: "An environment which is determined by materials which bear significant concentrations of salts." [] comment: The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request. subset: envoEmpo is_a: ENVO:01000314 ! high osmolarity environment is_a: ENVO:01000998 ! environmental system determined by a material property_value: IAO:0000118 "Saline" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/"} [Term] id: ENVO:01001044 name: soil environment def: "An environmental system which has its properties and dynamics determined by soil." [] subset: envoEmpo subset: envoOmics is_a: ENVO:01000997 ! environmental system determined by a quality is_a: ENVO:01000998 ! environmental system determined by a material intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 ENVO:00001998 ! determined by soil relationship: RO:0002507 ENVO:00001998 ! determined by soil property_value: IAO:0000118 "Soil (non-saline)" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/"} [Term] id: ENVO:01001048 name: sediment environment def: "An environmental system which has its properties and dynamics determined by sediment." [] subset: envoEmpo subset: envoOmics is_a: ENVO:01000997 ! environmental system determined by a quality is_a: ENVO:01000998 ! environmental system determined by a material intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 ENVO:00002007 ! determined by sediment relationship: RO:0002507 ENVO:00002007 ! determined by sediment [Term] id: ENVO:01001052 name: aerosol environment def: "An environmental system which has its properties and dynamics determined by an aerosol." [] subset: envoEmpo subset: envoOmics is_a: ENVO:01000997 ! environmental system determined by a quality is_a: ENVO:01000998 ! environmental system determined by a material intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002507 ENVO:00010505 ! determined by aerosol relationship: RO:0002507 ENVO:00010505 ! determined by aerosol [Term] id: ENVO:01001053 name: saline aerosol environment def: "An environmental system which has its properties and dynamics determined by a saline aerosol." [] subset: envoEmpo subset: envoOmics is_a: ENVO:01001040 ! saline environment is_a: ENVO:01001052 ! aerosol environment property_value: IAO:0000118 "Aerosol (saline)" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/", comment="seaspray or other aerosolized saline material (>5 psu)"} [Term] id: ENVO:01001054 name: non-saline aerosol environment def: "An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes." [] subset: envoEmpo subset: envoOmics is_a: ENVO:01001052 ! aerosol environment property_value: IAO:0000118 "Aerosol (non-saline)" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/", comment="aerosolized dust or liquid"} [Term] id: ENVO:01001057 name: environment associated with a plant part or small plant def: "An environmental system determined by part of a living or dead plant, or a whole small plant." [] subset: envoEmpo subset: envoMeo subset: envoOmics is_a: ENVO:01001110 ! ecosystem property_value: IAO:0000118 "Plant corpus" xsd:string {xref="http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/"} [Term] id: ENVO:01001068 name: meteoroid def: "An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids." [https://en.wikipedia.org/wiki/Meteoroid] subset: envoAstro is_a: ENVO:01000799 ! astronomical body relationship: has_quality PATO:0000587 ! decreased size [Term] id: ENVO:01001069 name: metallic material def: "A material which is composed primarily of one or more pure metals and which shows their properties." [] {comment="https://en.wikipedia.org/wiki/Metal"} comment: While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity. synonym: "metal" RELATED [] is_a: ENVO:00010483 ! environmental material relationship: composed_primarily_of CHEBI:33521 ! metal atom relationship: has_quality PATO:0000963 ! opaque relationship: RO:0000087 CHEBI:15022 ! has role electron donor property_value: editor_note "Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals." xsd:string [Term] id: ENVO:01001084 name: particulate matter formation process def: "A process during which microscopic solid or liquid objects are formed." [https://en.wikipedia.org/wiki/Particulates] synonym: "particle formation" RELATED [] is_a: ENVO:03000043 ! material transformation process relationship: RO:0002234 ENVO:01000060 ! has output particulate matter [Term] id: ENVO:01001085 name: atmospheric aerosol formation def: "An aerosol formation process which occurs in an atmosphere." [https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "atmospheric aerosol formation" EXACT [] is_a: ENVO:01001654 ! aerosol formation process is_a: ENVO:02500003 ! atmospheric process intersection_of: ENVO:01001654 ! aerosol formation process intersection_of: occurs_in ENVO:01000267 ! atmosphere [Term] id: ENVO:01001086 name: formation of a solid aerosol in an atmosphere def: "A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere." [https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "formation of solid particles in an atmosphere" RELATED [] is_a: ENVO:01001085 ! atmospheric aerosol formation intersection_of: ENVO:01001085 ! atmospheric aerosol formation intersection_of: RO:0002234 ENVO:01001089 ! has output aerosolised solids relationship: RO:0002234 ENVO:01001089 ! has output aerosolised solids [Term] id: ENVO:01001087 name: formation of a liquid aerosol in an atmosphere def: "A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere." [https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "formation of liquid droplets in an atmosphere" RELATED [] synonym: "formation of liquid particles in an atmosphere" RELATED [] is_a: ENVO:01001085 ! atmospheric aerosol formation intersection_of: ENVO:01001085 ! atmospheric aerosol formation intersection_of: RO:0002234 ENVO:01001088 ! has output aerosolised liquids relationship: RO:0002234 ENVO:01001088 ! has output aerosolised liquids [Term] id: ENVO:01001088 name: aerosolised liquids def: "An aerosol which has non-gaseous parts that are primarily composed of liquid droplets." [https://en.wikipedia.org/wiki/Aerosol] subset: envoAtmo synonym: "liquid aerosol" EXACT [] xref: SWEETRealm:Aerosol is_a: ENVO:00010505 ! aerosol relationship: surrounded_by ENVO:00002005 ! air [Term] id: ENVO:01001089 name: aerosolised solids def: "An aerosol which has non-gaseous parts that are primarily composed of solid particles." [https://en.wikipedia.org/wiki/Aerosol] subset: envoAtmo synonym: "solid aerosol" EXACT [] xref: SWEETRealm:Aerosol is_a: ENVO:00010505 ! aerosol relationship: surrounded_by ENVO:00002005 ! air [Term] id: ENVO:01001090 name: formation of a solid aerosol from gaseous material in an atmosphere def: "A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere." [https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "atmospheric formation of a solid aerosol" BROAD [] synonym: "formation of a solid aerosol in an atmosphere" BROAD [] synonym: "formation of a solid aerosol in the atmosphere" BROAD [] synonym: "formation of solid particles from gaseous material in an atmosphere" RELATED [] is_a: ENVO:01001086 ! formation of a solid aerosol in an atmosphere intersection_of: ENVO:01001086 ! formation of a solid aerosol in an atmosphere intersection_of: RO:0002233 ENVO:01000797 ! has input gaseous environmental material intersection_of: RO:0002234 ENVO:01001089 ! has output aerosolised solids relationship: RO:0002233 ENVO:01000797 ! has input gaseous environmental material [Term] id: ENVO:01001091 name: formation of a liquid aerosol from gaseous material in an atmosphere def: "A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere." [https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "atmospheric formation of a liquid aerosol" EXACT [] synonym: "formation of a liquid aerosol in an atmosphere" EXACT [] synonym: "formation of a liquid aerosol in the atmosphere" EXACT [] synonym: "formation of liquid droplets from gaseous material in an atmosphere" RELATED [] synonym: "formation of liquid particles from gaseous material in an atmosphere" RELATED [] is_a: ENVO:01001087 ! formation of a liquid aerosol in an atmosphere intersection_of: ENVO:01001087 ! formation of a liquid aerosol in an atmosphere intersection_of: RO:0002233 ENVO:01000797 ! has input gaseous environmental material intersection_of: RO:0002234 ENVO:01001088 ! has output aerosolised liquids relationship: RO:0002233 ENVO:01000797 ! has input gaseous environmental material [Term] id: ENVO:01001110 name: ecosystem alt_id: LTER:173 {xref="https://vocab.lternet.edu/vocab/vocab/index.php?tema=173&/ecosystems"} def: "An environmental system which includes both living and non-living components." [https://en.wikipedia.org/wiki/Ecosystem] comment: This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. is_a: ENVO:01000254 ! environmental system [Term] id: ENVO:01001122 name: gas planet def: "A planet which is primarily composed of hydrogen and helium." [http://solarsystem.nasa.gov/planets/whatisaplanet, https://en.wikipedia.org/wiki/List_of_planet_types, https://en.wikipedia.org/wiki/Planet] comment: Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants. subset: envoAstro is_a: ENVO:01000800 ! planet is_a: ENVO:01001686 ! mass of environmental material relationship: composed_primarily_of ENVO:01001155 ! astrogeological gas [Term] id: ENVO:01001125 name: ice def: "An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure." [] comment: Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure. is_a: ENVO:00010483 ! environmental material [Term] id: ENVO:01001136 name: ocean planet def: "A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water." [https://en.wikipedia.org/wiki/Ocean_planet] comment: While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b. subset: envoAstro synonym: "aquaplanet" EXACT [] synonym: "panthalassic planet" EXACT [] synonym: "water world" EXACT [] is_a: ENVO:01000800 ! planet property_value: editor_note "An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class." xsd:string [Term] id: ENVO:01001137 name: ice planet def: "A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice." [https://en.wikipedia.org/wiki/Ice_planet] comment: While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. {xref="https://en.wikipedia.org/wiki/Ice_planet"} subset: envoAstro synonym: "cryoplanet" EXACT [] is_a: ENVO:01000800 ! planet [Term] id: ENVO:01001138 name: carbon dioxide ice def: "Ice which is primarily composed of carbon dioxide." [https://en.wikipedia.org/wiki/Ice] subset: envoAstro synonym: "dry ice" RELATED [] is_a: ENVO:01001125 ! ice intersection_of: ENVO:01001125 ! ice intersection_of: composed_primarily_of CHEBI:16526 ! carbon dioxide relationship: composed_primarily_of CHEBI:16526 ! carbon dioxide [Term] id: ENVO:01001147 name: helium planet def: "A gas planet which has an atmosphere composed primarily of helium." [https://en.wikipedia.org/wiki/Helium_planet] comment: A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet. {xref="https://en.wikipedia.org/wiki/Helium_planet"} subset: envoAstro is_a: ENVO:01001122 ! gas planet property_value: editor_note "The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated." xsd:string [Term] id: ENVO:01001154 name: volatile astrogeological material def: "A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet." [https://en.wikipedia.org/wiki/Volatiles] comment: Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets. {xref="https://en.wikipedia.org/wiki/Volatiles"} subset: envoAstro synonym: "volatile" RELATED [] is_a: ENVO:00010483 ! environmental material property_value: editor_note "Add and axiomatise with moon and lunar crust" xsd:string [Term] id: ENVO:01001155 name: astrogeological gas def: "An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium." [https://en.wikipedia.org/wiki/Volatiles] comment: This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin. subset: envoAstro synonym: "gas" RELATED [] is_a: ENVO:01001154 ! volatile astrogeological material [Term] id: ENVO:01001164 name: geodiversity def: "A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms." [https://en.wikipedia.org/wiki/Geodiversity] comment: Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. {xref=""} is_a: PATO:0001241 ! physical object quality [Term] id: ENVO:01001176 name: environment associated with an aquatic invertebrate def: "An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system." [] subset: envoMeo subset: envoOmics xref: http://purl.jp/bio/11/meo/MEO_0000871 {comment="Not currently live, may need to be switched to alternative PURLs."} is_a: ENVO:01001002 ! animal-associated environment [Term] id: ENVO:01001191 name: water surface def: "The surface layer of a volume of water." [] synonym: "surface of a body of water" EXACT [] synonym: "water body surface" EXACT [] xref: EcoLexicon:surface_water xref: https://en.wikipedia.org/wiki/Surface_water xref: SWEETRealm:SurfaceWater is_a: ENVO:01000325 ! aquatic layer is_a: ENVO:01001310 ! liquid surface layer intersection_of: ENVO:01001310 ! liquid surface layer intersection_of: part_of ENVO:00002006 ! liquid water relationship: part_of ENVO:00002006 ! liquid water [Term] id: ENVO:01001192 name: sediment surface def: "The surface layer of a mass of sediment." [] synonym: "surface of a sedimentary mass" EXACT [] synonym: "surface sediment" EXACT [] is_a: ENVO:00010504 ! surface layer intersection_of: ENVO:00010504 ! surface layer intersection_of: part_of ENVO:00002007 ! sediment relationship: part_of ENVO:00002007 ! sediment [Term] id: ENVO:01001199 name: terrestrial environmental zone def: "An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it." [] is_a: ENVO:01000408 ! environmental zone intersection_of: ENVO:01000408 ! environmental zone intersection_of: part_of ENVO:01000635 ! planetary landmass relationship: part_of ENVO:00000446 ! terrestrial biome relationship: part_of ENVO:01000635 ! planetary landmass [Term] id: ENVO:01001200 name: anthropised terrestrial environmental zone def: "A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities." [] is_a: ENVO:01001199 ! terrestrial environmental zone intersection_of: ENVO:01001199 ! terrestrial environmental zone intersection_of: part_of ENVO:01000219 ! anthropogenic terrestrial biome relationship: part_of ENVO:01000219 ! anthropogenic terrestrial biome [Term] id: ENVO:01001201 name: marine environmental zone def: "An environmental zone which is bounded by material parts of a marine environment." [] comment: This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density. is_a: ENVO:01000408 ! environmental zone intersection_of: ENVO:01000408 ! environmental zone intersection_of: part_of ENVO:01000320 ! marine environment relationship: part_of ENVO:01000320 ! marine environment [Term] id: ENVO:01001211 name: stellar radiation def: "An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star." [https://en.wikipedia.org/wiki/Electromagnetic_radiation, https://en.wikipedia.org/wiki/Solar_irradiance] subset: environmental_hazards subset: envoAstro synonym: "solar radiation" NARROW [NCIT:C44445] xref: NCIT:C44445 is_a: ENVO:01001026 ! electromagnetic radiation intersection_of: ENVO:01001026 ! electromagnetic radiation intersection_of: RO:0002608 ENVO:01000801 ! process has causal agent star relationship: RO:0002608 ENVO:01000801 ! process has causal agent star [Term] id: ENVO:01001226 name: terrestrial natural environment def: "A natural environment which is located on a land mass." [] is_a: ENVO:01000951 ! natural environment intersection_of: ENVO:01000951 ! natural environment intersection_of: part_of ENVO:01000635 ! planetary landmass relationship: part_of ENVO:01000635 ! planetary landmass [Term] id: ENVO:01001227 name: aquatic natural environment def: "A natural environment which is within a water body." [] is_a: ENVO:01000951 ! natural environment intersection_of: ENVO:01000951 ! natural environment intersection_of: part_of ENVO:00000063 ! water body relationship: part_of ENVO:00000063 ! water body [Term] id: ENVO:01001273 name: liquid layer def: "A layer which is primarily composed of some liquid material." [] is_a: ENVO:01001678 ! fluid layer intersection_of: ENVO:01001678 ! fluid layer intersection_of: composed_primarily_of ENVO:01000815 ! liquid environmental material relationship: composed_primarily_of ENVO:01000815 ! liquid environmental material [Term] id: ENVO:01001275 name: solid layer def: "A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid." [] is_a: ENVO:01000281 ! layer intersection_of: ENVO:01000281 ! layer intersection_of: composed_primarily_of ENVO:01000814 ! solid environmental material relationship: composed_primarily_of ENVO:01000814 ! solid environmental material [Term] id: ENVO:01001276 name: water ice layer def: "A solid layer which is primarily composed of some water-based ice." [] is_a: ENVO:00000131 ! glacial feature is_a: ENVO:01001275 ! solid layer intersection_of: ENVO:01001275 ! solid layer intersection_of: composed_primarily_of ENVO:01000277 ! water ice relationship: composed_primarily_of ENVO:01000277 ! water ice [Term] id: ENVO:01001299 name: atmospheric zone def: "An environmental zone which is part of an atmosphere." [] synonym: "atmospheric area" EXACT [] is_a: ENVO:01000408 ! environmental zone intersection_of: ENVO:01000408 ! environmental zone intersection_of: part_of ENVO:01000267 ! atmosphere relationship: part_of ENVO:01000267 ! atmosphere [Term] id: ENVO:01001308 name: hydroform def: "A geographic feature which is primarily composed of a continuous volume of liquid water held in shape or sustained by an environmental process." [] comment: Similar, in spirit, to landform. is_a: ENVO:01001477 ! liquid astronomical body part intersection_of: ENVO:01001477 ! liquid astronomical body part intersection_of: composed_primarily_of ENVO:00002006 ! liquid water intersection_of: part_of ENVO:00000063 ! water body relationship: composed_primarily_of ENVO:00002006 ! liquid water relationship: contains_process ENVO:01000982 ! water flow process relationship: part_of ENVO:00000063 ! water body property_value: editor_note "Should create links to envrionmental process with new relation like \"sustained_by\"" xsd:string {created_by="ORCID:0000-0002-4366-3088"} [Term] id: ENVO:01001309 name: liquid air-water interface layer def: "A liquid surface layer which is in contact with air." [] is_a: ENVO:01001310 ! liquid surface layer intersection_of: ENVO:01001310 ! liquid surface layer intersection_of: adjacent_to ENVO:00002005 ! air relationship: adjacent_to ENVO:00002005 ! air [Term] id: ENVO:01001310 name: liquid surface layer def: "A surface layer which is composed primarily of some liquid." [] is_a: ENVO:01001273 ! liquid layer is_a: ENVO:01001673 ! fluid surface layer intersection_of: ENVO:01001673 ! fluid surface layer intersection_of: composed_primarily_of ENVO:01000815 ! liquid environmental material [Term] id: ENVO:01001311 name: solid surface layer def: "A surface layer which is composed primarily of solid environmental material." [] is_a: ENVO:00010504 ! surface layer is_a: ENVO:01001275 ! solid layer intersection_of: ENVO:00010504 ! surface layer intersection_of: composed_primarily_of ENVO:01000814 ! solid environmental material [Term] id: ENVO:01001319 name: saline water body def: "A body of water which is primarily composed of saline water." [] comment: This class has its subclasses populated by inference. synonym: "saline body of water" EXACT [] is_a: ENVO:00000063 ! water body intersection_of: ENVO:00000063 ! water body intersection_of: composed_primarily_of ENVO:00002010 ! saline water relationship: composed_primarily_of ENVO:00002010 ! saline water [Term] id: ENVO:01001334 name: advective transport process def: "A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged." [https://en.wikipedia.org/wiki/Advection, https://en.wikipedia.org/wiki/Intensive_and_extensive_properties] comment: Advective processes are disjoint from diffusive processes. Typically, fluids are advected. synonym: "advective transport" EXACT [] is_a: ENVO:03000010 ! material transport process [Term] id: ENVO:01001346 name: erosion def: "An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited." [https://en.wikipedia.org/wiki/Erosion] is_a: ENVO:03000010 ! material transport process relationship: RO:0000057 ENVO:00010483 ! has participant environmental material relationship: RO:0000057 ENVO:01000638 ! has participant planetary crust [Term] id: ENVO:01001357 name: desert def: "A landform which has been rendered barren or partially barren by environmental extremes, especially by low rainfall." [] is_a: ENVO:00000191 ! solid astronomical body part relationship: overlaps ENVO:00000097 ! desert area [Term] id: ENVO:01001366 name: aerosolised particle formation process def: "A process during which particles suspended in a gaseous medium are formed." [https://en.wikipedia.org/wiki/Aerosol, https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "new particle formation process" EXACT [] is_a: ENVO:01001084 ! particulate matter formation process relationship: part_of ENVO:01001654 ! aerosol formation process relationship: RO:0002233 ENVO:01000797 ! has input gaseous environmental material [Term] id: ENVO:01001367 name: primary aerosol formation process def: "A material transport process during which solid or liquid particles are directly introduced into a volume of gas." [https://en.wikipedia.org/wiki/Aerosol, https://en.wikipedia.org/wiki/Particulates] synonym: "primary aerosol formation" RELATED [] is_a: ENVO:03000010 ! material transport process relationship: RO:0002234 ENVO:00010505 ! has output aerosol [Term] id: ENVO:01001434 name: anthropogenic ecosystem conversion process def: "A process during which an ecosystem - natural or anthropised - is changed by the actions of humans." [] is_a: ENVO:02500027 ! anthropogenic environmental process created_by: http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:01001476 name: body of liquid is_a: ENVO:01001477 ! liquid astronomical body part created_by: http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:01001477 name: liquid astronomical body part def: "A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes." [https://en.wikipedia.org/wiki/Landform] is_a: ENVO:01001479 ! fluid astronomical body part is_a: ENVO:01001784 ! compound astronomical body part intersection_of: ENVO:01001479 ! fluid astronomical body part intersection_of: composed_primarily_of ENVO:01000815 ! liquid environmental material relationship: composed_primarily_of ENVO:01000815 ! liquid environmental material created_by: http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:01001478 name: gaseous astronomical body part def: "A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes." [https://en.wikipedia.org/wiki/Landform] is_a: ENVO:01001479 ! fluid astronomical body part is_a: ENVO:01001784 ! compound astronomical body part intersection_of: ENVO:01001479 ! fluid astronomical body part intersection_of: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: composed_primarily_of ENVO:01000797 ! gaseous environmental material created_by: http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:01001479 name: fluid astronomical body part def: "A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes." [https://en.wikipedia.org/wiki/Landform] is_a: ENVO:01000813 ! astronomical body part created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2018-10-04T13:59:22Z [Term] id: ENVO:01001483 name: surface of an astronomical body def: "A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space." [] comment: a useful class: this can be used to define sub-terrestrial and sub-marine entities is_a: ENVO:00010504 ! surface layer intersection_of: ENVO:00010504 ! surface layer intersection_of: part_of ENVO:01000799 ! astronomical body relationship: part_of ENVO:01000799 ! astronomical body created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2018-10-04T16:55:57Z [Term] id: ENVO:01001488 name: aircraft def: "A vehicle which is able to travel through air in an atmosphere." [https://en.wikipedia.org/wiki/Aircraft] is_a: ENVO:01000604 ! vehicle created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2018-10-04T19:28:01Z [Term] id: ENVO:01001501 name: radiation from a manufactured product def: "An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product." [https://en.wikipedia.org/wiki/Electromagnetic_radiation, https://en.wikipedia.org/wiki/Solar_irradiance] subset: environmental_hazards subset: envoAstro synonym: "anthropogenic radiation" BROAD [] synonym: "artificial radiation" EXACT [] is_a: ENVO:01001026 ! electromagnetic radiation intersection_of: ENVO:01001026 ! electromagnetic radiation intersection_of: RO:0002608 ENVO:00003074 ! process has causal agent manufactured product relationship: RO:0002608 ENVO:00003074 ! process has causal agent manufactured product created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-01-09T09:07:24Z [Term] id: ENVO:01001510 name: material congelation process def: "A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects." [https://en.wikipedia.org/wiki/Congelation] comment: Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. {xref="https://en.wikipedia.org/wiki/Congelation"} synonym: "congelation" EXACT [] synonym: "congelation process" EXACT [] is_a: ENVO:03000043 ! material transformation process created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-01-14T18:47:32Z [Term] id: ENVO:01001524 name: frozen land def: "Land which is below the freezing point of water." [https://orcid.org/0000-0003-4808-4736] comment: Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. {xref="https://orcid.org/0000-0003-4808-4736"} synonym: "frozen ground" EXACT [] xref: http://sweetontology.net/realmCryo/FrozenGround is_a: ENVO:01001785 ! land intersection_of: ENVO:01001785 ! land intersection_of: has_quality PATO:0001985 ! frozen relationship: has_quality PATO:0001985 ! frozen created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-01-14T21:18:19Z [Term] id: ENVO:01001526 name: frozen soil def: "Soil which is below the freezing point of water." [] is_a: ENVO:00001998 ! soil intersection_of: ENVO:00001998 ! soil intersection_of: has_quality PATO:0001985 ! frozen relationship: has_quality PATO:0001985 ! frozen relationship: part_of ENVO:01001524 ! frozen land created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-01-14T21:26:59Z [Term] id: ENVO:01001548 name: freezing def: "A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point." [https://en.wikipedia.org/wiki/Freezing] subset: envoPolar xref: http://sweetontology.net/procStateChange/Freezing is_a: ENVO:01001510 ! material congelation process created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-01-31T21:13:16Z [Term] id: ENVO:01001549 name: freezing of water into water ice def: "A freezing process during which liquid water is transformed into water ice." [] is_a: ENVO:01001548 ! freezing is_a: ENVO:02500031 ! hydrological process intersection_of: ENVO:01001548 ! freezing intersection_of: RO:0002233 ENVO:00002006 ! has input liquid water intersection_of: RO:0002234 ENVO:01000277 ! has output water ice relationship: RO:0002233 ENVO:00002006 ! has input liquid water relationship: RO:0002234 ENVO:01000277 ! has output water ice created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-01-31T21:16:46Z [Term] id: ENVO:01001554 name: surface layer of a water body def: "A water surface that is part of a water body." [] is_a: ENVO:01001191 ! water surface is_a: ENVO:01001483 ! surface of an astronomical body intersection_of: ENVO:01001191 ! water surface intersection_of: part_of ENVO:00000063 ! water body relationship: part_of ENVO:00000063 ! water body created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-02-27T21:22:13Z [Term] id: ENVO:01001570 name: terrestrial ecoregion def: "An ecoregion which is located on a landmass." [] xref: https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions is_a: ENVO:01000276 ! ecoregion relationship: adjacent_to ENVO:01000635 ! planetary landmass created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-03-05T17:40:44Z [Term] id: ENVO:01001581 name: sea surface layer def: "A surface layer which is part of an ocean or sea." [] comment: At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases.\nSea surface layer is also used to refer to the surfaces of oceans. subset: envoMarine subset: envoPlastics is_a: ENVO:01000295 ! marine layer is_a: ENVO:01001554 ! surface layer of a water body property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-2996-719X property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-8166-0486 property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0003-1072-8081 created_by: http://orcid.org/0000-0002-4366-3088 creation_date: 2019-03-06T01:22:01Z [Term] id: ENVO:01001609 name: cryospheric layer def: "A layer which is part of a cryosphere." [] subset: envoPolar is_a: ENVO:01000281 ! layer intersection_of: ENVO:01000281 ! layer intersection_of: part_of ENVO:01000818 ! cryosphere relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: part_of ENVO:01000818 ! cryosphere creation_date: 2019-04-09T13:05:25Z [Term] id: ENVO:01001614 name: ice-bearing permafrost def: "Permafrost which contains inclusions of water-based ice." [] is_a: ENVO:00000134 ! permafrost intersection_of: ENVO:00000134 ! permafrost intersection_of: has_part ENVO:01000277 ! water ice relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: has_part ENVO:01000277 ! water ice creation_date: 2019-04-09T13:45:40Z [Term] id: ENVO:01001617 name: snow accumulation process def: "A material accumulation process during which the mass of snow on a surface increases." [http://orcid.org/0000-0003-4808-4736] comment: This term is used both as a process and as an amount of mass added. Semantically speaking these are two distinct concepts (e.g., accumulation results in accumulation_amount of ice or snow gain), though accumulation_amount would more likely be an attribute.\n\nThe scope of this term varies depending on the definition. Some definitions constrain themselves snow or ice added to glaciers; while others also include ice fields, snow cover, and/or floating ice. How to resolve this depends on the scope desired.\n\nSome definitions include additional discussion of the the physics involved which would be useful for connecting glacier ontologies to atmospheric, hydrologic, etc. ontologies. This information should be captured no matter how the inconsistencies above are resolved. xref: http://sweetontology.net/phenCryo/Accumulation is_a: ENVO:03000009 ! material accumulation process relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: results_in_formation_of ENVO:03000111 ! snow mass relationship: RO:0000057 ENVO:00010504 ! has participant surface layer relationship: RO:0000057 ENVO:01000406 ! has participant snow creation_date: 2019-04-24T18:29:18Z [Term] id: ENVO:01001618 name: ice accumulation process def: "A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass." [http://orcid.org/0000-0003-4808-4736] xref: http://sweetontology.net/phenCryo/Accumulation is_a: ENVO:02500031 ! hydrological process is_a: ENVO:03000009 ! material accumulation process relationship: dc-creator http://orcid.org/0000-0002-4366-3088 creation_date: 2019-04-24T18:48:53Z [Term] id: ENVO:01001619 name: snow and ice accumulation process def: "A material accumulation process during which a accumulation of snow and ice forms or increases in mass." [http://orcid.org/0000-0003-4808-4736] xref: http://sweetontology.net/phenCryo/Accumulation is_a: ENVO:02500031 ! hydrological process intersection_of: ENVO:03000009 ! material accumulation process intersection_of: results_in_formation_of ENVO:01001620 ! mass of ice and snow relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: results_in_formation_of ENVO:01001620 ! mass of ice and snow creation_date: 2019-04-24T18:59:45Z [Term] id: ENVO:01001620 name: mass of ice and snow def: "A object which is composed primarily of water-based snow and ice." [] xref: http://sweetontology.net/phenCryo/Accumulation is_a: ENVO:01000293 ! ice mass relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0002354 ENVO:01001619 ! formed as result of snow and ice accumulation process creation_date: 2019-04-24T19:08:03Z [Term] id: ENVO:01001639 name: formation of a solid aerosol from liquid material in an atmosphere def: "A process during which microscopic solid particulates are formed from liquid materials in an atmosphere." [https://en.wikipedia.org/wiki/Particulates] subset: envoAtmo synonym: "atmospheric formation of a solid aerosol" BROAD [] synonym: "formation of a solid aerosol in an atmosphere" BROAD [] synonym: "formation of a solid aerosol in the atmosphere" BROAD [] synonym: "formation of solid particles from liquid material in an atmosphere" EXACT [] is_a: ENVO:01001086 ! formation of a solid aerosol in an atmosphere intersection_of: ENVO:01001086 ! formation of a solid aerosol in an atmosphere intersection_of: RO:0002233 ENVO:01000815 ! has input liquid environmental material intersection_of: RO:0002234 ENVO:01001089 ! has output aerosolised solids relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0002233 ENVO:01000815 ! has input liquid environmental material creation_date: 2019-05-30T21:07:51Z [Term] id: ENVO:01001645 name: gaseous part of an atmosphere def: "That part of an atmosphere which is composed of gaseous material." [] xref: http://vocab.nerc.ac.uk/collection/S23/current/S23C013/ is_a: ENVO:01001478 ! gaseous astronomical body part intersection_of: ENVO:01001478 ! gaseous astronomical body part intersection_of: part_of ENVO:01000267 ! atmosphere relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: part_of ENVO:01000267 ! atmosphere creation_date: 2019-06-02T07:52:47Z [Term] id: ENVO:01001646 name: amorphous solid def: "A solid material which does not have a regularly organised internal structure." [] xref: http://vocab.nerc.ac.uk/collection/S23/current/S23C014/ is_a: ENVO:01000814 ! solid environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 creation_date: 2019-06-02T11:07:47Z [Term] id: ENVO:01001652 name: atmospheric aerosol def: "An aerosol that is suspended in an atmosphere." [] xref: http://vocab.nerc.ac.uk/collection/S23/current/S23C005/ is_a: ENVO:00010505 ! aerosol intersection_of: ENVO:00010505 ! aerosol intersection_of: part_of ENVO:01000267 ! atmosphere relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: part_of ENVO:01000267 ! atmosphere creation_date: 2019-06-03T12:24:09Z [Term] id: ENVO:01001654 name: aerosol formation process def: "A material transformation process during which solid or liquid particles form and are suspended in a mass of air, thus creating an aerosol." [] is_a: ENVO:03000043 ! material transformation process intersection_of: ENVO:03000043 ! material transformation process intersection_of: RO:0002234 ENVO:00010505 ! has output aerosol relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: has_part ENVO:01001366 ! aerosolised particle formation process relationship: RO:0002234 ENVO:00010505 ! has output aerosol property_value: http://purl.org/dc/elements/1.1/date 2019-06-24T13:43:29Z xsd:dateTime [Term] id: ENVO:01001673 name: fluid surface layer def: "A surface layer which is composed primarily of some liquid or gas." [] is_a: ENVO:00010504 ! surface layer is_a: ENVO:01001677 ! fluid interface layer relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T08:28:42Z xsd:dateTime [Term] id: ENVO:01001677 name: fluid interface layer def: "A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface." [http://glossary.ametsoc.org/wiki/Interface] is_a: ENVO:01001678 ! fluid layer is_a: ENVO:01001684 ! interface layer relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-07-22T17:29:44Z xsd:dateTime [Term] id: ENVO:01001678 name: fluid layer def: "A layer which is composed primarily of some fluid." [] is_a: ENVO:01000281 ! layer relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-07-22T17:35:08Z xsd:dateTime [Term] id: ENVO:01001679 name: fluid front def: "A fluid interface which separates two fluid masses with differing properties." [http://glossary.ametsoc.org/wiki/Front, http://ww2010.atmos.uiuc.edu/(Gh)/guides/mtr/af/frnts/home.rxml, https://en.wikipedia.org/wiki/Front_(oceanography), https://en.wikipedia.org/wiki/Weather_front] is_a: ENVO:01001677 ! fluid interface layer relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-07-22T17:43:32Z xsd:dateTime [Term] id: ENVO:01001680 name: gaseous front def: "A fluid front which is composed primarily of gaseous material and separates at least two gaseous masses." [] is_a: ENVO:01001679 ! fluid front intersection_of: ENVO:01001679 ! fluid front intersection_of: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-07-22T17:50:08Z xsd:dateTime [Term] id: ENVO:01001681 name: weather front def: "A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena." [http://glossary.ametsoc.org/wiki/Front, https://en.wikipedia.org/wiki/Weather_front] comment: This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms." {xref="http://glossary.ametsoc.org/wiki/Front"} subset: envoAtmo synonym: "meteorological front" EXACT [] is_a: ENVO:01000543 ! atmospheric layer is_a: ENVO:01001680 ! gaseous front intersection_of: ENVO:01001680 ! gaseous front intersection_of: composed_primarily_of ENVO:00002005 ! air intersection_of: part_of ENVO:01000267 ! atmosphere relationship: adjacent_to ENVO:01001682 {minCardinality="2"} ! air mass relationship: composed_primarily_of ENVO:00002005 ! air relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0002500 ENVO:02500003 ! causal agent in process atmospheric process property_value: http://purl.org/dc/elements/1.1/date 2019-07-22T17:57:21Z xsd:dateTime [Term] id: ENVO:01001682 name: air mass def: "An object which is composed of a continuous mass of air." [] subset: envoAtmo is_a: ENVO:01001689 ! mass of gas intersection_of: ENVO:01001689 ! mass of gas intersection_of: composed_primarily_of ENVO:00002005 ! air relationship: composed_primarily_of ENVO:00002005 ! air relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T07:54:32Z xsd:dateTime [Term] id: ENVO:01001683 name: gaseous surface layer def: "A fluid surface layer which is composed primarily of some gaseous material." [] is_a: ENVO:01001673 ! fluid surface layer intersection_of: ENVO:01001673 ! fluid surface layer intersection_of: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T08:30:01Z xsd:dateTime [Term] id: ENVO:01001684 name: interface layer def: "A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface." [] is_a: ENVO:01000281 ! layer relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:28:10Z xsd:dateTime [Term] id: ENVO:01001686 name: mass of environmental material def: "An object which is composed primarily of an environmental material" [] comment: This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. is_a: BFO:0000030 ! object intersection_of: BFO:0000030 ! object intersection_of: composed_primarily_of ENVO:00010483 ! environmental material relationship: composed_primarily_of ENVO:00010483 ! environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:38:29Z xsd:dateTime [Term] id: ENVO:01001687 name: mass of solid material def: "An object which is composed primarily of a solid environmental material" [] comment: This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. is_a: ENVO:01001686 ! mass of environmental material intersection_of: ENVO:01001686 ! mass of environmental material intersection_of: composed_primarily_of ENVO:01000814 ! solid environmental material relationship: composed_primarily_of ENVO:01000814 ! solid environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:41:27Z xsd:dateTime [Term] id: ENVO:01001688 name: mass of fluid def: "An object which is composed primarily of a fluid." [] comment: This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. synonym: "fluid mass" EXACT [] is_a: ENVO:01001686 ! mass of environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:42:35Z xsd:dateTime [Term] id: ENVO:01001689 name: mass of gas def: "An object which is composed primarily of a gas." [] comment: This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. synonym: "gaseous mass" EXACT [] is_a: ENVO:01001688 ! mass of fluid intersection_of: ENVO:01001688 ! mass of fluid intersection_of: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: composed_primarily_of ENVO:01000797 ! gaseous environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:44:01Z xsd:dateTime [Term] id: ENVO:01001690 name: mass of liquid def: "An object which is composed primarily of a liquid." [] comment: This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. synonym: "liquid mass" EXACT [] is_a: ENVO:01001688 ! mass of fluid intersection_of: ENVO:01001688 ! mass of fluid intersection_of: composed_primarily_of ENVO:01000815 ! liquid environmental material relationship: composed_primarily_of ENVO:01000815 ! liquid environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:45:03Z xsd:dateTime [Term] id: ENVO:01001691 name: mass of compounded environmental materials def: "An mass of environmental materials which has appreciable quantities of several individual materials, such that the removal of one would convert the mass into a different entity." [] is_a: ENVO:01001686 ! mass of environmental material intersection_of: ENVO:01001686 ! mass of environmental material intersection_of: composed_primarily_of ENVO:00010483 {minCardinality="2"} ! environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T09:47:10Z xsd:dateTime [Term] id: ENVO:01001698 name: polar front def: "A weather front which separates air masses of tropical and polar origin." [http://glossary.ametsoc.org/wiki/Polar_front] subset: envoAtmo subset: envoPolar is_a: ENVO:01001681 ! weather front relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-08-20T13:46:42Z xsd:dateTime [Term] id: ENVO:01001747 name: mass fluid flow is_a: ENVO:01001334 ! advective transport process relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-09-05T05:47:26Z xsd:dateTime [Term] id: ENVO:01001776 name: subsurface zone of an astronomical body def: "An environmental zone which includes those regions of an astronomical body which are not exposed to its atmosphere or space." [] is_a: ENVO:01000408 ! environmental zone relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: part_of ENVO:01000799 ! astronomical body property_value: http://purl.org/dc/elements/1.1/date 2019-10-07T14:22:38Z xsd:dateTime [Term] id: ENVO:01001780 name: desert ecosystem def: "An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert." [] is_a: ENVO:01001110 ! ecosystem intersection_of: ENVO:01001110 ! ecosystem intersection_of: RO:0002507 ENVO:01001357 ! determined by desert relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0002507 ENVO:01001357 ! determined by desert property_value: http://purl.org/dc/elements/1.1/date 2019-10-17T08:21:08Z xsd:dateTime [Term] id: ENVO:01001781 name: part of a landmass def: "A solid astronomical body part which is part of the landmass of that body." [] is_a: ENVO:00000191 ! solid astronomical body part intersection_of: ENVO:00000191 ! solid astronomical body part intersection_of: part_of ENVO:01000635 ! planetary landmass relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: part_of ENVO:01000635 ! planetary landmass property_value: http://purl.org/dc/elements/1.1/date 2019-10-17T08:27:17Z xsd:dateTime [Term] id: ENVO:01001782 name: landmass def: "A large continuous area of land, either surrounded by sea or contiguous with another landmass." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://en.wiktionary.org/wiki/landmass"} is_a: ENVO:01001785 ! land relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-10-17T08:31:26Z xsd:dateTime [Term] id: ENVO:01001784 name: compound astronomical body part def: "A part of an astronomical body which is primarily composed of a continuous medium bearing liquid, gaseous, and solid material in varying quantities." [https://en.wikipedia.org/wiki/Landform] is_a: ENVO:01000813 ! astronomical body part relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-10-17T08:36:00Z xsd:dateTime [Term] id: ENVO:01001785 name: land def: "A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water." [https://en.wiktionary.org/wiki/land] is_a: ENVO:01001311 ! solid surface layer is_a: ENVO:01001483 ! surface of an astronomical body relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-10-21T10:42:26Z xsd:dateTime [Term] id: ENVO:01001787 name: aquatic ecosystem is_a: ENVO:01001110 ! ecosystem intersection_of: ENVO:01001110 ! ecosystem intersection_of: RO:0002507 ENVO:00000063 ! determined by water body relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0002507 ENVO:00000063 ! determined by water body property_value: http://purl.org/dc/elements/1.1/date 2019-10-21T11:05:45Z xsd:dateTime [Term] id: ENVO:01001788 name: marine ecosystem is_a: ENVO:01000320 ! marine environment is_a: ENVO:01001787 ! aquatic ecosystem intersection_of: ENVO:01001787 ! aquatic ecosystem intersection_of: RO:0002507 ENVO:00001999 ! determined by marine water body relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2019-10-21T11:06:11Z xsd:dateTime [Term] id: ENVO:01001795 name: ecosystem process def: "An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem." [] is_a: ENVO:02500000 ! environmental system process intersection_of: ENVO:02500000 ! environmental system process intersection_of: RO:0002608 ENVO:01001110 ! process has causal agent ecosystem relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0002608 ENVO:01001110 ! process has causal agent ecosystem property_value: http://purl.org/dc/elements/1.1/date 2019-10-21T11:52:55Z xsd:dateTime [Term] id: ENVO:01001836 name: montane biome def: "A biome which is subject to montane altitudinal conditions." [] is_a: ENVO:00000428 ! biome intersection_of: ENVO:00000428 ! biome intersection_of: has_quality ENVO:01000342 ! montane relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: has_quality ENVO:01000342 ! montane property_value: http://purl.org/dc/elements/1.1/date 2019-11-06T16:00:33Z xsd:dateTime [Term] id: ENVO:01001838 name: arid biome def: "A biome which is subject to arid environmental conditions." [] is_a: ENVO:00000428 ! biome intersection_of: ENVO:00000428 ! biome intersection_of: has_quality ENVO:01000230 ! arid relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: has_quality ENVO:01000230 ! arid property_value: http://purl.org/dc/elements/1.1/date 2019-11-06T16:06:47Z xsd:dateTime [Term] id: ENVO:01001852 name: energy transfer process def: "A process during which one entity loses energy to another entity." [] is_a: ENVO:02500000 ! environmental system process relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2020-02-13T13:34:28Z xsd:dateTime [Term] id: ENVO:01001856 name: liquid accumulation process def: "A material accumulation process during which the volume of liquid entity increases." [] is_a: ENVO:03000009 ! material accumulation process intersection_of: ENVO:03000009 ! material accumulation process intersection_of: RO:0000057 ENVO:01000815 ! has participant liquid environmental material relationship: dc-creator http://orcid.org/0000-0002-4366-3088 relationship: RO:0000057 ENVO:01000815 ! has participant liquid environmental material property_value: http://purl.org/dc/elements/1.1/date 2020-05-18T14:39:20Z xsd:dateTime [Term] id: ENVO:01001865 name: concentration of carbon dioxide in an atmosphere def: "The concentration of carbon dioxide when measured in air that is part of an atmosphere." [] subset: envoAtmo subset: envoNceas is_a: PATO:0000033 ! concentration of relationship: dc-creator http://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/elements/1.1/date 2020-05-19T22:51:38Z xsd:dateTime [Term] id: ENVO:02000140 name: fluid environmental material def: "A liquid or a gas." [https://github.com/EnvironmentOntology/envo/issues/940] synonym: "fluid" NARROW [] is_a: ENVO:00010483 ! environmental material union_of: ENVO:01000797 ! gaseous environmental material union_of: ENVO:01000798 ! plasma union_of: ENVO:01000815 ! liquid environmental material [Term] id: ENVO:02500000 name: environmental system process def: "A process in which includes the components of an environmental system as participants." [] comment: This is a convenience class for organisation and should not be used for annotation. is_a: BFO:0000015 ! process [Term] id: ENVO:02500003 name: atmospheric process def: "A process which occurs within an atmosphere." [] comment: This class will be populated by inference and is primarily organisational. is_a: ENVO:02500000 ! environmental system process intersection_of: ENVO:02500000 ! environmental system process intersection_of: occurs_in ENVO:01000267 ! atmosphere relationship: occurs_in ENVO:01000267 ! atmosphere [Term] id: ENVO:02500027 name: anthropogenic environmental process def: "An environmental process which is driven by the action of humans." [] is_a: ENVO:02500000 ! environmental system process intersection_of: ENVO:02500000 ! environmental system process intersection_of: RO:0002608 NCBITaxon:9606 ! process has causal agent Homo sapiens relationship: RO:0002608 NCBITaxon:9606 ! process has causal agent Homo sapiens [Term] id: ENVO:02500028 name: planetary erosion def: "An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited." [https://en.wikipedia.org/wiki/Erosion] subset: envoPolar is_a: ENVO:01001346 ! erosion [Term] id: ENVO:02500031 name: hydrological process def: "An environmental process which has water - in any of its states - as a participant." [] comment: This classes asserted subclasses will be moved away as it should be an inferred class. is_a: ENVO:02500000 ! environmental system process [Term] id: ENVO:03000008 name: compaction process def: "A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together." [https://en.wikipedia.org/wiki/Compaction] subset: envoPolar is_a: ENVO:02500000 ! environmental system process property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000009 name: material accumulation process def: "A process during which the mass of one or more materials, present within a given site, increases." [] comment: Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process. subset: envoPolar is_a: ENVO:02500000 ! environmental system process property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000010 name: material transport process def: "A process during which material is displaced from its original location and transported either to a new location or back to the original location." [] comment: Experimental class for structural purposes not recommended for annotation. subset: envoPolar is_a: ENVO:02500000 ! environmental system process property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000015 name: geographic basin def: "A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed." [https://en.wikipedia.org/wiki/Basin] subset: envoPolar is_a: ENVO:00000309 ! depression relationship: overlaps ENVO:01000638 ! planetary crust property_value: editor_note "The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000033 name: marine sediment def: "Sediment which has been transported through the marine water column, settling on the seafloor." [https://en.wikipedia.org/wiki/Pelagic_sediment#_note-8] comment: Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input. subset: envoPolar synonym: "marine sediments" EXACT [] is_a: ENVO:00002007 ! sediment relationship: adjacent_to ENVO:00001999 ! marine water body relationship: output_of ENVO:03000036 ! sedimentation in a water body property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000036 name: sedimentation in a water body def: "A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface." [] subset: envoPolar is_a: ENVO:03000009 ! material accumulation process relationship: ends ENVO:03000010 ! material transport process relationship: has_part ENVO:01000875 ! precipitation process relationship: occurs_in ENVO:00000063 ! water body relationship: RO:0000057 ENVO:01000060 ! has participant particulate matter property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000043 name: material transformation process def: "A process during which a portion of some environmental material is converted into a different material or a collection of materials." [] comment: Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another. subset: envoPolar is_a: ENVO:02500000 ! environmental system process relationship: RO:0002233 ENVO:00010483 ! has input environmental material relationship: RO:0002234 ENVO:00010483 ! has output environmental material property_value: editor_note "A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies." xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000055 name: desublimation of water vapour into ice def: "A desublimation process during which water vapour is frozen into water ice." [] subset: envoPolar is_a: ENVO:01000726 ! desublimation process is_a: ENVO:02500031 ! hydrological process relationship: RO:0002233 ENVO:00002006 ! has input liquid water property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000110 name: cryoform def: "A geographic feature which is primarily composed of a continuous mass of snow and/or ice." [] subset: envoPolar is_a: ENVO:00000191 ! solid astronomical body part property_value: editor_note "Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported." xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03000111 name: snow mass def: "A mass of snow." [] subset: envoPolar synonym: "accumulation of snow" BROAD [] synonym: "snow accumulation" BROAD [] xref: http://sweetontology.net/phenCryo/Accumulation is_a: ENVO:00000131 ! glacial feature is_a: ENVO:01001691 ! mass of compounded environmental materials intersection_of: ENVO:01001691 ! mass of compounded environmental materials intersection_of: composed_primarily_of ENVO:01000406 ! snow relationship: composed_primarily_of ENVO:01000406 ! snow relationship: RO:0002354 ENVO:01001617 ! formed as result of snow accumulation process property_value: IAO:0000117 http://orcid.org/0000-0002-3410-4655 xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 [Term] id: ENVO:03520007 name: snow crystal def: "A water ice crystal which is constituted by water molecules aligned in a hexagonal array." [http://www.snowcrystals.com/science/science.html, https://www.athropolis.com/arctic-facts/fact-snow-crystal.htm, https://www.noaa.gov/stories/how-do-snowflakes-form-science-behind-snow] synonym: "snowflake" BROAD [] {comment="Snow crystals and snowflakes are often noted as synonyms, however, the term \"snowflake\" is generally used more loosely. Some sites mention that snow crystals refer to individual crystals of ice, while the term \"snowflake\" can refer both to an individual crystal of ice and to a bundle of snow crystals. Please see here [https://github.com/EnvironmentOntology/envo/issues/998#issuecomment-685649444]"} is_a: ENVO:01000846 ! water ice crystal relationship: dc-creator http://orcid.org/0000-0002-2996-719X [Term] id: ENVO:04000003 name: concentration of carbon dioxide in soil def: "The concentration of carbon dioxide when measured in soil." [] subset: envoNceas is_a: PATO:0000033 ! concentration of relationship: dc-creator http://orcid.org/0000-0003-1264-1166 property_value: http://purl.org/dc/elements/1.1/date 2019-03-14T21:13:30Z xsd:dateTime [Term] id: ENVO:04000004 name: concentration of carbon dioxide in air def: "The concentration of carbon dioxide when measured in air." [] subset: envoNceas is_a: PATO:0000033 ! concentration of relationship: dc-creator http://orcid.org/0000-0003-1264-1166 property_value: http://purl.org/dc/elements/1.1/date 2019-03-14T21:24:04Z xsd:dateTime [Term] id: ENVO:04000006 name: concentration of carbon dioxide in seawater def: "The concentration of carbon dioxide when measured in seawater." [] subset: envoNceas is_a: PATO:0000033 ! concentration of relationship: dc-creator http://orcid.org/0000-0003-1264-1166 property_value: http://purl.org/dc/elements/1.1/date 2019-03-14T21:35:30Z xsd:dateTime [Term] id: ENVO:04000010 name: soil surface layer def: "A surface layer which is composed primarily of soil." [] subset: envoNceas is_a: ENVO:01001311 ! solid surface layer is_a: ENVO:01001483 ! surface of an astronomical body intersection_of: ENVO:01001311 ! solid surface layer intersection_of: composed_primarily_of ENVO:00001998 ! soil relationship: composed_primarily_of ENVO:00001998 ! soil relationship: dc-creator http://orcid.org/0000-0003-1264-1166 relationship: part_of ENVO:01000820 ! pedosphere property_value: http://purl.org/dc/elements/1.1/date 2019-04-12T17:35:13Z xsd:dateTime [Term] id: ENVO:09200000 name: temperature of environmental material def: "The temperature of some environmental material." [] synonym: "environmental material temperature" EXACT [] is_a: PATO:0000146 ! temperature intersection_of: PATO:0000146 ! temperature intersection_of: RO:0000052 ENVO:00010483 ! inheres in environmental material relationship: RO:0000052 ENVO:00010483 ! inheres in environmental material [Term] id: ENVO:09200001 name: temperature of air def: "The temperature of some air." [] synonym: "air temperature" EXACT [] is_a: ENVO:09200000 ! temperature of environmental material intersection_of: PATO:0000146 ! temperature intersection_of: RO:0000052 ENVO:00002005 ! inheres in air relationship: RO:0000052 ENVO:00002005 ! inheres in air [Term] id: ENVO:09200002 name: environmental system process quality def: "The quality of a environmental system process." [] synonym: "quality of environmental system process" EXACT [] is_a: PATO:0001236 ! process quality intersection_of: PATO:0001236 ! process quality intersection_of: RO:0000052 ENVO:02500000 ! inheres in environmental system process relationship: RO:0000052 ENVO:02500000 ! inheres in environmental system process [Term] id: ENVO:09200004 name: porosity of soil def: "The porosity of some soil." [] synonym: "soil porosity" EXACT [] is_a: ENVO:09200009 ! structure of soil is_a: PATO:0000973 ! porosity intersection_of: PATO:0000973 ! porosity intersection_of: RO:0000052 ENVO:00001998 ! inheres in soil [Term] id: ENVO:09200008 name: composition of soil def: "The composition of some soil." [] synonym: "soil composition" EXACT [] is_a: ENVO:09200009 ! structure of soil is_a: PATO:0000025 ! composition intersection_of: PATO:0000025 ! composition intersection_of: RO:0000052 ENVO:00001998 ! inheres in soil [Term] id: ENVO:09200009 name: structure of soil def: "The structure of some soil." [] synonym: "soil structure" EXACT [] is_a: PATO:0000141 ! structure intersection_of: PATO:0000141 ! structure intersection_of: RO:0000052 ENVO:00001998 ! inheres in soil relationship: RO:0000052 ENVO:00001998 ! inheres in soil [Term] id: ENVO:09200012 name: temperature of soil def: "The temperature of some soil." [] synonym: "soil temperature" EXACT [] is_a: ENVO:09200000 ! temperature of environmental material intersection_of: PATO:0000146 ! temperature intersection_of: RO:0000052 ENVO:00001998 ! inheres in soil relationship: RO:0000052 ENVO:00001998 ! inheres in soil [Term] id: ENVO:09200014 name: temperature of water def: "The temperature of some water." [] synonym: "water temperature" EXACT [] is_a: ENVO:09200000 ! temperature of environmental material intersection_of: PATO:0000146 ! temperature intersection_of: RO:0000052 ENVO:00002006 ! inheres in liquid water relationship: RO:0000052 ENVO:00002006 ! inheres in liquid water [Term] id: ENVO:09200017 name: composition of water def: "The composition of some water." [] synonym: "water composition" EXACT [] is_a: PATO:0000025 ! composition intersection_of: PATO:0000025 ! composition intersection_of: RO:0000052 ENVO:00002006 ! inheres in liquid water relationship: RO:0000052 ENVO:00002006 ! inheres in liquid water [Term] id: ENVO:2100000 name: anatomical entity environment def: "An environment which is determined by an anatomical entity." [] is_a: ENVO:01000254 ! environmental system intersection_of: ENVO:01000254 ! environmental system intersection_of: RO:0002509 UBERON:0001062 ! determined by part of anatomical entity relationship: part_of ENVO:01001000 ! environmental system determined by an organism relationship: RO:0002509 UBERON:0001062 ! determined by part of anatomical entity [Term] id: ENVO:3100011 name: concentration of dioxygen in liquid water def: "The concentration of dioxygen when measured in liquid water." [] synonym: "liquid water dioxygen concentration" EXACT [] is_a: PATO:0000033 ! concentration of [Term] id: GO:0000003 name: reproduction is_a: GO:0008150 ! biological_process [Term] id: GO:0000012 name: single strand break repair namespace: biological_process def: "The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair." [PMID:18626472] is_a: GO:0006281 ! DNA repair [Term] id: GO:0000228 name: nuclear chromosome is_a: GO:0005694 ! chromosome intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0031981 ! nuclear lumen [Term] id: GO:0000229 name: cytoplasmic chromosome is_a: GO:0005694 ! chromosome intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000710 name: meiotic mismatch repair namespace: biological_process def: "A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules. Correction of the mismatch can result in non-Mendelian segregation of alleles following meiosis." [GOC:elh, PMID:10357855] is_a: GO:0006298 ! mismatch repair [Term] id: GO:0000719 name: photoreactive repair namespace: biological_process def: "The repair of UV-induced T-T, C-T and C-C dimers by directly reversing the damage to restore the original pyrimidines." [GOC:elh, PMID:10915863] synonym: "pyrimidine-dimer repair by photolyase" NARROW [] is_a: GO:0006290 ! pyrimidine dimer repair [Term] id: GO:0000720 name: pyrimidine dimer repair by nucleotide-excision repair namespace: biological_process def: "The repair of UV-induced T-T, C-T, and C-C dimers by the recognition and removal of the damaged DNA strand from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase." [GOC:elh] comment: Note that the repair of pyrimidine dimers by nucleotide excision repair involves the same gene products that are involved in general nucleotide excision repair. Consider also annotating to other children of the biological process term 'nucleotide-excision repair ; GO:0006289'. is_a: GO:0006289 ! nucleotide-excision repair is_a: GO:0006290 ! pyrimidine dimer repair [Term] id: GO:0000724 name: double-strand break repair via homologous recombination namespace: biological_process alt_id: GO:0016924 def: "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC:elh, PMID:10357855] synonym: "HDR" EXACT [GOC:vk] synonym: "homologous recombinational repair" EXACT [] synonym: "homology-directed repair" EXACT [GOC:vk] synonym: "HRR" EXACT [] synonym: "Rad51-dependent recombinational repair" EXACT [GOC:mah] synonym: "Rhp51-dependent recombinational repair" EXACT [] is_a: GO:0000725 ! recombinational repair is_a: GO:0006302 ! double-strand break repair [Term] id: GO:0000725 name: recombinational repair namespace: biological_process def: "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region." [GOC:elh] xref: Wikipedia:Recombinational_repair is_a: GO:0006281 ! DNA repair [Term] id: GO:0000727 name: double-strand break repair via break-induced replication namespace: biological_process def: "The error-free repair of a double-strand break in DNA in which the centromere-proximal end of a broken chromosome searches for a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template, and progresses to the end of the chromosome." [GOC:elh, PMID:10357855] is_a: GO:0000724 ! double-strand break repair via homologous recombination [Term] id: GO:0000785 name: chromatin is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0000792 name: heterochromatin is_a: GO:0000785 ! chromatin [Term] id: GO:0001501 name: skeletal system development is_a: GO:0048731 ! system development [Term] id: GO:0001503 name: ossification is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0001508 name: action potential is_a: GO:0042391 ! regulation of membrane potential [Term] id: GO:0001525 name: angiogenesis is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0048514 ! blood vessel morphogenesis [Term] id: GO:0001568 name: blood vessel development is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0001944 ! vasculature development [Term] id: GO:0001569 name: branching involved in blood vessel morphogenesis is_a: GO:0048754 ! branching morphogenesis of an epithelial tube intersection_of: GO:0048754 ! branching morphogenesis of an epithelial tube intersection_of: part_of GO:0048514 ! blood vessel morphogenesis relationship: part_of GO:0001525 ! angiogenesis [Term] id: GO:0001659 name: temperature homeostasis is_a: GO:0048871 ! multicellular organismal homeostasis [Term] id: GO:0001667 name: ameboidal-type cell migration is_a: GO:0016477 ! cell migration [Term] id: GO:0001704 name: formation of primary germ layer is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0007369 ! gastrulation [Term] id: GO:0001705 name: ectoderm formation is_a: GO:0001704 ! formation of primary germ layer relationship: part_of GO:0007398 ! ectoderm development [Term] id: GO:0001706 name: endoderm formation is_a: GO:0001704 ! formation of primary germ layer relationship: part_of GO:0007492 ! endoderm development [Term] id: GO:0001707 name: mesoderm formation is_a: GO:0001704 ! formation of primary germ layer relationship: part_of GO:0048332 ! mesoderm morphogenesis [Term] id: GO:0001763 name: morphogenesis of a branching structure is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0001838 name: embryonic epithelial tube formation is_a: GO:0072175 ! epithelial tube formation relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium [Term] id: GO:0001841 name: neural tube formation is_a: GO:0001838 ! embryonic epithelial tube formation relationship: part_of GO:0021915 ! neural tube development [Term] id: GO:0001944 name: vasculature development is_a: GO:0048731 ! system development relationship: part_of GO:0072359 ! circulatory system development [Term] id: GO:0001957 name: intramembranous ossification is_a: GO:0036072 ! direct ossification [Term] id: GO:0002009 name: morphogenesis of an epithelium is_a: GO:0048729 ! tissue morphogenesis relationship: part_of GO:0060429 ! epithelium development [Term] id: GO:0002027 name: regulation of heart rate is_a: GO:0008016 ! regulation of heart contraction is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0002053 name: positive regulation of mesenchymal cell proliferation is_a: GO:0008284 ! positive regulation of cell population proliferation is_a: GO:0010464 ! regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010463 ! mesenchymal cell proliferation relationship: positively_regulates GO:0010463 ! mesenchymal cell proliferation [Term] id: GO:0002087 name: regulation of respiratory gaseous exchange by nervous system process is_a: GO:0044065 ! regulation of respiratory system process is_a: GO:0050877 ! nervous system process intersection_of: GO:0050877 ! nervous system process intersection_of: regulates GO:0007585 ! respiratory gaseous exchange by respiratory system [Term] id: GO:0002244 name: hematopoietic progenitor cell differentiation is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0030097 ! hemopoiesis [Term] id: GO:0002262 name: myeloid cell homeostasis is_a: GO:0002376 ! immune system process is_a: GO:0048872 ! homeostasis of number of cells [Term] id: GO:0002376 name: immune system process is_a: GO:0008150 ! biological_process [Term] id: GO:0002520 name: immune system development is_a: GO:0002376 ! immune system process is_a: GO:0048731 ! system development [Term] id: GO:0002682 name: regulation of immune system process is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002376 ! immune system process relationship: regulates GO:0002376 ! immune system process [Term] id: GO:0002683 name: negative regulation of immune system process is_a: GO:0002682 ! regulation of immune system process is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002376 ! immune system process relationship: negatively_regulates GO:0002376 ! immune system process [Term] id: GO:0002684 name: positive regulation of immune system process is_a: GO:0002682 ! regulation of immune system process is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002376 ! immune system process relationship: positively_regulates GO:0002376 ! immune system process [Term] id: GO:0003006 name: developmental process involved in reproduction 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:0003008 name: system process is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0003012 name: muscle system process is_a: GO:0003008 ! system process [Term] id: GO:0003013 name: circulatory system process is_a: GO:0003008 ! system process [Term] id: GO:0003015 name: heart process is_a: GO:0003013 ! circulatory system process [Term] id: GO:0003016 name: respiratory system process is_a: GO:0003008 ! system process relationship: part_of GO:0007585 ! respiratory gaseous exchange by respiratory system [Term] id: GO:0003330 name: regulation of extracellular matrix constituent secretion is_a: GO:1903053 ! regulation of extracellular matrix organization is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070278 ! extracellular matrix constituent secretion relationship: regulates GO:0070278 ! extracellular matrix constituent secretion [Term] id: GO:0003331 name: positive regulation of extracellular matrix constituent secretion is_a: GO:0003330 ! regulation of extracellular matrix constituent secretion is_a: GO:1903055 ! positive regulation of extracellular matrix organization is_a: GO:1903532 ! positive regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070278 ! extracellular matrix constituent secretion relationship: positively_regulates GO:0070278 ! extracellular matrix constituent secretion [Term] id: GO:0003332 name: negative regulation of extracellular matrix constituent secretion is_a: GO:0003330 ! regulation of extracellular matrix constituent secretion is_a: GO:1903054 ! negative regulation of extracellular matrix organization is_a: GO:1903531 ! negative regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070278 ! extracellular matrix constituent secretion relationship: negatively_regulates GO:0070278 ! extracellular matrix constituent secretion [Term] id: GO:0003674 name: molecular_function is_a: BFO:0000015 ! process property_value: IAO:0000589 "molecular process" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003824 name: catalytic activity is_a: GO:0003674 ! molecular_function property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [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_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic 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:0005576 name: extracellular region is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0005577 name: fibrinogen complex is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005615 ! extracellular space [Term] id: GO:0005581 name: collagen trimer is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0005583 name: fibrillar collagen trimer is_a: GO:0005581 ! collagen trimer intersection_of: GO:0005581 ! collagen trimer intersection_of: part_of GO:0098643 ! banded collagen fibril relationship: part_of GO:0098643 ! banded collagen fibril [Term] id: GO:0005587 name: collagen type IV trimer is_a: GO:0098642 ! network-forming collagen trimer is_a: GO:0098651 ! basement membrane collagen trimer [Term] id: GO:0005604 name: basement membrane is_a: GO:0062023 ! collagen-containing extracellular matrix [Term] id: GO:0005615 name: extracellular space is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0005622 name: intracellular anatomical structure namespace: cellular_component def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "internal to cell" EXACT [] synonym: "intracellular" EXACT [] synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular is_a: GO:0110165 ! cellular anatomical entity property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/17776 xsd:anyURI [Term] id: GO:0005634 name: nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle is_a: GO:0044464 ! obsolete cell part [Term] id: GO:0005635 name: nuclear envelope is_a: GO:0031967 ! organelle envelope relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0012505 ! endomembrane system [Term] id: GO:0005694 name: chromosome namespace: cellular_component def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [Term] id: GO:0005730 name: nucleolus is_a: GO:0043232 ! intracellular non-membrane-bounded organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] id: GO:0005737 name: cytoplasm is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0005773 name: vacuole is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005775 name: vacuolar lumen is_a: GO:0070013 ! intracellular organelle lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: part_of GO:0005773 ! vacuole relationship: part_of GO:0005773 ! vacuole [Term] id: GO:0005886 name: plasma membrane is_a: GO:0016020 ! membrane relationship: part_of GO:0071944 ! cell periphery [Term] id: GO:0005911 name: cell-cell junction is_a: GO:0070161 ! anchoring junction [Term] id: GO:0005929 name: cilium is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0120025 ! plasma membrane bounded cell projection relationship: has_part GO:0030990 ! intraciliary transport particle [Term] id: GO:0005938 name: cell cortex is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0071944 ! cell periphery relationship: part_of GO:0071944 ! cell periphery [Term] id: GO:0006139 name: nucleobase-containing compound metabolic process namespace: biological_process alt_id: GO:0055134 def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_pir subset: goslim_plant synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "cellular DNA metabolism" EXACT [] synonym: "DNA metabolism" EXACT [] is_a: GO:0044260 ! cellular macromolecule metabolic process is_a: GO:0090304 ! nucleic acid metabolic process [Term] id: GO:0006281 name: DNA repair namespace: biological_process def: "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486] subset: goslim_drosophila subset: goslim_pir subset: goslim_pombe subset: goslim_yeast xref: Wikipedia:DNA_repair is_a: GO:0006259 ! DNA metabolic process is_a: GO:0006974 ! cellular response to DNA damage stimulus [Term] id: GO:0006282 name: regulation of DNA repair namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA repair." [GOC:go_curators] subset: goslim_metagenomics is_a: GO:0051052 ! regulation of DNA metabolic process is_a: GO:2001020 ! regulation of response to DNA damage stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006281 ! DNA repair relationship: regulates GO:0006281 ! DNA repair [Term] id: GO:0006283 name: transcription-coupled nucleotide-excision repair namespace: biological_process def: "The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway." [PMID:10197977, PMID:11900249] synonym: "TC-NER" EXACT [PMID:10197977] synonym: "TCR" RELATED [GOC:vw, PMID:18794354] synonym: "transcription-coupled NER" EXACT [GOC:mah] synonym: "transcription-coupled repair" EXACT [GOC:vw, PMID:18794354] is_a: GO:0006289 ! nucleotide-excision repair [Term] id: GO:0006284 name: base-excision repair namespace: biological_process def: "In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase." [ISBN:0815316194] synonym: "BER" EXACT [] xref: Wikipedia:Base_excision_repair is_a: GO:0006281 ! DNA repair [Term] id: GO:0006289 name: nucleotide-excision repair namespace: biological_process alt_id: GO:0045001 def: "A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts)." [PMID:10197977] comment: Note that although intrastrand cross-link repair is not exactly synonymous with nucleotide excision repair, nucleotide excision repair includes the repair of intrastrand cross-links. The synonym field is being used to reflect the broad substrate specificity of nucleotide excision repair. synonym: "intrastrand cross-link repair" RELATED [] synonym: "NER" EXACT [] synonym: "pyrimidine-dimer repair, DNA damage excision" EXACT [] is_a: GO:0006281 ! DNA repair [Term] id: GO:0006290 name: pyrimidine dimer repair namespace: biological_process def: "The repair of UV-induced T-T, C-T and C-C dimers." [ISBN:0815316194] is_a: GO:0006281 ! DNA repair [Term] id: GO:0006298 name: mismatch repair namespace: biological_process alt_id: GO:0006300 def: "A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination." [ISBN:0198506732, PMID:11687886] synonym: "long patch mismatch repair system" NARROW [] synonym: "mismatch repair, MutL-like pathway" RELATED [] synonym: "MMR" EXACT [] synonym: "MutS/MutL/MutH pathway" RELATED [] xref: Wikipedia:DNA_mismatch_repair is_a: GO:0006281 ! DNA repair [Term] id: GO:0006301 name: postreplication repair namespace: biological_process def: "The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication." [GOC:elh] synonym: "postreplication DNA repair" EXACT [] xref: Wikipedia:Postreplication_repair is_a: GO:0006281 ! DNA repair [Term] id: GO:0006302 name: double-strand break repair namespace: biological_process def: "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC:elh] comment: Note that the processes of nuclear double-strand break repair and mitochondrial double-strand break repair are genetically separable (PMID:22214610). To annotate gene products involved in mitochondrial double-strand break repair, please use GO:0097551 'mitochondrial double-strand break repair'. is_a: GO:0006281 ! DNA repair [Term] id: GO:0006303 name: double-strand break repair via nonhomologous end joining namespace: biological_process def: "The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear." [GOC:rph, PMID:10827453, PMID:24837021] synonym: "NHEJ" EXACT [] is_a: GO:0006302 ! double-strand break repair [Term] id: GO:0006725 name: cellular aromatic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732] subset: goslim_pir synonym: "aromatic compound metabolism" EXACT [] synonym: "aromatic hydrocarbon metabolic process" NARROW [] synonym: "aromatic hydrocarbon metabolism" NARROW [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006807 name: nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen." [GOC:jl, ISBN:0198506732] subset: goslim_metagenomics subset: goslim_pir synonym: "nitrogen compound metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006810 name: transport is_a: GO:0051234 ! establishment of localization [Term] id: GO:0006858 name: extracellular transport is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: occurs_in GO:0005576 ! extracellular region relationship: occurs_in GO:0005576 ! extracellular region [Term] id: GO:0006869 name: lipid transport is_a: GO:0071702 ! organic substance transport relationship: part_of GO:0010876 ! lipid localization [Term] id: GO:0006928 name: movement of cell or subcellular component is_a: GO:0009987 ! cellular process [Term] id: GO:0006936 name: muscle contraction is_a: GO:0003012 ! muscle system process [Term] id: GO:0006937 name: regulation of muscle contraction is_a: GO:0090257 ! regulation of muscle system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006936 ! muscle contraction relationship: regulates GO:0006936 ! muscle contraction [Term] id: GO:0006941 name: striated muscle contraction is_a: GO:0006936 ! muscle contraction [Term] id: GO:0006942 name: regulation of striated muscle contraction is_a: GO:0006937 ! regulation of muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006941 ! striated muscle contraction relationship: regulates GO:0006941 ! striated muscle contraction [Term] id: GO:0006950 name: response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006974 name: cellular response to DNA damage stimulus namespace: biological_process alt_id: GO:0034984 def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:go_curators] subset: goslim_yeast synonym: "cellular DNA damage response" EXACT [] synonym: "DNA damage response" EXACT [] synonym: "response to DNA damage stimulus" BROAD [] synonym: "response to genotoxic stress" EXACT [] is_a: GO:0033554 ! cellular response to stress [Term] id: GO:0006996 name: organelle organization is_a: GO:0016043 ! cellular component organization [Term] id: GO:0007154 name: cell communication is_a: GO:0009987 ! cellular process [Term] id: GO:0007267 name: cell-cell signaling is_a: GO:0007154 ! cell communication is_a: GO:0023052 ! signaling [Term] id: GO:0007268 name: chemical synaptic transmission is_a: GO:0098916 ! anterograde trans-synaptic signaling [Term] id: GO:0007275 name: multicellular organism development is_a: GO:0032501 ! multicellular organismal process is_a: GO:0048856 ! anatomical structure development [Term] id: GO:0007276 name: gamete generation is_a: GO:0048609 ! multicellular organismal reproductive process relationship: part_of GO:0019953 ! sexual reproduction [Term] id: GO:0007369 name: gastrulation is_a: GO:0048598 ! embryonic morphogenesis relationship: has_part GO:0001705 ! ectoderm formation relationship: has_part GO:0001706 ! endoderm formation relationship: has_part GO:0001707 ! mesoderm formation [Term] id: GO:0007398 name: ectoderm development is_a: GO:0009888 ! tissue development [Term] id: GO:0007399 name: nervous system development is_a: GO:0048731 ! system development [Term] id: GO:0007492 name: endoderm development is_a: GO:0009888 ! tissue development [Term] id: GO:0007498 name: mesoderm development is_a: GO:0009888 ! tissue development [Term] id: GO:0007585 name: respiratory gaseous exchange by respiratory system is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0007586 name: digestion is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0007600 name: sensory perception is_a: GO:0050877 ! nervous system process [Term] id: GO:0007601 name: visual perception is_a: GO:0050953 ! sensory perception of light stimulus [Term] id: GO:0007610 name: behavior is_a: GO:0050896 ! response to stimulus [Term] id: GO:0008015 name: blood circulation is_a: GO:0003013 ! circulatory system process [Term] id: GO:0008016 name: regulation of heart contraction is_a: GO:1903522 ! regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060047 ! heart contraction relationship: regulates GO:0060047 ! heart contraction [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 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_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic 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 created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process alt_id: GO:0044236 alt_id: GO:0044710 def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_manually_annotate subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] synonym: "multicellular organism metabolic process" NARROW [] synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0008283 name: cell population proliferation is_a: GO:0009987 ! cellular process [Term] id: GO:0008284 name: positive regulation of cell population proliferation is_a: GO:0042127 ! regulation of cell population proliferation is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008283 ! cell population proliferation relationship: positively_regulates GO:0008283 ! cell population proliferation [Term] id: GO:0008285 name: negative regulation of cell population proliferation is_a: GO:0042127 ! regulation of cell population proliferation is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008283 ! cell population proliferation relationship: negatively_regulates GO:0008283 ! cell population proliferation [Term] id: GO:0009314 name: response to radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:jl, Wikipedia:Electromagnetic_radiation] comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength. synonym: "response to electromagnetic radiation stimulus" EXACT [] synonym: "response to radiation stimulus" EXACT [] is_a: GO:0009628 ! response to abiotic stimulus relationship: RO:0002608 ENVO:01001023 ! process has causal agent radiation [Term] id: GO:0009416 name: response to light stimulus is_a: GO:0009314 ! response to radiation [Term] id: GO:0009581 name: detection of external stimulus is_a: GO:0009605 ! response to external stimulus is_a: GO:0051606 ! detection of stimulus [Term] id: GO:0009582 name: detection of abiotic stimulus is_a: GO:0009628 ! response to abiotic stimulus is_a: GO:0051606 ! detection of stimulus [Term] id: GO:0009583 name: detection of light stimulus is_a: GO:0009416 ! response to light stimulus is_a: GO:0009581 ! detection of external stimulus is_a: GO:0009582 ! detection of abiotic stimulus [Term] id: GO:0009584 name: detection of visible light is_a: GO:0009583 ! detection of light stimulus [Term] id: GO:0009605 name: response to external stimulus is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009628 name: response to abiotic stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus." [GOC:hb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_metagenomics subset: goslim_plant synonym: "response to abiotic stress" NARROW [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/16572 xsd:anyURI [Term] id: GO:0009653 name: anatomical structure morphogenesis is_a: GO:0032502 ! developmental process relationship: part_of GO:0048856 ! anatomical structure development [Term] id: GO:0009790 name: embryo development is_a: GO:0007275 ! multicellular organism development [Term] id: GO:0009791 name: post-embryonic development is_a: GO:0032501 ! multicellular organismal process relationship: part_of GO:0007275 ! multicellular organism development [Term] id: GO:0009792 name: embryo development ending in birth or egg hatching is_a: GO:0009790 ! embryo development [Term] id: GO:0009888 name: tissue development is_a: GO:0048856 ! anatomical structure development [Term] id: GO:0009892 name: negative regulation of metabolic process namespace: biological_process alt_id: GO:0044252 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] synonym: "down regulation of metabolic process" EXACT [] synonym: "down-regulation of metabolic process" EXACT [] synonym: "downregulation of metabolic process" EXACT [] synonym: "inhibition of metabolic process" NARROW [] synonym: "inhibition of organismal metabolic process" NARROW [] synonym: "negative regulation of metabolism" EXACT [] synonym: "negative regulation of multicellular organismal metabolic process" NARROW [] synonym: "negative regulation of organismal metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008152 ! metabolic process relationship: negatively_regulates GO:0008152 ! metabolic process [Term] id: GO:0009893 name: positive regulation of metabolic process namespace: biological_process alt_id: GO:0044253 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] synonym: "activation of metabolic process" NARROW [] synonym: "positive regulation of metabolism" EXACT [] synonym: "positive regulation of multicellular organismal metabolic process" NARROW [] synonym: "positive regulation of organismal metabolism" NARROW [] synonym: "stimulation of metabolic process" NARROW [] synonym: "stimulation of organismal metabolic process" NARROW [] synonym: "up regulation of metabolic process" EXACT [] synonym: "up-regulation of metabolic process" EXACT [] synonym: "up-regulation of organismal metabolic process" NARROW [] synonym: "upregulation of metabolic process" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008152 ! metabolic process relationship: positively_regulates GO:0008152 ! metabolic process [Term] id: GO:0009914 name: hormone transport is_a: GO:0006810 ! transport is_a: GO:0010817 ! regulation of hormone levels [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] 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 created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] id: GO:0010165 name: response to X-ray namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC:sm, Wikipedia:X-ray] synonym: "response to X-ray radiation stimulus" EXACT [] is_a: GO:0010212 ! response to ionizing radiation [Term] id: GO:0010212 name: response to ionizing radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID:12509526] synonym: "response to ionising radiation" EXACT [] synonym: "response to ionizing radiation stimulus" EXACT [] is_a: GO:0009314 ! response to radiation relationship: RO:0002608 RBO:00000116 ! process has causal agent ionizing radiation [Term] id: GO:0010213 name: non-photoreactive DNA repair namespace: biological_process def: "A DNA repair process that is involved in repairing UV-induced DNA damage under non-photoreactivating conditions. The mechanism by which this repair process operates has not yet been completely elucidated." [GOC:syr] synonym: "light-independent DNA repair" EXACT [GOC:syr] is_a: GO:0006281 ! DNA repair [Term] id: GO:0010332 name: response to gamma radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum." [GOC:tair_curators] synonym: "response to gamma ray" RELATED [] synonym: "response to gamma-ray photon" RELATED [] is_a: GO:0010212 ! response to ionizing radiation [Term] id: GO:0010463 name: mesenchymal cell proliferation is_a: GO:0008283 ! cell population proliferation [Term] id: GO:0010464 name: regulation of mesenchymal cell proliferation is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010463 ! mesenchymal cell proliferation relationship: regulates GO:0010463 ! mesenchymal cell proliferation [Term] id: GO:0010470 name: regulation of gastrulation is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:0045995 ! regulation of embryonic development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007369 ! gastrulation relationship: regulates GO:0007369 ! gastrulation [Term] id: GO:0010604 name: positive regulation of macromolecule metabolic process namespace: biological_process def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0043170 ! macromolecule metabolic process relationship: positively_regulates GO:0043170 ! macromolecule metabolic process [Term] id: GO:0010605 name: negative regulation of macromolecule metabolic process namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0043170 ! macromolecule metabolic process relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process [Term] id: GO:0010638 name: positive regulation of organelle organization is_a: GO:0033043 ! regulation of organelle organization is_a: GO:0051130 ! positive regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006996 ! organelle organization relationship: positively_regulates GO:0006996 ! organelle organization [Term] id: GO:0010639 name: negative regulation of organelle organization is_a: GO:0033043 ! regulation of organelle organization is_a: GO:0051129 ! negative regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006996 ! organelle organization relationship: negatively_regulates GO:0006996 ! organelle organization [Term] id: GO:0010646 name: regulation of cell communication is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007154 ! cell communication relationship: regulates GO:0007154 ! cell communication [Term] id: GO:0010647 name: positive regulation of cell communication is_a: GO:0010646 ! regulation of cell communication is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007154 ! cell communication relationship: positively_regulates GO:0007154 ! cell communication [Term] id: GO:0010648 name: negative regulation of cell communication is_a: GO:0010646 ! regulation of cell communication is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007154 ! cell communication relationship: negatively_regulates GO:0007154 ! cell communication [Term] id: GO:0010776 name: meiotic mismatch repair involved in meiotic gene conversion namespace: biological_process def: "A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules resulting in meiotic gene conversion. Meiotic gene conversion is the cell cycle process in which genetic information is transferred from one helix to another." [GOC:dph, GOC:tb] is_a: GO:0000710 ! meiotic mismatch repair [Term] id: GO:0010777 name: meiotic mismatch repair involved in reciprocal meiotic recombination namespace: biological_process def: "A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules resulting in meiotic recombination. Meiotic recombination is the cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate." [GOC:dph, GOC:tb] is_a: GO:0000710 ! meiotic mismatch repair [Term] id: GO:0010817 name: regulation of hormone levels is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0010876 name: lipid localization is_a: GO:0033036 ! macromolecule localization [Term] id: GO:0010927 name: cellular component assembly involved in morphogenesis is_a: GO:0022607 ! cellular component assembly is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: GO:0022607 ! cellular component assembly intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0032989 ! cellular component morphogenesis [Term] id: GO:0012505 name: endomembrane system is_a: GO:0110165 ! cellular anatomical entity relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane [Term] id: GO:0012506 name: vesicle membrane is_a: GO:0031090 ! organelle membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0031982 ! vesicle relationship: part_of GO:0031982 ! vesicle [Term] id: GO:0015669 name: gas transport is_a: GO:0006810 ! transport [Term] id: GO:0015671 name: oxygen transport is_a: GO:0015669 ! gas transport [Term] id: GO:0016020 name: membrane is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0016043 name: cellular component organization is_a: GO:0071840 ! cellular component organization or biogenesis [Term] id: GO:0016050 name: vesicle organization is_a: GO:0006996 ! organelle organization [Term] id: GO:0016301 name: kinase activity is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016331 name: morphogenesis of embryonic epithelium is_a: GO:0002009 ! morphogenesis of an epithelium is_a: GO:0048598 ! embryonic morphogenesis [Term] id: GO:0016477 name: cell migration is_a: GO:0048870 ! cell motility [Term] id: GO:0016525 name: negative regulation of angiogenesis is_a: GO:0045765 ! regulation of angiogenesis is_a: GO:2000181 ! negative regulation of blood vessel morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001525 ! angiogenesis relationship: negatively_regulates GO:0001525 ! angiogenesis [Term] id: GO:0016740 name: transferase activity is_a: GO:0003824 ! catalytic activity property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016772 name: transferase activity, transferring phosphorus-containing groups is_a: GO:0016740 ! transferase activity property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0017145 name: stem cell division is_a: GO:0051301 ! cell division [Term] id: GO:0019098 name: reproductive behavior is_a: GO:0007610 ! behavior is_a: GO:0048609 ! multicellular organismal reproductive process intersection_of: GO:0007610 ! behavior intersection_of: part_of GO:0000003 ! reproduction [Term] id: GO:0019219 name: regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process is_a: GO:0080090 ! regulation of primary metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006139 ! nucleobase-containing compound metabolic process relationship: regulates GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0019222 name: regulation of metabolic process namespace: biological_process alt_id: GO:0044246 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] subset: goslim_metagenomics synonym: "regulation of metabolism" EXACT [] synonym: "regulation of multicellular organismal metabolic process" NARROW [] synonym: "regulation of organismal metabolic process" NARROW [GOC:tb] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008152 ! metabolic process relationship: regulates GO:0008152 ! metabolic process [Term] id: GO:0019226 name: transmission of nerve impulse is_a: GO:0035637 ! multicellular organismal signaling is_a: GO:0050877 ! nervous system process relationship: has_part GO:0001508 ! action potential relationship: has_part GO:0007268 ! chemical synaptic transmission relationship: part_of GO:0007154 ! cell communication [Term] id: GO:0019953 name: sexual reproduction is_a: GO:0000003 ! reproduction is_a: GO:0044703 ! multi-organism reproductive process [Term] id: GO:0019985 name: translesion synthesis namespace: biological_process def: "The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide." [GOC:elh, GOC:vw, PMID:10535901] synonym: "bypass DNA synthesis" EXACT [GOC:elh] is_a: GO:0006301 ! postreplication repair [Term] id: GO:0021915 name: neural tube development is_a: GO:0035295 ! tube development is_a: GO:0060429 ! epithelium development relationship: part_of GO:0007399 ! nervous system development relationship: part_of GO:0043009 ! chordate embryonic development [Term] id: GO:0022412 name: cellular process involved in reproduction in multicellular organism is_a: GO:0009987 ! cellular process is_a: GO:0022414 ! reproductive process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0032504 ! multicellular organism reproduction relationship: part_of GO:0032504 ! multicellular organism reproduction [Term] id: GO:0022414 name: reproductive process is_a: GO:0008150 ! biological_process intersection_of: GO:0008150 ! biological_process intersection_of: part_of GO:0000003 ! reproduction relationship: part_of GO:0000003 ! reproduction [Term] id: GO:0022600 name: digestive system process is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: part_of GO:0007586 ! digestion relationship: part_of GO:0007586 ! digestion [Term] id: GO:0022603 name: regulation of anatomical structure morphogenesis is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009653 ! anatomical structure morphogenesis relationship: regulates GO:0009653 ! anatomical structure morphogenesis [Term] id: GO:0022607 name: cellular component assembly is_a: GO:0016043 ! cellular component organization relationship: part_of GO:0044085 ! cellular component biogenesis [Term] id: GO:0023051 name: regulation of signaling is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0023052 ! signaling relationship: regulates GO:0023052 ! signaling [Term] id: GO:0023052 name: signaling is_a: GO:0008150 ! biological_process [Term] id: GO:0023056 name: positive regulation of signaling is_a: GO:0023051 ! regulation of signaling is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0023052 ! signaling relationship: positively_regulates GO:0023052 ! signaling [Term] id: GO:0023057 name: negative regulation of signaling is_a: GO:0023051 ! regulation of signaling is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0023052 ! signaling relationship: negatively_regulates GO:0023052 ! signaling [Term] id: GO:0023061 name: signal release is_a: GO:0032940 ! secretion by cell intersection_of: GO:0032940 ! secretion by cell intersection_of: part_of GO:0007267 ! cell-cell signaling relationship: part_of GO:0007267 ! cell-cell signaling [Term] id: GO:0030016 name: myofibril is_a: GO:0043292 ! contractile fiber [Term] id: GO:0030017 name: sarcomere is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0030016 ! myofibril [Term] id: GO:0030054 name: cell junction is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0030097 name: hemopoiesis is_a: GO:0048534 ! hematopoietic or lymphoid organ development [Term] id: GO:0030099 name: myeloid cell differentiation is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0030097 ! hemopoiesis [Term] id: GO:0030154 name: cell differentiation is_a: GO:0048869 ! cellular developmental process [Term] id: GO:0030198 name: extracellular matrix organization is_a: GO:0043062 ! extracellular structure organization is_a: GO:0045229 ! external encapsulating structure organization [Term] id: GO:0030218 name: erythrocyte differentiation is_a: GO:0030099 ! myeloid cell differentiation relationship: part_of GO:0034101 ! erythrocyte homeostasis [Term] id: GO:0030219 name: megakaryocyte differentiation is_a: GO:0030099 ! myeloid cell differentiation [Term] id: GO:0030278 name: regulation of ossification is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001503 ! ossification relationship: regulates GO:0001503 ! ossification [Term] id: GO:0030279 name: negative regulation of ossification is_a: GO:0030278 ! regulation of ossification is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001503 ! ossification relationship: negatively_regulates GO:0001503 ! ossification [Term] id: GO:0030312 name: external encapsulating structure is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0071944 ! cell periphery [Term] id: GO:0030334 name: regulation of cell migration is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016477 ! cell migration relationship: regulates GO:0016477 ! cell migration [Term] id: GO:0030335 name: positive regulation of cell migration is_a: GO:0030334 ! regulation of cell migration is_a: GO:2000147 ! positive regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016477 ! cell migration relationship: positively_regulates GO:0016477 ! cell migration [Term] id: GO:0030336 name: negative regulation of cell migration is_a: GO:0030334 ! regulation of cell migration is_a: GO:2000146 ! negative regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016477 ! cell migration relationship: negatively_regulates GO:0016477 ! cell migration [Term] id: GO:0030659 name: cytoplasmic vesicle membrane is_a: GO:0012506 ! vesicle membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0031410 ! cytoplasmic vesicle relationship: part_of GO:0031410 ! cytoplasmic vesicle [Term] id: GO:0030990 name: intraciliary transport particle is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0031012 name: extracellular matrix is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0031090 name: organelle membrane is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0043227 ! membrane-bounded organelle relationship: part_of GO:0043227 ! membrane-bounded organelle [Term] id: GO:0031323 name: regulation of cellular metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] synonym: "regulation of cellular metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044237 ! cellular metabolic process relationship: regulates GO:0044237 ! cellular metabolic process [Term] id: GO:0031324 name: negative regulation of cellular metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] synonym: "down regulation of cellular metabolic process" EXACT [] synonym: "down-regulation of cellular metabolic process" EXACT [] synonym: "downregulation of cellular metabolic process" EXACT [] synonym: "inhibition of cellular metabolic process" NARROW [] synonym: "negative regulation of cellular metabolism" EXACT [] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0044237 ! cellular metabolic process relationship: negatively_regulates GO:0044237 ! cellular metabolic process [Term] id: GO:0031325 name: positive regulation of cellular metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] synonym: "activation of cellular metabolic process" NARROW [] synonym: "positive regulation of cellular metabolism" EXACT [] synonym: "stimulation of cellular metabolic process" NARROW [] synonym: "up regulation of cellular metabolic process" EXACT [] synonym: "up-regulation of cellular metabolic process" EXACT [] synonym: "upregulation of cellular metabolic process" EXACT [] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044237 ! cellular metabolic process relationship: positively_regulates GO:0044237 ! cellular metabolic process [Term] id: GO:0031410 name: cytoplasmic vesicle is_a: GO:0097708 ! intracellular vesicle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0031644 name: regulation of nervous system process is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0050877 ! nervous system process relationship: regulates GO:0050877 ! nervous system process [Term] id: GO:0031645 name: negative regulation of nervous system process is_a: GO:0031644 ! regulation of nervous system process is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0050877 ! nervous system process relationship: negatively_regulates GO:0050877 ! nervous system process [Term] id: GO:0031646 name: positive regulation of nervous system process is_a: GO:0031644 ! regulation of nervous system process is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0050877 ! nervous system process relationship: positively_regulates GO:0050877 ! nervous system process [Term] id: GO:0031965 name: nuclear membrane is_a: GO:0031090 ! organelle membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005635 ! nuclear envelope [Term] id: GO:0031967 name: organelle envelope is_a: GO:0031975 ! envelope relationship: part_of GO:0043227 ! membrane-bounded organelle relationship: part_of GO:0043229 ! intracellular organelle [Term] id: GO:0031974 name: membrane-enclosed lumen is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0031975 name: envelope is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0031981 name: nuclear lumen is_a: GO:0070013 ! intracellular organelle lumen relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0031982 name: vesicle is_a: GO:0043227 ! membrane-bounded organelle [Term] id: GO:0032101 name: regulation of response to external stimulus is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009605 ! response to external stimulus relationship: regulates GO:0009605 ! response to external stimulus [Term] id: GO:0032102 name: negative regulation of response to external stimulus is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0048585 ! negative regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009605 ! response to external stimulus relationship: negatively_regulates GO:0009605 ! response to external stimulus [Term] id: GO:0032103 name: positive regulation of response to external stimulus is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0048584 ! positive regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009605 ! response to external stimulus relationship: positively_regulates GO:0009605 ! response to external stimulus [Term] id: GO:0032368 name: regulation of lipid transport is_a: GO:0051049 ! regulation of transport is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006869 ! lipid transport relationship: regulates GO:0006869 ! lipid transport [Term] id: GO:0032369 name: negative regulation of lipid transport is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0051051 ! negative regulation of transport is_a: GO:1905953 ! negative regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006869 ! lipid transport relationship: negatively_regulates GO:0006869 ! lipid transport [Term] id: GO:0032370 name: positive regulation of lipid transport is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0051050 ! positive regulation of transport is_a: GO:1905954 ! positive regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006869 ! lipid transport relationship: positively_regulates GO:0006869 ! lipid transport [Term] id: GO:0032386 name: regulation of intracellular transport is_a: GO:0051049 ! regulation of transport is_a: GO:0060341 ! regulation of cellular localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0046907 ! intracellular transport relationship: regulates GO:0046907 ! intracellular transport [Term] id: GO:0032387 name: negative regulation of intracellular transport is_a: GO:0032386 ! regulation of intracellular transport is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0046907 ! intracellular transport relationship: negatively_regulates GO:0046907 ! intracellular transport [Term] id: GO:0032388 name: positive regulation of intracellular transport is_a: GO:0032386 ! regulation of intracellular transport is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0046907 ! intracellular transport relationship: positively_regulates GO:0046907 ! intracellular transport [Term] id: GO:0032501 name: multicellular organismal process is_a: GO:0008150 ! biological_process [Term] id: GO:0032502 name: developmental process is_a: GO:0008150 ! biological_process [Term] id: GO:0032504 name: multicellular organism reproduction is_a: GO:0000003 ! reproduction is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0032838 name: plasma membrane bounded cell projection cytoplasm is_a: GO:0099568 ! cytoplasmic region intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0120025 ! plasma membrane bounded cell projection relationship: part_of GO:0120025 ! plasma membrane bounded cell projection [Term] id: GO:0032879 name: regulation of localization is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051179 ! localization relationship: regulates GO:0051179 ! localization [Term] id: GO:0032940 name: secretion by cell is_a: GO:0046903 ! secretion is_a: GO:0140352 ! export from cell [Term] id: GO:0032989 name: cellular component morphogenesis is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0016043 ! cellular component organization is_a: GO:0048869 ! cellular developmental process [Term] id: GO:0032991 name: protein-containing complex is_a: GO:0005575 ! cellular_component [Term] id: GO:0033036 name: macromolecule localization is_a: GO:0051179 ! localization [Term] id: GO:0033043 name: regulation of organelle organization is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006996 ! organelle organization relationship: regulates GO:0006996 ! organelle organization [Term] id: GO:0033554 name: cellular response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0006950 ! response to stress is_a: GO:0051716 ! cellular response to stimulus [Term] id: GO:0034101 name: erythrocyte homeostasis is_a: GO:0002262 ! myeloid cell homeostasis [Term] id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] subset: goslim_chembl subset: goslim_generic synonym: "cellular nitrogen compound metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0035148 name: tube formation is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0035239 ! tube morphogenesis [Term] id: GO:0035239 name: tube morphogenesis is_a: GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0035295 ! tube development [Term] id: GO:0035295 name: tube development is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0007275 ! multicellular organism development [Term] id: GO:0035637 name: multicellular organismal signaling is_a: GO:0023052 ! signaling is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0035861 name: site of double-strand break namespace: cellular_component def: "A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix." [GOC:bf, GOC:mah, GOC:vw, PMID:20096808, PMID:21035408] synonym: "DNA damage foci" RELATED [GOC:vw] synonym: "DNA damage focus" RELATED [GOC:mah, PMID:20096808, PMID:21035408] synonym: "ionizing radiation-induced foci" RELATED [PMID:20096808, PMID:21035408] synonym: "IRIF" RELATED [PMID:20096808, PMID:21035408] synonym: "site of DSB" EXACT [PMID:21035408] is_a: GO:0090734 ! site of DNA damage created_by: bf creation_date: 2011-05-17T03:04:42Z [Term] id: GO:0035929 name: steroid hormone secretion is_a: GO:0060986 ! endocrine hormone secretion is_a: GO:0140353 ! lipid export from cell [Term] id: GO:0035935 name: androgen secretion is_a: GO:0035929 ! steroid hormone secretion [Term] id: GO:0036072 name: direct ossification is_a: GO:0001503 ! ossification [Term] id: GO:0036297 name: interstrand cross-link repair namespace: biological_process def: "Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication." [GOC:vw, PMID:16464006, PMID:22064477] synonym: "ICL repair" EXACT [PMID:20658649] is_a: GO:0006281 ! DNA repair created_by: bf creation_date: 2012-08-07T11:05:19Z [Term] id: GO:0036298 name: recombinational interstrand cross-link repair namespace: biological_process def: "Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA by a mechanism that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region." [GOC:vw, PMID:20658649] synonym: "recombination-dependent interstrand cross-link repair" EXACT [GOC:vw] is_a: GO:0000725 ! recombinational repair is_a: GO:0036297 ! interstrand cross-link repair created_by: bf creation_date: 2012-08-07T11:11:59Z [Term] id: GO:0036299 name: non-recombinational interstrand cross-link repair namespace: biological_process def: "Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA by a mechanism that does not involve homologous DNA recombination." [GOC:vw, PMID:11154259, PMID:22064477] synonym: "recombination-independent ICL repair" EXACT [GOC:vw] synonym: "recombination-independent interstrand cross-link repair" EXACT [GOC:vw] is_a: GO:0036297 ! interstrand cross-link repair created_by: bf creation_date: 2012-08-07T11:11:59Z [Term] id: GO:0036477 name: somatodendritic compartment is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0040011 name: locomotion is_a: GO:0008150 ! biological_process [Term] id: GO:0040012 name: regulation of locomotion is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0040011 ! locomotion relationship: regulates GO:0040011 ! locomotion [Term] id: GO:0040013 name: negative regulation of locomotion is_a: GO:0040012 ! regulation of locomotion is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0040011 ! locomotion relationship: negatively_regulates GO:0040011 ! locomotion [Term] id: GO:0040016 name: embryonic cleavage is_a: GO:0051301 ! cell division relationship: part_of GO:0009790 ! embryo development [Term] id: GO:0040017 name: positive regulation of locomotion is_a: GO:0040012 ! regulation of locomotion is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0040011 ! locomotion relationship: positively_regulates GO:0040011 ! locomotion [Term] id: GO:0040019 name: positive regulation of embryonic development is_a: GO:0045995 ! regulation of embryonic development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009790 ! embryo development relationship: positively_regulates GO:0009790 ! embryo development [Term] id: GO:0042074 name: cell migration involved in gastrulation is_a: GO:0001667 ! ameboidal-type cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0007369 ! gastrulation relationship: part_of GO:0007369 ! gastrulation [Term] id: GO:0042127 name: regulation of cell population proliferation is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008283 ! cell population proliferation relationship: regulates GO:0008283 ! cell population proliferation [Term] id: GO:0042275 name: error-free postreplication DNA repair namespace: biological_process def: "The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA via processes such as template switching, which does not remove the replication-blocking lesions but does not increase the endogenous mutation rate." [GOC:elh, GOC:jl, PMID:11459630] comment: Note that 'error-free' does not mean that literally zero errors occur during DNA synthesis, but that the error rate is low, comparable to that of DNA synthesis during replication. synonym: "error-free PRR" EXACT [] synonym: "error-free replication restart" RELATED [] is_a: GO:0006301 ! postreplication repair [Term] id: GO:0042276 name: error-prone translesion synthesis namespace: biological_process def: "The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites." [GOC:elh, GOC:jl, PMID:11485998] synonym: "error-prone postreplication DNA repair" RELATED [GOC:elh] synonym: "mutagenic postreplication DNA repair" RELATED [GOC:elh] synonym: "mutagenic PRR" EXACT [] is_a: GO:0019985 ! translesion synthesis [Term] id: GO:0042391 name: regulation of membrane potential is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0042592 name: homeostatic process is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0042995 name: cell projection is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0043005 name: neuron projection is_a: GO:0120025 ! plasma membrane bounded cell projection [Term] id: GO:0043009 name: chordate embryonic development is_a: GO:0009792 ! embryo development ending in birth or egg hatching [Term] id: GO:0043025 name: neuronal cell body is_a: GO:0044297 ! cell body relationship: part_of GO:0036477 ! somatodendritic compartment [Term] id: GO:0043062 name: extracellular structure organization is_a: GO:0016043 ! cellular component organization [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0043283 alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: goslim_pir synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] synonym: "multicellular organismal macromolecule metabolic process" NARROW [] synonym: "organismal macromolecule metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process [Term] id: GO:0043226 name: organelle namespace: cellular_component 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." [GOC:go_curators] subset: goslim_chembl subset: goslim_generic subset: goslim_pir xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0043227 name: membrane-bounded organelle is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane relationship: has_part GO:0016020 ! membrane [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] synonym: "biological condensate" NARROW [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/21881 xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component 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." [GOC:go_curators] subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043230 name: extracellular organelle is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005576 ! extracellular region relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0043231 name: intracellular membrane-bounded organelle is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0043229 ! intracellular organelle intersection_of: GO:0043227 ! membrane-bounded organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 name: intracellular non-membrane-bounded organelle namespace: cellular_component 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." [GOC:go_curators] subset: goslim_mouse subset: goslim_pir synonym: "intracellular non-membrane-enclosed organelle" EXACT [] is_a: GO:0043228 ! non-membrane-bounded organelle is_a: GO:0043229 ! intracellular organelle intersection_of: GO:0043228 ! non-membrane-bounded organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043233 name: organelle lumen is_a: GO:0031974 ! membrane-enclosed lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: part_of GO:0043226 ! organelle relationship: part_of GO:0043226 ! organelle [Term] id: GO:0043264 name: extracellular non-membrane-bounded organelle is_a: GO:0043228 ! non-membrane-bounded organelle is_a: GO:0043230 ! extracellular organelle intersection_of: GO:0043228 ! non-membrane-bounded organelle intersection_of: part_of GO:0005576 ! extracellular region [Term] id: GO:0043292 name: contractile fiber is_a: GO:0043232 ! intracellular non-membrane-bounded organelle is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0043504 name: mitochondrial DNA repair namespace: biological_process def: "The process of restoring mitochondrial DNA after damage." [PMID:12565799, PMID:15189144, PMID:16050976] is_a: GO:0006281 ! DNA repair [Term] id: GO:0043576 name: regulation of respiratory gaseous exchange is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: regulates GO:0007585 ! respiratory gaseous exchange by respiratory system [Term] id: GO:0044057 name: regulation of system process is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003008 ! system process relationship: regulates GO:0003008 ! system process [Term] id: GO:0044058 name: regulation of digestive system process is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0022600 ! digestive system process relationship: regulates GO:0022600 ! digestive system process [Term] id: GO:0044060 name: regulation of endocrine process is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0050886 ! endocrine process relationship: regulates GO:0050886 ! endocrine process [Term] id: GO:0044065 name: regulation of respiratory system process is_a: GO:0043576 ! regulation of respiratory gaseous exchange is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003016 ! respiratory system process relationship: regulates GO:0003016 ! respiratory system process [Term] id: GO:0044085 name: cellular component biogenesis is_a: GO:0071840 ! cellular component organization or biogenesis [Term] id: GO:0044087 name: regulation of cellular component biogenesis is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044085 ! cellular component biogenesis relationship: regulates GO:0044085 ! cellular component biogenesis [Term] id: GO:0044089 name: positive regulation of cellular component biogenesis is_a: GO:0044087 ! regulation of cellular component biogenesis is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044085 ! cellular component biogenesis relationship: positively_regulates GO:0044085 ! cellular component biogenesis [Term] id: GO:0044092 name: negative regulation of molecular function is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003674 ! molecular_function relationship: negatively_regulates GO:0003674 ! molecular_function [Term] id: GO:0044093 name: positive regulation of molecular function is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003674 ! molecular_function relationship: positively_regulates GO:0003674 ! molecular_function [Term] id: GO:0044237 name: cellular metabolic process namespace: biological_process def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] synonym: "cellular metabolism" EXACT [] synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] subset: goslim_pir synonym: "primary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0044260 name: cellular macromolecule metabolic process namespace: biological_process alt_id: GO:0034960 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells." [GOC:mah] synonym: "cellular biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "cellular macromolecule metabolism" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044297 name: cell body is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0044464 name: cell part name: obsolete cell part is_a: CARO:0000003 ! connected anatomical structure [Term] id: GO:0044703 name: multi-organism reproductive process is_a: GO:0022414 ! reproductive process is_a: GO:0051704 ! multi-organism process [Term] id: GO:0045002 name: double-strand break repair via single-strand annealing namespace: biological_process def: "Repair of a DSB made between two repeated sequences oriented in the same direction occurs primarily by the single strand annealing pathway. The ends of the break are processed by a 5' to 3' exonuclease, exposing complementary single-strand regions of the direct repeats that can anneal, resulting in a deletion of the unique DNA between the direct repeats." [PMID:11606529] is_a: GO:0006302 ! double-strand break repair [Term] id: GO:0045003 name: double-strand break repair via synthesis-dependent strand annealing namespace: biological_process def: "SDSA is a major mechanism of double-strand break repair in mitosis which allows for the error-free repair of a double-strand break without the exchange of adjacent sequences. The broken DNA searches for and base pairs with a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template. Newly synthesized DNA is then displaced from the template and anneal with its complement on the other side of the double-strand break." [PMID:10357855] synonym: "mitotic gene conversion" RELATED [] synonym: "SDSA" BROAD [] is_a: GO:0000724 ! double-strand break repair via homologous recombination [Term] id: GO:0045004 name: DNA replication proofreading namespace: biological_process def: "Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity." [GOC:ai] is_a: GO:0006281 ! DNA repair [Term] id: GO:0045202 name: synapse is_a: GO:0030054 ! cell junction [Term] id: GO:0045229 name: external encapsulating structure organization is_a: GO:0016043 ! cellular component organization [Term] id: GO:0045595 name: regulation of cell differentiation is_a: GO:0050793 ! regulation of developmental process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030154 ! cell differentiation relationship: regulates GO:0030154 ! cell differentiation [Term] id: GO:0045596 name: negative regulation of cell differentiation is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051093 ! negative regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030154 ! cell differentiation relationship: negatively_regulates GO:0030154 ! cell differentiation [Term] id: GO:0045597 name: positive regulation of cell differentiation is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051094 ! positive regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030154 ! cell differentiation relationship: positively_regulates GO:0030154 ! cell differentiation [Term] id: GO:0045637 name: regulation of myeloid cell differentiation is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030099 ! myeloid cell differentiation relationship: regulates GO:0030099 ! myeloid cell differentiation [Term] id: GO:0045638 name: negative regulation of myeloid cell differentiation is_a: GO:0045596 ! negative regulation of cell differentiation is_a: GO:0045637 ! regulation of myeloid cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030099 ! myeloid cell differentiation relationship: negatively_regulates GO:0030099 ! myeloid cell differentiation [Term] id: GO:0045639 name: positive regulation of myeloid cell differentiation is_a: GO:0045597 ! positive regulation of cell differentiation is_a: GO:0045637 ! regulation of myeloid cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030099 ! myeloid cell differentiation relationship: positively_regulates GO:0030099 ! myeloid cell differentiation [Term] id: GO:0045646 name: regulation of erythrocyte differentiation is_a: GO:0045637 ! regulation of myeloid cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030218 ! erythrocyte differentiation relationship: regulates GO:0030218 ! erythrocyte differentiation [Term] id: GO:0045647 name: negative regulation of erythrocyte differentiation is_a: GO:0045638 ! negative regulation of myeloid cell differentiation is_a: GO:0045646 ! regulation of erythrocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030218 ! erythrocyte differentiation relationship: negatively_regulates GO:0030218 ! erythrocyte differentiation [Term] id: GO:0045648 name: positive regulation of erythrocyte differentiation is_a: GO:0045639 ! positive regulation of myeloid cell differentiation is_a: GO:0045646 ! regulation of erythrocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030218 ! erythrocyte differentiation relationship: positively_regulates GO:0030218 ! erythrocyte differentiation [Term] id: GO:0045652 name: regulation of megakaryocyte differentiation is_a: GO:0045637 ! regulation of myeloid cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030219 ! megakaryocyte differentiation relationship: regulates GO:0030219 ! megakaryocyte differentiation [Term] id: GO:0045653 name: negative regulation of megakaryocyte differentiation is_a: GO:0045638 ! negative regulation of myeloid cell differentiation is_a: GO:0045652 ! regulation of megakaryocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030219 ! megakaryocyte differentiation relationship: negatively_regulates GO:0030219 ! megakaryocyte differentiation [Term] id: GO:0045654 name: positive regulation of megakaryocyte differentiation is_a: GO:0045639 ! positive regulation of myeloid cell differentiation is_a: GO:0045652 ! regulation of megakaryocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030219 ! megakaryocyte differentiation relationship: positively_regulates GO:0030219 ! megakaryocyte differentiation [Term] id: GO:0045738 name: negative regulation of DNA repair namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair." [GOC:go_curators] synonym: "down regulation of DNA repair" EXACT [] synonym: "down-regulation of DNA repair" EXACT [] synonym: "downregulation of DNA repair" EXACT [] synonym: "inhibition of DNA repair" NARROW [] is_a: GO:0006282 ! regulation of DNA repair is_a: GO:0051053 ! negative regulation of DNA metabolic process is_a: GO:2001021 ! negative regulation of response to DNA damage stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006281 ! DNA repair relationship: negatively_regulates GO:0006281 ! DNA repair [Term] id: GO:0045739 name: positive regulation of DNA repair namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA repair." [GOC:go_curators] synonym: "activation of DNA repair" NARROW [] synonym: "stimulation of DNA repair" NARROW [] synonym: "up regulation of DNA repair" EXACT [] synonym: "up-regulation of DNA repair" EXACT [] synonym: "upregulation of DNA repair" EXACT [] is_a: GO:0006282 ! regulation of DNA repair is_a: GO:0051054 ! positive regulation of DNA metabolic process is_a: GO:2001022 ! positive regulation of response to DNA damage stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006281 ! DNA repair relationship: positively_regulates GO:0006281 ! DNA repair [Term] id: GO:0045759 name: negative regulation of action potential is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0098900 ! regulation of action potential intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001508 ! action potential relationship: negatively_regulates GO:0001508 ! action potential [Term] id: GO:0045760 name: positive regulation of action potential is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0098900 ! regulation of action potential intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001508 ! action potential relationship: positively_regulates GO:0001508 ! action potential [Term] id: GO:0045765 name: regulation of angiogenesis is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:1901342 ! regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001525 ! angiogenesis relationship: regulates GO:0001525 ! angiogenesis [Term] id: GO:0045766 name: positive regulation of angiogenesis is_a: GO:0045765 ! regulation of angiogenesis is_a: GO:1904018 ! positive regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001525 ! angiogenesis relationship: positively_regulates GO:0001525 ! angiogenesis [Term] id: GO:0045778 name: positive regulation of ossification is_a: GO:0030278 ! regulation of ossification is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001503 ! ossification relationship: positively_regulates GO:0001503 ! ossification [Term] id: GO:0045822 name: negative regulation of heart contraction is_a: GO:0008016 ! regulation of heart contraction is_a: GO:1903523 ! negative regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060047 ! heart contraction relationship: negatively_regulates GO:0060047 ! heart contraction [Term] id: GO:0045823 name: positive regulation of heart contraction is_a: GO:0008016 ! regulation of heart contraction is_a: GO:1903524 ! positive regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060047 ! heart contraction relationship: positively_regulates GO:0060047 ! heart contraction [Term] id: GO:0045932 name: negative regulation of muscle contraction is_a: GO:0006937 ! regulation of muscle contraction is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006936 ! muscle contraction relationship: negatively_regulates GO:0006936 ! muscle contraction [Term] id: GO:0045933 name: positive regulation of muscle contraction is_a: GO:0006937 ! regulation of muscle contraction is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006936 ! muscle contraction relationship: positively_regulates GO:0006936 ! muscle contraction [Term] id: GO:0045934 name: negative regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] synonym: "down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process relationship: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0045935 name: positive regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] synonym: "activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process relationship: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0045988 name: negative regulation of striated muscle contraction is_a: GO:0006942 ! regulation of striated muscle contraction is_a: GO:0045932 ! negative regulation of muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006941 ! striated muscle contraction relationship: negatively_regulates GO:0006941 ! striated muscle contraction [Term] id: GO:0045989 name: positive regulation of striated muscle contraction is_a: GO:0006942 ! regulation of striated muscle contraction is_a: GO:0045933 ! positive regulation of muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006941 ! striated muscle contraction relationship: positively_regulates GO:0006941 ! striated muscle contraction [Term] id: GO:0045992 name: negative regulation of embryonic development is_a: GO:0045995 ! regulation of embryonic development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009790 ! embryo development relationship: negatively_regulates GO:0009790 ! embryo development [Term] id: GO:0045995 name: regulation of embryonic development is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009790 ! embryo development relationship: regulates GO:0009790 ! embryo development [Term] id: GO:0046483 name: heterocycle metabolic process namespace: biological_process def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198506732] subset: goslim_pir synonym: "heterocycle metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0046787 name: viral DNA repair namespace: biological_process def: "The process of restoring viral DNA after damage or errors in replication." [ISBN:0781718325] is_a: GO:0006281 ! DNA repair [Term] id: GO:0046879 name: hormone secretion is_a: GO:0009914 ! hormone transport is_a: GO:0023061 ! signal release [Term] id: GO:0046883 name: regulation of hormone secretion is_a: GO:0010646 ! regulation of cell communication is_a: GO:0010817 ! regulation of hormone levels is_a: GO:0023051 ! regulation of signaling is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0046879 ! hormone secretion relationship: regulates GO:0046879 ! hormone secretion [Term] id: GO:0046887 name: positive regulation of hormone secretion is_a: GO:0010647 ! positive regulation of cell communication is_a: GO:0023056 ! positive regulation of signaling is_a: GO:0046883 ! regulation of hormone secretion is_a: GO:1903532 ! positive regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0046879 ! hormone secretion relationship: positively_regulates GO:0046879 ! hormone secretion [Term] id: GO:0046888 name: negative regulation of hormone secretion is_a: GO:0010648 ! negative regulation of cell communication is_a: GO:0023057 ! negative regulation of signaling is_a: GO:0046883 ! regulation of hormone secretion is_a: GO:1903531 ! negative regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0046879 ! hormone secretion relationship: negatively_regulates GO:0046879 ! hormone secretion [Term] id: GO:0046903 name: secretion is_a: GO:0006810 ! transport [Term] id: GO:0046907 name: intracellular transport is_a: GO:0006810 ! transport is_a: GO:0051641 ! cellular localization is_a: GO:0051649 ! establishment of localization in cell intersection_of: GO:0006810 ! transport intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure relationship: occurs_in GO:0005622 ! intracellular anatomical structure [Term] id: GO:0048103 name: somatic stem cell division is_a: GO:0017145 ! stem cell division [Term] id: GO:0048332 name: mesoderm morphogenesis is_a: GO:0048729 ! tissue morphogenesis relationship: part_of GO:0007498 ! mesoderm development [Term] id: GO:0048513 name: animal organ development is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0048731 ! system development [Term] id: GO:0048514 name: blood vessel morphogenesis is_a: GO:0035239 ! tube morphogenesis relationship: part_of GO:0001568 ! blood vessel development [Term] id: GO:0048518 name: positive regulation of biological process namespace: biological_process alt_id: GO:0043119 def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of biological process" NARROW [] synonym: "positive regulation of physiological process" EXACT [] synonym: "stimulation of biological process" NARROW [] synonym: "up regulation of biological process" EXACT [] synonym: "up-regulation of biological process" EXACT [] synonym: "upregulation of biological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008150 ! biological_process relationship: positively_regulates GO:0008150 ! biological_process [Term] id: GO:0048519 name: negative regulation of biological process namespace: biological_process alt_id: GO:0043118 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "down regulation of biological process" EXACT [] synonym: "down-regulation of biological process" EXACT [] synonym: "downregulation of biological process" EXACT [] synonym: "inhibition of biological process" NARROW [] synonym: "negative regulation of physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008150 ! biological_process relationship: negatively_regulates GO:0008150 ! biological_process [Term] id: GO:0048520 name: positive regulation of behavior is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:0050795 ! regulation of behavior intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007610 ! behavior relationship: positively_regulates GO:0007610 ! behavior [Term] id: GO:0048521 name: negative regulation of behavior is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:0050795 ! regulation of behavior intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007610 ! behavior relationship: negatively_regulates GO:0007610 ! behavior [Term] id: GO:0048522 name: positive regulation of cellular process namespace: biological_process alt_id: GO:0051242 def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] synonym: "activation of cellular process" NARROW [] synonym: "positive regulation of cellular physiological process" EXACT [] synonym: "stimulation of cellular process" NARROW [] synonym: "up regulation of cellular process" EXACT [] synonym: "up-regulation of cellular process" EXACT [] synonym: "upregulation of cellular process" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009987 ! cellular process relationship: positively_regulates GO:0009987 ! cellular process [Term] id: GO:0048523 name: negative regulation of cellular process namespace: biological_process alt_id: GO:0051243 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] synonym: "down regulation of cellular process" EXACT [] synonym: "down-regulation of cellular process" EXACT [] synonym: "downregulation of cellular process" EXACT [] synonym: "inhibition of cellular process" NARROW [] synonym: "negative regulation of cellular physiological process" EXACT [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009987 ! cellular process relationship: negatively_regulates GO:0009987 ! cellular process [Term] id: GO:0048534 name: hematopoietic or lymphoid organ development is_a: GO:0048513 ! animal organ development relationship: part_of GO:0002520 ! immune system development [Term] id: GO:0048580 name: regulation of post-embryonic development is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009791 ! post-embryonic development relationship: regulates GO:0009791 ! post-embryonic development [Term] id: GO:0048581 name: negative regulation of post-embryonic development is_a: GO:0048580 ! regulation of post-embryonic development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009791 ! post-embryonic development relationship: negatively_regulates GO:0009791 ! post-embryonic development [Term] id: GO:0048582 name: positive regulation of post-embryonic development is_a: GO:0048580 ! regulation of post-embryonic development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009791 ! post-embryonic development relationship: positively_regulates GO:0009791 ! post-embryonic development [Term] id: GO:0048583 name: regulation of response to stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0050896 ! response to stimulus relationship: regulates GO:0050896 ! response to stimulus [Term] id: GO:0048584 name: positive regulation of response to stimulus namespace: biological_process def: "Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "activation of response to stimulus" NARROW [] synonym: "stimulation of response to stimulus" NARROW [] synonym: "up regulation of response to stimulus" EXACT [] synonym: "up-regulation of response to stimulus" EXACT [] synonym: "upregulation of response to stimulus" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0050896 ! response to stimulus relationship: positively_regulates GO:0050896 ! response to stimulus [Term] id: GO:0048585 name: negative regulation of response to stimulus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "down regulation of response to stimulus" EXACT [] synonym: "down-regulation of response to stimulus" EXACT [] synonym: "downregulation of response to stimulus" EXACT [] synonym: "inhibition of response to stimulus" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0050896 ! response to stimulus relationship: negatively_regulates GO:0050896 ! response to stimulus [Term] id: GO:0048598 name: embryonic morphogenesis is_a: GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0009790 ! embryo development [Term] id: GO:0048609 name: multicellular organismal reproductive process is_a: GO:0022414 ! reproductive process relationship: part_of GO:0032504 ! multicellular organism reproduction [Term] id: GO:0048646 name: anatomical structure formation involved in morphogenesis is_a: GO:0032502 ! developmental process relationship: part_of GO:0009653 ! anatomical structure morphogenesis [Term] id: GO:0048729 name: tissue morphogenesis is_a: GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0009888 ! tissue development [Term] id: GO:0048731 name: system development is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0007275 ! multicellular organism development [Term] id: GO:0048754 name: branching morphogenesis of an epithelial tube is_a: GO:0035239 ! tube morphogenesis is_a: GO:0061138 ! morphogenesis of a branching epithelium relationship: part_of GO:0060562 ! epithelial tube morphogenesis [Term] id: GO:0048770 name: pigment granule is_a: GO:0031410 ! cytoplasmic vesicle [Term] id: GO:0048856 name: anatomical structure development is_a: GO:0032502 ! developmental process [Term] id: GO:0048869 name: cellular developmental process is_a: GO:0009987 ! cellular process is_a: GO:0032502 ! developmental process [Term] id: GO:0048870 name: cell motility is_a: GO:0006928 ! movement of cell or subcellular component is_a: GO:0040011 ! locomotion relationship: part_of GO:0051674 ! localization of cell [Term] id: GO:0048871 name: multicellular organismal homeostasis is_a: GO:0032501 ! multicellular organismal process is_a: GO:0042592 ! homeostatic process [Term] id: GO:0048872 name: homeostasis of number of cells is_a: GO:0042592 ! homeostatic process [Term] id: GO:0050789 name: regulation of biological process namespace: biological_process alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir synonym: "regulation of physiological process" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008150 ! biological_process relationship: regulates GO:0008150 ! biological_process [Term] id: GO:0050793 name: regulation of developmental process is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032502 ! developmental process relationship: regulates GO:0032502 ! developmental process [Term] id: GO:0050794 name: regulation of cellular process namespace: biological_process alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] synonym: "regulation of cellular physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009987 ! cellular process relationship: regulates GO:0009987 ! cellular process [Term] id: GO:0050795 name: regulation of behavior is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007610 ! behavior relationship: regulates GO:0007610 ! behavior [Term] id: GO:0050804 name: modulation of chemical synaptic transmission is_a: GO:0099177 ! regulation of trans-synaptic signaling intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007268 ! chemical synaptic transmission relationship: regulates GO:0007268 ! chemical synaptic transmission [Term] id: GO:0050805 name: negative regulation of synaptic transmission is_a: GO:0010648 ! negative regulation of cell communication is_a: GO:0023057 ! negative regulation of signaling is_a: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007268 ! chemical synaptic transmission relationship: negatively_regulates GO:0007268 ! chemical synaptic transmission [Term] id: GO:0050806 name: positive regulation of synaptic transmission is_a: GO:0010647 ! positive regulation of cell communication is_a: GO:0023056 ! positive regulation of signaling is_a: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007268 ! chemical synaptic transmission relationship: positively_regulates GO:0007268 ! chemical synaptic transmission [Term] id: GO:0050877 name: nervous system process is_a: GO:0003008 ! system process [Term] id: GO:0050886 name: endocrine process is_a: GO:0003008 ! system process [Term] id: GO:0050896 name: response to stimulus namespace: biological_process alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0050906 name: detection of stimulus involved in sensory perception is_a: GO:0051606 ! detection of stimulus intersection_of: GO:0051606 ! detection of stimulus intersection_of: part_of GO:0007600 ! sensory perception relationship: part_of GO:0007600 ! sensory perception [Term] id: GO:0050908 name: detection of light stimulus involved in visual perception is_a: GO:0009584 ! detection of visible light is_a: GO:0050962 ! detection of light stimulus involved in sensory perception intersection_of: GO:0009583 ! detection of light stimulus intersection_of: part_of GO:0007601 ! visual perception relationship: part_of GO:0007601 ! visual perception [Term] id: GO:0050953 name: sensory perception of light stimulus is_a: GO:0007600 ! sensory perception [Term] id: GO:0050962 name: detection of light stimulus involved in sensory perception is_a: GO:0009583 ! detection of light stimulus is_a: GO:0050906 ! detection of stimulus involved in sensory perception intersection_of: GO:0009583 ! detection of light stimulus intersection_of: part_of GO:0007600 ! sensory perception relationship: part_of GO:0050953 ! sensory perception of light stimulus [Term] id: GO:0051046 name: regulation of secretion is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0046903 ! secretion relationship: regulates GO:0046903 ! secretion [Term] id: GO:0051047 name: positive regulation of secretion is_a: GO:0051046 ! regulation of secretion is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0046903 ! secretion relationship: positively_regulates GO:0046903 ! secretion [Term] id: GO:0051048 name: negative regulation of secretion is_a: GO:0051046 ! regulation of secretion is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0046903 ! secretion relationship: negatively_regulates GO:0046903 ! secretion [Term] id: GO:0051049 name: regulation of transport is_a: GO:0032879 ! regulation of localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006810 ! transport relationship: regulates GO:0006810 ! transport [Term] id: GO:0051050 name: positive regulation of transport is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006810 ! transport relationship: positively_regulates GO:0006810 ! transport [Term] id: GO:0051051 name: negative regulation of transport is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006810 ! transport relationship: negatively_regulates GO:0006810 ! transport [Term] id: GO:0051052 name: regulation of DNA metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] subset: goslim_yeast synonym: "regulation of DNA metabolism" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006259 ! DNA metabolic process relationship: regulates GO:0006259 ! DNA metabolic process [Term] id: GO:0051053 name: negative regulation of DNA metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] synonym: "down regulation of DNA metabolic process" EXACT [] synonym: "down-regulation of DNA metabolic process" EXACT [] synonym: "downregulation of DNA metabolic process" EXACT [] synonym: "inhibition of DNA metabolic process" NARROW [] synonym: "negative regulation of DNA metabolism" EXACT [] is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006259 ! DNA metabolic process relationship: negatively_regulates GO:0006259 ! DNA metabolic process [Term] id: GO:0051054 name: positive regulation of DNA metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] synonym: "activation of DNA metabolic process" NARROW [] synonym: "positive regulation of DNA metabolism" EXACT [] synonym: "stimulation of DNA metabolic process" NARROW [] synonym: "up regulation of DNA metabolic process" EXACT [] synonym: "up-regulation of DNA metabolic process" EXACT [] synonym: "upregulation of DNA metabolic process" EXACT [] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006259 ! DNA metabolic process relationship: positively_regulates GO:0006259 ! DNA metabolic process [Term] id: GO:0051093 name: negative regulation of developmental process is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032502 ! developmental process relationship: negatively_regulates GO:0032502 ! developmental process [Term] id: GO:0051094 name: positive regulation of developmental process is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032502 ! developmental process relationship: positively_regulates GO:0032502 ! developmental process [Term] id: GO:0051128 name: regulation of cellular component organization is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016043 ! cellular component organization relationship: regulates GO:0016043 ! cellular component organization [Term] id: GO:0051129 name: negative regulation of cellular component organization is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016043 ! cellular component organization relationship: negatively_regulates GO:0016043 ! cellular component organization [Term] id: GO:0051130 name: positive regulation of cellular component organization is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016043 ! cellular component organization relationship: positively_regulates GO:0016043 ! cellular component organization [Term] id: GO:0051171 name: regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "regulation of nitrogen metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006807 ! nitrogen compound metabolic process relationship: regulates GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0051172 name: negative regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "down regulation of nitrogen metabolic process" EXACT [] synonym: "down-regulation of nitrogen metabolic process" EXACT [] synonym: "downregulation of nitrogen metabolic process" EXACT [] synonym: "inhibition of nitrogen metabolic process" NARROW [] synonym: "negative regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "negative regulation of nitrogen metabolism" EXACT [] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006807 ! nitrogen compound metabolic process relationship: negatively_regulates GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0051173 name: positive regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "activation of nitrogen metabolic process" NARROW [] synonym: "positive regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "positive regulation of nitrogen metabolism" EXACT [] synonym: "stimulation of nitrogen metabolic process" NARROW [] synonym: "up regulation of nitrogen metabolic process" EXACT [] synonym: "up-regulation of nitrogen metabolic process" EXACT [] synonym: "upregulation of nitrogen metabolic process" EXACT [] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006807 ! nitrogen compound metabolic process relationship: positively_regulates GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0051179 name: localization is_a: GO:0008150 ! biological_process [Term] id: GO:0051216 name: cartilage development is_a: GO:0048513 ! animal organ development relationship: part_of GO:0001501 ! skeletal system development relationship: part_of GO:0061448 ! connective tissue development [Term] id: GO:0051234 name: establishment of localization is_a: GO:0051179 ! localization [Term] id: GO:0051239 name: regulation of multicellular organismal process is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032501 ! multicellular organismal process relationship: regulates GO:0032501 ! multicellular organismal process [Term] id: GO:0051240 name: positive regulation of multicellular organismal process is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032501 ! multicellular organismal process relationship: positively_regulates GO:0032501 ! multicellular organismal process [Term] id: GO:0051241 name: negative regulation of multicellular organismal process is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032501 ! multicellular organismal process relationship: negatively_regulates GO:0032501 ! multicellular organismal process [Term] id: GO:0051270 name: regulation of cellular component movement is_a: GO:0032879 ! regulation of localization is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006928 ! movement of cell or subcellular component relationship: regulates GO:0006928 ! movement of cell or subcellular component [Term] id: GO:0051271 name: negative regulation of cellular component movement is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051270 ! regulation of cellular component movement intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006928 ! movement of cell or subcellular component relationship: negatively_regulates GO:0006928 ! movement of cell or subcellular component [Term] id: GO:0051272 name: positive regulation of cellular component movement is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051270 ! regulation of cellular component movement intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006928 ! movement of cell or subcellular component relationship: positively_regulates GO:0006928 ! movement of cell or subcellular component [Term] id: GO:0051301 name: cell division is_a: GO:0009987 ! cellular process [Term] id: GO:0051302 name: regulation of cell division is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051301 ! cell division relationship: regulates GO:0051301 ! cell division [Term] id: GO:0051606 name: detection of stimulus is_a: GO:0050896 ! response to stimulus [Term] id: GO:0051641 name: cellular localization is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization [Term] id: GO:0051649 name: establishment of localization in cell is_a: GO:0051234 ! establishment of localization relationship: part_of GO:0051641 ! cellular localization [Term] id: GO:0051674 name: localization of cell is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization [Term] id: GO:0051704 name: multi-organism process is_a: GO:0008150 ! biological_process [Term] id: GO:0051716 name: cellular response to stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0009987 ! cellular process is_a: GO:0050896 ! response to stimulus [Term] id: GO:0051781 name: positive regulation of cell division is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051302 ! regulation of cell division intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051301 ! cell division relationship: positively_regulates GO:0051301 ! cell division [Term] id: GO:0051782 name: negative regulation of cell division is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051302 ! regulation of cell division intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051301 ! cell division relationship: negatively_regulates GO:0051301 ! cell division [Term] id: GO:0051931 name: regulation of sensory perception is_a: GO:0031644 ! regulation of nervous system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007600 ! sensory perception relationship: regulates GO:0007600 ! sensory perception [Term] id: GO:0051960 name: regulation of nervous system development is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007399 ! nervous system development relationship: regulates GO:0007399 ! nervous system development [Term] id: GO:0051961 name: negative regulation of nervous system development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:0051960 ! regulation of nervous system development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007399 ! nervous system development relationship: negatively_regulates GO:0007399 ! nervous system development [Term] id: GO:0051962 name: positive regulation of nervous system development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:0051960 ! regulation of nervous system development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007399 ! nervous system development relationship: positively_regulates GO:0007399 ! nervous system development [Term] id: GO:0051969 name: regulation of transmission of nerve impulse is_a: GO:0010646 ! regulation of cell communication is_a: GO:0023051 ! regulation of signaling is_a: GO:0031644 ! regulation of nervous system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0019226 ! transmission of nerve impulse relationship: regulates GO:0019226 ! transmission of nerve impulse [Term] id: GO:0051970 name: negative regulation of transmission of nerve impulse is_a: GO:0010648 ! negative regulation of cell communication is_a: GO:0023057 ! negative regulation of signaling is_a: GO:0031645 ! negative regulation of nervous system process is_a: GO:0051969 ! regulation of transmission of nerve impulse intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0019226 ! transmission of nerve impulse relationship: negatively_regulates GO:0019226 ! transmission of nerve impulse [Term] id: GO:0051971 name: positive regulation of transmission of nerve impulse is_a: GO:0010647 ! positive regulation of cell communication is_a: GO:0023056 ! positive regulation of signaling is_a: GO:0031646 ! positive regulation of nervous system process is_a: GO:0051969 ! regulation of transmission of nerve impulse intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0019226 ! transmission of nerve impulse relationship: positively_regulates GO:0019226 ! transmission of nerve impulse [Term] id: GO:0055117 name: regulation of cardiac muscle contraction is_a: GO:0006942 ! regulation of striated muscle contraction is_a: GO:0008016 ! regulation of heart contraction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060048 ! cardiac muscle contraction relationship: regulates GO:0060048 ! cardiac muscle contraction [Term] id: GO:0055118 name: negative regulation of cardiac muscle contraction is_a: GO:0045822 ! negative regulation of heart contraction is_a: GO:0045988 ! negative regulation of striated muscle contraction is_a: GO:0055117 ! regulation of cardiac muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060048 ! cardiac muscle contraction relationship: negatively_regulates GO:0060048 ! cardiac muscle contraction [Term] id: GO:0060047 name: heart contraction is_a: GO:0003015 ! heart process relationship: part_of GO:0008015 ! blood circulation [Term] id: GO:0060048 name: cardiac muscle contraction is_a: GO:0006941 ! striated muscle contraction relationship: part_of GO:0060047 ! heart contraction [Term] id: GO:0060255 name: regulation of macromolecule metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043170 ! macromolecule metabolic process relationship: regulates GO:0043170 ! macromolecule metabolic process [Term] id: GO:0060341 name: regulation of cellular localization is_a: GO:0032879 ! regulation of localization is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051641 ! cellular localization relationship: regulates GO:0051641 ! cellular localization [Term] id: GO:0060429 name: epithelium development is_a: GO:0009888 ! tissue development [Term] id: GO:0060452 name: positive regulation of cardiac muscle contraction is_a: GO:0045823 ! positive regulation of heart contraction is_a: GO:0045989 ! positive regulation of striated muscle contraction is_a: GO:0055117 ! regulation of cardiac muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060048 ! cardiac muscle contraction relationship: positively_regulates GO:0060048 ! cardiac muscle contraction [Term] id: GO:0060456 name: positive regulation of digestive system process is_a: GO:0044058 ! regulation of digestive system process is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0022600 ! digestive system process relationship: positively_regulates GO:0022600 ! digestive system process [Term] id: GO:0060457 name: negative regulation of digestive system process is_a: GO:0044058 ! regulation of digestive system process is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0022600 ! digestive system process relationship: negatively_regulates GO:0022600 ! digestive system process [Term] id: GO:0060562 name: epithelial tube morphogenesis is_a: GO:0002009 ! morphogenesis of an epithelium is_a: GO:0035239 ! tube morphogenesis [Term] id: GO:0060688 name: regulation of morphogenesis of a branching structure is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001763 ! morphogenesis of a branching structure relationship: regulates GO:0001763 ! morphogenesis of a branching structure [Term] id: GO:0060986 name: endocrine hormone secretion is_a: GO:0046879 ! hormone secretion relationship: part_of GO:0050886 ! endocrine process [Term] id: GO:0061035 name: regulation of cartilage development is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051216 ! cartilage development relationship: regulates GO:0051216 ! cartilage development [Term] id: GO:0061036 name: positive regulation of cartilage development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:0061035 ! regulation of cartilage development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051216 ! cartilage development relationship: positively_regulates GO:0051216 ! cartilage development [Term] id: GO:0061037 name: negative regulation of cartilage development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:0061035 ! regulation of cartilage development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051216 ! cartilage development relationship: negatively_regulates GO:0051216 ! cartilage development [Term] id: GO:0061138 name: morphogenesis of a branching epithelium is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium [Term] id: GO:0061448 name: connective tissue development is_a: GO:0009888 ! tissue development [Term] id: GO:0062023 name: collagen-containing extracellular matrix is_a: GO:0031012 ! extracellular matrix [Term] id: GO:0065007 name: biological regulation namespace: biological_process def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process [Term] id: GO:0065008 name: regulation of biological quality is_a: GO:0065007 ! biological regulation [Term] id: GO:0065009 name: regulation of molecular function is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003674 ! molecular_function relationship: regulates GO:0003674 ! molecular_function [Term] id: GO:0065010 name: extracellular membrane-bounded organelle is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0043230 ! extracellular organelle intersection_of: GO:0043227 ! membrane-bounded organelle intersection_of: part_of GO:0005576 ! extracellular region [Term] id: GO:0070013 name: intracellular organelle lumen is_a: GO:0043233 ! organelle lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: part_of GO:0043229 ! intracellular organelle relationship: part_of GO:0043229 ! intracellular organelle [Term] id: GO:0070161 name: anchoring junction is_a: GO:0030054 ! cell junction [Term] id: GO:0070278 name: extracellular matrix constituent secretion is_a: GO:0032940 ! secretion by cell relationship: part_of GO:0030198 ! extracellular matrix organization [Term] id: GO:0070716 name: mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication namespace: biological_process def: "A mismatch repair process that corrects errors introduced that ensures the accuracy of DNA replication." [GOC:BHF, GOC:mah] synonym: "mismatch repair involved in maintenance of fidelity during DNA-dependent DNA replication" RELATED [GOC:dph, GOC:tb] is_a: GO:0006298 ! mismatch repair created_by: mah creation_date: 2009-06-09T04:00:29Z [Term] id: GO:0070911 name: global genome nucleotide-excision repair namespace: biological_process def: "The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome." [PMID:10197977, PMID:18794354] synonym: "GG-NER" EXACT [PMID:10197977] synonym: "GGR" EXACT [GOC:vw, PMID:18794354] synonym: "global genome NER" EXACT [GOC:mah] synonym: "global genomic nucleotide-excision repair" EXACT [GOC:mah, GOC:vw] synonym: "global genomic repair" EXACT [GOC:vw, PMID:18794354] is_a: GO:0006289 ! nucleotide-excision repair created_by: mah creation_date: 2009-09-09T03:13:11Z [Term] id: GO:0070914 name: UV-damage excision repair namespace: biological_process def: "A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs)." [GOC:mah, PMID:9619100] synonym: "AER" RELATED [GOC:mah, PMID:10704216] synonym: "alternative excision repair" RELATED [GOC:mah, PMID:10704216] synonym: "UV-damaged DNA endonuclease-dependent excision repair" EXACT [GOC:vw] synonym: "UVDE-dependent excision repair" EXACT [GOC:vw, PMID:9619100] synonym: "UVER" EXACT [GOC:vw, PMID:9619100] is_a: GO:0006281 ! DNA repair created_by: mah creation_date: 2009-09-10T03:14:06Z [Term] id: GO:0070925 name: organelle assembly is_a: GO:0006996 ! organelle organization is_a: GO:0022607 ! cellular component assembly [Term] id: GO:0070987 name: error-free translesion synthesis namespace: biological_process def: "The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level." [GOC:elh] comment: Note that 'error-free' does not mean that literally zero errors occur during DNA synthesis, but that the error rate is low, comparable to that of DNA synthesis during replication. is_a: GO:0019985 ! translesion synthesis created_by: mah creation_date: 2009-10-29T02:45:42Z [Term] id: GO:0071214 name: cellular response to abiotic stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "cellular response to abiotic stress" NARROW [GOC:mah] is_a: GO:0009628 ! response to abiotic stimulus is_a: GO:0104004 ! cellular response to environmental stimulus created_by: mah creation_date: 2009-12-03T01:02:11Z [Term] id: GO:0071478 name: cellular response to radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:mah] comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength. synonym: "cellular response to electromagnetic radiation stimulus" EXACT [GOC:mah] synonym: "cellular response to radiation stimulus" EXACT [GOC:mah] is_a: GO:0009314 ! response to radiation is_a: GO:0071214 ! cellular response to abiotic stimulus created_by: mah creation_date: 2009-12-18T01:59:37Z [Term] id: GO:0071479 name: cellular response to ionizing radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [GOC:mah] synonym: "cellular response to ionising radiation" EXACT [GOC:mah] synonym: "cellular response to ionizing radiation stimulus" EXACT [GOC:mah] is_a: GO:0010212 ! response to ionizing radiation is_a: GO:0071478 ! cellular response to radiation created_by: mah creation_date: 2009-12-18T02:00:31Z [Term] id: GO:0071480 name: cellular response to gamma radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum." [GOC:mah] synonym: "cellular response to gamma ray" RELATED [GOC:mah] synonym: "cellular response to gamma-ray photon" RELATED [GOC:mah] is_a: GO:0010332 ! response to gamma radiation is_a: GO:0071479 ! cellular response to ionizing radiation created_by: mah creation_date: 2009-12-18T02:00:50Z [Term] id: GO:0071481 name: cellular response to X-ray namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC:mah] synonym: "cellular response to X-ray radiation stimulus" EXACT [GOC:mah] is_a: GO:0010165 ! response to X-ray is_a: GO:0071479 ! cellular response to ionizing radiation created_by: mah creation_date: 2009-12-18T02:00:59Z [Term] id: GO:0071702 name: organic substance transport is_a: GO:0006810 ! transport [Term] id: GO:0071704 name: organic substance metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] synonym: "organic molecular entity metabolic process" EXACT [] synonym: "organic molecular entity metabolism" EXACT [] synonym: "organic substance metabolism" EXACT [] is_a: GO:0008152 ! metabolic process created_by: mah creation_date: 2010-03-08T03:32:18Z [Term] id: GO:0071840 name: cellular component organization or biogenesis is_a: GO:0009987 ! cellular process [Term] id: GO:0071944 name: cell periphery is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0071953 name: elastic fiber is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0031012 ! extracellular matrix [Term] id: GO:0071971 name: extracellular exosome assembly is_a: GO:0016050 ! vesicle organization is_a: GO:0070925 ! organelle assembly relationship: part_of GO:0097734 ! extracellular exosome biogenesis [Term] id: GO:0072175 name: epithelial tube formation is_a: GO:0035148 ! tube formation relationship: part_of GO:0060562 ! epithelial tube morphogenesis [Term] id: GO:0072201 name: negative regulation of mesenchymal cell proliferation is_a: GO:0008285 ! negative regulation of cell population proliferation is_a: GO:0010464 ! regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010463 ! mesenchymal cell proliferation relationship: negatively_regulates GO:0010463 ! mesenchymal cell proliferation [Term] id: GO:0072359 name: circulatory system development is_a: GO:0048731 ! system development [Term] id: GO:0080090 name: regulation of primary metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [PMID:19211694] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044238 ! primary metabolic process relationship: regulates GO:0044238 ! primary metabolic process created_by: dhl creation_date: 2009-04-22T04:30:52Z [Term] id: GO:0080134 name: regulation of response to stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006950 ! response to stress relationship: regulates GO:0006950 ! response to stress created_by: dhl creation_date: 2009-05-06T04:51:28Z [Term] id: GO:0080135 name: regulation of cellular response to stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] is_a: GO:0050794 ! regulation of cellular process is_a: GO:0080134 ! regulation of response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0033554 ! cellular response to stress relationship: regulates GO:0033554 ! cellular response to stress created_by: dhl creation_date: 2009-05-06T05:02:52Z [Term] id: GO:0090257 name: regulation of muscle system process is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003012 ! muscle system process relationship: regulates GO:0003012 ! muscle system process [Term] id: GO:0090304 name: nucleic acid metabolic process namespace: biological_process def: "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0043170 ! macromolecule metabolic process created_by: tb creation_date: 2010-04-07T10:18:47Z [Term] id: GO:0090734 name: site of DNA damage namespace: cellular_component def: "A region of a chromosome at which DNA damage has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix." [GOC:pg] xref: Wikipedia:DNA_repair is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome created_by: tb creation_date: 2017-02-03T17:24:08Z [Term] id: GO:0097014 name: ciliary plasm is_a: GO:0032838 ! plasma membrane bounded cell projection cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0005929 ! cilium relationship: part_of GO:0005929 ! cilium [Term] id: GO:0097060 name: synaptic membrane is_a: GO:0098590 ! plasma membrane region intersection_of: GO:0098590 ! plasma membrane region intersection_of: part_of GO:0045202 ! synapse relationship: part_of GO:0045202 ! synapse [Term] id: GO:0097551 name: mitochondrial double-strand break repair namespace: biological_process def: "The repair of double-strand breaks in mitochondrial DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC:di, PMID:22214610] comment: Note that the processes of nuclear double-strand break repair and mitochondrial double-strand break repair are genetically separable. synonym: "mtDSB repair" EXACT [] is_a: GO:0006302 ! double-strand break repair created_by: pr creation_date: 2014-01-22T10:06:54Z [Term] id: GO:0097552 name: mitochondrial double-strand break repair via homologous recombination namespace: biological_process def: "The repair of a double-strand break in mitochondrial DNA in which the broken DNA molecule is repaired using homologous sequences." [GOC:di, PMID:22214610] comment: Note that the processes of nuclear double-strand break repair and mitochondrial double-strand break repair are genetically separable. synonym: "mtDSB repair via homologous recombination" EXACT [] is_a: GO:0000725 ! recombinational repair is_a: GO:0097551 ! mitochondrial double-strand break repair created_by: pr creation_date: 2014-01-22T10:09:10Z [Term] id: GO:0097680 name: double-strand break repair via classical nonhomologous end joining namespace: biological_process def: "An instance of double-strand break repair via nonhomologous end joining that requires a number of factors important for V(D)J recombination, including the KU70/80 heterodimer (KU), XRCC4, ligase IV, and DNA-PKcs in mammals. It does not produce translocations (as opposed to the alternative nonhomologous end joining)." [GOC:rph, PMID:18584027] synonym: "C-NHEJ" RELATED [] synonym: "canonical nonhomologous end joining" EXACT [] is_a: GO:0006303 ! double-strand break repair via nonhomologous end joining created_by: pr creation_date: 2014-12-17T15:15:18Z [Term] id: GO:0097681 name: double-strand break repair via alternative nonhomologous end joining namespace: biological_process def: "An instance of double-strand break repair via nonhomologous end joining that is independent of factors important for V(D)J recombination (as opposed to classical nonhomologous end joining). It often results in a deletion with microhomology (i.e. 5-25bp homology) at the repair junction. Among different subclasses of nonhomologous end joining (NHEJ), alternative NHEJ appears to play a significant role in the etiology of mutations that arise during cancer development and treatment." [GOC:rph, PMID:18584027, PMID:21655080, Wikipedia:Microhomology-mediated_end_joining] synonym: "A-NHEJ" RELATED [] synonym: "alt-NHEJ" RELATED [] synonym: "double-strand break repair via microhomology-mediated end joining" EXACT [] synonym: "MMEJ" RELATED [] is_a: GO:0006303 ! double-strand break repair via nonhomologous end joining created_by: pr creation_date: 2014-12-17T15:17:45Z [Term] id: GO:0097698 name: telomere maintenance via base-excision repair namespace: biological_process def: "A telomere maintenance process that occurs by base-excision repair of telomeric DNA in response to DNA damage. Telomeric sequences are particularly susceptible to oxidative DNA damage, due to their G-rich nature." [GOC:BHF, GOC:BHF_telomere, GOC:jbu, PMID:24703901] is_a: GO:0006284 ! base-excision repair created_by: pr creation_date: 2016-01-07T11:15:39Z [Term] id: GO:0097708 name: intracellular vesicle is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0097734 name: extracellular exosome biogenesis is_a: GO:0140112 ! extracellular vesicle biogenesis [Term] id: GO:0098590 name: plasma membrane region is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane [Term] id: GO:0098642 name: network-forming collagen trimer is_a: GO:0005581 ! collagen trimer intersection_of: GO:0005581 ! collagen trimer intersection_of: part_of GO:0098645 ! collagen network relationship: part_of GO:0098645 ! collagen network [Term] id: GO:0098643 name: banded collagen fibril is_a: GO:0098644 ! complex of collagen trimers is_a: GO:0099512 ! supramolecular fiber [Term] id: GO:0098644 name: complex of collagen trimers is_a: GO:0099080 ! supramolecular complex relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix [Term] id: GO:0098645 name: collagen network is_a: GO:0098644 ! complex of collagen trimers is_a: GO:0099081 ! supramolecular polymer [Term] id: GO:0098651 name: basement membrane collagen trimer is_a: GO:0005581 ! collagen trimer intersection_of: GO:0005581 ! collagen trimer intersection_of: part_of GO:0005604 ! basement membrane relationship: part_of GO:0005604 ! basement membrane [Term] id: GO:0098796 name: membrane protein complex is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0016020 ! membrane relationship: part_of GO:0016020 ! membrane [Term] id: GO:0098797 name: plasma membrane protein complex is_a: GO:0098796 ! membrane protein complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane [Term] id: GO:0098900 name: regulation of action potential is_a: GO:0042391 ! regulation of membrane potential is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0001508 ! action potential relationship: regulates GO:0001508 ! action potential [Term] id: GO:0098916 name: anterograde trans-synaptic signaling is_a: GO:0099537 ! trans-synaptic signaling [Term] id: GO:0099080 name: supramolecular complex is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0099081 name: supramolecular polymer is_a: GO:0099080 ! supramolecular complex [Term] id: GO:0099177 name: regulation of trans-synaptic signaling is_a: GO:0010646 ! regulation of cell communication is_a: GO:0023051 ! regulation of signaling intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0099537 ! trans-synaptic signaling relationship: regulates GO:0099537 ! trans-synaptic signaling [Term] id: GO:0099512 name: supramolecular fiber is_a: GO:0099081 ! supramolecular polymer [Term] id: GO:0099536 name: synaptic signaling is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse relationship: occurs_in GO:0045202 ! synapse [Term] id: GO:0099537 name: trans-synaptic signaling is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0099550 name: trans-synaptic signaling, modulating synaptic transmission is_a: GO:0099537 ! trans-synaptic signaling intersection_of: GO:0099537 ! trans-synaptic signaling intersection_of: regulates GO:0007268 ! chemical synaptic transmission relationship: regulates GO:0007268 ! chemical synaptic transmission [Term] id: GO:0099568 name: cytoplasmic region is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0099643 name: signal release from synapse is_a: GO:0023061 ! signal release intersection_of: GO:0023061 ! signal release intersection_of: occurs_in GO:0045202 ! synapse relationship: occurs_in GO:0045202 ! synapse relationship: part_of GO:0099536 ! synaptic signaling [Term] id: GO:0099738 name: cell cortex region is_a: GO:0005938 ! cell cortex is_a: GO:0099568 ! cytoplasmic region intersection_of: GO:0005938 ! cell cortex intersection_of: part_of GO:0005938 ! cell cortex relationship: part_of GO:0005938 ! cell cortex [Term] id: GO:0104004 name: cellular response to environmental stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an environmental stimulus." [GOC:dos] is_a: GO:0051716 ! cellular response to stimulus created_by: dos creation_date: 2017-02-17T16:02:42Z [Term] id: GO:0106300 name: protein-DNA covalent cross-linking repair namespace: biological_process def: "The removal of covalent cross-link between DNA and a protein." [PMID:31921408] synonym: "resolution of protein-DNA covalent cross-linking" EXACT [] is_a: GO:0006281 ! DNA repair created_by: hjd creation_date: 2020-08-26T14:23:42Z [Term] id: GO:0110165 name: cellular anatomical entity namespace: cellular_component 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 but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] is_a: GO:0005575 ! cellular_component created_by: kmv creation_date: 2019-08-12T18:01:37Z [Term] id: GO:0120025 name: plasma membrane bounded cell projection is_a: GO:0042995 ! cell projection intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region [Term] id: GO:0120111 name: neuron projection cytoplasm is_a: GO:0032838 ! plasma membrane bounded cell projection cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0043005 ! neuron projection relationship: part_of GO:0043005 ! neuron projection [Term] id: GO:0140112 name: extracellular vesicle biogenesis is_a: GO:0044085 ! cellular component biogenesis [Term] id: GO:0140352 name: export from cell is_a: GO:0006810 ! transport is_a: GO:0009987 ! cellular process [Term] id: GO:0140353 name: lipid export from cell is_a: GO:0006869 ! lipid transport is_a: GO:0140352 ! export from cell [Term] id: GO:0140513 name: nuclear protein-containing complex is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus [Term] id: GO:1901255 name: nucleotide-excision repair involved in interstrand cross-link repair namespace: biological_process def: "Any nucleotide-excision repair that is involved in interstrand cross-link repair." [GOC:TermGenie, PMID:22064477] synonym: "NER involved in ICL repair" EXACT [GOC:TermGenie] synonym: "NER involved in interstrand cross-link repair" EXACT [GOC:TermGenie] synonym: "nucleotide-excision repair involved in ICL repair" EXACT [GOC:TermGenie] is_a: GO:0006289 ! nucleotide-excision repair created_by: vw creation_date: 2012-08-09T06:09:50Z [Term] id: GO:1901342 name: regulation of vasculature development is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001944 ! vasculature development relationship: regulates GO:0001944 ! vasculature development [Term] id: GO:1901343 name: negative regulation of vasculature development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:1901342 ! regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001944 ! vasculature development relationship: negatively_regulates GO:0001944 ! vasculature development [Term] id: GO:1901360 name: organic cyclic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0071704 ! organic substance metabolic process created_by: bf creation_date: 2012-09-14T09:03:51Z [Term] id: GO:1901532 name: regulation of hematopoietic progenitor cell differentiation is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002244 ! hematopoietic progenitor cell differentiation relationship: regulates GO:0002244 ! hematopoietic progenitor cell differentiation [Term] id: GO:1901533 name: negative regulation of hematopoietic progenitor cell differentiation is_a: GO:0045596 ! negative regulation of cell differentiation is_a: GO:1901532 ! regulation of hematopoietic progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation relationship: negatively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation [Term] id: GO:1901534 name: positive regulation of hematopoietic progenitor cell differentiation is_a: GO:0045597 ! positive regulation of cell differentiation is_a: GO:1901532 ! regulation of hematopoietic progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation relationship: positively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation [Term] id: GO:1902115 name: regulation of organelle assembly is_a: GO:0033043 ! regulation of organelle organization is_a: GO:0044087 ! regulation of cellular component biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070925 ! organelle assembly relationship: regulates GO:0070925 ! organelle assembly [Term] id: GO:1902116 name: negative regulation of organelle assembly is_a: GO:0010639 ! negative regulation of organelle organization is_a: GO:1902115 ! regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070925 ! organelle assembly relationship: negatively_regulates GO:0070925 ! organelle assembly [Term] id: GO:1902117 name: positive regulation of organelle assembly is_a: GO:0010638 ! positive regulation of organelle organization is_a: GO:0044089 ! positive regulation of cellular component biogenesis is_a: GO:1902115 ! regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070925 ! organelle assembly relationship: positively_regulates GO:0070925 ! organelle assembly [Term] id: GO:1903053 name: regulation of extracellular matrix organization is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030198 ! extracellular matrix organization relationship: regulates GO:0030198 ! extracellular matrix organization [Term] id: GO:1903054 name: negative regulation of extracellular matrix organization is_a: GO:0051129 ! negative regulation of cellular component organization is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030198 ! extracellular matrix organization relationship: negatively_regulates GO:0030198 ! extracellular matrix organization [Term] id: GO:1903055 name: positive regulation of extracellular matrix organization is_a: GO:0051130 ! positive regulation of cellular component organization is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030198 ! extracellular matrix organization relationship: positively_regulates GO:0030198 ! extracellular matrix organization [Term] id: GO:1903522 name: regulation of blood circulation is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008015 ! blood circulation relationship: regulates GO:0008015 ! blood circulation [Term] id: GO:1903523 name: negative regulation of blood circulation is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:1903522 ! regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008015 ! blood circulation relationship: negatively_regulates GO:0008015 ! blood circulation [Term] id: GO:1903524 name: positive regulation of blood circulation is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:1903522 ! regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008015 ! blood circulation relationship: positively_regulates GO:0008015 ! blood circulation [Term] id: GO:1903530 name: regulation of secretion by cell is_a: GO:0050794 ! regulation of cellular process is_a: GO:0051046 ! regulation of secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032940 ! secretion by cell relationship: regulates GO:0032940 ! secretion by cell [Term] id: GO:1903531 name: negative regulation of secretion by cell is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051048 ! negative regulation of secretion is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032940 ! secretion by cell relationship: negatively_regulates GO:0032940 ! secretion by cell [Term] id: GO:1903532 name: positive regulation of secretion by cell is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051047 ! positive regulation of secretion is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032940 ! secretion by cell relationship: positively_regulates GO:0032940 ! secretion by cell [Term] id: GO:1903551 name: regulation of extracellular exosome assembly is_a: GO:1902115 ! regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071971 ! extracellular exosome assembly relationship: regulates GO:0071971 ! extracellular exosome assembly [Term] id: GO:1903552 name: negative regulation of extracellular exosome assembly is_a: GO:1902116 ! negative regulation of organelle assembly is_a: GO:1903551 ! regulation of extracellular exosome assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071971 ! extracellular exosome assembly relationship: negatively_regulates GO:0071971 ! extracellular exosome assembly [Term] id: GO:1903553 name: positive regulation of extracellular exosome assembly is_a: GO:1902117 ! positive regulation of organelle assembly is_a: GO:1903551 ! regulation of extracellular exosome assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071971 ! extracellular exosome assembly relationship: positively_regulates GO:0071971 ! extracellular exosome assembly [Term] id: GO:1903561 name: extracellular vesicle is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region [Term] id: GO:1903706 name: regulation of hemopoiesis is_a: GO:0002682 ! regulation of immune system process is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030097 ! hemopoiesis relationship: regulates GO:0030097 ! hemopoiesis [Term] id: GO:1903707 name: negative regulation of hemopoiesis is_a: GO:0002683 ! negative regulation of immune system process is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030097 ! hemopoiesis relationship: negatively_regulates GO:0030097 ! hemopoiesis [Term] id: GO:1903708 name: positive regulation of hemopoiesis is_a: GO:0002684 ! positive regulation of immune system process is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030097 ! hemopoiesis relationship: positively_regulates GO:0030097 ! hemopoiesis [Term] id: GO:1903823 name: telomere single strand break repair namespace: biological_process def: "Single strand break repair that takes place in a telomere." [GO_REF:0000062, GOC:TermGenie, PMID:24374808] synonym: "single strand break repair in telomere" EXACT [GOC:TermGenie] synonym: "telomere single-strand break repair" EXACT [] synonym: "telomere SSBR" RELATED [] synonym: "telomeric single strand break repair" EXACT [] is_a: GO:0000012 ! single strand break repair created_by: jl creation_date: 2015-01-19T16:12:29Z [Term] id: GO:1903941 name: negative regulation of respiratory gaseous exchange is_a: GO:0043576 ! regulation of respiratory gaseous exchange is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: negatively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system [Term] id: GO:1903942 name: positive regulation of respiratory gaseous exchange is_a: GO:0043576 ! regulation of respiratory gaseous exchange is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: positively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system [Term] id: GO:1904018 name: positive regulation of vasculature development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:1901342 ! regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001944 ! vasculature development relationship: positively_regulates GO:0001944 ! vasculature development [Term] id: GO:1904675 name: regulation of somatic stem cell division is_a: GO:2000035 ! regulation of stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048103 ! somatic stem cell division relationship: regulates GO:0048103 ! somatic stem cell division [Term] id: GO:1904676 name: negative regulation of somatic stem cell division is_a: GO:0051782 ! negative regulation of cell division is_a: GO:1904675 ! regulation of somatic stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048103 ! somatic stem cell division relationship: negatively_regulates GO:0048103 ! somatic stem cell division [Term] id: GO:1904677 name: positive regulation of somatic stem cell division is_a: GO:0051781 ! positive regulation of cell division is_a: GO:1904675 ! regulation of somatic stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048103 ! somatic stem cell division relationship: positively_regulates GO:0048103 ! somatic stem cell division [Term] id: GO:1905276 name: regulation of epithelial tube formation is_a: GO:1905330 ! regulation of morphogenesis of an epithelium is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072175 ! epithelial tube formation relationship: regulates GO:0072175 ! epithelial tube formation [Term] id: GO:1905277 name: negative regulation of epithelial tube formation is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:1905276 ! regulation of epithelial tube formation is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072175 ! epithelial tube formation relationship: negatively_regulates GO:0072175 ! epithelial tube formation [Term] id: GO:1905278 name: positive regulation of epithelial tube formation is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:1905276 ! regulation of epithelial tube formation is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072175 ! epithelial tube formation relationship: positively_regulates GO:0072175 ! epithelial tube formation [Term] id: GO:1905330 name: regulation of morphogenesis of an epithelium is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002009 ! morphogenesis of an epithelium relationship: regulates GO:0002009 ! morphogenesis of an epithelium [Term] id: GO:1905331 name: negative regulation of morphogenesis of an epithelium is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002009 ! morphogenesis of an epithelium relationship: negatively_regulates GO:0002009 ! morphogenesis of an epithelium [Term] id: GO:1905332 name: positive regulation of morphogenesis of an epithelium is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002009 ! morphogenesis of an epithelium relationship: positively_regulates GO:0002009 ! morphogenesis of an epithelium [Term] id: GO:1905553 name: regulation of blood vessel branching is_a: GO:0045765 ! regulation of angiogenesis is_a: GO:0060688 ! regulation of morphogenesis of a branching structure is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001569 ! branching involved in blood vessel morphogenesis relationship: regulates GO:0001569 ! branching involved in blood vessel morphogenesis [Term] id: GO:1905554 name: negative regulation of vessel branching is_a: GO:0016525 ! negative regulation of angiogenesis is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium is_a: GO:1905553 ! regulation of blood vessel branching intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis relationship: negatively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis [Term] id: GO:1905555 name: positive regulation of blood vessel branching is_a: GO:0045766 ! positive regulation of angiogenesis is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium is_a: GO:1905553 ! regulation of blood vessel branching intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis relationship: positively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis [Term] id: GO:1905843 name: regulation of cellular response to gamma radiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular response to gamma radiation." [GO_REF:0000058, GOC:TermGenie, PMID:23505386] synonym: "regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] is_a: GO:0050794 ! regulation of cellular process is_a: GO:2001228 ! regulation of response to gamma radiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071480 ! cellular response to gamma radiation relationship: regulates GO:0071480 ! cellular response to gamma radiation created_by: rz creation_date: 2017-01-19T10:24:39Z [Term] id: GO:1905844 name: negative regulation of cellular response to gamma radiation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to gamma radiation." [GO_REF:0000058, GOC:TermGenie, PMID:23505386] synonym: "down regulation of cellular response to gamma radiation" EXACT [GOC:TermGenie] synonym: "down regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "down regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "down-regulation of cellular response to gamma radiation" EXACT [GOC:TermGenie] synonym: "down-regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "down-regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "downregulation of cellular response to gamma radiation" EXACT [GOC:TermGenie] synonym: "downregulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "downregulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "inhibition of cellular response to gamma radiation" NARROW [GOC:TermGenie] synonym: "inhibition of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "inhibition of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "negative regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "negative regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:1905843 ! regulation of cellular response to gamma radiation is_a: GO:2001229 ! negative regulation of response to gamma radiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071480 ! cellular response to gamma radiation relationship: negatively_regulates GO:0071480 ! cellular response to gamma radiation created_by: rz creation_date: 2017-01-19T10:24:48Z [Term] id: GO:1905845 name: positive regulation of cellular response to gamma radiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cellular response to gamma radiation." [GO_REF:0000058, GOC:TermGenie, PMID:23505386] synonym: "activation of cellular response to gamma radiation" NARROW [GOC:TermGenie] synonym: "activation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "activation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "positive regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "positive regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "up regulation of cellular response to gamma radiation" EXACT [GOC:TermGenie] synonym: "up regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "up regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "up-regulation of cellular response to gamma radiation" EXACT [GOC:TermGenie] synonym: "up-regulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "up-regulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] synonym: "upregulation of cellular response to gamma radiation" EXACT [GOC:TermGenie] synonym: "upregulation of cellular response to gamma ray" RELATED [GOC:TermGenie] synonym: "upregulation of cellular response to gamma-ray photon" RELATED [GOC:TermGenie] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:1905843 ! regulation of cellular response to gamma radiation is_a: GO:2001230 ! positive regulation of response to gamma radiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071480 ! cellular response to gamma radiation relationship: positively_regulates GO:0071480 ! cellular response to gamma radiation created_by: rz creation_date: 2017-01-19T10:24:57Z [Term] id: GO:1905902 name: regulation of mesoderm formation is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001707 ! mesoderm formation relationship: regulates GO:0001707 ! mesoderm formation [Term] id: GO:1905903 name: negative regulation of mesoderm formation is_a: GO:1905902 ! regulation of mesoderm formation is_a: GO:2000381 ! negative regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001707 ! mesoderm formation relationship: negatively_regulates GO:0001707 ! mesoderm formation [Term] id: GO:1905904 name: positive regulation of mesoderm formation is_a: GO:1905902 ! regulation of mesoderm formation is_a: GO:2000382 ! positive regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001707 ! mesoderm formation relationship: positively_regulates GO:0001707 ! mesoderm formation [Term] id: GO:1905952 name: regulation of lipid localization is_a: GO:0032879 ! regulation of localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010876 ! lipid localization relationship: regulates GO:0010876 ! lipid localization [Term] id: GO:1905953 name: negative regulation of lipid localization is_a: GO:0048519 ! negative regulation of biological process is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010876 ! lipid localization relationship: negatively_regulates GO:0010876 ! lipid localization [Term] id: GO:1905954 name: positive regulation of lipid localization is_a: GO:0048518 ! positive regulation of biological process is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010876 ! lipid localization relationship: positively_regulates GO:0010876 ! lipid localization [Term] id: GO:1990396 name: single-strand break repair via homologous recombination namespace: biological_process def: "The error-free repair of a single-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC:bhm, PMID:24339919] is_a: GO:0000012 ! single strand break repair is_a: GO:0000725 ! recombinational repair is_a: GO:0042275 ! error-free postreplication DNA repair created_by: bhm creation_date: 2014-06-09T10:47:04Z [Term] id: GO:1990414 name: replication-born double-strand break repair via sister chromatid exchange namespace: biological_process def: "The repair of a replication-born double-strand DNA break in which the DNA molecule is repaired using the homologous sequence of the sister chromatid which serves as a template to repair the breaks." [GOC:rb, PMID:12820977, PMID:16888651] synonym: "replication-born DSB repair by SCE" EXACT [] is_a: GO:0000724 ! double-strand break repair via homologous recombination created_by: rb creation_date: 2014-07-10T21:20:34Z [Term] id: GO:1990516 name: ribonucleotide excision repair namespace: biological_process def: "The pathway by which a ribonucleotide is removed from DNA and replaced by a deoxyribonucleotide. The ribonucleotide is incised by RNase H2, and further excised by an endonuclease. The resulting 1 nt gap is then repaired by DNA polymerase and DNA ligase." [PMID:12475934, PMID:22864116] is_a: GO:0070716 ! mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication created_by: al creation_date: 2014-10-14T12:24:37Z [Term] id: GO:1990918 name: double-strand break repair involved in meiotic recombination namespace: biological_process def: "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix that contributes to reciprocal meiotic recombination." [GOC:mah, PMID:15238514] is_a: GO:0006302 ! double-strand break repair created_by: al creation_date: 2015-12-11T01:01:14Z [Term] id: GO:2000026 name: regulation of multicellular organismal development is_a: GO:0050793 ! regulation of developmental process is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007275 ! multicellular organism development relationship: regulates GO:0007275 ! multicellular organism development [Term] id: GO:2000035 name: regulation of stem cell division is_a: GO:0051302 ! regulation of cell division intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0017145 ! stem cell division relationship: regulates GO:0017145 ! stem cell division [Term] id: GO:2000145 name: regulation of cell motility is_a: GO:0040012 ! regulation of locomotion is_a: GO:0051270 ! regulation of cellular component movement intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048870 ! cell motility relationship: regulates GO:0048870 ! cell motility [Term] id: GO:2000146 name: negative regulation of cell motility is_a: GO:0040013 ! negative regulation of locomotion is_a: GO:0051271 ! negative regulation of cellular component movement is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048870 ! cell motility relationship: negatively_regulates GO:0048870 ! cell motility [Term] id: GO:2000147 name: positive regulation of cell motility is_a: GO:0040017 ! positive regulation of locomotion is_a: GO:0051272 ! positive regulation of cellular component movement is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048870 ! cell motility relationship: positively_regulates GO:0048870 ! cell motility [Term] id: GO:2000181 name: negative regulation of blood vessel morphogenesis is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:1901343 ! negative regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048514 ! blood vessel morphogenesis relationship: negatively_regulates GO:0048514 ! blood vessel morphogenesis [Term] id: GO:2000241 name: regulation of reproductive process is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0022414 ! reproductive process relationship: regulates GO:0022414 ! reproductive process [Term] id: GO:2000242 name: negative regulation of reproductive process is_a: GO:0048519 ! negative regulation of biological process is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0022414 ! reproductive process relationship: negatively_regulates GO:0022414 ! reproductive process [Term] id: GO:2000243 name: positive regulation of reproductive process is_a: GO:0048518 ! positive regulation of biological process is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0022414 ! reproductive process relationship: positively_regulates GO:0022414 ! reproductive process [Term] id: GO:2000380 name: regulation of mesoderm development is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007498 ! mesoderm development relationship: regulates GO:0007498 ! mesoderm development [Term] id: GO:2000381 name: negative regulation of mesoderm development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:2000380 ! regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007498 ! mesoderm development relationship: negatively_regulates GO:0007498 ! mesoderm development [Term] id: GO:2000382 name: positive regulation of mesoderm development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:2000380 ! regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007498 ! mesoderm development relationship: positively_regulates GO:0007498 ! mesoderm development [Term] id: GO:2000383 name: regulation of ectoderm development is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007398 ! ectoderm development relationship: regulates GO:0007398 ! ectoderm development [Term] id: GO:2000384 name: negative regulation of ectoderm development is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:2000383 ! regulation of ectoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007398 ! ectoderm development relationship: negatively_regulates GO:0007398 ! ectoderm development [Term] id: GO:2000385 name: positive regulation of ectoderm development is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:2000383 ! regulation of ectoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007398 ! ectoderm development relationship: positively_regulates GO:0007398 ! ectoderm development [Term] id: GO:2000542 name: negative regulation of gastrulation is_a: GO:0010470 ! regulation of gastrulation is_a: GO:0045992 ! negative regulation of embryonic development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007369 ! gastrulation relationship: negatively_regulates GO:0007369 ! gastrulation [Term] id: GO:2000543 name: positive regulation of gastrulation is_a: GO:0010470 ! regulation of gastrulation is_a: GO:0040019 ! positive regulation of embryonic development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007369 ! gastrulation relationship: positively_regulates GO:0007369 ! gastrulation [Term] id: GO:2000683 name: regulation of cellular response to X-ray namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular response to X-ray." [GOC:obol] synonym: "regulation of cellular response to X-ray radiation stimulus" EXACT [GOC:obol] is_a: GO:0048583 ! regulation of response to stimulus is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071481 ! cellular response to X-ray relationship: regulates GO:0071481 ! cellular response to X-ray created_by: yaf creation_date: 2011-05-10T01:40:41Z [Term] id: GO:2000684 name: negative regulation of cellular response to X-ray namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to X-ray." [GOC:obol] synonym: "negative regulation of cellular response to X-ray radiation stimulus" EXACT [GOC:obol] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:2000683 ! regulation of cellular response to X-ray intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071481 ! cellular response to X-ray relationship: negatively_regulates GO:0071481 ! cellular response to X-ray created_by: yaf creation_date: 2011-05-10T01:40:45Z [Term] id: GO:2000685 name: positive regulation of cellular response to X-ray namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cellular response to X-ray." [GOC:obol] synonym: "positive regulation of cellular response to X-ray radiation stimulus" EXACT [GOC:obol] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:2000683 ! regulation of cellular response to X-ray intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071481 ! cellular response to X-ray relationship: positively_regulates GO:0071481 ! cellular response to X-ray created_by: yaf creation_date: 2011-05-10T01:40:49Z [Term] id: GO:2000831 name: regulation of steroid hormone secretion is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0044060 ! regulation of endocrine process is_a: GO:0046883 ! regulation of hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035929 ! steroid hormone secretion relationship: regulates GO:0035929 ! steroid hormone secretion [Term] id: GO:2000832 name: negative regulation of steroid hormone secretion is_a: GO:0032369 ! negative regulation of lipid transport is_a: GO:0046888 ! negative regulation of hormone secretion is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035929 ! steroid hormone secretion relationship: negatively_regulates GO:0035929 ! steroid hormone secretion [Term] id: GO:2000833 name: positive regulation of steroid hormone secretion is_a: GO:0032370 ! positive regulation of lipid transport is_a: GO:0046887 ! positive regulation of hormone secretion is_a: GO:0051240 ! positive regulation of multicellular organismal process is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035929 ! steroid hormone secretion relationship: positively_regulates GO:0035929 ! steroid hormone secretion [Term] id: GO:2000834 name: regulation of androgen secretion is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035935 ! androgen secretion relationship: regulates GO:0035935 ! androgen secretion [Term] id: GO:2000835 name: negative regulation of androgen secretion is_a: GO:2000832 ! negative regulation of steroid hormone secretion is_a: GO:2000834 ! regulation of androgen secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035935 ! androgen secretion relationship: negatively_regulates GO:0035935 ! androgen secretion [Term] id: GO:2000836 name: positive regulation of androgen secretion is_a: GO:2000833 ! positive regulation of steroid hormone secretion is_a: GO:2000834 ! regulation of androgen secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035935 ! androgen secretion relationship: positively_regulates GO:0035935 ! androgen secretion [Term] id: GO:2001020 name: regulation of response to DNA damage stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol] synonym: "regulation of cellular DNA damage response" EXACT [GOC:obol] synonym: "regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol] synonym: "regulation of DNA damage response" EXACT [GOC:obol] synonym: "regulation of response to genotoxic stress" EXACT [GOC:obol] is_a: GO:0080135 ! regulation of cellular response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006974 ! cellular response to DNA damage stimulus relationship: regulates GO:0006974 ! cellular response to DNA damage stimulus created_by: yaf creation_date: 2011-08-19T10:20:25Z [Term] id: GO:2001021 name: negative regulation of response to DNA damage stimulus namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol] synonym: "negative regulation of cellular DNA damage response" EXACT [GOC:obol] synonym: "negative regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol] synonym: "negative regulation of DNA damage response" EXACT [GOC:obol] synonym: "negative regulation of response to genotoxic stress" EXACT [GOC:obol] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:2001020 ! regulation of response to DNA damage stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006974 ! cellular response to DNA damage stimulus relationship: negatively_regulates GO:0006974 ! cellular response to DNA damage stimulus created_by: yaf creation_date: 2011-08-19T10:20:29Z [Term] id: GO:2001022 name: positive regulation of response to DNA damage stimulus namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol] synonym: "positive regulation of cellular DNA damage response" EXACT [GOC:obol] synonym: "positive regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol] synonym: "positive regulation of DNA damage response" EXACT [GOC:obol] synonym: "positive regulation of response to genotoxic stress" EXACT [GOC:obol] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:2001020 ! regulation of response to DNA damage stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006974 ! cellular response to DNA damage stimulus relationship: positively_regulates GO:0006974 ! cellular response to DNA damage stimulus created_by: yaf creation_date: 2011-08-19T10:20:33Z [Term] id: GO:2001228 name: regulation of response to gamma radiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of response to gamma radiation." [GOC:obol] synonym: "regulation of response to gamma ray" RELATED [GOC:obol] synonym: "regulation of response to gamma-ray photon" RELATED [GOC:obol] is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010332 ! response to gamma radiation relationship: regulates GO:0010332 ! response to gamma radiation created_by: yaf creation_date: 2011-11-20T04:51:07Z [Term] id: GO:2001229 name: negative regulation of response to gamma radiation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to gamma radiation." [GOC:obol] synonym: "negative regulation of response to gamma ray" RELATED [GOC:obol] synonym: "negative regulation of response to gamma-ray photon" RELATED [GOC:obol] is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:2001228 ! regulation of response to gamma radiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010332 ! response to gamma radiation relationship: negatively_regulates GO:0010332 ! response to gamma radiation created_by: yaf creation_date: 2011-11-20T04:51:14Z [Term] id: GO:2001230 name: positive regulation of response to gamma radiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of response to gamma radiation." [GOC:obol] synonym: "positive regulation of response to gamma ray" RELATED [GOC:obol] synonym: "positive regulation of response to gamma-ray photon" RELATED [GOC:obol] is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:2001228 ! regulation of response to gamma radiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010332 ! response to gamma radiation relationship: positively_regulates GO:0010332 ! response to gamma radiation created_by: yaf creation_date: 2011-11-20T04:51:17Z [Term] id: IAO:0000003 name: measurement unit label def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] is_a: IAO:0000009 ! datum label property_value: editor_note "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string property_value: editor_note "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: example_of_usage "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000005 name: objective specification def: "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] is_a: IAO:0000033 ! directive information entity property_value: editor_note "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" xsd:string property_value: editor_note "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that." xsd:string property_value: editor_note "Answers the question, why did you do this experiment?" xsd:string property_value: example_of_usage "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." xsd:string property_value: IAO:0000111 "objective specification" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Barry Smith" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000118 "goal specification" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process/Roles Branch" xsd:string property_value: IAO:0000119 "OBI_0000217" xsd:string [Term] id: IAO:0000007 name: action specification def: "A directive information entity that describes an action the bearer will take." [] is_a: IAO:0000033 ! directive information entity property_value: example_of_usage "Pour the contents of flask 1 into flask 2" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string [Term] id: IAO:0000009 name: datum label def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] is_a: IAO:0000030 ! information content entity property_value: editor_note http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n xsd:string property_value: IAO:0000111 "datum label" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "GROUP: IAO" xsd:string property_value: IAO:0000232 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" xsd:string [Term] id: IAO:0000010 name: software def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." [] is_a: IAO:0000104 ! plan specification property_value: editor_note "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" xsd:string property_value: IAO:0000111 "software" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [Term] id: IAO:0000015 name: information carrier def: "A quality of an information bearer that imparts the information content" [] is_a: BFO:0000019 ! quality intersection_of: BFO:0000019 ! quality intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity relationship: RO:0000059 IAO:0000030 ! concretizes information content entity property_value: editor_note "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." xsd:string property_value: editor_note "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." xsd:string property_value: example_of_usage "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." xsd:string property_value: IAO:0000111 "information carrier" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string [Term] id: IAO:0000027 name: data item def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] 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: editor_note "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string property_value: editor_note "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string property_value: editor_note "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: editor_note "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string property_value: editor_note "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: example_of_usage "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000114 IAO:0000125 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 property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [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: editor_note "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string property_value: editor_note "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\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: example_of_usage "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000119 "OBI_0000142" xsd:string [Term] id: IAO:0000032 name: scalar measurement datum def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." [] is_a: IAO:0000109 ! measurement datum relationship: OBI:0001938 OBI:0001931 ! has value specification scalar value specification property_value: editor_note "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string property_value: editor_note "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string property_value: example_of_usage "10 feet. 3 ml." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000033 name: directive information entity def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." [] is_a: IAO:0000030 ! information content entity relationship: IAO:0000136 BFO:0000017 ! is about realizable entity property_value: editor_note "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: editor_note "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it." xsd:string property_value: editor_note "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string property_value: editor_note "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan" 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 [Term] id: IAO:0000037 name: dot plot def: "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions." [] is_a: IAO:0000038 ! graph property_value: example_of_usage "Dot plot of SSC-H and FSC-H." xsd:string property_value: IAO:0000111 "dot plot" xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000123" xsd:string [Term] id: IAO:0000038 name: graph def: "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." [] is_a: IAO:0000309 ! diagram property_value: IAO:0000111 "graph" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000240" xsd:string [Term] id: IAO:0000064 name: algorithm def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification property_value: example_of_usage "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string property_value: IAO:0000111 "algorithm" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" xsd:string property_value: IAO:0000119 "OBI_0000270" 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: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 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:0000096 name: source code module def: "A source code module is a directive information entity that specifies, using a programming language, some algorithm." [] is_a: IAO:0000033 ! directive information entity property_value: example_of_usage "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script." xsd:string property_value: IAO:0000111 "source code module" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000039" xsd:string [Term] id: IAO:0000098 name: data format specification def: "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" [] is_a: IAO:0000033 ! directive information entity property_value: editor_note "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" xsd:string property_value: IAO:0000111 "data format specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000187" xsd:string [Term] id: IAO:0000100 name: data set def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] is_a: IAO:0000027 ! data item property_value: editor_note "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: editor_note "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string property_value: example_of_usage "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string property_value: IAO:0000111 "data set" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000042" xsd:string [Term] id: IAO:0000101 name: image def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." [] is_a: IAO:0000308 ! figure property_value: IAO:0000111 "image" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 person:Allyson xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000030" 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:0000104 name: plan specification def: "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them is_a: IAO:0000033 ! directive information entity relationship: has_part IAO:0000005 ! objective specification relationship: has_part IAO:0000007 ! action specification property_value: editor_note "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: editor_note "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string property_value: editor_note "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" xsd:string property_value: example_of_usage "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string property_value: IAO:0000111 "plan specification" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string property_value: IAO:0000119 "OBI_0000344" xsd:string [Term] id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] is_a: IAO:0000027 ! data item relationship: OBI:0001938 OBI:0001933 ! has value specification value specification property_value: editor_note "2/2/2009 is_specified_output of some assay?" xsd:string property_value: example_of_usage "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000305" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: IAO:0000178 name: material information bearer def: "A material entity in which a concretization of an information content entity inheres." [] is_a: BFO:0000040 ! material entity property_value: example_of_usage "a brain" xsd:string property_value: example_of_usage "a hard drive" xsd:string property_value: example_of_usage "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string property_value: IAO:0000111 "material information bearer" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: IAO" xsd:string [Term] id: IAO:0000179 name: histogram def: "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "histogram" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [Term] id: IAO:0000180 name: heatmap def: "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "heatmap" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [Term] id: IAO:0000183 name: dendrogram def: "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." [] is_a: IAO:0000038 ! graph property_value: example_of_usage "Dendrograms are often used in computational biology to\nillustrate the clustering of genes." xsd:string property_value: IAO:0000111 "dendrogram" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Dendrogram" xsd:string [Term] id: IAO:0000184 name: scatter plot def: "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." [] is_a: IAO:0000038 ! graph property_value: example_of_usage "Comparison of gene expression values in two samples can be displayed in a scatter plot" xsd:string property_value: IAO:0000111 "scatter plot" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000118 "scattergraph" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Scatterplot" 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: editor_note "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:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000308 name: figure def: "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." [] is_a: IAO:0000030 ! information content entity property_value: example_of_usage "Any picture, diagram or table" xsd:string property_value: IAO:0000111 "figure" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000309 name: diagram def: "A figure that expresses one or more propositions" [] is_a: IAO:0000308 ! figure property_value: example_of_usage "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space." xsd:string property_value: IAO:0000111 "diagram" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000310 name: document def: "A collection of information content entities intended to be understood together as a whole" [] is_a: IAO:0000030 ! information content entity property_value: example_of_usage "A journal article, patent application, laboratory notebook, or a book" xsd:string property_value: IAO:0000111 "document" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000408 name: length measurement datum def: "A scalar measurement datum that is the result of measurement of length quality" [] is_a: IAO:0000032 ! scalar measurement datum relationship: IAO:0000039 UO:0000001 ! has measurement unit label length unit relationship: IAO:0000221 PATO:0000122 ! is quality measurement of length property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" 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: example_of_usage "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:0000111 "denotator type" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [Term] id: NBO:0000001 name: body part movement is_a: NBO:0000338 ! kinesthetic behavior [Term] id: NBO:0000007 name: mouth movement is_a: NBO:0000001 ! body part movement [Term] id: NBO:0000073 name: chewing is_a: NBO:0000747 ! jaw movement [Term] id: NBO:0000313 name: behavior process is_a: GO:0007610 ! behavior [Term] id: NBO:0000338 name: kinesthetic behavior is_a: NBO:0000313 ! behavior process [Term] id: NBO:0000747 name: jaw movement is_a: NBO:0000007 ! mouth movement [Term] id: NCBITaxon:1 name: root namespace: ncbi_taxonomy synonym: "all" RELATED synonym [] xref: GC_ID:1 is_a: BFO:0000040 ! material entity [Term] id: NCBITaxon:10239 name: Viruses is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Viruses" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:117570 name: Teleostomi is_a: NCBITaxon:7776 ! Gnathostomata relationship: in_taxon NCBITaxon:117570 ! Teleostomi [Term] id: NCBITaxon:117571 name: Euteleostomi synonym: "bony vertebrates" EXACT [] is_a: NCBITaxon:117570 ! Teleostomi relationship: in_taxon NCBITaxon:117571 ! Euteleostomi property_value: IAO:0000111 "Euteleostomi" xsd:string property_value: IAO:0000118 "bony vertebrates" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:131567 name: cellular organisms namespace: ncbi_taxonomy synonym: "biota" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1 ! root [Term] id: NCBITaxon:1338369 name: Dipnotetrapodomorpha is_a: NCBITaxon:8287 ! Sarcopterygii [Term] id: NCBITaxon:1437010 name: Boreoeutheria synonym: "Boreotheria" RELATED [] is_a: NCBITaxon:9347 ! Eutheria [Term] id: NCBITaxon:2 name: Bacteria synonym: "bacteria" RELATED [] synonym: "eubacteria" EXACT [] synonym: "Monera" RELATED [] synonym: "Procaryotae" RELATED [] synonym: "Prokaryota" RELATED [] synonym: "Prokaryotae" RELATED [] synonym: "prokaryote" RELATED [] synonym: "prokaryotes" RELATED [] is_a: NCBITaxon:131567 ! cellular organisms is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Bacteria" xsd:string property_value: IAO:0000118 "eubacteria" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:207598 name: Homininae synonym: "Homo/Pan/Gorilla group" RELATED [] is_a: NCBITaxon:9604 ! Hominidae [Term] id: NCBITaxon:2157 name: Archaea is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Archaea" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2759 name: Eukaryota namespace: ncbi_taxonomy synonym: "Eucarya" RELATED synonym [] synonym: "Eucaryotae" RELATED synonym [] synonym: "eucaryotes" EXACT genbank_common_name [] synonym: "Eukarya" RELATED synonym [] synonym: "Eukaryotae" RELATED synonym [] synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms is_a: OBI:0100026 ! organism relationship: in_taxon NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:superkingdom property_value: IAO:0000111 "Eukaryota" xsd:string property_value: IAO:0000118 "eucaryotes" xsd:string property_value: IAO:0000118 "eukaryotes" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:314146 name: Euarchontoglires is_a: NCBITaxon:1437010 ! Boreoeutheria property_value: IAO:0000111 "Euarchontoglires" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:314293 name: Simiiformes synonym: "Anthropoidea" RELATED [] is_a: NCBITaxon:376913 ! Haplorrhini [Term] id: NCBITaxon:314295 name: Hominoidea synonym: "ape" EXACT [] synonym: "apes" EXACT [] is_a: NCBITaxon:9526 ! Catarrhini [Term] id: NCBITaxon:32523 name: Tetrapoda synonym: "tetrapods" EXACT [] is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha property_value: IAO:0000111 "Tetrapoda" xsd:string property_value: IAO:0000118 "tetrapods" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32524 name: Amniota synonym: "amniotes" EXACT [] is_a: NCBITaxon:32523 ! Tetrapoda property_value: IAO:0000111 "Amniota" xsd:string property_value: IAO:0000118 "amniotes" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 name: Theria synonym: "Theria" EXACT [] is_a: NCBITaxon:40674 ! Mammalia [Term] id: NCBITaxon:33090 name: Viridiplantae synonym: "Chlorobionta" RELATED [] synonym: "Chlorophyta/Embryophyta group" EXACT [] synonym: "chlorophyte/embryophyte group" EXACT [] synonym: "Chloroplastida" RELATED [] synonym: "green plants" EXACT [] synonym: "green plants" RELATED [] is_a: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:33154 name: Opisthokonta namespace: ncbi_taxonomy synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota relationship: in_taxon NCBITaxon:33154 ! Opisthokonta property_value: IAO:0000111 "Opisthokonta" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33208 name: Metazoa synonym: "Animalia" RELATED [] synonym: "animals" RELATED [] synonym: "metazoans" EXACT [] synonym: "multicellular animals" EXACT [] is_a: NCBITaxon:33154 ! Opisthokonta relationship: in_taxon NCBITaxon:33208 ! Metazoa [Term] id: NCBITaxon:33213 name: Bilateria is_a: NCBITaxon:6072 ! Eumetazoa relationship: in_taxon NCBITaxon:33213 ! Bilateria property_value: IAO:0000111 "Bilateria" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33511 name: Deuterostomia synonym: "deuterostomes" EXACT [] is_a: NCBITaxon:33213 ! Bilateria relationship: in_taxon NCBITaxon:33511 ! Deuterostomia [Term] id: NCBITaxon:376913 name: Haplorrhini is_a: NCBITaxon:9443 ! Primates [Term] id: NCBITaxon:40674 name: Mammalia synonym: "mammals" EXACT [] synonym: "mammals" RELATED [] is_a: NCBITaxon:32524 ! Amniota property_value: IAO:0000111 "Mammalia" xsd:string property_value: IAO:0000118 "mammals" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:6072 name: Eumetazoa is_a: NCBITaxon:33208 ! Metazoa relationship: in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: NCBITaxon:7711 name: Chordata synonym: "chordates" EXACT [] synonym: "chordates" RELATED [] is_a: NCBITaxon:33511 ! Deuterostomia relationship: in_taxon NCBITaxon:7711 ! Chordata [Term] id: NCBITaxon:7742 name: Vertebrata synonym: "Vertebrata" EXACT [] synonym: "vertebrates" EXACT [] synonym: "vertebrates" RELATED [] is_a: NCBITaxon:89593 ! Craniata relationship: in_taxon NCBITaxon:7742 ! Vertebrata property_value: IAO:0000111 "Vertebrata " xsd:string property_value: IAO:0000118 "Vertebrata" xsd:string property_value: IAO:0000118 "vertebrates" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 name: Gnathostomata synonym: "Gnathostomata" EXACT [] synonym: "jawed vertebrates" EXACT [] is_a: NCBITaxon:7742 ! Vertebrata relationship: in_taxon NCBITaxon:7776 ! Gnathostomata [Term] id: NCBITaxon:8287 name: Sarcopterygii is_a: NCBITaxon:117571 ! Euteleostomi relationship: in_taxon NCBITaxon:8287 ! Sarcopterygii [Term] id: NCBITaxon:89593 name: Craniata synonym: "Craniata" EXACT [] is_a: NCBITaxon:7711 ! Chordata relationship: in_taxon NCBITaxon:89593 ! Craniata [Term] id: NCBITaxon:9347 name: Eutheria synonym: "eutherian mammals" EXACT [] synonym: "placental mammals" EXACT [] synonym: "Placentalia" RELATED [] synonym: "placentals" EXACT [] synonym: "placentals" RELATED [] is_a: NCBITaxon:32525 ! Theria [Term] id: NCBITaxon:9443 name: Primates synonym: "Primata" RELATED [] synonym: "primate" EXACT [] synonym: "primates" RELATED [] is_a: NCBITaxon:314146 ! Euarchontoglires [Term] id: NCBITaxon:9526 name: Catarrhini is_a: NCBITaxon:314293 ! Simiiformes [Term] id: NCBITaxon:9604 name: Hominidae synonym: "great apes" EXACT [] synonym: "Pongidae" RELATED [] is_a: NCBITaxon:314295 ! Hominoidea [Term] id: NCBITaxon:9605 name: Homo synonym: "humans" EXACT [] is_a: NCBITaxon:207598 ! Homininae [Term] id: NCBITaxon:9606 name: Homo sapiens synonym: "human" EXACT [] synonym: "man" EXACT [] is_a: NCBITaxon:9605 ! Homo property_value: IAO:0000111 "Homo sapiens" xsd:string property_value: IAO:0000118 "human" xsd:string property_value: IAO:0000118 "human being" xsd:string property_value: IAO:0000118 "man" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: OBI:0000011 name: planned process alt_id: CHMO:0001840 def: "A process that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: editor_note "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string property_value: editor_note "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string property_value: example_of_usage "Injecting mice with a vaccine in order to test its efficacy" xsd:string property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "branch derived" xsd:string property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0000014 name: regulator role def: "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders" [] is_a: OBI:0000017 ! regulatory role property_value: example_of_usage "Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805" xsd:string property_value: IAO:0000111 "regulator role" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Jennifer Fostel" xsd:string property_value: IAO:0000118 "regulator" xsd:string property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000017 name: regulatory role def: "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body." [] is_a: BFO:0000023 ! role property_value: example_of_usage "Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008" xsd:string property_value: IAO:0000111 "regulatory role" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "GROUP: Role branch" xsd:string property_value: IAO:0000119 "OBI, CDISC" xsd:string property_value: IAO:0000232 "govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent" xsd:string [Term] id: OBI:0000018 name: material supplier role def: "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation." [] is_a: OBI:0000947 ! service provider role property_value: editor_note "Supplier role is a special kind of service, e.g. biobank" xsd:string property_value: example_of_usage "Jackson Labs is an organization which provide mice as experimental material" xsd:string property_value: IAO:0000111 "material supplier role" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Jennifer Fostel" xsd:string property_value: IAO:0000118 "material provider role" xsd:string property_value: IAO:0000118 "supplier" xsd:string [Term] id: OBI:0000023 name: classified data set def: "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels." [] is_a: IAO:0000100 ! data set relationship: OBI:0000312 OBI:0000663 ! is_specified_output_of class prediction data transformation property_value: IAO:0000111 "classified data set" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000117 "PERSON: Monnie McGee" xsd:string property_value: IAO:0000118 "data set with assigned class labels" xsd:string [Term] id: OBI:0000047 name: processed material def: "Is a material entity that is created or changed during material processing." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing property_value: example_of_usage "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string property_value: IAO:0000111 "processed material" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string [Term] id: OBI:0000070 name: assay alt_id: CHMO:0000000 alt_id: CHMO:0001133 def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [obi:pppb] synonym: "measurement method" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000094 name: material processing def: "A planned process which results in physical changes in a specified input material" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0000047 ! has_specified_output processed material relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: example_of_usage "A cell lysis, production of a cloning vector, creating a buffer." xsd:string property_value: IAO:0000111 "material processing" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca Serra" xsd:string property_value: IAO:0000118 "material transformation" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0000112 name: specimen role def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] is_a: BFO:0000023 ! role property_value: editor_note "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." xsd:string property_value: editor_note "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." xsd:string property_value: editor_note "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string property_value: editor_note "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." xsd:string property_value: example_of_usage "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string property_value: IAO:0000111 "specimen role" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000245 name: organization def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] is_a: BFO:0000040 ! material entity property_value: editor_note "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." xsd:string property_value: example_of_usage "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string property_value: IAO:0000111 "organization" 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: Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "PERSON: Susanna Sansone" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [Term] id: OBI:0000272 name: protocol def: "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process." [] is_a: IAO:0000104 ! plan specification property_value: example_of_usage "PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR." xsd:string property_value: IAO:0000111 "protocol" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)" xsd:string property_value: OBI:0001847 "study protocol" xsd:string [Term] id: OBI:0000338 name: drawing a conclusion based on data def: "A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item relationship: OBI:0000299 OBI:0001909 ! has_specified_output conclusion based on data property_value: example_of_usage "Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. " xsd:string property_value: IAO:0000111 "interpreting data" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [Term] id: OBI:0000374 name: excitation function def: "A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons." [] is_a: BFO:0000034 ! function property_value: IAO:0000111 "excitation function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [Term] id: OBI:0000450 name: regulatory agency def: "A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government." [] is_a: OBI:0000245 ! organization intersection_of: OBI:0000245 ! organization intersection_of: RO:0000087 OBI:0000014 ! has role regulator role relationship: RO:0000087 OBI:0000014 ! has role regulator role property_value: example_of_usage "The US Environmental Protection Agency" xsd:string property_value: IAO:0000111 "regulatory agency" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: en.wikipedia.org/wiki/Regulator" xsd:string [Term] id: OBI:0000456 name: material transformation objective def: "an objective specifiction that creates an specific output object from input materials." [] is_a: IAO:0000005 ! objective specification property_value: example_of_usage "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS." xsd:string property_value: IAO:0000111 "material transformation objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "artifact creation objective" xsd:string property_value: IAO:0000119 "GROUP: OBI PlanAndPlannedProcess Branch" xsd:string [Term] id: OBI:0000457 name: manufacturing def: "Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000417 OBI:0000458 ! achieves_planned_objective manufacturing objective property_value: editor_note "Manufacturing implies reproducibility and responsibility AR" xsd:string property_value: editor_note "This includes a single scientist making a processed material for personal use." xsd:string property_value: IAO:0000111 "manufacturing" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI PlanAndPlannedProcess Branch" xsd:string [Term] id: OBI:0000458 name: manufacturing objective def: "is the objective to manufacture a material of a certain function (device)" [] is_a: OBI:0000456 ! material transformation objective property_value: IAO:0000111 "manufacturing objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI PlanAndPlannedProcess Branch" xsd:string [Term] id: OBI:0000571 name: manufacturer role def: "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process." [] is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000457 ! realized in manufacturing property_value: example_of_usage "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role." xsd:string property_value: IAO:0000111 "manufacturer role" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000648 name: clustered data set def: "A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels." [] is_a: IAO:0000100 ! data set relationship: OBI:0000312 OBI:0200175 ! is_specified_output_of class discovery data transformation property_value: example_of_usage "A clustered data set is the output of a K means clustering data transformation" xsd:string property_value: IAO:0000111 "clustered data set" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000117 "PERSON: Monnie McGee" xsd:string property_value: IAO:0000118 "data set with assigned discovered class labels" xsd:string property_value: IAO:0000232 "AR thinks could be a data item instead" xsd:string [Term] id: OBI:0000659 name: specimen collection process def: "A planned process with the objective of collecting a specimen." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective property_value: editor_note "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" xsd:string property_value: editor_note "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string property_value: editor_note "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." xsd:string property_value: editor_note "Philly2013: The specimen_role for the specimen is created during the specimen collection process." xsd:string property_value: example_of_usage "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string property_value: IAO:0000111 "specimen collection process" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000118 "specimen collection" xsd:string property_value: IAO:0000232 "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" xsd:string property_value: IAO:0000232 "6/9/09: used at workshop" xsd:string [Term] id: OBI:0000663 name: class prediction data transformation def: "A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction." [] is_a: OBI:0200000 ! data transformation property_value: IAO:0000111 "class prediction data transformation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "supervised classification data transformation" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0000684 name: specimen collection objective def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] is_a: IAO:0000005 ! objective specification property_value: example_of_usage "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string property_value: IAO:0000111 "specimen collection objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [Term] id: OBI:0000700 name: support vector machine def: "A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space." [] is_a: OBI:0000663 ! class prediction data transformation relationship: OBI:0000417 OBI:0200179 ! achieves_planned_objective class prediction objective property_value: IAO:0000111 "support vector machine" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Ryan Brinkman" xsd:string property_value: IAO:0000118 "SVM" xsd:string property_value: IAO:0000119 "PERSON: Ryan Brinkman" xsd:string [Term] id: OBI:0000704 name: decision tree induction objective def: "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made." [] is_a: OBI:0200166 ! data transformation objective property_value: IAO:0000111 "decision tree induction objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string [Term] id: OBI:0000707 name: decision tree building data transformation def: "A decision tree building data transformation is a data transformation that has objective decision tree induction." [] is_a: OBI:0200000 ! data transformation relationship: OBI:0000417 OBI:0000704 ! achieves_planned_objective decision tree induction objective property_value: IAO:0000111 "decision tree building data transformation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0000713 name: GenePattern software def: "a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks." [] is_a: IAO:0000010 ! software property_value: IAO:0000111 "GenePattern software" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string property_value: IAO:0000119 "WEB: http://www.broadinstitute.org/cancer/software/genepattern/" xsd:string [Term] id: OBI:0000726 name: peak matching def: "Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold" [] is_a: OBI:0200000 ! data transformation property_value: IAO:0000111 "peak matching" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Ryan Brinkman" xsd:string property_value: IAO:0000119 "PERSON: Ryan Brinkman" xsd:string [Term] id: OBI:0000727 name: k-nearest neighbors def: "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "k-nearest neighbors" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "k-NN" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0000749 name: CART def: "A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure." [] is_a: OBI:0000707 ! decision tree building data transformation property_value: IAO:0000111 "CART" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "classification and regression trees" xsd:string property_value: IAO:0000119 "BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining." xsd:string [Term] id: OBI:0000792 name: statistical model validation def: "A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set." [] is_a: OBI:0200171 ! partitioning data transformation relationship: OBI:0000417 OBI:0200188 ! achieves_planned_objective cross validation objective property_value: example_of_usage "Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia" xsd:string property_value: IAO:0000111 "statistical model validation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 xsd:string [Term] id: OBI:0000835 name: manufacturer def: "A person or organization that has a manufacturer role" [] is_a: BFO:0000040 ! material entity relationship: RO:0000087 OBI:0000571 ! has role manufacturer role property_value: IAO:0000111 "manufacturer" xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: OBI:0000947 name: service provider role def: "is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person" [] is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000011 ! realized in planned process property_value: example_of_usage "Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer." xsd:string property_value: IAO:0000111 "service provider role" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON:Helen Parkinson" xsd:string [Term] id: OBI:0000953 name: processed specimen def: "A specimen that has been intentionally physically modified." [] comment: A tissue sample that has been sliced and stained for a histology study. is_a: OBI:0000047 ! processed material is_a: OBI:0100051 ! specimen intersection_of: OBI:0000047 ! processed material intersection_of: OBI:0100051 ! specimen property_value: example_of_usage "A tissue sample that has been sliced and stained for a histology study.\nA blood specimen that has been centrifuged to obtain the white blood cells." xsd:string property_value: IAO:0000111 "processed specimen" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [Term] id: OBI:0000963 name: categorical label def: "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale." [] is_a: IAO:0000009 ! datum label property_value: example_of_usage "The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. " xsd:string property_value: IAO:0000111 "categorical label" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [Term] id: OBI:0000968 name: device alt_id: CHMO:0000998 def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [obi:obi] is_a: CHMO:0000993 ! portion of material is_a: OBI:0000047 ! processed material relationship: RO:0000085 BFO:0000034 ! has function function property_value: editor_note "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. " xsd:string property_value: example_of_usage "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string property_value: example_of_usage "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string property_value: IAO:0000111 "device" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string property_value: IAO:0000118 "instrument" xsd:string property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string [Term] id: OBI:0000984 name: dose def: "A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses." [] is_a: IAO:0000109 ! measurement datum property_value: example_of_usage "An organism has been injected 1ml of vaccine" xsd:string property_value: IAO:0000111 "dose" xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: OBI:0001000 name: questionnaire def: "A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study." [] is_a: IAO:0000310 ! document property_value: editor_note "JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. \nJZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. " xsd:string property_value: editor_note "Need to clarify if this is a document or a directive information entity (or what their connection is))" xsd:string property_value: IAO:0000111 "questionnaire" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Jessica Turner" xsd:string property_value: IAO:0000119 "Merriam-Webster" xsd:string [Term] id: OBI:0001138 name: X-ray source alt_id: CHMO:0000944 def: "A device that is used to generate X-rays." [obi:es] synonym: "X-ray generator" EXACT [] is_a: OBI:0000968 ! device relationship: RO:0000085 OBI:0000374 ! has function excitation function property_value: IAO:0000111 "X-ray source" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000118 "x-ray generator" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/X-ray_generator xsd:string [Term] id: OBI:0001909 name: conclusion based on data def: "An information content entity that is inferred from data." [] is_a: IAO:0000030 ! information content entity relationship: OBI:0000124 IAO:0000027 ! is_supported_by_data data item relationship: OBI:0000312 OBI:0000338 ! is_specified_output_of drawing a conclusion based on data property_value: editor_note "In the Philly 2013 workshop, we recognized the limitations of \"conclusion textual entity\", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. " xsd:string property_value: example_of_usage "The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting.\nThe following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. \"13 is prime\"." xsd:string property_value: IAO:0000111 "conclusion based on data" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Group:2013 Philly Workshop group" xsd:string property_value: IAO:0000119 "Group:2013 Philly Workshop group" xsd:string [Term] id: OBI:0001930 name: categorical value specification def: "A value specification that is specifies one category out of a fixed number of nominal categories" [] is_a: OBI:0001933 ! value specification property_value: IAO:0000111 "categorical value specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [Term] id: OBI:0001931 name: scalar value specification def: "A value specification that consists of two parts: a numeral and a unit label" [] is_a: OBI:0001933 ! value specification property_value: IAO:0000111 "scalar value specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [Term] id: OBI:0001933 name: value specification def: "An information content entity that specifies a value within a classification scheme or on a quantitative scale." [] is_a: IAO:0000030 ! information content entity property_value: editor_note "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement." xsd:string property_value: example_of_usage "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass." xsd:string property_value: IAO:0000111 "value specification" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [Term] id: OBI:0002076 name: collection of specimens def: "A material entity that has two or more specimens as its parts." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: has_member OBI:0100051 {all_only="true"} ! specimen property_value: editor_note "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" xsd:string property_value: example_of_usage "Blood cells collected from multiple donors over the course of a study." xsd:string property_value: http://purl.org/dc/elements/1.1/source "Biobank" xsd:string property_value: IAO:0000111 "collection of specimens" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "OBIB, OBI" xsd:string [Term] id: OBI:0002205 name: histologic grade according to AJCC 7th edition def: "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system." [] is_a: OBI:0001930 ! categorical value specification property_value: example_of_usage " G4: Undifferentiated" xsd:string property_value: example_of_usage "G1:Well differentiated " xsd:string property_value: IAO:0000111 "histologic grade according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002210 name: histologic grade according to the Fuhrman Nuclear Grading System def: "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "histologic grade according to the Fuhrman Nuclear Grading System" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Histologic Grade (Fuhrman Nuclear Grading System)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002215 name: histologic grade for ovarian tumor def: "A categorical value specification that is a histologic grade assigned to a ovarian tumor." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "histologic grade for ovarian tumor" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002216 name: histologic grade for ovarian tumor according to a two-tier grading system def: "A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. " [] is_a: OBI:0002215 ! histologic grade for ovarian tumor property_value: IAO:0000111 "histologic grade for ovarian tumor according to a two-tier grading system" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002219 name: histologic grade for ovarian tumor according to the World Health Organization def: "A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO)." [] is_a: OBI:0002215 ! histologic grade for ovarian tumor property_value: IAO:0000111 "histologic grade for ovarian tumor according to the World Health Organization" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002224 name: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for colon and rectum according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002232 name: pathologic primary tumor stage for lung according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for lung according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread lung primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002243 name: pathologic primary tumor stage for kidney according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for kidney according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002256 name: pathologic primary tumor stage for ovary according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for ovary according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002270 name: pathologic lymph node stage for colon and rectum according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for colon and rectum according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002279 name: pathologic lymph node stage for lung according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for lung according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002284 name: pathologic lymph node stage for kidney according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for kidney according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002287 name: pathologic lymph node stage for ovary according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for ovary according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002290 name: pathologic distant metastases stage for colon according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for colon according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: colon distant metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002298 name: pathologic distant metastases stage for lung according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for lung according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: lung distant metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002306 name: pathologic distant metastases stage for kidney according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for kidney according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: kidney distant Metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002310 name: pathologic distant metastases stage for ovary according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for ovary according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: ovarian distant metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002314 name: clinical tumor stage group according to AJCC 7th edition def: "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "clinical tumor stage group according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Clinical tumor stage group (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002326 name: International Federation of Gynecology and Obstetrics cervical cancer stage value specification def: "A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "International Federation of Gynecology and Obstetrics cervical cancer stage value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Clinical FIGO stage" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002341 name: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "International Federation of Gynecology and Obstetrics ovarian cancer stage value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002356 name: performance status value specification def: "A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life)." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "performance status value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Performance Status Scale" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Performance_status xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002357 name: Eastern Cooperative Oncology Group score value specification def: "A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient." [] is_a: OBI:0002356 ! performance status value specification property_value: IAO:0000111 "Eastern Cooperative Oncology Group score value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "ECOG score" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002363 name: Karnofsky score vaue specification def: "A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment." [] is_a: OBI:0002356 ! performance status value specification property_value: IAO:0000111 "Karnofsky score vaue specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Karnofsky Score" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [Term] id: OBI:0002983 name: altitude measurement datum def: "A length measurement datum between a point at sea or ground level and some point above it." [] is_a: IAO:0000408 ! length measurement datum property_value: IAO:0000111 "altitude measurement datum" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert" xsd:string property_value: IAO:0000119 "Adapted from https://www.merriam-webster.com/dictionary/altitude" xsd:string [Term] id: OBI:0002989 name: material supplier def: "A person or organization that provides material supplies to other people or organizations." [] is_a: BFO:0000040 ! material entity relationship: RO:0000087 OBI:0000018 ! has role material supplier role property_value: IAO:0000111 "material supplier" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Rebecca Jackson" xsd:string property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1289 xsd:string [Term] id: OBI:0100026 name: organism def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] is_a: BFO:0000040 ! material entity union_of: NCBITaxon:10239 ! Viruses union_of: NCBITaxon:2 ! Bacteria union_of: NCBITaxon:2157 ! Archaea union_of: NCBITaxon:2759 ! Eukaryota property_value: editor_note "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string property_value: editor_note "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string property_value: example_of_usage "animal" xsd:string property_value: example_of_usage "fungus" xsd:string property_value: example_of_usage "plant" xsd:string property_value: example_of_usage "virus" xsd:string property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string [Term] id: OBI:0100051 name: specimen def: "A material entity that has the specimen role." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role relationship: RO:0000087 OBI:0000112 ! has role specimen role property_value: editor_note "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string property_value: example_of_usage "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string property_value: IAO:0000111 "specimen" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [Term] id: OBI:0200000 name: data transformation def: "A planned process that produces output data from input data." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective property_value: example_of_usage "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string property_value: IAO:0000111 "data transformation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "Richard Scheuermann" xsd:string property_value: IAO:0000117 "Ryan Brinkman" xsd:string property_value: IAO:0000117 "Tina Hernandez-Boussard" xsd:string property_value: IAO:0000118 "data analysis" xsd:string property_value: IAO:0000118 "data processing" xsd:string property_value: IAO:0000119 "Branch editors" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0200033 name: leave one out cross validation method def: "is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data" [] is_a: OBI:0000792 ! statistical model validation property_value: editor_note "2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178" xsd:string property_value: example_of_usage "The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368" xsd:string property_value: IAO:0000111 "leave one out cross validation method" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string [Term] id: OBI:0200041 name: k-means clustering def: "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "k-means clustering" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/K-means" xsd:string [Term] id: OBI:0200042 name: hierarchical clustering def: "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "hierarchical clustering" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering" xsd:string [Term] id: OBI:0200050 name: dimensionality reduction def: "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "dimensionality reduction" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "data projection" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string property_value: IAO:0000119 "PERSON: Melanie Courtot" xsd:string [Term] id: OBI:0200051 name: principal components analysis dimensionality reduction def: "A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones." [] is_a: OBI:0200050 ! dimensionality reduction property_value: IAO:0000111 "principal components analysis dimensionality reduction" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "pca data reduction" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string property_value: IAO:0000119 "PERSON: Melanie Courtot" xsd:string [Term] id: OBI:0200111 name: data visualization def: "An planned process that creates images, diagrams or animations from the input data." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item property_value: example_of_usage "Generation of a heatmap from a microarray dataset" xsd:string property_value: IAO:0000111 "data visualization" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Tina Boussard" xsd:string property_value: IAO:0000118 "data encoding as image" xsd:string property_value: IAO:0000118 "visualization" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string property_value: IAO:0000119 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000119 "PERSON: Tina Boussard" xsd:string property_value: IAO:0000232 "Possible future hierarchy might include this:\ninformation_encoding\n>data_encoding\n>>image_encoding" xsd:string [Term] id: OBI:0200166 name: data transformation objective def: "An objective specification to transformation input data into output data" [] is_a: IAO:0000005 ! objective specification property_value: editor_note "Modified definition in 2013 Philly OBI workshop" xsd:string property_value: example_of_usage "normalize objective" xsd:string property_value: IAO:0000111 "data transformation objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0200171 name: partitioning data transformation def: "A partitioning data transformation is a data transformation that has objective partitioning." [] is_a: OBI:0200000 ! data transformation relationship: OBI:0000417 OBI:0200172 ! achieves_planned_objective partitioning objective property_value: IAO:0000111 "partitioning data transformation" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0200172 name: partitioning objective def: "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set." [] is_a: OBI:0200166 ! data transformation objective property_value: example_of_usage "A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets." xsd:string property_value: IAO:0000111 "partitioning objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string [Term] id: OBI:0200175 name: class discovery data transformation def: "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery." [] is_a: OBI:0200000 ! data transformation property_value: IAO:0000111 "class discovery data transformation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "clustering data transformation" xsd:string property_value: IAO:0000118 "unsupervised classification data transformation" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0200178 name: class discovery objective def: "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic." [] is_a: OBI:0200166 ! data transformation objective property_value: IAO:0000111 "class discovery objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "clustering objective" xsd:string property_value: IAO:0000118 "discriminant analysis objective" xsd:string property_value: IAO:0000118 "unsupervised classification objective" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0200179 name: class prediction objective def: "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and\nclass labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data." [] is_a: OBI:0200166 ! data transformation objective property_value: IAO:0000111 "class prediction objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "classification objective" xsd:string property_value: IAO:0000118 "supervised classification objective" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0200188 name: cross validation objective def: "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis." [] is_a: OBI:0200172 ! partitioning objective property_value: IAO:0000111 "cross validation objective" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "rotation estimation objective" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Cross_validation" xsd:string [Term] id: OBI:0200190 name: clustered data visualization def: "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type." [] is_a: OBI:0200111 ! data visualization relationship: OBI:0000293 OBI:0000648 ! has_specified_input clustered data set property_value: IAO:0000111 "clustered data visualization" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string [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 property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000025 name: composition def: "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts." [] synonym: "composed of" EXACT [] synonym: "compositionality" EXACT [] synonym: "content" EXACT [] synonym: "structure, composition" EXACT [] is_a: PATO:0000141 ! structure [Term] id: PATO:0000033 name: concentration of def: "A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance." [] synonym: "concentration" EXACT [] is_a: PATO:0002182 ! molecular quality [Term] id: PATO:0000048 name: hardness def: "A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced" [] synonym: "impenetrability" RELATED [] synonym: "toughness" RELATED [] is_a: PATO:0001546 ! quality of a solid [Term] id: PATO:0000051 name: morphology def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] is_a: PATO:0001241 ! physical object quality property_value: IAO:0000111 "morphology" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000052 name: shape 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)." [] synonym: "relational shape quality" EXACT [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000068 name: qualitative is_a: PATO:0000001 ! quality [Term] id: PATO:0000069 name: deviation (from_normal) def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [] is_a: PATO:0000068 ! qualitative [Term] id: PATO:0000117 name: size def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000122 name: length def: "A 1-D extent quality which is equal to the distance between two points." [] is_a: PATO:0000051 ! morphology property_value: IAO:0000111 "length" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000125 name: mass def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000136 name: closure is_a: PATO:0000051 ! morphology [Term] id: PATO:0000140 name: position def: "A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity." [] synonym: "location" EXACT [] synonym: "placement" EXACT [] synonym: "relational spatial quality" EXACT [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000141 name: structure def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [] synonym: "conformation" BROAD [] synonym: "relational structural quality" EXACT [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000146 name: temperature def: "A physical quality of the thermal energy of a system." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000386 name: hard def: "A hardness quality of being rigid and resistant to pressure." [] synonym: "firm" RELATED [] synonym: "impenetrable" RELATED [] synonym: "tough" RELATED [] is_a: PATO:0000048 ! hardness is_a: PATO:0002305 ! increased object quality [Term] id: PATO:0000389 name: acute namespace: quality def: "A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course." [dictionary:reference] subset: hpo_slim subset: mpath_slim subset: value_slim is_a: PATO:0001309 ! duration property_value: RO:0002604 PATO:0001863 [Term] id: PATO:0000402 name: branched is_a: PATO:0002009 ! branchiness [Term] id: PATO:0000407 name: flat is_a: PATO:0002254 ! flattened [Term] id: PATO:0000587 name: decreased size def: "A size quality which is relatively low." [] synonym: "hypoplasia" NARROW [] synonym: "reduced" RELATED [] synonym: "small" RELATED [] synonym: "tiny" RELATED [] synonym: "underdeveloped" NARROW [] is_a: PATO:0000117 ! size is_a: PATO:0002303 ! decreased object quality [Term] id: PATO:0000608 name: closed is_a: PATO:0000136 ! closure [Term] id: PATO:0000957 name: opacity def: "An optical quality which obtains by virtue of the ability of the bearer to absorb visible light." [] is_a: PATO:0001300 ! optical quality [Term] id: PATO:0000963 name: opaque def: "A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy." [] synonym: "clouding" RELATED [] synonym: "cloudy" RELATED [] synonym: "non-transparent" EXACT [] is_a: PATO:0000957 ! opacity [Term] id: PATO:0000964 name: transparent is_a: PATO:0000957 ! opacity [Term] id: PATO:0000973 name: porosity def: "A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices." [] is_a: PATO:0000141 ! structure [Term] id: PATO:0000984 name: porous def: "A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices." [] is_a: PATO:0000973 ! porosity [Term] id: PATO:0000992 name: viscosity def: "A physical quality of a liquid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow." [] is_a: PATO:0001548 ! quality of a liquid [Term] id: PATO:0000998 name: viscous def: "A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity." [] is_a: PATO:0000992 ! viscosity [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 property_value: IAO:0000111 "physical quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001031 name: elasticity is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001154 name: elongated def: "A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width." [] is_a: PATO:0000052 ! shape [Term] id: PATO:0001171 name: elastic is_a: PATO:0001031 ! elasticity [Term] id: PATO:0001236 name: process quality namespace: quality alt_id: PATO:0001239 alt_id: PATO:0001240 def: "A quality which inheres in an process." [PATOC:GVG] comment: See comments of relational quality of a physical entity. synonym: "quality of a process" EXACT [] synonym: "quality of occurrent" EXACT [] synonym: "quality of process" EXACT [] synonym: "relational quality of occurrent" EXACT [] is_a: PATO:0000001 ! quality disjoint_from: PATO:0001241 ! physical object quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [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: BFO:0000019 ! quality is_a: PATO:0000001 ! quality property_value: IAO:0000111 "physical object quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001291 name: electromagnetic (EM) radiation quality def: "A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation." [] is_a: PATO:0001739 ! radiation quality [Term] id: PATO:0001300 name: optical quality def: "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." [] is_a: PATO:0001291 ! electromagnetic (EM) radiation quality [Term] id: PATO:0001306 name: decreased temperature def: "A temperature which is relatively low." [] synonym: "cold" EXACT [] synonym: "low temperature" EXACT [] is_a: PATO:0000146 ! temperature is_a: PATO:0002303 ! decreased object quality [Term] id: PATO:0001309 name: duration namespace: quality alt_id: PATO:0000081 def: "A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point." [PATOC:mellybelly] subset: attribute_slim subset: hpo_slim synonym: "period" EXACT [] synonym: "time" RELATED [] is_a: PATO:0002062 ! physical quality of a process [Term] id: PATO:0001332 name: amorphous def: "A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology." [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0001411 name: structured def: "A structural quality inhering in a bearer by virtue of the bearer's having distinct structure." [] is_a: PATO:0000141 ! structure [Term] id: PATO:0001412 name: unstructured def: "A structural quality inhering in a bearer by virtue of the bearer's lacking distinct structure." [] is_a: PATO:0000141 ! structure [Term] id: PATO:0001476 name: decreased position def: "A positional which is relatively low." [] synonym: "low position" RELATED [] is_a: PATO:0000140 ! position is_a: PATO:0002303 ! decreased object quality [Term] id: PATO:0001481 name: sloped def: "A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction." [] is_a: PATO:0000052 ! shape [Term] id: PATO:0001543 name: flexibility def: "A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking." [] is_a: PATO:0001546 ! quality of a solid [Term] id: PATO:0001545 name: inflexible def: "A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking." [] synonym: "stiff" EXACT [] synonym: "stiffness" RELATED [] is_a: PATO:0001543 ! flexibility [Term] id: PATO:0001546 name: quality of a solid def: "A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable." [] synonym: "solidity" EXACT [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001547 name: quality of a gas def: "A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape." [] synonym: "gaseous" EXACT [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001548 name: quality of a liquid def: "A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape." [] synonym: "liquidity" EXACT [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001563 name: increased mass def: "A mass which is higher than normal or average." [] synonym: "high mass" EXACT [] synonym: "large mass" EXACT [] is_a: PATO:0000125 ! mass is_a: PATO:0002305 ! increased object quality [Term] id: PATO:0001579 name: contractility is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001591 name: curvature is_a: PATO:0000052 ! shape [Term] id: PATO:0001655 name: osmolarity def: "A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution." [] is_a: PATO:0000033 ! concentration of [Term] id: PATO:0001657 name: increased osmolarity def: "A osmolarity which is relatively high." [] synonym: "high osmolarity" EXACT [] is_a: PATO:0001655 ! osmolarity is_a: PATO:0002305 ! increased object quality [Term] id: PATO:0001687 name: elevation def: "A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface." [] is_a: PATO:0000140 ! position [Term] id: PATO:0001689 name: decreased elevation def: "An elevation which is relatively low." [] synonym: "low elevation" EXACT [] is_a: PATO:0001476 ! decreased position is_a: PATO:0001687 ! elevation [Term] id: PATO:0001690 name: contractile is_a: PATO:0001579 ! contractility [Term] id: PATO:0001693 name: increased viscosity def: "A viscosity which relatively high." [] synonym: "high viscosity" EXACT [] is_a: PATO:0000998 ! viscous is_a: PATO:0002305 ! increased object quality [Term] id: PATO:0001739 name: radiation quality namespace: quality def: "A quality that inheres in an bearer by virtue of how that bearer interacts with radiation." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001744 name: radiation exposure namespace: quality def: "A radiation quality inhering in a bearer by virtue of what the bearer receives as a result of being exposed to ionizing radiation." [hps:hps] subset: attribute_slim subset: scalar_slim is_a: PATO:0001739 ! radiation quality [Term] id: PATO:0001759 name: granular def: "A composition quality inhering in a bearer by virtue of the bearer's containing granules." [] is_a: PATO:0000025 ! composition [Term] id: PATO:0001863 name: chronic namespace: quality def: "A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration." [PATOC:cjm] subset: hpo_slim subset: mpath_slim subset: value_slim is_a: PATO:0001309 ! duration property_value: RO:0002604 PATO:0000389 [Term] id: PATO:0001873 name: cylindrical is_a: PATO:0002007 ! convex 3-D shape [Term] id: PATO:0001985 name: frozen def: "A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point." [] is_a: PATO:0000146 ! temperature [Term] id: PATO:0001987 name: saccular is_a: PATO:0002014 ! structure, cavities [Term] id: PATO:0001992 name: cellularity is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0001993 name: multicellular is_a: PATO:0001992 ! cellularity [Term] id: PATO:0001995 name: organismal quality is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0002007 name: convex 3-D shape is_a: PATO:0002266 ! 3-D shape [Term] id: PATO:0002009 name: branchiness is_a: PATO:0000052 ! shape [Term] id: PATO:0002014 name: structure, cavities is_a: PATO:0000141 ! structure [Term] id: PATO:0002045 name: dendritic is_a: PATO:0000402 ! branched [Term] id: PATO:0002062 name: physical quality of a process namespace: quality subset: attribute_slim is_a: PATO:0001236 ! process quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-06-05T09:16:46Z [Term] id: PATO:0002078 name: hollow is_a: PATO:0002014 ! structure, cavities [Term] id: PATO:0002124 name: laminar def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." [] is_a: PATO:0000141 ! structure [Term] id: PATO:0002143 name: sloped downward is_a: PATO:0001481 ! sloped [Term] id: PATO:0002181 name: displaced def: "A positional quality inhering in a bearer by virtue the bearer's being changed in position." [] is_a: PATO:0000140 ! position [Term] id: PATO:0002182 name: molecular quality def: "A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc." [] synonym: "relational molecular quality" EXACT [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0002198 name: quality of a substance def: "A quality inhering in a bearer by virtue of its constitution." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0002254 name: flattened is_a: PATO:0001591 ! curvature [Term] id: PATO:0002266 name: 3-D shape is_a: PATO:0000052 ! shape [Term] id: PATO:0002299 name: tubular is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow [Term] id: PATO:0002300 name: increased quality def: "A quality that has a value that is increased compared to normal or average." [] is_a: PATO:0000069 ! deviation (from_normal) [Term] id: PATO:0002301 name: decreased quality def: "A quality that has a value that is decreased compared to normal or average." [] is_a: PATO:0000069 ! deviation (from_normal) [Term] id: PATO:0002303 name: decreased object quality def: "A quality of an object that has a value that is decreased compared to normal or average." [] is_a: PATO:0001241 ! physical object quality is_a: PATO:0002301 ! decreased quality [Term] id: PATO:0002305 name: increased object quality def: "A quality of an object that has a value that is increased compared to normal or average." [] is_a: PATO:0001241 ! physical object quality is_a: PATO:0002300 ! increased quality [Term] id: PATO:0002422 name: acinar is_a: PATO:0000141 ! structure [Term] id: PATO:0002462 name: collagenous is_a: PATO:0000025 ! composition [Term] id: PCO:0000000 name: collection of organisms def: "A material entity that consists of two or more organisms, viruses, or viroids." [] comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity intersection_of: BFO:0000027 ! object aggregate intersection_of: has_member CARO:0001010 {all_only="true"} ! organism or virus or viroid intersection_of: has_member CARO:0001010 {minCardinality="2"} ! organism or virus or viroid relationship: has_member CARO:0001010 ! organism or virus or viroid relationship: has_member CARO:0001010 ! organism or virus or viroid property_value: example_of_usage "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string property_value: IAO:0000118 "organism collection" xsd:string [Term] id: PCO:0000001 name: population of organisms def: "A collection of organisms, all of the same species, that live in the same place." [] comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. is_a: PCO:0000018 ! single-species collection of organisms relationship: RO:0002303 ENVO:01000739 ! has habitat habitat property_value: example_of_usage "" xsd:string property_value: example_of_usage "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 ISBN:0878932739 xsd:string [Term] id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. subset: envoPolar is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string [Term] id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms property_value: editor_note "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000031 name: organismal entity def: "A material entity that is one or more organisms, viruses or viroids." [] is_a: BFO:0000040 ! material entity union_of: CARO:0001010 ! organism or virus or viroid union_of: PCO:0000000 ! collection of organisms property_value: IAO:0000114 IAO:0000120 [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms intersection_of: PCO:0000000 ! collection of organisms intersection_of: has_member CARO:0001010 {cardinality="2"} ! organism or virus or viroid [Term] id: PO:0000003 name: whole plant namespace: plant_anatomy def: "A plant structure (PO:0005679) which is a whole organism." [POC:curators] comment: Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). subset: reference subset: TraitNet synonym: "bush (narrow)" NARROW [] synonym: "clonal colony (related)" RELATED [] synonym: "colony (related)" RELATED [] synonym: "frutex (narrow)" NARROW [FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba] synonym: "frutices (narrow)" NARROW Plural [FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b] synonym: "gametophyte (narrow)" NARROW [] synonym: "genet (broad)" BROAD [] synonym: "herb (narrow)" NARROW [] synonym: "liana (narrow)" NARROW [] synonym: "planta entera (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "prothalli (narrow)" NARROW Plural [FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0] synonym: "prothallium (narrow)" NARROW [] synonym: "prothallus (narrow)" NARROW [FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8] synonym: "ramet (broad)" BROAD [] synonym: "seedling (narrow)" NARROW [] synonym: "shrub (narrow)" NARROW [] synonym: "sporophyte (narrow)" NARROW [] synonym: "suffrutex (narrow)" NARROW [FNA:99508f62-7116-4e2b-90c0-19ff55ebd967] synonym: "suffrutices (narrow)" NARROW Plural [FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2] synonym: "tree (narrow)" NARROW [] synonym: "vine (narrow)" NARROW [] synonym: "woody clump (narrow)" NARROW [FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0] synonym: "植物体全体 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:538 xref: PO_GIT:69 is_a: PO:0009011 ! plant structure [Term] id: PO:0009011 name: plant structure namespace: plant_anatomy def: "A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant." [CARO:0000003, POC:curators] comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. {xref="PO:cooperl"} subset: TraitNet synonym: "estructura vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "植物 構造 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:57 is_a: PO:0025131 ! plant anatomical entity [Term] id: PO:0025131 name: plant anatomical entity namespace: plant_anatomy def: "An anatomical entity that is or was part of a plant." [BFO:0000004, CARO:0000000, POC:curators] comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. {xref="CAROC:Brownsville2014"} synonym: "entidad anatómica vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "植物 解剖学（形態）的実体 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:224 is_a: BFO:0000040 ! material entity relationship: only_in_taxon NCBITaxon:33090 {source="cjm"} ! Viridiplantae created_by: rwalls creation_date: 2010-11-15T11:41:38Z [Term] id: PR:000000001 name: protein is_a: PR:000018263 ! amino acid chain [Term] id: PR:000001003 name: CD34 molecule is_a: PR:000000001 ! protein [Term] id: PR:000001327 name: cadherin is_a: PR:000000001 ! protein [Term] id: PR:000001444 name: cadherin-5 is_a: PR:000001327 ! cadherin [Term] id: PR:000001945 name: transferrin receptor protein 1 is_a: PR:000000001 ! protein [Term] id: PR:000001971 name: vascular endothelial growth factor receptor is_a: PR:000000001 ! protein [Term] id: PR:000002112 name: vascular endothelial growth factor receptor 2 is_a: PR:000001971 ! vascular endothelial growth factor receptor [Term] id: PR:000007499 name: fibroblast growth factor 8 is_a: PR:000000001 ! protein [Term] id: PR:000014841 name: sonic hedgehog protein is_a: PR:000000001 ! protein [Term] id: PR:000016043 name: T-cell acute lymphocytic leukemia protein 1 is_a: PR:000000001 ! protein [Term] id: PR:000018263 name: amino acid chain is_a: CHEBI:50047 ! organic amino compound [Term] id: RBO:00000001 name: ionizing radiation categorized by source def: "Ionizing radiation classified by the material entity which generates or emits it." [] is_a: RBO:00000116 ! ionizing radiation [Term] id: RBO:00000002 name: space radiation def: "Radiation originating outside the Earth's atmosphere." [] is_a: RBO:00000001 ! ionizing radiation categorized by source [Term] id: RBO:00000003 name: ground radiation def: "Radiation produced on Earth or on another planetary body by natural or artificial means." [] is_a: RBO:00000001 ! ionizing radiation categorized by source property_value: example_of_usage "One of the principal sources of ground radiation is radon gas." xsd:string [Term] id: RBO:00000004 name: tissue equivalent material def: "Material presenting, when irradiated, interaction properties similar to those of soft tissue." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000119 "ICRP glossary (http://icrpaedia.org/Tissue_equivalent_material)" xsd:string [Term] id: RBO:00000005 name: Fe-56 ion radiation def: "Atomic nuclei, each with 26 protons and 30 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000006 name: C-12 ion radiation def: "Atomic nuclei, each with 6 protons and 6 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000007 name: Si-28 ion radiation def: "Atomic nuclei, each with 14 protons and 14 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000008 name: He-4 ion radiation def: "Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000009 name: Ne-20 ion radiation def: "Atomic nuclei, each with 10 protons and 10 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000010 name: light ion def: "An atomic nucleus, fully stripped of its orbital electrons, and containing 2, 3, 4, 5, or 6 protons." [] is_a: CHEBI:33252 ! atomic nucleus is_a: RBO:00005003 ! charged particle [Term] id: RBO:00000011 name: active dosimeter def: "A radiation measuring device which records dose at the time of detection, with data available in real time" [] is_a: RBO:00000115 ! radiation dosimeter device property_value: example_of_usage "Ionization chambers and silicon solid state detectors can be used as active dosimeters." xsd:string [Term] id: RBO:00000012 name: passive dosimeter def: "A radiation measuring device which integrates the amount of radiation to which it is exposed. Passive detectors are interrogated at a later time to determine the dose." [] is_a: RBO:00000115 ! radiation dosimeter device property_value: example_of_usage "Thermoluminescent dosimeters and plastic nuclear track detectors are passive detectors." xsd:string [Term] id: RBO:00000013 name: background ionizing radiation def: "The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra" [] is_a: ENVO:01001023 ! radiation [Term] id: RBO:00000014 name: effective dose def: "The sum of the equivalent doses to all organs in the body, each adjusted to account for the sensitivity of the organ to radiation. Effective dose is calculated for the whole body. Effective dose is expressed in millisieverts (mSv)." [] is_a: RBO:010016 ! radiation dose property_value: example_of_usage "The effective dose was calculated to be 300 mSv." xsd:string [Term] id: RBO:00000015 name: mixed radiation field def: "The process of exposing the same sample to more than one type and/or energy of radiation, in sequence or simultaneously." [] synonym: "mixed field|mixed radiation" EXACT [] is_a: RBO:00000049 ! particle accelerator radiation property_value: example_of_usage "The samples were exposed to a mixed radiation field consisting of several ions at different energies." xsd:string property_value: IAO:0000111 "mixed radiation" xsd:string [Term] id: RBO:00000016 name: radiation environment def: "Radiation classified by where the exposure to the radiation is occurring." [] is_a: ENVO:01000254 ! environmental system [Term] id: RBO:00000017 name: Earth surface def: "That part of the Earth exposed to the Earth atmosphere." [] is_a: RBO:00000016 ! radiation environment [Term] id: RBO:00000018 name: Earth atmosphere def: "The region between the Earth's surface and an altitude of approximately 100 km" [] is_a: RBO:00000016 ! radiation environment [Term] id: RBO:00000019 name: low Earth orbit def: "The region of outer space between the Earth's atmosphere and the innermost Earth radiation belt" [] synonym: "LEO" EXACT [] is_a: ENVO:01000637 ! outer space property_value: IAO:0000111 "LEO" xsd:string [Term] id: RBO:00000020 name: beyond low Earth orbit def: "That part of outer space beyond the Earth's radiation belts." [] synonym: "BLEO" EXACT [] is_a: ENVO:01000637 ! outer space property_value: IAO:0000111 "BLEO" xsd:string [Term] id: RBO:00000021 name: fractionated radiation exposure def: "A radiation dose administered in two or more exposures at specified time intervals" [] is_a: RBO:00000082 ! radiobiology study type property_value: IAO:0000111 "fractionated" xsd:string [Term] id: RBO:00000022 name: millirad def: "A unit of absorbed dose equal to 1/1000 of a rad" [] synonym: "mrad" EXACT [] is_a: UO:1000135 ! rad based unit [Term] id: RBO:00000023 name: equivalent dose def: "The product of the mean absorbed dose in an organ or tissue and the radiation weighting factor (w_R )of the radiation type of interest" [] is_a: RBO:010016 ! radiation dose property_value: example_of_usage "The equivalent dose was calculated to be 300 mSv." xsd:string [Term] id: RBO:00000024 name: dose fraction def: "The absorbed radiation dose administered in a single one of a series comprising a fractionated radiation exposure" [] is_a: RBO:010016 ! radiation dose property_value: example_of_usage "The total dose was administered in five dose fractions." xsd:string [Term] id: RBO:00000026 name: cosmic radiation def: "Penetrating ionizing radiation, both particulate and electromagnetic, that originates in outer space" [] is_a: RBO:00000002 ! space radiation [Term] id: RBO:00000027 name: galactic cosmic radiation def: "Galactic cosmic radiation consists of high-energy charged particles originating from outside the solar system" [] is_a: RBO:00000026 ! cosmic radiation property_value: example_of_usage "Galactic cosmic radiation is one of the principal sources of radiation dose outside low-earth orbit" xsd:string [Term] id: RBO:00000028 name: solar cosmic radiation def: "Solar cosmic radiation is high-energy charged particles that originate from the sun." [] is_a: RBO:00000026 ! cosmic radiation property_value: example_of_usage "Solar cosmic radiation contributes to the radiation dose to humans in space." xsd:string [Term] id: RBO:00000029 name: dose rate def: "The measurement datum representing a dose to an organism or object per unit time." [] is_a: IAO:0000109 ! measurement datum property_value: example_of_usage "The dose rate was 0.5 mGy/min." xsd:string [Term] id: RBO:00000033 name: spacecraft def: "Vehicles, crewed or uncrewed, which are designed to orbit about the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space." [] is_a: OBI:0000968 ! device property_value: example_of_usage "The Apollo spacecraft took 24 astronauts to the Moon between 1968 and 1972." xsd:string property_value: IAO:0000119 "NASA Thesaurus, 1988" xsd:string [Term] id: RBO:00000044 name: spacecraft module def: "a self-contained unit of a spacecraft" [] is_a: RBO:00000033 ! spacecraft [Term] id: RBO:00000045 name: International Space Station module def: "A self-contained unit of the International Space Station." [] is_a: RBO:00000044 ! spacecraft module property_value: example_of_usage "The experiment was conducted in the International Space Station module Columbus" xsd:string property_value: example_of_usage "The experiment was conducted on the Russian module of the ISS." xsd:string property_value: IAO:0000111 "ISS module" xsd:string [Term] id: RBO:00000046 name: space station def: "A spacecraft capable of supporting a human crew in orbit for an extended period of time. It lacks major propulsion or landing systems. Stations must have docking ports to allow other spacecraft to dock to transfer crew and supplies." [] is_a: RBO:00000033 ! spacecraft property_value: example_of_usage "Mir was a space station that operated in low Earth orbit from 1986 to 2001, operated by the Soviet Union and later by Russia." xsd:string property_value: IAO:0000119 "Wikipedia" xsd:string [Term] id: RBO:00000047 name: particle accelerator beamline def: "The path leading from a particle accelerator to an experimental station used in experiments in particle physics, materials science, chemistry, and molecular biology, or in irradiation tests or to produce isotopes." [] is_a: RBO:00000121 ! particle accelerator property_value: example_of_usage "The HIMAC accelerator has a beamline dedicated for radiation biology experiments." xsd:string property_value: IAO:0000119 "Wikipedia" xsd:string [Term] id: RBO:00000049 name: particle accelerator radiation def: "Radiation produced by a particle accelerator." [] is_a: RBO:00000003 ! ground radiation [Term] id: RBO:00000050 name: nuclear reactor radiation def: "Radiation produced by a nuclear reactor." [] is_a: RBO:00000003 ! ground radiation [Term] id: RBO:00000051 name: Cesium-137 gamma radiation def: "High energy photons emitted during nuclear decay of the Cesium-137 isotope." [] synonym: "Cs-137" EXACT [] is_a: RBO:00000120 ! gamma radiation property_value: IAO:0000111 "Cs-137 gamma" xsd:string [Term] id: RBO:00000052 name: Cobalt-60 gamma radiation def: "High energy photons emitted during nuclear decay of the Cobalt-60 isotope." [] synonym: "Co-60" EXACT [] is_a: RBO:00000120 ! gamma radiation property_value: IAO:0000111 "Co-60 gamma" xsd:string [Term] id: RBO:00000058 name: Cobalt-57 gamma radiation def: "High energy photons emitted during nuclear decay of the Cobalt-57 isotope." [] synonym: "Co-57" EXACT [] xref: obo:RBO_00000060 is_a: RBO:00000120 ! gamma radiation property_value: IAO:0000111 "Co-57 gamma" xsd:string [Term] id: RBO:00000060 name: radionuclide is_a: CHEBI:33250 ! atom [Term] id: RBO:00000061 name: actinide is_a: RBO:00000060 ! radionuclide [Term] id: RBO:00000062 name: actinium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000063 name: americium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000064 name: californium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000065 name: neptunium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000066 name: plutonium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000067 name: thorium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000068 name: uranium is_a: RBO:00000061 ! actinide [Term] id: RBO:00000069 name: ultraviolet radiation def: "Electromagnetic radiation with photon energies approximately 3-120 eV. High energy UV radiation can be ioinizing." [] is_a: RBO:00000114 ! ionizing electromagnetic radiation property_value: IAO:0000111 "UV" xsd:string property_value: IAO:0000118 "UV radiation" xsd:string property_value: IAO:0000119 http://son.nasa.gov/tass/content/electrospectrum.htm xsd:string [Term] id: RBO:00000070 name: radioprotectant is_a: CHEBI:24432 ! biological role [Term] id: RBO:00000071 name: radionuclide chelator is_a: CHEBI:24432 ! biological role [Term] id: RBO:00000072 name: co-carcinogen is_a: CHEBI:24432 ! biological role [Term] id: RBO:00000073 name: radiation response modifier is_a: CHEBI:24432 ! biological role [Term] id: RBO:00000074 name: peptide radiation response modifier is_a: RBO:00000073 ! radiation response modifier [Term] id: RBO:00000075 name: small molecule radiation response modifier is_a: RBO:00000073 ! radiation response modifier [Term] id: RBO:00000076 name: nuclear industry worker is_a: RBO:00000111 ! occupational role [Term] id: RBO:00000077 name: astronaut is_a: RBO:00000111 ! occupational role [Term] id: RBO:00000078 name: military is_a: RBO:00000111 ! occupational role [Term] id: RBO:00000079 name: medical professional is_a: RBO:00000111 ! occupational role [Term] id: RBO:00000080 name: dentist is_a: RBO:00000079 ! medical professional [Term] id: RBO:00000081 name: radiologist is_a: RBO:00000079 ! medical professional [Term] id: RBO:00000082 name: radiobiology study type is_a: OBI:0000011 ! planned process [Term] id: RBO:00000083 name: epidemiological study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000084 name: environmental study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000085 name: lifespan study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000086 name: carcinogenesis study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000087 name: tissue damage study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000088 name: dna damage and repair study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000089 name: physiological study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000090 name: anatomical study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000091 name: external exposure study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000092 name: internal contamination study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000093 name: mixed exposure route study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000094 name: acute external exposure study is_a: RBO:00000091 ! external exposure study [Term] id: RBO:00000095 name: chronic external exposure study is_a: RBO:00000091 ! external exposure study [Term] id: RBO:00000096 name: chronic internal contamination study is_a: RBO:00000092 ! internal contamination study [Term] id: RBO:00000097 name: acute internal contamination study is_a: RBO:00000092 ! internal contamination study [Term] id: RBO:00000098 name: acute mixed exposure route study is_a: RBO:00000093 ! mixed exposure route study [Term] id: RBO:00000099 name: chronic mixed exposure route study is_a: RBO:00000093 ! mixed exposure route study [Term] id: RBO:00000100 name: gene expression study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000101 name: proteomics study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000102 name: marker discovery study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000103 name: therapeutics study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000104 name: survival study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000105 name: metabolomics study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000106 name: nuclear accident study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000107 name: toxicity study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000108 name: endocrine study is_a: RBO:00000089 ! physiological study [Term] id: RBO:00000109 name: offspring study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000110 name: biokinetics study is_a: RBO:00000082 ! radiobiology study type [Term] id: RBO:00000111 name: occupational role is_a: BFO:0000023 ! role [Term] id: RBO:00000112 name: high linear energy transfer radiation def: "Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1]." [] xref: NCIT:C17052 is_a: RBO:00000116 ! ionizing radiation property_value: IAO:0000119 "NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf" xsd:string [Term] id: RBO:00000113 name: low linear energy transfer radiation def: "X and gamma rays or light charged particles such as electrons that produce sparse ionizing events far apart on a molecular scale." [] synonym: "low LET|low-LET" EXACT [] xref: NCIT:C17052 is_a: RBO:00000116 ! ionizing radiation property_value: IAO:0000119 "NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf" xsd:string [Term] id: RBO:00000114 name: ionizing electromagnetic radiation def: "Electromagnetic radiation having sufficient energy to remove one or more electrons from an atom" [] is_a: RBO:00000116 ! ionizing radiation [Term] id: RBO:00000115 name: radiation dosimeter device def: "A device that is used to measure the amount of ionizing radiation exposure or absorption." [] synonym: "dosimeter" EXACT [] xref: NCIT:C150121 is_a: OBI:0000968 ! device property_value: IAO:0000111 "radiation dosimeter" xsd:string property_value: IAO:0000118 "radiation dosimeter" xsd:string property_value: IAO:0000119 "NCIT" xsd:string [Term] id: RBO:00000116 name: ionizing radiation def: "Particle or electromagnetic radiation with sufficient energy to liberate one or more electrons from an atom." [] synonym: "ionising radiation" EXACT [] xref: NCIT:C17052 is_a: ENVO:01001023 ! radiation property_value: IAO:0000118 "ionising radiation" xsd:string [Term] id: RBO:00000117 name: charged particle radiation def: "Charged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] xref: NCIT:C18982 is_a: ENVO:01001024 ! particle radiation property_value: IAO:0000111 "charged particle" xsd:string property_value: IAO:0000118 "charged particle" xsd:string [Term] id: RBO:00000118 name: risk estimate xref: NCIT:C19015 is_a: OBI:0001909 ! conclusion based on data [Term] id: RBO:00000119 name: lifetime risk estimate xref: NCIT:C19662 is_a: RBO:00000118 ! risk estimate [Term] id: RBO:00000120 name: gamma radiation def: "electromagnetic radiation with photon energies greater than approximately 100 keV" [] xref: NCIT:C44386 is_a: RBO:00000114 ! ionizing electromagnetic radiation property_value: IAO:0000119 http://son.nasa.gov/tass/content/electrospectrum.htm xsd:string [Term] id: RBO:00000121 name: particle accelerator def: "A device used to impart kinetic energy to subatomic particles by means of electric and magnetic fields" [] xref: NCIT:C94854 is_a: OBI:0000968 ! device is_a: RBO:00005014 ! radiation source [Term] id: RBO:00000122 name: nuclear reactor def: "A device in which nuclear fission may be initiated and controlled in a self-sustaining chain reaction to generate energy or produce useful radiation." [] xref: MESH:D009688 is_a: OBI:0000968 ! device is_a: RBO:00005014 ! radiation source [Term] id: RBO:00000123 name: biological process xref: GO:0008150 is_a: BFO:0000015 ! process [Term] id: RBO:00000124 name: cellular process xref: GO:0009987 is_a: RBO:00000123 ! biological process [Term] id: RBO:00000125 name: O-16 ion radiation def: "Atomic nuclei, each with 8 protons and 8 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000126 name: Ar-40 ion radiation def: "Atomic nuclei, each with 18 protons and 22 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000127 name: Ti-48 ion radiation def: "Atomic nuclei, each with 22 protons and 26 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000128 name: Kr-84 ion radiation def: "Atomic nuclei, each with 36 protons and 48 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000129 name: Nb-93 ion radiation def: "Atomic nuclei, each with 41 protons and 52 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000130 name: Ag-107 ion radiation def: "Atomic nuclei, each with 47 protons and 60 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000131 name: Xe-129 ion radiation def: "Atomic nuclei, each with 54 protons and 75 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000132 name: Ta-181 ion radiation def: "Atomic nuclei, each with 73 protons and 108 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000133 name: Au-197 ion radiation def: "Atomic nuclei, each with 79 protons and 118 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00000134 name: N-14 ion radiation def: "Atomic nuclei, each with 7 protons and 7 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)" [] is_a: RBO:00005001 ! heavy ion radiation [Term] id: RBO:00005001 name: heavy ion radiation def: "Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means" [] is_a: RBO:00000117 ! charged particle radiation [Term] id: RBO:00005002 name: light ion radiation def: "Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means" [] is_a: RBO:00000117 ! charged particle radiation [Term] id: RBO:00005003 name: charged particle def: "A particle with a positive or negative electric charge" [] is_a: BFO:0000040 ! material entity [Term] id: RBO:00005004 name: Iron-56 nucleus def: "An atomic nucleus with 26 protons and 30 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005005 name: Silicon-28 nucleus def: "An atomic nucleus with 14 protons and 14 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005006 name: Carbon-12 nucleus def: "An atomic nucleus with 6 protons and 6 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005007 name: Helium-4 nucleus def: "An atomic nucleus with 2 protons and 2 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005008 name: Neon-20 nucleus def: "An atomic nucleus with 10 protons and 10 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005009 name: space flight def: "Activity carried out by crewed or robotic vehicles outside the Earth's atmmosphere." [] synonym: "Space flight" EXACT [] is_a: ENVO:03000010 ! material transport process property_value: IAO:0000111 "space flight" xsd:string property_value: IAO:0000118 "spaceflight" xsd:string [Term] id: RBO:00005010 name: absorbed radiation dose def: "The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium." [] is_a: RBO:010016 ! radiation dose property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005011 name: absorbed radiation dose rate def: "The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium per unit time." [] is_a: RBO:00000029 ! dose rate property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005012 name: ionizing radiation energy def: "The kinetic energy carried by a particle or photon of ionizing radiation. " [] is_a: RBO:00000116 ! ionizing radiation property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005013 name: x-ray radiation def: "Electromagnetic radiation with photon energies approximately between 0.1 and 120 keV. The upper end of the x-ray spectrum overlaps with the lower end of the gamma ray spectrum." [] is_a: RBO:00000114 ! ionizing electromagnetic radiation property_value: IAO:0000111 "x-ray" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "x-ray" xsd:string property_value: IAO:0000119 http://son.nasa.gov/tass/content/electrospectrum.htm xsd:string [Term] id: RBO:00005014 name: radiation source def: "A material entity which emits radiation" [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005015 name: sham irradiation def: "A protocol in which a sample is kept under conditions identical to irradiated samples, without exposure" [] is_a: OBI:0000272 ! protocol property_value: IAO:0000111 "sham irradiation" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "sham" xsd:string [Term] id: RBO:00005016 name: radiation fractionation protocol def: "A protocol for administering a total radiation dose in two or more increments separated by a specified time interval" [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "fractionation protocol" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "fractionation protocol" xsd:string [Term] id: RBO:00005017 name: cis-lunar space def: "The region of space between the Earth and the Moon" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "cis-lunar space" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005018 name: lunar orbit def: "A region of space defined by a regular, repeating path of a specified object about Earth's moon" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "lunar orbit" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005019 name: lunar surface def: "The area of the lunar landmass exposed to space" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "lunar surface" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005020 name: cis-Mars space def: "The region of space between the Earth and Mars" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "cis-Mars space" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005021 name: Mars orbit def: "A region of space defined by a regular, repeating path of a specified object about Mars" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "Mars orbit" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005022 name: Mars surface def: "The area of the Mars landmass exposed to the Martian atmosphere" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "Mars surface" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005023 name: interplanetary space def: "The region of space in the Solar System between planets" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "interplanetary space" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005024 name: planet surface def: "The outermost solid or liquid area of a planet" [] is_a: RBO:00000016 ! radiation environment property_value: IAO:0000111 "planet surface" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005025 name: non-irradiated def: "An organism or material entity kept unexposed to radiation, for purposes of comparison to a similar organism or material entity that has been exposed to radiation " [] is_a: PATO:0001744 ! radiation exposure property_value: IAO:0000111 "non-irradiated" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005026 name: ground analog study def: "A study at a ground facility designed so as to replicate one or more conditions in space (e.g. radiation, microgravity, isolation)" [] is_a: RBO:00000082 ! radiobiology study type property_value: IAO:0000111 "ground analog experiment" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "ground analog" xsd:string [Term] id: RBO:00005027 name: ground control study def: "An study at a ground facility designed so as to replicate conditions in space (e.g. radiation, microgravity, isolation) with the exception of one condition, so as to ascertain the effects of that condition on an organism or instrument" [] is_a: RBO:00000082 ! radiobiology study type property_value: IAO:0000111 "ground control" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "ground control" xsd:string [Term] id: RBO:00005028 name: irradiation protocol def: "A protocol for administering radiation to a sample " [] is_a: ENVO:01001488 ! aircraft property_value: IAO:0000111 "irradiation protocol" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005029 name: radiation fraction def: "One of the series of individual doses administered to a sample in a fractionated irradiation." [] is_a: RBO:00000024 ! dose fraction property_value: IAO:0000111 "radiation fraction" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "fraction" xsd:string [Term] id: RBO:00005030 name: radiation fraction interval def: "Time between fractions in a fractionated irradiation." [] is_a: RBO:00000029 ! dose rate property_value: IAO:0000111 "radiation fraction interval" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005031 name: high altitude def: "The region of the atmosphere above 8000 feet above sea level. Altitudes above 12000 feet are sometimes referred to as very high altitude, and above 18000 feet as extremely high altitude." [] is_a: OBI:0002983 ! altitude measurement datum property_value: IAO:0000111 "high altitude" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 https://www.medicinenet.com/high_altitude/definition.htm xsd:string [Term] id: RBO:00005032 name: sham-irradiated def: "A radiation quality resulting from a material entity being kept under similar conditions as an irradiated material entity" [] is_a: RBO:00005025 ! non-irradiated property_value: IAO:0000111 "sham" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005033 name: parabolic flight aircraft def: "An aircraft which flies a series of parabolic arcs to simulate micrgravity." [] is_a: ENVO:01001488 ! aircraft property_value: IAO:0000111 "parabolic flight" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "Vomit Comet" xsd:string [Term] id: RBO:00005034 name: high altitude research aircraft def: "An aircraft which flies at altitudes greater than commercial aircraft altitudes for research purposes." [] is_a: ENVO:01001488 ! aircraft property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005035 name: uncrewed aerial vehicle def: "An research aircraft designed to operate without crew members, either autonomously or under control from a ground station" [] is_a: ENVO:01001488 ! aircraft property_value: IAO:0000111 "UAV" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "UAV" xsd:string [Term] id: RBO:00005036 name: highly charged energetic nuclei def: "Fully ionized atomic nuclei with 2 or more protons and energies in excess of tens of MeV per nucleon" [] is_a: RBO:00005003 ! charged particle property_value: IAO:0000111 "HZE" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "HZE" xsd:string [Term] id: RBO:00005037 name: adaptive radiation response study def: "A study of a response to radiation conditioned by prior administration of radiation of a different type and/or at a different dose or dose rate" [] is_a: RBO:00000082 ! radiobiology study type property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "adaptive" xsd:string [Term] id: RBO:00005038 name: average fractionated dose rate def: "The total dose administered in a series of radiation fractions divided by the elapsed time between the beginning of the first exposure fraction and the end of the last exposure fraction" [] is_a: RBO:00000029 ! dose rate property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005039 name: gamma irradiator def: "A device which exposes samples to gamma radiation." [] is_a: RBO:00005014 ! radiation source property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005040 name: particle charge def: "The electric charge of a particle used in an irradiation" [] is_a: UO:0000219 ! electric charge property_value: IAO:0000111 "charge" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005041 name: radiation dosimetry def: "The measurement of the amount of radiation taken up by a sample." [] is_a: CHMO:0002796 ! dosimetry property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005042 name: microbeam def: "A microbeam is a narrow beam of radiation, of micrometer or sub-micrometer dimensions. Together with integrated imaging techniques, microbeams allow precisely defined quantities of damage to be introduced at precisely defined locations." [] is_a: RBO:00000121 ! particle accelerator property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "Wikipedia" xsd:string [Term] id: RBO:00005048 name: Niobium-93 nucleus def: "An atomic nucleus with 41 protons and 52 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005049 name: Silver-107 nucleus def: "An atomic nucleus with 47 protons and 60 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005050 name: Xenon-129 nucleus def: "An atomic nucleus with 54 protons and 75 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005051 name: Tantalum-181 nucleus def: "An atomic nucleus with 73 protons and 108 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005052 name: Gold-197 nucleus def: "An atomic nucleus with 79 protons and 118 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005053 name: Nitrogen-14 nucleus def: "An atomic nucleus with 7 protons and 7 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005054 name: Oxygen-16 nucleus def: "An atomic nucleus with 8 protons and 8 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005055 name: Argon-40 nucleus def: "An atomic nucleus with 18 protons and 22 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005056 name: Titanium-48 nucleus def: "An atomic nucleus with 22 protons and 26 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005057 name: Krypton-84 nucleus def: "An atomic nucleus with 36 protons and 48 neutrons " [] is_a: RBO:010012 ! heavy ion [Term] id: RBO:00005066 name: miliigray per second def: "A derived absorbed dose unit which is equal to one milligray absorbed per second" [] is_a: UO:0000129 ! absorbed dose unit property_value: IAO:0000111 "mGy/sec" xsd:string property_value: IAO:0000118 "mGy/sec " xsd:string [Term] id: RBO:00005067 name: Indirect cellular response to stimulus def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell" [] is_a: GO:0051716 ! cellular response to stimulus property_value: example_of_usage "This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen." xsd:string property_value: IAO:0000111 "Indirect cellular response to stimulus" xsd:string property_value: IAO:0000119 "Paul Schofield" xsd:string [Term] id: RBO:00005068 name: Indirect cellular response to radiation def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells." [] is_a: RBO:00005067 ! Indirect cellular response to stimulus relationship: RO:0002404 ENVO:01001023 ! causally downstream of radiation property_value: example_of_usage "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" xsd:string property_value: IAO:0000119 "Paul Schofield" xsd:string [Term] id: RBO:00005069 name: Indirect cellular response to ionising radiation def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells." [] is_a: RBO:00005068 ! Indirect cellular response to radiation property_value: example_of_usage "Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component." xsd:string property_value: IAO:0000119 "Paul Schofield" xsd:string [Term] id: RBO:00005070 name: ionizing radiation device def: "A device for exposing materials or biological organisms to ionizing radiation for research or therapeutic purposes." [] is_a: RBO:00005014 ! radiation source [Term] id: RBO:00005071 name: high-altitude balloon def: "High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level." [] is_a: ENVO:01001488 ! aircraft property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "Wikipedia" xsd:string [Term] id: RBO:00005072 name: Space flight def: "Travel beyond the Earth's atmosphere" [] is_a: PATO:0002062 ! physical quality of a process property_value: IAO:0000111 "spaceflight" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:00005074 name: non-targeted effects of ionising radiation def: "Non-targeted effects of ionising radiation are characterised by cellular responses that occur in cells in which energy from ionizing radiation has not been deposited. The distinct classes of non-targeted effects include Genomic Instability, and Bystander effect which latter includes Abscopal effects and Bystander-mediated adaptive response. These can also arise non-clonally in the progeny of irradiated somatic or germ cells, resulting in radiation-induced genomic instability and transgenerational genomic instability respectively. (Kadhim M, Salomaa S, Wright E, et al. Non-targeted effects of ionising radiation--implications for low dose risk. Mutat Res. 2013;752(2):84-98. doi:10.1016/j.mrrev.2012.12.001)" [] is_a: RBO:00005069 ! Indirect cellular response to ionising radiation property_value: IAO:0000111 "non-targeted effects of ionising radiation" xsd:string property_value: IAO:0000117 "Paul Schofield ORCID: 0000-0002-5111-7263" xsd:string property_value: IAO:0000118 "non-targeted effects" xsd:string property_value: IAO:0000118 "NTE" xsd:string [Term] id: RBO:010000 name: as low as reasonably achievable def: "A principle of radiation protection philosophy that requires that exposures to ionizing radiation be kept as low as reasonably achievable, economic and social factors being taken into account. The protection from radiation exposure is ALARA when the expen" [] synonym: "ALARA" EXACT [] is_a: IAO:0000104 ! plan specification property_value: example_of_usage "One of the measures to ensure ALARA is to minimize the time spent working around radioactive materials." xsd:string property_value: IAO:0000111 "ALARA" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "ALARA" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010001 name: radiation attenuation def: "The reduction of radiation intensity upon passage of radiation through matter" [] is_a: BFO:0000182 ! history property_value: example_of_usage "Attenuation in concrete or leadshielding is a common method of radiation protection on Earth, but is impractical in space due to mass constraints." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010002 name: biodosimetry def: "Use of a biological response as an indicator of a dose of an effective agent (e.g., the extent of decline in peripheral blood lymphocytes of humans exposed to ionizing radiation can be used as an indicator of the absorbed dose to the whole body from that " [] is_a: CHMO:0002796 ! dosimetry property_value: example_of_usage "Biodosimetry was used to measure the exposure of some victims of the Chernobyl nuclear accident." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010003 name: bystander effect def: "The term used to describe the effects on cells in proximity to irradiated cells, but through which radiation has not passed. In experimental radiation biology, the bystander effect can be investigated by targeting individual cells, or by using doses low enough that the probability for a given cell to be hit by a particle is less than one." [] is_a: RBO:00005074 ! non-targeted effects of ionising radiation property_value: example_of_usage "The bystander effect can be studied by identifying cells that were traversed by a charged particle." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010006 name: delta ray def: "Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a " [] synonym: "delta electron" EXACT [] is_a: RBO:00000117 ! charged particle radiation property_value: example_of_usage "Delta ray energies increase with the velocity of the incident particle." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "delta electron" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010007 name: dose equivalent def: "The product of the absorbed dose (D) at a point and the quality factor (Q) at that point for the radiation type (i.e., H = DQ). The unit of H is J-kg^[-1] with the special name sievert (Sv)" [] is_a: RBO:010016 ! radiation dose property_value: example_of_usage "The average annual dose equivalent for crew members on the ISS is approximately 300 mSv." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010008 name: excess lifetime risk of cancer def: "The increased risk from induced cancer due to exposure when the effects over an entire lifetime are accounted for. Individuals who would have died of cancer anyway but die early because of exposure are not included" [] is_a: RBO:00000119 ! lifetime risk estimate property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010009 name: fast neutron def: "Neutrons of energies above a few hundred kiloelectron volts (keV)" [] is_a: ENVO:01001024 ! particle radiation property_value: example_of_usage "The sample was irradiated with fast neutrons." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010010 name: fluence def: "The number of particles or photons per unit of cross-sectional area perpendicular to the direction of the particle (units of m^2 or cm^2) (i.e., particles-m^[-2] or particles-cm^[-2])." [] is_a: IAO:0000109 ! measurement datum property_value: example_of_usage "The value of the fluence was approximately 1 particle per cm2." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010011 name: flux def: "The quotient of dN by dt, where dN is the increment of the particle number in the time interval dt. The unit for flux is reciprocal second (s^[-1].)" [] is_a: IAO:0000109 ! measurement datum property_value: example_of_usage "The flux of cosmic ray muons per cm2 at the surface of the Earth is approximately 1.0." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010012 name: heavy ion def: "An atomic nucleus, fully stripped of its orbital electrons, containing 2 or more protons. Nuclei containing between 2 protons (helium) and 6 protons (carbon) are sometimes referred to as light ions." [] is_a: CHEBI:33252 ! atomic nucleus property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "In RBO--needs def from NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010013 name: linear energy transfer def: "The energy deposited by an ionizing charged particle or photon in any medium per unit path length." [] synonym: "LET" EXACT [] is_a: IAO:0000109 ! measurement datum property_value: example_of_usage "Biological effects are a function of LET." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "LET" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010014 name: organ dose def: "The mean absorbed radiation dose in a specified tissue or organ of the human body." [] is_a: RBO:010016 ! radiation dose property_value: example_of_usage "Radiation protection standards take into account organ dose as well as whole body dose." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010015 name: quality factor def: "Dimensionless factor developed for purposes of radiation protection and assessing health risks in general terms that accounts for the relative biological effectiveness of different radiations in producing stochastic effects and is used to relate absorbed " [] is_a: OBI:0001909 ! conclusion based on data property_value: example_of_usage "Neutrons have a high quality factor compared to photons." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010016 name: radiation dose def: "A measurement datum of the quantity of radiation absorbed by a substance or organism. The term \"radiation dose\" may for example refer to absorbed dose, organ dose, dose equivalent or equivalent dose, depending upon context and weighting factor(s)." [] is_a: OBI:0000984 ! dose property_value: example_of_usage "The samples received a dose of 1 Gy. (The use of the gray unit implies that \"dose\" refers to a measured quantity, typically absorbed dose or organ dose.)" xsd:string property_value: example_of_usage "The samples received a dose of 1 Sv. (The use of the sievert unit implies that \"dose\" refers to a der" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string [Term] id: RBO:010017 name: radiation quality def: "Currently under discussion: [A general term referring to the relative biological effectiveness of the radiation of interest. For example, the absorbed dose from an exposure to neutron radiation may be quantitatively the same as that from an exposure to ga" [] is_a: PATO:0001018 ! physical quality property_value: example_of_usage "Radiation quality has been commonly expressed in terms of the LET of the ionizing particles that deliver the absorbed dose. (Rossi, 1959)" xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010018 name: radiation weighting factor def: "A factor used to allow for differences in the biological effectiveness between different radiations when calculating equivalent dose (H_T) (see equivalent dose). These factors are independent of the tissue or organ irradiated." [] is_a: OBI:0001909 ! conclusion based on data property_value: example_of_usage "Radiation weighting factors may change as more data on biological effects are obtained." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010019 name: relative biological effectiveness def: "Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r" [] synonym: "RBE" EXACT [] is_a: IAO:0000109 ! measurement datum property_value: example_of_usage "Neutrons have been found to have a higher RBE than electrons. " xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000118 "RBE" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RBO:010020 name: tissue equivalence def: "Denotes a substance with absorbing and scattering properties for a given radiation that sufficiently match those of a particular biological tissue." [] is_a: PATO:0001018 ! physical quality property_value: example_of_usage "Tissue equivalent materials can be used to study radiation effects at depth in the human body." xsd:string property_value: IAO:0000117 "Jack Miller" xsd:string property_value: IAO:0000119 "NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)" xsd:string [Term] id: RO:0002577 name: system def: "A material entity consisting of multiple components that are causally integrated." [] is_a: BFO:0000040 ! material entity property_value: editor_note "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string [Term] id: UBERON:0000000 name: processual entity namespace: uberon def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] subset: upper_level disjoint_from: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000009 name: submucosa namespace: uberon def: "A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]." [Wikipedia:Submucosa] subset: pheno_slim subset: uberon_slim synonym: "organ submucosa" EXACT [FMA:85391] synonym: "region of submucosa" EXACT [FMA:85392] synonym: "submucosa of organ" EXACT [FMA:85391] synonym: "submucosa of region of organ" EXACT [FMA:85392] synonym: "submucous layer" RELATED [BTO:0002107] synonym: "tela submucosa" RELATED [BTO:0002107] synonym: "tunica submucosa" RELATED [] xref: BTO:0002107 xref: FMA:85391 xref: FMA:85392 xref: NCIT:C13167 xref: SCTID:68439008 xref: UMLS:C0225344 {source="ncithesaurus:Submucosa"} xref: Wikipedia:Submucosa is_a: UBERON:0004923 ! organ component layer relationship: composed_primarily_of UBERON:0002384 ! connective tissue relationship: immediately_deep_to UBERON:0000344 ! mucosa relationship: only_in_taxon NCBITaxon:7711 ! Chordata property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xsd:anyURI property_value: UBPROP:0000007 "submucosal" xsd:string [Term] id: UBERON:0000010 name: peripheral nervous system namespace: uberon 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." [GO:0007422] subset: cumbo subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "pars peripherica" EXACT LATIN [FMA:9903, FMA:TA, Wikipedia:Peripheral_nervous_system] synonym: "PNS" BROAD ABBREVIATION [] synonym: "systema nervosum periphericum" EXACT LATIN [FMA:9903, FMA:TA, Wikipedia:Peripheral_nervous_system] xref: AAO:0000429 xref: BAMS:PNS xref: BILA:0000081 xref: BIRNLEX:1111 xref: BTO:0001028 xref: CALOHA:TS-0808 xref: EFO:0000891 xref: EHDAA2:0001445 xref: EHDAA:2893 xref: EMAPA:16665 xref: EV:0100335 xref: FBbt:00005098 xref: FMA:9903 xref: GAID:715 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3232 xref: MA:0000218 xref: MAT:0000338 xref: MESH:D017933 xref: MIAA:0000338 xref: NCIT:C12465 xref: SCTID:362292005 xref: TAO:0000142 xref: UMLS:C0206417 {source="ncithesaurus:Peripheral_Nervous_System"} xref: UMLS:C0206417 {source="BIRNLEX:1111"} xref: UMLS:C1305921 {source="BIRNLEX:1111"} xref: VHOG:0000399 xref: Wikipedia:Peripheral_nervous_system xref: XAO:0000178 xref: ZFA:0000142 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png xsd:anyURI property_value: UBPROP:0000001 "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000142", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000429", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} property_value: UBPROP:0000003 "(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000399", ontology="VHOG", source="DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000014 name: zone of skin namespace: uberon def: "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Skin] subset: pheno_slim synonym: "portion of skin" EXACT [] synonym: "region of skin" EXACT [] synonym: "skin" EXACT [MA:0000151] synonym: "skin region" EXACT [] synonym: "skin zone" EXACT [] xref: EHDAA2:0001844 xref: EHDAA:6530 xref: EMAPA:17525 xref: EV:0100152 xref: FMA:86166 xref: GAID:933 xref: MA:0000151 xref: MAT:0000284 xref: MESH:D012867 xref: MIAA:0000284 xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA xref: SCTID:20795001 xref: VHOG:0000860 xref: Wikipedia:Skin is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: has_part UBERON:0001003 ! skin epidermis relationship: has_part UBERON:0002067 ! dermis relationship: part_of UBERON:0002097 ! skin of body property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg xsd:anyURI property_value: IAO:0000232 "Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee" xsd:string property_value: UBPROP:0000003 "(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000860", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive" xsd:string [Term] id: UBERON:0000015 name: non-material anatomical boundary namespace: uberon def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CARO:0000010] comment: Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. subset: upper_level synonym: "anatomical boundary" EXACT [CARO:0000010] xref: AEO:0000192 xref: CARO:0000010 xref: FMA:50705 is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity [Term] id: UBERON:0000019 name: camera-type eye namespace: uberon def: "An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid." [GO:0043010, https://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "camera-type eye plus associated structures" RELATED [] synonym: "eye" BROAD [FMA:54448] synonym: "eyes" RELATED PLURAL [TAO:0000107] synonym: "orbital part of face" RELATED [FMA:54448] synonym: "orbital region" RELATED [FMA:54448] synonym: "regio orbitalis" EXACT LATIN [FMA:54448, FMA:TA] synonym: "vertebrate eye" NARROW [] xref: AAO:0010340 xref: BIRNLEX:1169 xref: BTO:0004688 xref: EHDAA2:0000484 xref: EHDAA:936 xref: EMAPA:16198 xref: FMA:54448 xref: MA:0000261 xref: NCIT:C12401 xref: OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA xref: SCTID:181143004 xref: TAO:0000107 xref: UMLS:C0015392 {source="BIRNLEX:1169"} xref: UMLS:C0015392 {source="ncithesaurus:Eye"} xref: UMLS:C1280202 {source="BIRNLEX:1169"} xref: VHOG:0000275 xref: XAO:0000179 xref: ZFA:0000107 is_a: UBERON:0000047 ! simple eye is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015212 ! lateral structure relationship: develops_from UBERON:0003072 {evidence="definitional"} ! optic cup relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000965 ! lens of camera-type eye relationship: has_part UBERON:0000966 ! retina relationship: in_lateral_side_of UBERON:0000033 ! head relationship: part_of UBERON:0004088 ! orbital region property_value: UBPROP:0000001 "A cavitated compound organ that transduces light waves into neural signals.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000107", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000275", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000020 name: sense organ namespace: uberon def: "An organ that is capable of transducing sensory stimulus to the nervous system." [https://github.com/obophenotype/uberon/issues/549, https://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "organ of sense organ system" EXACT [OBOL:accepted] synonym: "organ of sensory organ system" EXACT [OBOL:accepted] synonym: "organ of sensory system" EXACT [OBOL:accepted] synonym: "sense organ system organ" EXACT [OBOL:automatic] synonym: "sensillum" NARROW [WBbt:0006929] synonym: "sensor" RELATED [] synonym: "sensory organ" EXACT [] synonym: "sensory organ system organ" EXACT [OBOL:automatic] synonym: "sensory system organ" EXACT [OBOL:accepted] synonym: "Sinnesorgan" RELATED [BTO:0000202] xref: AEO:0000094 xref: BSA:0000121 xref: BTO:0000202 xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 xref: FBbt:00005155 xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 xref: MESH:D012679 xref: NCIT:C33224 xref: SCTID:244485009 xref: UMLS:C0935626 {source="ncithesaurus:Organ_of_the_Special_Sense"} xref: VHOG:0001407 xref: WBbt:0006929 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png xsd:anyURI property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall [Term] id: UBERON:0000025 name: tube namespace: uberon def: "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." [http://orcid.org/0000-0002-6601-2165] synonym: "anatomical tube" EXACT [] synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: has_quality PATO:0002299 ! tubular relationship: has_part UBERON:0013522 ! subdivision of tube relationship: has_quality PATO:0002299 ! tubular property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string property_value: UBPROP:0000007 "tubular" xsd:string [Term] id: UBERON:0000026 name: appendage namespace: uberon def: "Major subdivision of an organism that protrudes from the body[DOS, CARO]." [CARO:DOS] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "appendages" RELATED PLURAL [XAO:0000218] synonym: "extremitaet" RELATED [BTO:0001492] synonym: "extremity" RELATED [] synonym: "limbs/digits/tail" RELATED [MP:0000001] xref: AEO:0000193 xref: BILA:0000018 xref: BTO:0001492 xref: CARO:0010003 xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 xref: FBbt:00007000 xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 xref: MIAA:0000023 xref: NCIT:C61460 xref: OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA xref: UMLS:C0598782 {source="ncithesaurus:Appendage"} xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: UBPROP:0000001 "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." xsd:string {source="BILA:0000018"} property_value: UBPROP:0000001 "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." xsd:string {source="GO:0048736"} property_value: UBPROP:0000007 "appendicular" xsd:string property_value: UBPROP:0000008 "this is currently a subtype of organism subdivision - which would exclude feathers" xsd:string [Term] id: UBERON:0000030 name: lamina propria namespace: uberon def: "A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions." [Wikipedia:Lamina_propria] subset: uberon_slim synonym: "lamina propria mucosa" EXACT [] synonym: "lamina propria mucosae" EXACT [] synonym: "tunica propria" RELATED [BTO:0002330] xref: BTO:0002330 xref: FMA:62517 xref: NCIT:C32918 xref: SCTID:298225002 xref: UMLS:C1179187 {source="ncithesaurus:Lamina_Propria"} xref: Wikipedia:Lamina_propria is_a: UBERON:0004923 ! organ component layer relationship: composed_primarily_of UBERON:0011825 ! loose connective tissue relationship: immediately_deep_to UBERON:0000483 ! epithelium relationship: part_of UBERON:0000344 ! mucosa property_value: depicted:by GI:Organization.svg xsd:anyURI [Term] id: UBERON:0000031 name: lamina propria of trachea namespace: uberon def: "A lamina propria that is part of a respiratory airway." [OBOL:automatic] synonym: "lamina propria mucosa of trachea" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of windpipe" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of trachea" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of windpipe" EXACT [OBOL:automatic] synonym: "lamina propria of windpipe" EXACT [OBOL:automatic] synonym: "trachea lamina propria" EXACT [] synonym: "trachea lamina propria mucosa" EXACT [OBOL:automatic] synonym: "trachea lamina propria mucosae" EXACT [OBOL:automatic] synonym: "tracheal lamina propria" EXACT [] synonym: "windpipe lamina propria" EXACT [OBOL:automatic] synonym: "windpipe lamina propria mucosa" EXACT [OBOL:automatic] synonym: "windpipe lamina propria mucosae" EXACT [OBOL:automatic] xref: EMAPA:35877 xref: FMA:265157 xref: MA:0001858 xref: NCIT:C49305 xref: UMLS:C1710457 {source="ncithesaurus:Trachea_Lamina_Propria"} is_a: UBERON:0004779 ! respiratory system lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001005 ! respiratory airway relationship: part_of UBERON:0000379 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! tracheal mucosa [Term] id: UBERON:0000033 name: head namespace: uberon def: "The head is the anterior-most division of the body [GO]." [GO:0060322, Wikipedia:Head] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "adult head" NARROW [] synonym: "cephalic area" RELATED [SPD:0000016] synonym: "head (volume)" EXACT [FMA:7154] xref: AAO:0010335 xref: AEO:0000106 xref: BILA:0000115 xref: BIRNLEX:1230 xref: BTO:0000282 xref: CALOHA:TS-0436 xref: EFO:0000964 xref: EHDAA2:0003106 xref: EMAPA:31858 xref: FBbt:00000004 xref: FMA:7154 xref: GAID:61 xref: galen:Head xref: HAO:0000397 xref: MA:0000023 xref: MAT:0000294 xref: MESH:D006257 xref: MIAA:0000294 xref: NCIT:C12419 xref: OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg xref: OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA xref: SCTID:302548004 xref: SPD:0000016 xref: TAO:0001114 xref: TGMA:0000002 xref: UMLS:C0018670 {source="ncithesaurus:Head"} xref: UMLS:C0018670 {source="BIRNLEX:1230"} xref: VHOG:0001644 xref: WBbt:0005739 xref: Wikipedia:Head xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: has_skeleton UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! skull relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0007811 ! craniocervical region property_value: UBPROP:0000001 "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001644", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000042 name: serous membrane namespace: uberon def: "multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." [https://github.com/obophenotype/uberon/issues/86, Wikipedia:Serous_membrane] subset: uberon_slim subset: vertebrate_core synonym: "serosa" RELATED [Wikipedia:Serous_membrane] synonym: "tunica serosa" EXACT LATIN [FMA:9581] synonym: "wall of serous sac" EXACT [FMA:9581] xref: FMA:9581 xref: GAID:19 xref: MESH:D012704 xref: NCIT:C13169 xref: SCTID:362878009 xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xsd:anyURI property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: UBPROP:0000001 "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="Wikipedia:Serous_membrane"} property_value: UBPROP:0000001 "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string {source="Wikipedia:Serous_membrane"} property_value: UBPROP:0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000043 name: tendon namespace: uberon def: "Dense regular connective tissue that connects muscle to bone[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000073, Wikipedia:Tendon] subset: pheno_slim subset: uberon_slim synonym: "sinew" RELATED [Wikipedia:Tendon] synonym: "tendo" RELATED LATIN [Wikipedia:Tendon] xref: AEO:0000091 xref: BTO:0001356 xref: CALOHA:TS-1021 xref: EHDAA2:0003091 xref: EMAPA:35854 xref: EV:0100149 xref: FMA:9721 xref: GAID:276 xref: galen:Tendon xref: MA:0000115 xref: MESH:D013710 xref: NCIT:C13045 xref: OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA xref: SCTID:256667004 xref: UMLS:C0039508 {source="ncithesaurus:Tendon"} xref: VHOG:0001286 xref: VSAO:0000073 xref: Wikipedia:Tendon xref: XAO:0000173 xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue relationship: connects UBERON:0001474 ! bone element relationship: connects UBERON:0001630 ! muscle organ relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg xsd:anyURI property_value: UBPROP:0000001 "Dense regular connective tissue that connects muscle to bone.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000073", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000003 "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001286", ontology="VHOG", source="DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000047 name: simple eye namespace: uberon def: "An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity." [Wikipedia:Eye#Simple_eyes] subset: grouping_class subset: uberon_slim xref: TGMA:0000729 xref: Wikipedia:Eye#Simple_eyes is_a: UBERON:0000970 ! eye [Term] id: UBERON:0000055 name: vessel namespace: uberon def: "A tubular structure that contains, conveys body fluid, such as blood or lymph." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid [Term] id: UBERON:0000058 name: duct namespace: uberon def: "A tubular structure that transports secreted or excreted substances." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm#ducts] subset: grouping_class synonym: "anatomical duct" EXACT [] synonym: "ducts" RELATED PLURAL [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 xref: FBbt:00100314 xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 xref: SCTID:91726008 xref: TAO:0005171 xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 is_a: UBERON:0000063 ! organ subunit relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: has_quality PATO:0002299 ! tubular property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string [Term] id: UBERON:0000060 name: anatomical wall namespace: uberon alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [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: 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 relationship: existence_ends_during_or_before UBERON:0000071 ! death stage relationship: existence_starts_during_or_after UBERON:0000106 ! zygote stage [Term] id: UBERON:0000062 name: organ namespace: uberon def: "Anatomical structure that performs a specific function or group of functions [WP]." [Wikipedia:Organ_(anatomy)] subset: upper_level synonym: "anatomical unit" RELATED [] synonym: "body organ" RELATED [] synonym: "element" RELATED [http://orcid.org/0000-0002-6601-2165] xref: BIRNLEX:4 xref: CARO:0020004 xref: EFO:0000634 xref: EMAPA:35949 xref: ENVO:01000162 xref: FMA:67498 xref: MA:0003001 xref: NCIT:C13018 xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA xref: SCTID:272625005 xref: UMLS:C0178784 {source="ncithesaurus:Organ"} xref: WBbt:0003760 xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage relationship: has_boundary UBERON:0006984 ! anatomical surface relationship: part_of UBERON:0000467 ! anatomical system property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string [Term] id: UBERON:0000063 name: organ subunit namespace: uberon def: "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity." [http://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "organ region with fixed fiat boundary" RELATED [FMA:86140] synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} [Term] id: UBERON:0000064 name: organ part namespace: uberon def: "A multicellular structure that is a part of an organ." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: non_informative subset: upper_level synonym: "cardinal organ part" EXACT [FMA:82472] synonym: "regional part of organ" RELATED [BIRNLEX:16] xref: AAO:0011124 xref: BIRNLEX:16 xref: EFO:0000635 xref: FMA:82472 xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string [Term] id: UBERON:0000065 name: respiratory tract namespace: uberon def: "Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts" [https://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0001606 xref: EHDAA:1568 xref: EHDAA:2219 xref: EMAPA:16737 xref: FMA:265130 xref: OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA xref: SCTID:361110005 xref: VHOG:0000393 is_a: UBERON:0001005 ! respiratory airway is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut relationship: develops_from UBERON:0008947 ! respiratory primordium [Term] id: UBERON:0000066 name: fully formed stage namespace: uberon def: "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "adult stage" BROAD [] synonym: "fully formed animal stage" EXACT [] synonym: "juvenile-adult stage" EXACT [] xref: BilaDO:0000004 xref: BTO:0001043 xref: EFO:0001272 xref: FBdv:00005369 xref: WBls:0000041 xref: XtroDO:0000084 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000092 ! post-embryonic stage relationship: preceded_by UBERON:0000111 ! organogenesis stage relationship: precedes UBERON:0000071 ! death stage property_value: seeAlso https://github.com/obophenotype/uberon/issues/566 xsd:anyURI [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: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: part_of GO:0009790 ! embryo development relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage relationship: simultaneous_with GO:0009790 ! embryo development [Term] id: UBERON:0000071 name: death stage namespace: uberon def: "End of the life of an organism." [XAO:0000437] synonym: "death" RELATED [] xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: ends UBERON:0000104 ! life cycle property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} [Term] id: UBERON:0000072 name: proximo-distal subdivision of respiratory tract namespace: uberon def: "An section of a respiratory tract." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "respiratory tract" RELATED [MA:0000434] synonym: "subdivision of respiratory tract" RELATED [] xref: EMAPA:16737 xref: FMA:45660 xref: MA:0000434 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000065 ! respiratory tract property_value: UBPROP:0000012 "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole" xsd:string {external_ontology="MA"} [Term] id: UBERON:0000073 name: regional part of nervous system namespace: uberon def: "Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS." [BIRNLEX:1157] subset: non_informative subset: upper_level synonym: "part of nervous system" EXACT [BIRNLEX:1157] xref: BIRNLEX:1157 xref: NCIT:C13040 xref: SCTID:25087005 xref: UMLS:C1518256 {source="ncithesaurus:Nervous_System_Part"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system created_by: Melissa Haendel creation_date: 2009-06-18T09:00:04Z [Term] id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] synonym: "skeletal system subdivision" EXACT [FMA:85544] xref: FMA:85544 xref: galen:ComplexSkeletalStructure xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: composed_primarily_of UBERON:0004765 ! skeletal element relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system [Term] id: UBERON:0000076 name: external ectoderm namespace: uberon def: "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." [MGI:anna, MP:0012532] subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 xref: EHDAA:4784 xref: EHDAA:4790 xref: EHDAA:4796 xref: EHDAA:7860 xref: EMAPA:16096 xref: FMA:87656 xref: NCIT:C34309 xref: UMLS:C1515087 {source="ncithesaurus:Surface_Ectoderm"} xref: Wikipedia:External_ectoderm is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png xsd:anyURI property_value: editor_note "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string property_value: UBPROP:0000011 "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" xsd:string [Term] id: UBERON:0000077 name: mixed endoderm/mesoderm-derived structure namespace: uberon def: "An anatomical structure that develops from the endoderm and the mesoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000232 "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" xsd:string [Term] id: UBERON:0000078 name: mixed ectoderm/mesoderm/endoderm-derived structure namespace: uberon def: "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000232 "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" xsd:string [Term] id: UBERON:0000092 name: post-embryonic stage namespace: uberon def: "stage succeeding embryo, including mature structure" [https://orcid.org/0000-0002-6601-2165] synonym: "post-hatching stage" NARROW [] synonym: "postembryonic" RELATED [] synonym: "postembryonic stage" EXACT [] xref: BilaDO:0000003 xref: OGES:000010 xref: OGES:000014 xref: OGES:000024 xref: WBls:0000022 xref: WBls:0000093 xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of GO:0009791 ! post-embryonic development relationship: preceded_by UBERON:0000068 ! embryo stage relationship: simultaneous_with GO:0009791 ! post-embryonic development property_value: seeAlso https://github.com/obophenotype/uberon/issues/344 xsd:anyURI property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000094 name: membrane organ namespace: uberon def: "Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]" [FMA:7145] synonym: "membrane" BROAD [] synonym: "membrane of organ" EXACT [] xref: FMA:7145 is_a: UBERON:0000062 ! organ relationship: composed_primarily_of UBERON:0011823 {source="FMA-def"} ! dense connective tissue created_by: cjm creation_date: 2009-07-30T05:19:13Z [Term] id: UBERON:0000095 name: cardiac neural crest namespace: uberon def: "portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]" [Wikipedia:Cardiac_neural_crest] subset: vertebrate_core synonym: "cardiac neural crest complex" RELATED [Wikipedia:Cardiac_neural_crest] synonym: "complexus cristae neuralis cardiacus" RELATED [Wikipedia:Cardiac_neural_crest] xref: TAO:0002173 xref: Wikipedia:Cardiac_neural_crest xref: XAO:0004190 xref: ZFA:0001648 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest property_value: UBPROP:0000001 "A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]." xsd:string {source="DOI:10.1242/dev.091751"} property_value: UBPROP:0000012 "ZFA treats this as a subtype of NC." xsd:string {external_ontology="ZFA"} created_by: cjm creation_date: 2009-07-30T07:57:38Z [Term] id: UBERON:0000102 name: lung vasculature namespace: uberon def: "The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]." [GOC:GO] subset: pheno_slim synonym: "lung vascular network" EXACT [OBOL:automatic] synonym: "pulmonary vasculature" EXACT [FMA:73750] synonym: "vascular network of lung" EXACT [OBOL:automatic] synonym: "vasculature of lung" EXACT [OBOL:automatic] xref: FMA:73750 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002201 ! vasculature of trunk is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: UBERON:0000104 name: life cycle namespace: uberon def: "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism." [https://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "entire life cycle" EXACT [] synonym: "entire lifespan" EXACT [] synonym: "life" EXACT [] synonym: "lifespan" EXACT [] xref: FBdv:00000000 xref: HsapDv:0000001 xref: MmusDv:0000001 xref: ncithesaurus:Life xref: OGES:000011 is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage relationship: starts_with UBERON:0000106 ! zygote stage property_value: seeAlso https://github.com/obophenotype/uberon/issues/532 xsd:anyURI [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: 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: MmusDv:0000000 xref: ncithesaurus:Developmental_Stage xref: OlatDv:0000010 xref: PdumDv:0000090 xref: WBls:0000002 xref: XAO:1000000 xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle property_value: editor_note "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:0000106 name: zygote stage namespace: uberon def: "A stage at which the organism is a single cell produced by means of sexual reproduction." [Wikipedia:Zygote] subset: efo_slim synonym: "1-cell stage" EXACT [] synonym: "fertilized egg stage" EXACT [BTO:0000854] synonym: "fertilized egg stage" RELATED [] synonym: "one cell stage" EXACT [] synonym: "one-cell stage" RELATED [VHOG:0000745] synonym: "zygote" RELATED [VHOG:0000745] synonym: "zygotum" RELATED LATIN [Wikipedia:Zygote] xref: BilaDO:0000005 xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 xref: Wikipedia:Zygote xref: XAO:1000001 xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: starts UBERON:0000104 ! life cycle property_value: seeAlso EMAPA:16033 property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000107 name: cleavage stage namespace: uberon def: "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula." [GO:0040016, Wikipedia:Cleavage_(embryo)] subset: efo_slim xref: BilaDO:0000006 xref: BILS:0000107 xref: EFO:0001290 xref: FBdv:00000054 xref: MESH:A16.254.270 xref: MmusDv:0000004 xref: OGES:000015 xref: OGES:000020 xref: PdumDv:0000200 xref: Wikipedia:Cleavage_(embryo) xref: XAO:1000004 xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of GO:0040016 ! embryonic cleavage relationship: part_of UBERON:0000068 ! embryo stage relationship: simultaneous_with GO:0040016 ! embryonic cleavage [Term] id: UBERON:0000108 name: blastula stage namespace: uberon def: "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: efo_slim xref: BilaDO:0000007 xref: BILS:0000108 xref: EFO:0001282 xref: HsapDv:0000006 xref: MmusDv:0000007 xref: OGES:000003 xref: OGES:000016 xref: OGES:000021 xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg xref: WBls:0000005 xref: Wikipedia:Blastula xref: XAO:1000003 xref: ZFS:0000045 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png xsd:anyURI property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 name: gastrula stage namespace: uberon def: "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GO:0007369] subset: efo_slim synonym: "blastocystis trilaminaris stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar blastocyst stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar blastoderm stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar disk stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ stage" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar stage" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BilaDO:0000008 xref: BILS:0000109 xref: EFO:0001296 xref: FBdv:00005317 xref: HsapDv:0000010 xref: MmusDv:0000013 xref: OGES:000004 xref: OGES:000019 xref: WBls:0000010 xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of GO:0007369 ! gastrulation relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: simultaneous_with GO:0007369 ! gastrulation [Term] id: UBERON:0000110 name: neurula stage namespace: uberon def: "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GO:0001841] xref: BilaDO:0000009 xref: BILS:0000110 xref: HsapDv:0000012 xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of GO:0001841 ! neural tube formation relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: simultaneous_with GO:0001841 ! neural tube formation property_value: seeAlso https://github.com/obophenotype/uberon/issues/343 xsd:anyURI [Term] id: UBERON:0000111 name: organogenesis stage namespace: uberon def: "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." [Wikipedia:Organogenesis] synonym: "segmentation stage" RELATED [] xref: BilaDO:0000010 xref: BILS:0000111 xref: HsapDv:0000015 xref: MmusDv:0000018 xref: OGES:000005 xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of GO:0048513 ! animal organ development relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000110 ! neurula stage relationship: simultaneous_with GO:0048513 ! animal organ development property_value: seeAlso https://github.com/obophenotype/uberon/issues/533 xsd:anyURI [Term] id: UBERON:0000114 name: lung connective tissue namespace: uberon def: "the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin" [ISBN:0-683-40008-8, MGI:anna, MP:0002276, PMID:14635660] subset: pheno_slim synonym: "connective tissue of lung" EXACT [OBOL:automatic] synonym: "lung interstitial tissue" RELATED [MA:0001782] synonym: "lung interstitium" RELATED [] synonym: "pulmonary connective tissue" RELATED [EMAPA:35521] synonym: "pulmonary interstitial tissue" RELATED [] synonym: "pulmonary interstitium" EXACT [FMA:27533] xref: EMAPA:35521 xref: FMA:27533 xref: MA:0001782 xref: SCTID:201609008 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003580 ! lower respiratory tract connective tissue is_a: UBERON:0003837 ! thoracic segment connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002048 ! lung relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: develops_from UBERON:0004883 ! lung mesenchyme relationship: part_of UBERON:0002048 ! lung relationship: transformation_of UBERON:0004883 ! lung mesenchyme property_value: UBPROP:0000009 "it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces" xsd:string [Term] id: UBERON:0000115 name: lung epithelium namespace: uberon def: "The epithelial layer of the lung." [MP:0006382] subset: pheno_slim synonym: "epithelial tissue of lung" EXACT [OBOL:automatic] synonym: "epithelium of lung" EXACT [OBOL:automatic] synonym: "lung epithelial tissue" EXACT [OBOL:automatic] synonym: "pulmonary epithelium" RELATED [BTO:0001653] xref: BTO:0001653 xref: EMAPA:32860 xref: MA:0001783 is_a: UBERON:0004815 ! lower respiratory tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002048 ! lung relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: develops_from UBERON:0001041 ! foregut relationship: part_of UBERON:0002048 ! lung property_value: UBPROP:0000008 "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]" xsd:string [Term] id: UBERON:0000117 name: respiratory tube namespace: uberon def: "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea." [GO:0030323, http://orcid.org/0000-0002-6601-2165] synonym: "airway" RELATED [] synonym: "respiratory conducting tube" NARROW [MP:0004391] synonym: "segment of tracheobronchial tree" EXACT [FMA:12224] synonym: "segment of tracheobronchial tree" NARROW [FMA:12224] synonym: "tracheobronchial tree segment" NARROW [FMA:12224] xref: EMAPA:37946 {source="MA:th"} xref: FMA:12224 is_a: UBERON:0000025 ! tube is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000025 ! tube intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: has_part UBERON:0000483 ! epithelium relationship: part_of UBERON:0000065 ! respiratory tract property_value: UBPROP:0000012 "in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)" xsd:string {external_ontology="GO"} [Term] id: UBERON:0000118 name: lung bud namespace: uberon def: "Structure derived from foregut that becomes a lung[GO]." [GO:0060431, Wikipedia:Respiratory_bud] subset: pheno_slim synonym: "gemma pulmonalis" RELATED LATIN [Wikipedia:Lung_buds] synonym: "gemma respiratoria" RELATED LATIN [Wikipedia:Lung_buds] synonym: "lung bud" RELATED PLURAL [] synonym: "primary lung bud" RELATED [GO:0060572] synonym: "respiratory diverticulum" RELATED [Wikipedia:Lung_buds] xref: BTO:0001643 xref: EHDAA2:0004089 xref: NCIT:C34260 xref: NCIT:C34282 xref: SCTID:361427007 xref: UMLS:C1514420 {source="ncithesaurus:Primary_Bronchial_Bud"} xref: UMLS:C1514897 {source="ncithesaurus:Respiratory_Diverticulum"} xref: Wikipedia:Respiratory_bud is_a: UBERON:0005153 {source="GO:0060441"} ! epithelial bud is_a: UBERON:0005911 ! endo-epithelium relationship: adjacent_to UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: develops_from UBERON:0005597 ! lung primordium relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png xsd:anyURI property_value: editor_note "clarify successors - include bronchi?" xsd:string [Term] id: UBERON:0000122 name: neuron projection bundle namespace: uberon alt_id: UBERON:0005163 def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 xref: FBbt:00005099 xref: NLX:147821 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection relationship: part_of UBERON:0001016 ! nervous system [Term] id: UBERON:0000153 name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body relationship: anterior_to UBERON:0000154 ! posterior region of body relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0000161 name: orifice namespace: uberon def: "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]." [FMA:3724] synonym: "anatomical orifice" EXACT [FMA:3724] synonym: "anatomical ostium" BROAD [FMA:3724] synonym: "hilum" NARROW [] synonym: "ostium" BROAD [] xref: FMA:3724 xref: SCTID:91837002 is_a: UBERON:0004111 ! anatomical conduit property_value: UBPROP:0000012 "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000165 name: mouth namespace: uberon def: "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, Wikipedia:Mouth] subset: efo_slim subset: major_organ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "adult mouth" NARROW [] synonym: "cavital oralis" RELATED LATIN [Wikipedia:Mouth] synonym: "cavitas oris" RELATED [BTO:0001090] synonym: "cavum oris" RELATED [BTO:0001090] synonym: "mouth cavity" RELATED [BTO:0001090] synonym: "oral region" RELATED [EHDAA2:0001326] synonym: "oral vestibule" RELATED [BTO:0001090] synonym: "regio oralis" EXACT [BTO:0004698] synonym: "regio oralis" EXACT LATIN [FMA:49184, FMA:TA] synonym: "rima oris" RELATED [BTO:0001090] synonym: "stoma" RELATED [] synonym: "stomatodaeum" RELATED [VHOG:0000812] synonym: "trophic apparatus" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "vestibule of mouth" RELATED [BTO:0001090] synonym: "vestibulum oris" RELATED [BTO:0001090] xref: AAO:0010355 xref: BTO:0001090 xref: BTO:0004698 xref: CALOHA:TS-1315 xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 xref: FBbt:00003126 xref: FMA:49184 xref: GAID:75 xref: galen:Mouth xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg xref: MA:0000341 xref: MA:0002474 xref: MAT:0000038 xref: MESH:D009055 xref: MIAA:0000038 xref: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA xref: SCTID:21082005 xref: TADS:0000040 xref: TAO:0000547 xref: TAO:0000590 xref: TGMA:0000131 xref: VHOG:0000280 xref: VHOG:0000812 xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract relationship: develops_from UBERON:0035804 ! future mouth relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000033 ! head relationship: proximalmost_part_of UBERON:0001555 ! digestive tract property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/issues/661 xsd:anyURI property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "oral" xsd:string property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000166 name: oral opening namespace: uberon def: "The orifice that connects the mouth to the exterior of the body." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract] subset: uberon_slim subset: vertebrate_core synonym: "mouth" RELATED INCONSISTENT [] synonym: "oral fissure" EXACT [FMA:59806] synonym: "oral orifice" EXACT [FMA:59806] synonym: "oral part of face" RELATED [] xref: FMA:59806 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000161 {source="FMA"} ! orifice relationship: part_of UBERON:0000165 ! mouth property_value: UBPROP:0000003 "(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000280", ontology="VHOG", source="DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000167 name: oral cavity namespace: uberon def: "Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)" [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, https://orcid.org/0000-0002-6601-2165, ISBN:0073040584] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "bucca" RELATED [] synonym: "buccal cavity" EXACT [FMA:20292, ISBN:0073040584] synonym: "cavity of mouth" EXACT [] xref: AAO:0000053 xref: AAO:0000960 xref: BSA:0000107 xref: CALOHA:TS-1315 xref: EFO:0001975 xref: EHDAA2:0001324 xref: EHDAA:6970 xref: EMAPA:17411 xref: EMAPA:18399 xref: EV:0100057 xref: FMA:20292 xref: HAO:0000669 xref: NCIT:C12421 xref: SCTID:181220002 xref: TAO:0001027 xref: TGMA:0000102 xref: UMLS:C0226896 {source="ncithesaurus:Oral_Cavity"} xref: VHOG:0000188 xref: WBbt:0005255 xref: XAO:0000126 xref: ZFA:0001027 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0000165 ! mouth relationship: contributes_to_morphology_of UBERON:0000165 ! mouth relationship: luminal_space_of UBERON:0000165 ! mouth relationship: part_of UBERON:0000165 ! mouth property_value: UBPROP:0000001 "Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000960", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/oral+cavity"} property_value: UBPROP:0000003 "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000170 name: pair of lungs namespace: uberon def: "The pair of anatomical structures comprised of a left lung and right lung." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "lungs" EXACT [] synonym: "lungs pair" EXACT [] synonym: "pulmones" EXACT LATIN [FMA:68877, FMA:TA] synonym: "set of lungs" EXACT [] xref: FMA:68877 xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: has_member UBERON:0002167 ! right lung intersection_of: has_member UBERON:0002168 ! left lung relationship: has_member UBERON:0002167 ! right lung relationship: has_member UBERON:0002167 {minCardinality="1", maxCardinality="1"} ! right lung relationship: has_member UBERON:0002168 ! left lung relationship: has_member UBERON:0002168 {minCardinality="1", maxCardinality="1"} ! left lung relationship: located_in UBERON:0002224 ! thoracic cavity relationship: part_of UBERON:0001558 {source="FMA-abduced"} ! lower respiratory tract [Term] id: UBERON:0000171 name: respiration organ namespace: uberon def: "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [GO:0007585] subset: functional_classification subset: organ_slim synonym: "apparatus respiratorius organ" EXACT [OBOL:automatic] synonym: "breathing organ" EXACT [] synonym: "gas exchange organ" RELATED [] synonym: "organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "organ of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory organ" EXACT [] synonym: "respiratory system organ" EXACT [OBOL:automatic] xref: EMAPA:17607 xref: SCTID:272626006 xref: SPD:0000428 xref: TGMA:0001247 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0000178 name: blood namespace: uberon def: "A fluid that is composed of blood plasma and erythrocytes." [FMA:9670, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/9, Wikipedia:Blood] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "portion of blood" EXACT [] synonym: "vertebrate blood" EXACT [] synonym: "whole blood" RELATED [BTO:0000089] xref: AAO:0000046 xref: BTO:0000089 xref: CALOHA:TS-0079 xref: EFO:0000296 xref: EHDAA2:0000176 xref: EHDAA:418 xref: EMAPA:16332 xref: ENVO:02000027 xref: EV:0100047 xref: FMA:9670 xref: GAID:965 xref: galen:Blood xref: MA:0000059 xref: MESH:D001769 xref: MIAA:0000315 xref: NCIT:C12434 xref: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA xref: TAO:0000007 xref: UMLS:C0005767 {source="ncithesaurus:Blood"} xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: develops_from UBERON:0006596 ! presumptive blood relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/tmeehan property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000179 name: haemolymphatic fluid namespace: uberon def: "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." [http://orcid.org/0000-0002-6601-2165] synonym: "blood or blood analog" RELATED [] synonym: "circulating fluid" RELATED [] xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system created_by: cjm creation_date: 2009-04-08T04:38:19Z [Term] id: UBERON:0000304 name: tendon sheath namespace: uberon def: "A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath" [Wikipedia:Tendon_sheath] synonym: "synovial tendon sheath" EXACT [FMA:45087] synonym: "vagina tendinis" RELATED LATIN [Wikipedia:Tendon_sheath] xref: BTO:0000051 xref: FMA:45087 xref: FMA:76715 xref: NCIT:C96299 xref: SCTID:361885006 xref: UMLS:C0224856 {source="ncithesaurus:Tendon_Sheath"} xref: Wikipedia:Tendon_sheath is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000043 ! tendon relationship: bounding_layer_of UBERON:0000043 ! tendon relationship: has_part UBERON:0011233 ! synovial membrane of synovial tendon sheath relationship: has_part UBERON:0011234 ! fibrous membrane of synovial tendon sheath relationship: part_of UBERON:0000043 ! tendon property_value: editor_note "TODO - add layer relations. 'tendon sheath' GAT in FMA." xsd:string [Term] id: UBERON:0000307 name: blastula namespace: uberon alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] synonym: "blastula embryo" EXACT [BILA:0000059] xref: BILA:0000059 xref: BTO:0000128 xref: GAID:1294 xref: MESH:A16.254.270.274 xref: OGEM:000006 xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg xref: Wikipedia:Blastula is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage relationship: develops_from UBERON:0007010 ! cleaving embryo relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png xsd:anyURI property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000328 name: gut wall namespace: uberon def: "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity)." [http://orcid.org/0000-0002-6601-2165] synonym: "digestive tract wall" EXACT [] synonym: "wall of alimentary tract" RELATED [] synonym: "wall of digestive tract" EXACT [] synonym: "wall of gut" EXACT [FMA:45653] xref: BTO:0000547 xref: FMA:45653 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000232 "We model the digestive tract as consisting of two parts: the wall and the lumen." xsd:string [Term] id: UBERON:0000332 name: yellow bone marrow namespace: uberon def: "bone marrow in which the fat cells predominate in the meshes of the reticular network." [http://medical-dictionary.thefreedictionary.com/Yellow+Marrow] synonym: "fat marrow" RELATED [BTO:0000635] synonym: "medulla ossium flava" EXACT LATIN [BTO:0000635] synonym: "yellow marrow" EXACT [BTO:0000635] xref: BTO:0000635 xref: FMA:74596 xref: SCTID:328639002 xref: SCTID:5023006 is_a: UBERON:0002371 ! bone marrow intersection_of: UBERON:0002371 ! bone marrow intersection_of: composed_primarily_of CL:0000136 ! fat cell relationship: composed_primarily_of CL:0000136 ! fat cell relationship: part_of UBERON:0007195 ! stroma of bone marrow [Term] id: UBERON:0000344 name: mucosa namespace: uberon def: "A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]" [Wikipedia:Mucous_membrane] subset: pheno_slim synonym: "mucosa of organ" EXACT [FMA:85355] synonym: "mucosa of organ part" EXACT [FMA:85358] synonym: "mucosal region" EXACT [FMA:85358] synonym: "mucous membrane" EXACT [FMA:85355] synonym: "organ mucosa" EXACT [FMA:85355] synonym: "region of mucosa" RELATED [FMA:85358] synonym: "tunica mucosa" RELATED LATIN [Wikipedia:Mucous_membrane] synonym: "tunica mucosa" RELATED [BTO:0000886] xref: AEO:0000199 xref: BTO:0000886 xref: CALOHA:TS-2031 xref: EHDAA2_RETIRED:0003234 xref: EV:0100382 xref: FMA:85355 xref: FMA:85358 xref: GAID:297 xref: galen:Mucosa xref: MESH:D009092 xref: NCIT:C13166 xref: OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA xref: SCTID:361693009 xref: UMLS:C0026724 {source="ncithesaurus:Mucosa"} xref: Wikipedia:Mucous_membrane is_a: UBERON:0004923 ! organ component layer relationship: has_part UBERON:0000483 ! epithelium relationship: has_part UBERON:0002384 ! connective tissue relationship: only_in_taxon NCBITaxon:7711 ! Chordata property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xsd:anyURI property_value: UBPROP:0000007 "mucosal" xsd:string property_value: UBPROP:0000012 "FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000355 name: pharyngeal mucosa namespace: uberon alt_id: UBERON:0003344 def: "A mucosa that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] synonym: "mucosa of organ of pharynx" EXACT [OBOL:automatic] synonym: "mucosa of pharynx" EXACT [OBOL:automatic] synonym: "mucous membrane of pharynx" EXACT [OBOL:automatic] synonym: "mucous membrane of pharynx" EXACT [FMA:55031] synonym: "mucous membrane of the pharynx" RELATED [BTO:0001047] synonym: "organ mucosa of pharynx" EXACT [OBOL:automatic] synonym: "pharynx mucosa" EXACT [OBOL:automatic] synonym: "pharynx mucosa of organ" EXACT [OBOL:automatic] synonym: "pharynx mucous membrane" EXACT [OBOL:automatic] synonym: "pharynx organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa pharyngea" EXACT LATIN [FMA:55031, FMA:TA] synonym: "tunica mucosa pharyngis" EXACT [] xref: BTO:0001047 xref: EMAPA:26957 xref: FMA:55031 xref: MA:0003143 xref: SCTID:362121003 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004785 ! respiratory system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx [Term] id: UBERON:0000361 name: red bone marrow namespace: uberon def: "The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream." [http://medical-dictionary.thefreedictionary.com/red+marrow] synonym: "medulla ossium rubra" EXACT LATIN [BTO:0001160] synonym: "parenchyma of none marrow marrow" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "parenchymal red marrow" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "red marrow" EXACT [BTO:0001160] xref: BTO:0001160 xref: FMA:74595 xref: SCTID:328538003 xref: SCTID:75330005 is_a: UBERON:0002371 ! bone marrow intersection_of: UBERON:0002371 ! bone marrow intersection_of: composed_primarily_of CL:0000988 ! hematopoietic cell relationship: composed_primarily_of CL:0000988 ! hematopoietic cell relationship: part_of UBERON:0012429 ! hematopoietic tissue [Term] id: UBERON:0000379 name: tracheal mucosa namespace: uberon def: "A mucosa that is part of a respiratory airway." [OBOL:automatic] synonym: "mucosa of organ of trachea" EXACT [OBOL:automatic] synonym: "mucosa of organ of windpipe" EXACT [OBOL:automatic] synonym: "mucosa of trachea" EXACT [OBOL:automatic] synonym: "mucosa of windpipe" EXACT [OBOL:automatic] synonym: "mucous membrane of trachea" EXACT [FMA:7471] synonym: "mucous membrane of trachea" EXACT [OBOL:automatic] synonym: "mucous membrane of windpipe" EXACT [OBOL:automatic] synonym: "organ mucosa of trachea" EXACT [OBOL:automatic] synonym: "organ mucosa of windpipe" EXACT [OBOL:automatic] synonym: "trachea mucosa" EXACT [OBOL:automatic] synonym: "trachea mucosa of organ" EXACT [OBOL:automatic] synonym: "trachea mucous membrane" EXACT [OBOL:automatic] synonym: "trachea organ mucosa" EXACT [OBOL:automatic] synonym: "tracheal mucous membrane" EXACT [FMA:7471] synonym: "tunica mucosa (tracheae)" EXACT [FMA:7471] synonym: "tunica mucosa tracheae" EXACT LATIN [FMA:7471, FMA:TA] synonym: "windpipe mucosa" EXACT [OBOL:automatic] synonym: "windpipe mucosa of organ" EXACT [OBOL:automatic] synonym: "windpipe mucous membrane" EXACT [OBOL:automatic] synonym: "windpipe organ mucosa" EXACT [OBOL:automatic] xref: BTO:0001390 xref: FMA:7471 xref: SCTID:660006 is_a: UBERON:0004785 ! respiratory system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001005 ! respiratory airway relationship: part_of UBERON:0001005 ! respiratory airway [Term] id: UBERON:0000383 name: musculature of body namespace: uberon def: "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]." [VSAO:0000033] subset: efo_slim subset: pheno_slim synonym: "muscle system" EXACT [] synonym: "muscle system of body" EXACT [] synonym: "muscular system" EXACT [FMA:72954] synonym: "musculature system" EXACT [BILA:0000088] synonym: "muskelsystem" RELATED [BTO:0001485] synonym: "set of all muscles" EXACT [FMA:72954] synonym: "set of muscles of body" EXACT [FMA:72954] synonym: "vertebrate muscular system" EXACT [BTO:0001369] xref: AAO:0000307 xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 xref: EMAPA:35578 xref: FBbt:00005069 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 xref: MIAA:0000025 xref: VSAO:0000033 xref: XAO:0004042 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: composed_primarily_of UBERON:0001015 ! musculature relationship: capable_of GO:0003012 ! muscle system process relationship: composed_primarily_of UBERON:0001015 ! musculature relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002204 ! musculoskeletal system property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} [Term] id: UBERON:0000389 name: lens cortex namespace: uberon def: "Tissue that surrounds the lens nucleus" [http://www.thefreedictionary.com/lens+cortex] synonym: "cortex of lens" EXACT [FMA:58970] xref: BTO:0001632 xref: CALOHA:TS-0542 xref: FMA:58970 xref: MESH:A09.371.509.225 xref: SCTID:280626006 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000479 ! tissue intersection_of: surrounds UBERON:0000390 ! lens nucleus relationship: develops_from UBERON:0005614 ! lens anterior epithelium relationship: part_of UBERON:0000965 ! lens of camera-type eye relationship: surrounds UBERON:0000390 ! lens nucleus [Term] id: UBERON:0000390 name: lens nucleus namespace: uberon def: "The core of the crystalline lens, surrounded by the cortex." [BTO:0001633] synonym: "nucleus of lens" EXACT [FMA:58971] xref: BTO:0001633 xref: FMA:58971 xref: MESH:A09.371.509.670 xref: SCTID:280628007 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: surrounded_by UBERON:0000389 ! lens cortex relationship: develops_from UBERON:0005614 ! lens anterior epithelium relationship: part_of UBERON:0000965 ! lens of camera-type eye relationship: surrounded_by UBERON:0000389 ! lens cortex [Term] id: UBERON:0000409 name: serous gland namespace: uberon def: "A gland in which the principal secretory cells are serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] subset: organ_slim subset: pheno_slim xref: BTO:0001837 xref: EMAPA:37950 {source="MA:th"} xref: FMA:62889 xref: Wikipedia:Serous_gland is_a: UBERON:0002365 ! exocrine gland intersection_of: UBERON:0002365 ! exocrine gland intersection_of: has_part CL:0000313 ! serous secreting cell relationship: has_part CL:0000313 ! serous secreting cell relationship: has_part UBERON:0013232 ! serous acinus relationship: produces UBERON:0007794 ! secretion of serous gland property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png xsd:anyURI property_value: UBPROP:0000001 "glands that secrete watery albuminous material that often contains enzymes[MP:0008052]." xsd:string {source="MP:0008052"} [Term] id: UBERON:0000415 name: artery wall namespace: uberon def: "An anatomical wall that is part of an artery [Automatically generated definition]." [OBOL:automatic] synonym: "arterial wall" EXACT [FMA:14155] synonym: "wall of artery" EXACT [FMA:14155] xref: BTO:0002009 xref: FMA:14155 xref: galen:ArterialWall is_a: UBERON:0035965 ! wall of blood vessel intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery [Term] id: UBERON:0000456 name: secretion of exocrine gland namespace: uberon alt_id: UBERON:0006540 def: "A portion of organism substance that is produced by exocrine glands." [http://orcid.org/0000-0002-6601-2165] synonym: "bodily secretion" EXACT [MESH:D012634] synonym: "exocrine gland fluid" RELATED [] synonym: "exocrine gland fluid or secretion" RELATED [] synonym: "exocrine gland fluid/secretion" EXACT [MA:0002504] synonym: "exocrine gland secretion" RELATED [] synonym: "external secretion" RELATED [BTO:0002977] synonym: "secreted substance" EXACT [] synonym: "secretion" BROAD [FMA:9675] xref: AEO:0001005 xref: BTO:0002977 xref: BTO:0002979 xref: EMAPA:36535 xref: FMA:9675 xref: galen:Secretion xref: MA:0002504 xref: MESH:D012634 xref: NCIT:C34062 xref: UMLS:C1516992 {source="ncithesaurus:Exocrine_Gland_Fluid_or_Secretion"} is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0002365 ! exocrine gland relationship: produced_by UBERON:0002365 ! exocrine gland property_value: UBPROP:0000012 "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0000463 name: organism substance namespace: uberon def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [http://orcid.org/0000-0001-9114-8737] subset: pheno_slim subset: upper_level synonym: "body fluid or substance" EXACT [MA:0002450] synonym: "body substance" EXACT [FMA:9669] synonym: "organism substance" EXACT [CARO:0000004] synonym: "portion of body substance" EXACT [FMA:9669] synonym: "portion of organism substance" EXACT [ZFA:0001487] xref: AAO:0010839 xref: AEO:0000004 xref: BILA:0000004 xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 xref: FBbt:00007019 xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 xref: MA:0002450 xref: NCIT:C13236 xref: SPD:0000008 xref: TAO:0001487 xref: TGMA:0001824 xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity relationship: has_quality PATO:0002198 ! quality of a substance relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism [Term] id: UBERON:0000464 name: anatomical space namespace: uberon def: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "anatomical spaces" RELATED PLURAL [ZFA:0001643] synonym: "lumen" BROAD [] synonym: "lumen space" EXACT [] synonym: "space" BROAD [] xref: AAO:0010110 xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 xref: FBbt:00007017 xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 xref: TAO:0001668 xref: TGMA:0001825 xref: UMLS:C0524461 {source="ncithesaurus:Lumen_Space"} xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity relationship: surrounded_by UBERON:0000061 ! anatomical structure [Term] id: UBERON:0000465 name: material anatomical entity namespace: uberon def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] 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: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000466 name: immaterial anatomical entity namespace: uberon def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] xref: AAO:0010265 xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity [Term] id: UBERON:0000467 name: anatomical system namespace: uberon def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011] subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "anatomical systems" RELATED PLURAL [ZFA:0001439] synonym: "body system" EXACT [BIRNLEX:14] synonym: "connected anatomical system" EXACT [CARO:0000011] synonym: "organ system" EXACT [] synonym: "system" BROAD [GO:0048731] xref: AAO:0000007 xref: AEO:0000011 xref: BILA:0000011 xref: BIRNLEX:14 xref: BSA:0000049 xref: CALOHA:TS-2088 xref: CARO:0000011 xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 xref: FBbt:00004856 xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 xref: MA:0000003 xref: NCIT:C12919 xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ xref: SCTID:278195005 xref: TAO:0001439 xref: TGMA:0001831 xref: UMLS:C0460002 {source="ncithesaurus:Organ_System"} xref: VHOG:0001725 xref: WBbt:0005746 xref: WBbt:0005763 xref: Wikipedia:Organ_system xref: XAO:0003002 xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 name: multicellular organism namespace: uberon def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://orcid.org/0000-0001-9114-8737, Wikipedia:Multi-cellular_organism] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "animal" NARROW [BTO:0000042] synonym: "body" RELATED [AEO:0000103, BIRNLEX:18, FMA:256135, NCIT:C13041] synonym: "Koerper" RELATED [BTO:0001489] synonym: "multi-cellular organism" EXACT [CARO:0000012] synonym: "organism" BROAD [FBbt:00000001, VHOG:0000671, WBbt:0007833] synonym: "whole body" RELATED [BTO:0001489] synonym: "whole organism" RELATED [FBbt:00000001] xref: AAO:0010026 xref: AEO:0000191 xref: BILA:0000012 xref: BIRNLEX:18 xref: BSA:0000038 xref: BTO:0000042 xref: CARO:0000012 xref: EFO:0002906 xref: EHDAA2:0003103 xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 xref: FBbt:00000001 xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 xref: NCIT:C13041 xref: ncithesaurus:Whole_Organism xref: SCTID:243928005 xref: TADS:0000001 xref: TAO:0001094 xref: TGMA:0001832 xref: VHOG:0000671 xref: WBbt:0007833 xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string property_value: UBPROP:0000007 "organismal" xsd:string [Term] id: UBERON:0000474 name: female reproductive system namespace: uberon def: "The organs and associated structures associated with bearing offspring in a female animal." [http://orcid.org/0000-0002-6601-2165, MP:0001119, Wikipedia:Female_genitalia] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "female genital system" RELATED [] synonym: "female genital tract" RELATED [] synonym: "female genitalia" RELATED [] synonym: "female genitals" RELATED PLURAL [XAO:0000156] synonym: "female organism genitalia" EXACT [OBOL:automatic] synonym: "female organism reproductive system" EXACT [OBOL:automatic] synonym: "female reproductive tract" RELATED [MA:0000381] synonym: "genitalia of female organism" EXACT [OBOL:automatic] synonym: "gynaecological tissue" RELATED [BTO:0000083] synonym: "reproductive system of female organism" EXACT [OBOL:automatic] synonym: "systema genitale femininum" RELATED [BTO:0000083] xref: BTO:0000083 xref: CALOHA:TS-1303 xref: EFO:0000969 xref: EHDAA2:0000506 xref: EHDAA:8116 xref: EMAPA:17959 xref: EV:0100110 xref: FBbt:00004864 xref: FMA:45663 xref: GAID:364 xref: HAO:0000324 xref: MA:0000381 xref: MESH:D005836 xref: MIAA:0000028 xref: NCIT:C12402 xref: OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA xref: SCTID:361386004 xref: TGMA:0000635 xref: UMLS:C0700038 {source="ncithesaurus:Female_Reproductive_System"} xref: VHOG:0000726 xref: Wikipedia:Female_genitalia xref: WikipediaCategory:Female_reproductive_system xref: XAO:0000156 is_a: UBERON:0000990 ! reproductive system intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0003100 ! female organism property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg xsd:anyURI property_value: UBPROP:0000003 "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000726", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} [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: 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: OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA xref: TAO:0001308 xref: TGMA:0001840 xref: UMLS:C0229962 {source="ncithesaurus:Body_Part"} xref: VHOG:0001758 xref: Wikipedia:Body_part xref: XAO:0003013 xref: ZFA:0001308 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000075 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! subdivision of skeletal system relationship: has_part UBERON:0034929 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! external soft tissue zone relationship: part_of UBERON:0000468 ! multicellular organism property_value: editor_note "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: 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 disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure [Term] id: UBERON:0000477 name: anatomical cluster namespace: uberon def: "Anatomical group that has its parts adjacent to one another." [http://orcid.org/0000-0001-9114-8737] subset: upper_level xref: AAO:0010009 xref: AEO:0000041 xref: BILA:0000041 xref: CARO:0000041 xref: EHDAA2:0003041 xref: FBbt:00007277 xref: FMA:49443 xref: HAO:0000041 xref: TADS:0000605 xref: TAO:0001478 xref: TGMA:0001842 xref: VHOG:0001737 xref: XAO:0003160 xref: ZFA:0001478 is_a: UBERON:0001062 ! anatomical entity property_value: editor_note "Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]" xsd:string [Term] id: UBERON:0000478 name: extraembryonic structure namespace: uberon 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." [CARO:DOS, http://orcid.org/0000-0001-9114-8737, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] comment: see also conceptus extraembryonic component in EHDAA2. subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "extra-embryonic structure" EXACT [] synonym: "extraembryonic structures" RELATED PLURAL [ZFA:0000020] synonym: "extraembryonic tissue" RELATED [] xref: AAO:0010020 xref: AEO:0000042 xref: BILA:0000042 xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 xref: FBbt:00005835 xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 xref: SCTID:314908006 xref: TAO:0000020 xref: TGMA:0001843 xref: UMLS:C1282438 {source="ncithesaurus:Extraembryonic_Structure"} xref: VHOG:0000292 xref: XAO:0004005 xref: ZFA:0000020 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0016887 ! entire extraembryonic component relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0016887 ! entire extraembryonic component [Term] id: UBERON:0000479 name: tissue namespace: uberon 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." [CARO:0000043] subset: pheno_slim subset: upper_level synonym: "portion of tissue" EXACT [CARO:0000043] synonym: "simple tissue" NARROW [AEO:0000043] synonym: "tissue portion" EXACT [] xref: AAO:0000607 xref: AAO:0010054 xref: AEO:0000043 xref: BILA:0000043 xref: BIRNLEX:19 xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 xref: FBbt:00007003 xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 xref: MA:0003002 xref: MESH:D014024 xref: NCIT:C12801 xref: TAO:0001477 xref: TGMA:0001844 xref: UMLS:C0040300 {source="ncithesaurus:Tissue"} xref: VHOG:0001757 xref: WBbt:0005729 xref: XAO:0003040 xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism property_value: editor_note "changed label and definition to reflect CARO2" xsd:string [Term] id: UBERON:0000481 name: multi-tissue structure namespace: uberon def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [CARO:0000055, http://orcid.org/0000-0001-9114-8737] subset: upper_level synonym: "multi-tissue structures" RELATED PLURAL [ZFA:0001488] xref: AAO:0010048 xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 xref: FBbt:00007010 xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 xref: VHOG:0001762 xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue relationship: part_of NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0000483 name: epithelium namespace: uberon def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Epithelium] comment: Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "epithelial tissue" EXACT [] synonym: "portion of epithelium" EXACT [FMA:9639] xref: AAO:0000144 xref: AAO:0010055 xref: AEO:0000066 xref: BILA:0000066 xref: BTO:0000416 xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 xref: FBbt:00007005 xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 xref: MA:0003060 xref: MESH:D004848 xref: NCIT:C12710 xref: SCTID:31610004 xref: TAO:0001486 xref: UMLS:C0014609 {source="ncithesaurus:Epithelium"} xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of CL:0000066 ! epithelial cell union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium relationship: composed_primarily_of CL:0000066 ! epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depicted:by Tkanka:nablonkowa.png xsd:anyURI property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "epithelial" xsd:string [Term] id: UBERON:0000484 name: simple cuboidal epithelium namespace: uberon def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_cuboidal_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "epithelium simplex cuboideum" EXACT [] synonym: "simple cuboidal epithelia" RELATED PLURAL [ZFA:0001497] xref: AAO:0010064 xref: AEO:0000067 xref: BILA:0000067 xref: CARO:0000067 xref: EHDAA2:0003067 xref: FMA:45566 xref: HAO:0000067 xref: NCIT:C33553 xref: TAO:0001497 xref: UMLS:C0836134 {source="ncithesaurus:Simple_Cuboidal_Epithelium"} xref: Wikipedia:Simple_cuboidal_epithelium xref: XAO:0004009 xref: ZFA:0001497 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0010077 ! cuboidal epithelium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png xsd:anyURI property_value: editor_note "needs to be synchronized with CL - there is no distinct cuboidal cell in CL" xsd:string [Term] id: UBERON:0000485 name: simple columnar epithelium namespace: uberon def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [FMA:FMA, http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_columnar_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "columnar epithelium" BROAD [EHDAA2:0003068] synonym: "columnar epithlium" BROAD [AEO:0000068] synonym: "epithelium simplex columnare" EXACT [] synonym: "simple columnar epithelia" RELATED PLURAL [ZFA:0001496] synonym: "simple columnar epithelium" EXACT [] xref: AAO:0010063 xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 xref: FBbt:00007027 xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 xref: SCTID:32210007 xref: TAO:0001496 xref: UMLS:C0836135 {source="ncithesaurus:Simple_Columnar_Epithelium"} xref: Wikipedia:Simple_columnar_epithelium xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png xsd:anyURI [Term] id: UBERON:0000486 name: multilaminar epithelium namespace: uberon def: "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]" [FMA:FMA, http://orcid.org/0000-0001-9114-8737, Wikipedia:Stratified_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "laminated epithelium" RELATED [BTO:0002074] synonym: "stratified epithelium" EXACT [] xref: AAO:0010059 xref: AEO:0000069 xref: BILA:0000069 xref: BTO:0002074 xref: CARO:0000069 xref: EHDAA2:0003069 xref: FMA:45562 xref: HAO:0000069 xref: NCIT:C33622 xref: SCTID:309044005 xref: TAO:0001494 xref: UMLS:C0682575 {source="ncithesaurus:Stratified_Epithelium"} xref: Wikipedia:Stratified_epithelium xref: XAO:0004006 xref: ZFA:0001494 is_a: UBERON:0000483 ! epithelium property_value: UBPROP:0000001 "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="FMA:45562", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000487 name: simple squamous epithelium namespace: uberon def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [FMA:45565, http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_squamous_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "epithelium simplex squamosum" EXACT [] synonym: "simple squamous epithelia" RELATED PLURAL [ZFA:0001498] xref: AAO:0010066 xref: AEO:0000070 xref: BILA:0000070 xref: BTO:0002073 xref: CARO:0000070 xref: EHDAA2:0003070 xref: FMA:45565 xref: HAO:0000070 xref: NCIT:C13178 xref: TAO:0001498 xref: UMLS:C0836133 {source="ncithesaurus:Simple_Squamous_Epithelium"} xref: Wikipedia:Simple_squamous_epithelium xref: XAO:0004010 xref: ZFA:0001498 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell property_value: depicted:by Illu:epithelium.jpg xsd:anyURI property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000488 name: atypical epithelium namespace: uberon def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core synonym: "atypical epithelia" RELATED PLURAL [ZFA:0001493] synonym: "heterogenous epithelium" EXACT [] xref: AAO:0010057 xref: AEO:0000071 xref: BILA:0000071 xref: CARO:0000071 xref: EHDAA2:0003071 xref: FMA:61741 xref: HAO:0000071 xref: TAO:0001493 xref: XAO:0004004 xref: ZFA:0001493 is_a: UBERON:0000483 ! epithelium [Term] id: UBERON:0000489 name: cavitated compound organ namespace: uberon def: "Compound organ that contains one or more macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] subset: organ_slim subset: upper_level synonym: "cavitated compound organs" RELATED PLURAL [ZFA:0001490] synonym: "cavitated organ" EXACT [FMA:55671] xref: AAO:0010016 xref: AEO:0000072 xref: BILA:0000072 xref: CARO:0000072 xref: EHDAA2:0003072 xref: FMA:55671 xref: HAO:0000072 xref: TAO:0001490 xref: TGMA:0001857 xref: VHOG:0001730 xref: XAO:0003165 xref: ZFA:0001490 is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000490 name: unilaminar epithelium namespace: uberon def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [FMA:45561, http://orcid.org/0000-0001-9114-8737] subset: vertebrate_core synonym: "simple epithelium" EXACT [FMA:45561] synonym: "unilaminar epithelia" RELATED PLURAL [ZFA:0001495] xref: AAO:0010062 xref: AEO:0000073 xref: BILA:0000073 xref: BTO:0002073 xref: CARO:0000073 xref: EHDAA2:0003073 xref: FMA:45561 xref: HAO:0000073 xref: NCIT:C33554 xref: SCTID:309043004 xref: TAO:0001495 xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000915 name: thoracic segment of trunk namespace: uberon def: "Subdivision of trunk that lies between the head and the abdomen." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "anterior subdivision of trunk" RELATED [] synonym: "thorax" EXACT [MA:0000022] synonym: "upper body" RELATED [] synonym: "upper trunk" RELATED [FMA:259209] xref: EMAPA:35862 xref: FMA:259209 xref: MA:0000022 xref: SCTID:302551006 xref: Wikipedia:Thorax is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton relationship: has_skeleton UBERON:0014477 ! thoracic skeleton property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string [Term] id: UBERON:0000916 name: abdomen namespace: uberon def: "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "abdominopelvic region" EXACT [FMA:9577] synonym: "abdominopelvis" EXACT [FMA:9577] synonym: "adult abdomen" RELATED [] synonym: "belly" RELATED [] synonym: "celiac region" RELATED [] xref: BTO:0000020 xref: CALOHA:TS-0001 xref: EFO:0000968 xref: EMAPA:35102 xref: EV:0100011 xref: FMA:9577 xref: GAID:16 xref: galen:Abdomen xref: MA:0000029 xref: MAT:0000298 xref: MESH:A01.047 xref: MIAA:0000298 xref: OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk property_value: editor_note "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string property_value: UBPROP:0000007 "abdominal" xsd:string property_value: UBPROP:0000007 "celiac" xsd:string [Term] id: UBERON:0000922 name: embryo namespace: uberon 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." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "developing organism" RELATED [BILA:0000056] synonym: "developmental tissue" RELATED [] synonym: "embryonic organism" EXACT [BILA:0000056] xref: AAO:0011035 xref: AEO:0000169 xref: BILA:0000056 xref: BSA:0000039 xref: BTO:0000379 xref: CALOHA:TS-0229 xref: EFO:0001367 xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 xref: FBbt:00000052 xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 xref: NCIT:C28147 xref: OGEM:000001 xref: OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA xref: SCTID:57991002 xref: UMLS:C0013935 {source="ncithesaurus:Embryo"} xref: VHOG:0001766 xref: Wikipedia:Embryo xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_ends_with UBERON:0000068 ! embryo stage intersection_of: existence_starts_with UBERON:0000068 ! embryo stage relationship: existence_ends_with UBERON:0000068 ! embryo stage relationship: existence_starts_with UBERON:0000068 ! embryo stage property_value: depicted:by Wrinkledfrog:embryos.jpg xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/issues/503 xsd:anyURI property_value: UBPROP:0000007 "embryonic" xsd:string property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 name: germ layer namespace: uberon def: "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [https://github.com/obophenotype/uberon/issues/203, Wikipedia:Germ_layer] comment: Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] subset: uberon_slim subset: vertebrate_core synonym: "embryonic germ layer" RELATED [] synonym: "embryonic germ layers" RELATED [] synonym: "embryonic tissue" BROAD [FMA:69069] synonym: "germinal layer" EXACT [ncithesaurus:Germinal_Layer] synonym: "primary germ layer" NARROW [GO:0001704, ZFA:0001122] xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 xref: FBbt:00000110 xref: FMA:69069 xref: GAID:1303 xref: MESH:A16.254.425 xref: NCIT:C12950 xref: NCIT:C54105 xref: TAO:0001122 xref: UMLS:C0920502 {source="ncithesaurus:Embryonic_Tissue"} xref: UMLS:C1708239 {source="ncithesaurus:Germinal_Layer"} xref: VHOG:0001223 xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000924 name: ectoderm namespace: uberon def: "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [Wikipedia:Ectoderm] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "embryonic ectoderm" EXACT [VHOG:0000153] xref: AAO:0000137 xref: BILA:0000036 xref: BTO:0000315 xref: CALOHA:TS-0216 xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 xref: FBbt:00000111 xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 xref: MAT:0000173 xref: MESH:A16.254.425.273 xref: MIAA:0000173 xref: NCIT:C12703 xref: SCTID:362851007 xref: TAO:0000016 xref: UMLS:C0013574 {source="ncithesaurus:Ectoderm"} xref: VHOG:0000153 xref: Wikipedia:Ectoderm xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: develops_from UBERON:0006601 ! presumptive ectoderm relationship: has_part CL:0000221 ! ectodermal cell relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png xsd:anyURI property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "ectodermal" xsd:string [Term] id: UBERON:0000925 name: endoderm namespace: uberon def: "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [Wikipedia:Endoderm] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "entoderm" RELATED DEPRECATED [DOI:10.5962/bhl.title.1013] xref: AAO:0000139 xref: BILA:0000038 xref: BTO:0000800 xref: CALOHA:TS-0273 xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 xref: FBbt:00000125 xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 xref: MESH:A16.254.425.407 xref: MIAA:0000175 xref: NCIT:C12706 xref: SCTID:362855003 xref: TAO:0000017 xref: UMLS:C0014144 {source="ncithesaurus:Endoderm"} xref: VHOG:0000154 xref: Wikipedia:Endoderm xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: develops_from UBERON:0006595 ! presumptive endoderm relationship: has_part CL:0000223 ! endodermal cell relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png xsd:anyURI property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "endodermal" xsd:string [Term] id: UBERON:0000926 name: mesoderm namespace: uberon alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "embryonic mesoderm" RELATED [VHOG:0000152] synonym: "entire mesoderm" RELATED [https://orcid.org/0000-0002-6601-2165, SCTID:362854004] synonym: "mesodermal mantle" RELATED [] xref: AAO:0000304 xref: BILA:0000037 xref: BTO:0000839 xref: CALOHA:TS-0623 xref: EFO:0001981 xref: EHDAA2:0001128 xref: EHDAA:124 xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 xref: FBbt:00000126 xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 xref: MESH:A16.254.425.660 xref: MIAA:0000174 xref: NCIT:C12750 xref: SCTID:362854004 xref: TAO:0000041 xref: UMLS:C0025485 {source="ncithesaurus:Mesoderm"} xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer relationship: develops_from UBERON:0006603 ! presumptive mesoderm relationship: has_part CL:0000222 ! mesodermal cell relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "mesodermal" xsd:string property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} [Term] id: UBERON:0000930 name: stomodeum namespace: uberon def: "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/326, Wikipedia:Stomodeum] subset: grouping_class subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "mouth pit" RELATED [EMAPA:16263] synonym: "mouth primordium" EXACT [XAO:0000269] synonym: "oral ectoderm" RELATED [ZFA:0001290, ZFIN:ZDB-PUB-100726-23] synonym: "oral pit" RELATED [EMAPA:16263] synonym: "primitive oral cavity" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "stomatodeum" EXACT [Wikipedia:Stomodeum] synonym: "stomodaeum" EXACT [] synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 xref: FBbt:00000439 xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 xref: TGMA:0000135 xref: UMLS:C1514977 {source="ncithesaurus:Stomodeum"} xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0013522 ! subdivision of tube relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png xsd:anyURI property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} property_value: UBPROP:0000007 "stomodeal" xsd:string property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string [Term] id: UBERON:0000947 name: aorta namespace: uberon def: "The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation" [http://orcid.org/0000-0002-6601-2165, ISBN:0-683-40008-8, MESH:A07.231.114.056, MP:0000272, Wikipedia:Aorta] subset: efo_slim subset: grouping_class subset: pheno_slim subset: uberon_slim synonym: "arteria maxima" RELATED LATIN [Wikipedia:Aorta] synonym: "dorsal aorta" NARROW SENSU [Wikipedia:Aorta#In_other_animals, ZFA:0000014] synonym: "trunk of aortic tree" EXACT [] synonym: "trunk of systemic arterial tree" EXACT [] xref: AAO:0010213 xref: BTO:0000135 xref: CALOHA:TS-0046 xref: EFO:0000265 xref: EMAPA:18601 xref: EV:0100027 xref: FMA:3734 xref: GAID:469 xref: galen:Aorta xref: MA:0000062 xref: MAT:0000035 xref: MESH:D001011 xref: MIAA:0000035 xref: NCIT:C12669 xref: OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA xref: SCTID:181298001 xref: UMLS:C0003483 {source="ncithesaurus:Aorta"} xref: VHOG:0001523 xref: Wikipedia:Aorta xref: XAO:0003010 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel is_a: UBERON:0003519 ! thoracic cavity blood vessel is_a: UBERON:0013768 ! great vessel of heart relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system property_value: depicted:by Aorta:scheme.jpg xsd:anyURI property_value: editor_note "This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae." xsd:string {source="WP"} property_value: UBPROP:0000001 "The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010213", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001523", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "aortic" xsd:string property_value: UBPROP:0000008 "All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches" xsd:string [Term] id: UBERON:0000948 name: heart namespace: uberon def: "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Heart] comment: Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "branchial heart" NARROW SENSU [] synonym: "cardium" RELATED [EMAPA:16105] synonym: "chambered heart" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "vertebrate heart" EXACT [] xref: AAO:0010210 xref: BILA:0000020 xref: BTO:0000562 xref: CALOHA:TS-0445 xref: EFO:0000815 xref: EHDAA2:0000738 xref: EHDAA:420 xref: EMAPA:16105 xref: EV:0100018 xref: FMA:7088 xref: GAID:174 xref: galen:Heart xref: MA:0000072 xref: MAT:0000036 xref: MESH:D006321 xref: MIAA:0000036 xref: NCIT:C12727 xref: OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA xref: SCTID:302509004 xref: TAO:0000114 xref: UMLS:C0018787 {source="ncithesaurus:Heart"} xref: VHOG:0000276 xref: Wikipedia:Heart xref: XAO:0000064 xref: ZFA:0000114 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "cardiac" xsd:string [Term] id: UBERON:0000949 name: endocrine system namespace: uberon def: "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity." [NLM:endocrine+system, Wikipedia:Endocrine_system] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "endocrine glandular system" EXACT [EHDAA2:0002224] synonym: "endocrine system" EXACT [] synonym: "systema endocrinum" EXACT [] xref: AAO:0010279 xref: CALOHA:TS-1301 xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 xref: FBbt:00005068 xref: FMA:9668 xref: GAID:439 xref: MA:0000012 xref: MESH:D004703 xref: NCIT:C12705 xref: SCTID:278876000 xref: TAO:0001158 xref: UMLS:C0014136 {source="ncithesaurus:Endocrine_System"} xref: VHOG:0000098 xref: Wikipedia:Endocrine_system xref: XAO:0000158 xref: ZFA:0001158 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0050886 ! endocrine process disjoint_from: UBERON:0000990 ! reproductive system disjoint_from: UBERON:0001004 ! respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050886 ! endocrine process relationship: composed_primarily_of UBERON:0002368 ! endocrine gland relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: UBPROP:0000001 "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010279", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000098", ontology="VHOG", source="DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "endocrine" xsd:string [Term] id: UBERON:0000955 name: brain namespace: uberon def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Brain] subset: cumbo subset: efo_slim subset: major_organ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "encephalon" RELATED [BTO:0000142] synonym: "suprasegmental levels of nervous system" RELATED [NeuroNames:21] synonym: "suprasegmental structures" RELATED [NeuroNames:21] synonym: "synganglion" RELATED [] synonym: "the brain" RELATED [NeuroNames:21] xref: AAO:0010478 xref: ABA:Brain xref: BAMS:Br xref: BAMS:Brain xref: BILA:0000135 xref: BIRNLEX:796 xref: BTO:0000142 xref: CALOHA:TS-0095 xref: DHBA:10155 xref: EFO:0000302 xref: EHDAA2:0000183 xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 xref: FBbt:00005095 xref: FMA:50801 xref: GAID:571 xref: galen:Brain xref: HBA:4005 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 {source="BIRNLEX:796"} xref: MA:0000168 xref: MAT:0000098 xref: MBA:8 xref: MBA:997 xref: MESH:D001921 xref: MIAA:0000098 xref: NCIT:C12439 xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA xref: PBA:3999 xref: SCTID:258335003 xref: TAO:0000008 xref: UMLS:C0006104 {source="ncithesaurus:Brain"} xref: UMLS:C0006104 {source="BIRNLEX:796"} xref: UMLS:C1269537 {source="BIRNLEX:796"} xref: VHOG:0000157 xref: Wikipedia:Brain xref: XAO:0000010 xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: composed_primarily_of CL:0002319 ! neural cell relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! neural tube relationship: develops_from UBERON:0006238 ! future brain relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system property_value: editor_note "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000957 name: lamina namespace: uberon def: "Any thin layer or plate." [Wikipedia:Lamina_of_the_vertebral_arch] subset: non_informative subset: uberon_slim subset: upper_level synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: has_quality PATO:0002124 ! laminar relationship: has_quality PATO:0002124 ! laminar property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png xsd:anyURI property_value: editor_note "TODO - merge with cell layer?" xsd:string property_value: UBPROP:0000007 "laminar" xsd:string [Term] id: UBERON:0000964 name: cornea namespace: uberon def: "the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure" [ISBN:0-683-40008-8, MESH:A09.371.060.217, MP:0001312] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cornea of camera-type eye" EXACT [GO:0061303] synonym: "corneas" RELATED PLURAL [ZFA:0000640] synonym: "tunica cornea" RELATED [] xref: AAO:0010344 xref: BTO:0000286 xref: CALOHA:TS-0171 xref: EFO:0000377 xref: EHDAA2:0000316 xref: EHDAA:10199 xref: EMAPA:17161 xref: EV:0100341 xref: FMA:58238 xref: GAID:892 xref: MA:0000266 xref: MESH:D003315 xref: NCIT:C12342 xref: OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA xref: SCTID:181162001 xref: TAO:0000640 xref: UMLS:C0010031 {source="ncithesaurus:Cornea"} xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0003102 {source="XAO"} ! surface structure is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: continuous_with UBERON:0001773 ! sclera relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle relationship: develops_from UBERON:0004348 {evidence="definitional"} ! optic eminence relationship: develops_from UBERON:0005427 ! corneal primordium relationship: has_part UBERON:0001772 ! corneal epithelium relationship: has_part UBERON:0004370 ! anterior limiting lamina of cornea relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0012430 {source="FMA-isa"} ! tunica fibrosa of eyeball property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: UBPROP:0000007 "corneal" xsd:string property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" xsd:string [Term] id: UBERON:0000965 name: lens of camera-type eye namespace: uberon def: "Transparent part of camera-type eye that helps to refract light to be focused on the retina." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Lens_(anatomy)] comment: The lens is avascular and nourished by diffusion from the aqueous and vitreous subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "camera-type eye lens" EXACT [GO:0002088] synonym: "crystalline lens" RELATED [BTO:0000723] synonym: "eye lens" EXACT SENSU [] synonym: "lens" EXACT SENSU [] synonym: "lens crystallina" EXACT [Wikipedia:Lens_(anatomy)] synonym: "lenses" RELATED PLURAL [ZFA:0000035] synonym: "ocular lens" RELATED [BTO:0000723] xref: AAO:0010348 xref: BTO:0000723 xref: CALOHA:TS-0545 xref: EHDAA:9057 xref: EMAPA:17838 xref: EV:0100343 xref: FMA:58241 xref: MA:0000275 xref: MAT:0000141 xref: MESH:A09.371.509 xref: MIAA:0000141 xref: NCIT:C12743 xref: OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0000975 xref: SCTID:181169005 xref: TAO:0000035 xref: UMLS:C0023317 {source="ncithesaurus:Crystalline_Lens"} xref: VHOG:0000169 xref: Wikipedia:Lens_(anatomy) xref: XAO:0000008 xref: ZFA:0000035 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005389 ! transparent eye structure relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: developmentally_induced_by UBERON:0003902 ! retinal neural layer relationship: develops_from UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000169", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "This class excludes compound eye corneal lenses." xsd:string [Term] id: UBERON:0000966 name: retina namespace: uberon def: "The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [Wikipedia:Retina, ZFIN:curator] comment: Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "inner layer of eyeball" EXACT [] synonym: "Netzhaut" RELATED [BTO:0001175] synonym: "retina of camera-type eye" EXACT [GO:0060041] synonym: "retinas" RELATED PLURAL [ZFA:0000152] synonym: "tunica interna of eyeball" EXACT [] xref: AAO:0010352 xref: BAMS:R xref: BIRNLEX:1153 xref: BTO:0001175 xref: CALOHA:TS-0865 xref: EFO:0000832 xref: EHDAA2:0001627 xref: EHDAA:4757 xref: EMAPA:17168 xref: EV:0100348 xref: FMA:58301 xref: GAID:755 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1862 xref: MA:0000276 xref: MAT:0000142 xref: MBA:304325711 xref: MESH:D012160 xref: MIAA:0000142 xref: NCIT:C12343 xref: NIFSTD_RETIRED:birnlex_1156 xref: OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA xref: SCTID:181171005 xref: TAO:0000152 xref: UMLS:C0035298 {source="BIRNLEX:1153"} xref: UMLS:C0035298 {source="ncithesaurus:Retina"} xref: UMLS:C1278894 {source="BIRNLEX:1153"} xref: VHOG:0000229 xref: Wikipedia:Retina xref: XAO:0000009 xref: ZFA:0000152 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005388 ! photoreceptor array relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: has_part CL:0000573 {source="FMA"} ! retinal cone cell relationship: has_part CL:0000604 {source="FMA"} ! retinal rod cell relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png xsd:anyURI property_value: RO:0002161 NCBITaxon:6656 property_value: UBPROP:0000001 "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000152", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000229", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "retinal" xsd:string [Term] id: UBERON:0000970 name: eye namespace: uberon def: "An organ that detects light." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: functional_classification subset: major_organ subset: organ_slim subset: uberon_slim synonym: "light-detecting organ" RELATED [] synonym: "visual apparatus" RELATED [EV:0100336] xref: BILA:0000017 xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 xref: FBbt:00005162 xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 xref: MIAA:0000140 xref: OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA xref: Wikipedia:Eye is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000020 ! sense organ relationship: capable_of GO:0009584 ! detection of visible light relationship: has_part CL:0000149 {source="PMID:21062451"} ! visual pigment cell relationship: has_part CL:0000210 {source="PMID:21062451"} ! photoreceptor cell relationship: part_of UBERON:0002104 ! visual system property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string property_value: UBPROP:0000007 "ocular" xsd:string property_value: UBPROP:0000007 "optic" xsd:string property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string [Term] id: UBERON:0000974 name: neck namespace: uberon def: "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "collum" RELATED LATIN [Wikipedia:Neck] synonym: "neck (volume)" RELATED [FMA:7155] xref: AEO:0000108 xref: BTO:0000420 xref: CALOHA:TS-2045 xref: EFO:0000967 xref: EHDAA2:0003108 xref: EMAPA:35587 xref: FMA:7155 xref: GAID:86 xref: galen:Neck xref: MA:0000024 xref: MAT:0000297 xref: MESH:D009333 xref: MIAA:0000297 xref: NCIT:C13063 xref: OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA xref: SCTID:302550007 xref: UMLS:C0027530 {source="ncithesaurus:Neck"} xref: Wikipedia:Neck is_a: UBERON:0000475 ! organism subdivision relationship: anteriorly_connected_to UBERON:0000033 ! head relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0007811 ! craniocervical region relationship: posteriorly_connected_to UBERON:0002100 ! trunk property_value: depicted:by Female:neck.jpg xsd:anyURI property_value: IAO:0000232 "true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck." xsd:string property_value: RO:0002174 NCBITaxon:32443 {source="ISBN:9780674021839"} property_value: UBPROP:0000007 "cervical" xsd:string [Term] id: UBERON:0000982 name: skeletal joint namespace: uberon def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000101, Wikipedia:Joint] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "articular joint" RELATED [BTO:0001686] synonym: "articulation" BROAD [VSAO:0000101] synonym: "joint" BROAD [FMA:7490, VSAO:0000101] synonym: "joints" RELATED PLURAL [ZFA:0001596] xref: AEO:0000182 xref: BTO:0001686 xref: CALOHA:TS-2023 xref: EFO:0000948 xref: EMAPA:35456 xref: FMA:7490 xref: GAID:102 xref: galen:Joint xref: MA:0000319 xref: MAT:0000188 xref: MESH:D007596 xref: MIAA:0000188 xref: NCIT:C13044 xref: OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0003182 xref: SCTID:302536002 xref: TAO:0000367 xref: UMLS:C0022417 {source="ncithesaurus:Joint"} xref: VHOG:0001276 xref: VSAO:0000101 xref: Wikipedia:Joint xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation union_of: UBERON:0002217 ! synovial joint union_of: UBERON:0011134 ! nonsynovial joint disjoint_from: UBERON:0001474 ! bone element relationship: connects UBERON:0004765 ! skeletal element relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} [Term] id: UBERON:0000990 name: reproductive system namespace: uberon def: "Anatomical system that has as its parts the organs concerned with reproduction." [Wikipedia:Reproductive_system] subset: efo_slim subset: functional_classification subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "animal reproductive system" RELATED [BTO:0000081] synonym: "genital system" RELATED [] synonym: "genital tract" RELATED [] synonym: "genitalia" RELATED PLURAL [] synonym: "Geschlechtsorgan" RELATED [BTO:0000081] synonym: "organa genitalia" RELATED [BTO:0000081] synonym: "reproductive tissue" RELATED [BTO:0000081] synonym: "reproductive tract" RELATED [] synonym: "systemata genitalia" RELATED LATIN [Wikipedia:Reproductive_system] xref: AAO:0010258 xref: BILA:0000103 xref: BTO:0000081 xref: CALOHA:TS-1318 xref: EFO:0000809 xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 xref: FBbt:00004857 xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 xref: HAO:0000895 xref: MA:0000326 xref: MIAA:0000305 xref: NCIT:C12841 xref: OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA xref: SCTID:278875001 xref: TAO:0000632 xref: UMLS:C1261210 {source="ncithesaurus:Reproductive_System"} xref: VHOG:0000182 xref: WBbt:0005747 xref: Wikipedia:Reproductive_system xref: XAO:0000142 xref: ZFA:0000632 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of_part_of GO:0000003 ! reproduction disjoint_from: UBERON:0001004 ! respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0000003 ! reproduction relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000991 ! gonad property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg xsd:anyURI property_value: editor_note "consider splitting genitalia from reproductive system" xsd:string property_value: UBPROP:0000001 "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010258", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000182", ontology="VHOG", source="PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000202 FMA:75572 [Term] id: UBERON:0000991 name: gonad namespace: uberon def: "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." [ISBN:0140512888, Wikipedia:Gonad, ZFA:0000413, ZFIN:curator] subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gonada" EXACT [] synonym: "gonads" RELATED PLURAL [ZFA:0000413] xref: AAO:0000213 xref: BILA:0000123 xref: BSA:0000079 xref: BTO:0000534 xref: EMAPA:17383 xref: FBbt:00004858 xref: FMA:18250 xref: GAID:368 xref: HAO:0000379 xref: MA:0002420 xref: MESH:D006066 xref: NCIT:C12725 xref: OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA xref: SCTID:304623008 xref: TAO:0000413 xref: UMLS:C0018067 {source="ncithesaurus:Gonad"} xref: VHOG:0000397 xref: WBbt:0005175 xref: Wikipedia:Gonad xref: XAO:0003146 xref: ZFA:0000413 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: has_part CL:0000586 ! germ cell relationship: contains_process GO:0007276 ! gamete generation relationship: develops_from UBERON:0005564 ! gonad primordium relationship: has_part CL:0000586 ! germ cell property_value: UBPROP:0000001 "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000213", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000413", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000397", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "gonadal" xsd:string property_value: UBPROP:0000012 "FMA xref is a 'general anatomical term'" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000992 name: ovary namespace: uberon def: "the gonad of a female organism which contains germ cells" [ISBN:0-683-40008-8, MP:0001126, Wikipedia:Ovary] subset: efo_slim subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "animal ovary" EXACT [EFO:0000973] synonym: "female gonad" EXACT [] synonym: "female organism genitalia gonad" EXACT [OBOL:automatic] synonym: "female organism genitalia gonada" EXACT [OBOL:automatic] synonym: "female organism reproductive system gonad" EXACT [OBOL:automatic] synonym: "female organism reproductive system gonada" EXACT [OBOL:automatic] synonym: "female reproductive system gonad" EXACT [OBOL:automatic] synonym: "female reproductive system gonada" EXACT [OBOL:automatic] synonym: "genitalia of female organism gonad" EXACT [OBOL:automatic] synonym: "genitalia of female organism gonada" EXACT [OBOL:automatic] synonym: "gonad of female organism genitalia" EXACT [OBOL:automatic] synonym: "gonad of female organism reproductive system" EXACT [OBOL:automatic] synonym: "gonad of female reproductive system" EXACT [OBOL:automatic] synonym: "gonad of genitalia of female organism" EXACT [OBOL:automatic] synonym: "gonad of reproductive system of female organism" EXACT [OBOL:automatic] synonym: "gonada of female organism genitalia" EXACT [OBOL:automatic] synonym: "gonada of female organism reproductive system" EXACT [OBOL:automatic] synonym: "gonada of female reproductive system" EXACT [OBOL:automatic] synonym: "gonada of genitalia of female organism" EXACT [OBOL:automatic] synonym: "gonada of reproductive system of female organism" EXACT [OBOL:automatic] synonym: "ovaries" RELATED PLURAL [] synonym: "ovarium" RELATED LATIN [Wikipedia:Ovary] synonym: "ovum-producing ovary" EXACT SENSU [GO:0061039] synonym: "reproductive system of female organism gonad" EXACT [OBOL:automatic] synonym: "reproductive system of female organism gonada" EXACT [OBOL:automatic] xref: AAO:0000371 xref: BILA:0000125 xref: BSA:0000080 xref: BTO:0000975 xref: CALOHA:TS-0730 xref: EFO:0000973 xref: EHDAA2:0001360 xref: EHDAA:8124 xref: EMAPA:17962 xref: EV:0100111 xref: FBbt:00004865 xref: FMA:7209 xref: GAID:367 xref: MA:0000384 xref: MESH:D010053 xref: MIAA:0000125 xref: NCIT:C12404 xref: OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA xref: SCTID:181464007 xref: TAO:0000403 xref: UMLS:C0029939 {source="ncithesaurus:Ovary"} xref: VHOG:0000251 xref: Wikipedia:Ovary xref: XAO:0000258 xref: ZFA:0000403 is_a: UBERON:0000991 ! gonad is_a: UBERON:0003134 ! female reproductive organ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009117 ! indifferent gonad relationship: develops_from UBERON:0009117 ! indifferent gonad relationship: only_in_taxon NCBITaxon:33208 ! Metazoa property_value: depicted:by Female:anatomy.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png xsd:anyURI property_value: UBPROP:0000001 "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000371", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "Female reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000403", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000251", ontology="VHOG", source="DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "ovarian" xsd:string property_value: UBPROP:0000008 "Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" xsd:string {source="WP"} [Term] id: UBERON:0001003 name: skin epidermis namespace: uberon def: "The outer epithelial layer of the skin that is superficial to the dermis." [http://orcid.org/0000-0002-6601-2165, ISBN:0073040584] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "epidermis" BROAD [] synonym: "skin" BROAD [] synonym: "vertebrate epidermis" EXACT [] xref: AAO:0000143 xref: BTO:0000404 xref: CALOHA:TS-0283 xref: EFO:0000954 xref: EMAPA:17528 xref: EV:0100153 xref: FMA:70596 xref: GAID:932 xref: MA:0000153 xref: MAT:0000154 xref: MESH:D004817 xref: MIAA:0000154 xref: NCIT:C12708 xref: SCTID:361694003 xref: TAO:0000105 xref: UMLS:C0014520 {source="ncithesaurus:Epidermis"} xref: VHOG:0000077 xref: Wikipedia:Epidermis_(skin) xref: XAO:0000028 xref: ZFA:0000105 is_a: UBERON:0007376 ! outer epithelium is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:0007376 ! outer epithelium intersection_of: part_of UBERON:0002097 ! skin of body relationship: adjacent_to UBERON:0002067 ! dermis relationship: developmentally_replaces UBERON:0003055 ! periderm relationship: part_of UBERON:0002097 ! skin of body property_value: UBPROP:0000001 "A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000105", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000002 "relationship loss: subclass external integument structures (AAO:0000961)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO"} property_value: UBPROP:0000003 "(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000077", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "epidermal" xsd:string property_value: UBPROP:0000008 "Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes)." xsd:string [Term] id: UBERON:0001004 name: respiratory system namespace: uberon def: "Functional system which consists of structures involved in respiration." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Respiratory_system] subset: efo_slim subset: functional_classification subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "apparatus respiratorius" EXACT [] synonym: "apparatus respiratorius" RELATED [BTO:0000203] synonym: "Atmungssystem" RELATED [BTO:0000203] synonym: "respiratory system" EXACT [] synonym: "systema respiratorium" RELATED LATIN [Wikipedia:Respiratory_system] xref: AAO:0000541 xref: BTO:0000203 xref: CALOHA:TS-1319 xref: EFO:0000804 xref: EHDAA2:0001604 xref: EHDAA:2203 xref: EMAPA:16727 xref: EV:0100036 xref: FMA:7158 xref: GAID:78 xref: MA:0000327 xref: MAT:0000030 xref: MESH:D012137 xref: MIAA:0000030 xref: NCIT:C12779 xref: OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA xref: SCTID:278197002 xref: TAO:0000272 xref: UMLS:C0035237 {source="ncithesaurus:Respiratory_System"} xref: VHOG:0000202 xref: Wikipedia:Respiratory_system xref: XAO:0000117 xref: ZFA:0000272 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003016 ! respiratory system process relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: UBPROP:0000001 "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000541", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000202", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001005 name: respiratory airway namespace: uberon def: "An airway through which respiratory air passes in organisms." [Wikipedia:Trachea] subset: grouping_class subset: uberon_slim synonym: "airway" BROAD [http://orcid.org/0000-0002-6601-2165] synonym: "airways" BROAD PLURAL [http://orcid.org/0000-0002-6601-2165] xref: FMA:265130 xref: SCTID:361380005 xref: Wikipedia:Trachea is_a: UBERON:0003103 ! compound organ is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0034874 ! air in respiratory system relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000232 "This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends" xsd:string [Term] id: UBERON:0001007 name: digestive system namespace: uberon 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." [FB:gg, NLM:alimentary+system, Wikipedia:Digestive_system] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "alimentary system" RELATED [] synonym: "alimentary tract" RELATED [] synonym: "gastrointestinal system" RELATED [] synonym: "gut" RELATED [] xref: AAO:0000129 xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 xref: EV:0100056 xref: FBbt:00005055 xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem xref: MA:0002431 xref: MAT:0000018 xref: MESH:D004064 xref: MIAA:0000018 xref: ncithesaurus:Digestive_System xref: SCTID:278859004 xref: TADS:0000170 xref: TAO:0000339 xref: WBbt:0005748 xref: Wikipedia:Digestive_system xref: XAO:0000125 xref: ZFA:0000339 is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0022600 ! digestive system process disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0022600 ! digestive system process relationship: existence_ends_during UBERON:0000066 ! fully formed stage property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000007 "digestive" xsd:string property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001009 name: circulatory system namespace: uberon def: "organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] subset: uberon_slim synonym: "systema cardiovasculare" RELATED LATIN [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 xref: FBbt:00005057 xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg xsd:anyURI property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001013 name: adipose tissue namespace: uberon def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue" [http://orcid.org/0000-0002-6601-2165, MESH:A10.165.114, MGI:cwg, MP:0000003, Wikipedia:Adipose_tissue] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "adipose" RELATED [BTO:0001487] synonym: "bodyfat" RELATED [BTO:0001487] synonym: "fat" EXACT [MA:0000009] synonym: "fat tissue" EXACT [] synonym: "fatty depot" RELATED [] synonym: "fatty tissue" EXACT [] xref: AAO:0000001 xref: AEO:000020 xref: BTO:0001487 xref: CALOHA:TS-0013 xref: EFO:0000790 xref: EHDAA2:0003120 xref: EMAPA:35112 xref: EV:0100381 xref: FMA:20110 xref: GAID:920 xref: galen:FattyTissue xref: MA:0000009 xref: MAT:0000015 xref: MESH:D000273 xref: MIAA:0000015 xref: NCIT:C12472 xref: OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA xref: SCTID:55603005 xref: TAO:0002134 xref: UMLS:C0001527 {source="ncithesaurus:Adipose_Tissue"} xref: VHOG:0001284 xref: Wikipedia:Adipose_tissue xref: XAO:0003049 xref: ZFA:0005345 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: composed_primarily_of CL:0000136 ! fat cell disjoint_from: UBERON:0003714 ! neural tissue relationship: composed_primarily_of CL:0000136 ! fat cell property_value: UBPROP:0000001 "Connective tissue in which fat is stored.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002134", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000002 "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO"} property_value: UBPROP:0000003 "Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001284", ontology="VHOG", source="DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "adipose" xsd:string property_value: UBPROP:0000008 "In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen." xsd:string property_value: UBPROP:0000012 "in FMA this is dense irregular connective tissue" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001015 name: musculature namespace: uberon def: "A subdivision of the muscular system corresponding to a subdisivision of an organism." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Muscular_system] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle group" EXACT [] synonym: "muscle system" RELATED [] synonym: "muscles" RELATED [] synonym: "muscles set" EXACT [] synonym: "musculature" EXACT [] synonym: "musculature system" RELATED [] synonym: "musculi" EXACT LATIN [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 xref: NCIT:C13056 xref: OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA xref: TAO:0000548 xref: UMLS:C0026845 {source="ncithesaurus:Muscle"} xref: VSAO:0005038 xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011216 ! organ system subdivision relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png xsd:anyURI property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001016 name: nervous system namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "nerve net" NARROW [Wikipedia:Nerve_net] synonym: "neurological system" EXACT [GO:0050877] synonym: "systema nervosum" RELATED LATIN [Wikipedia:Nervous_system] xref: AAO:0000324 xref: BILA:0000079 xref: BIRNLEX:844 xref: BTO:0001484 xref: CALOHA:TS-1313 xref: EFO:0000802 xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 xref: FBbt:00005093 xref: FMA:7157 xref: GAID:466 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3236 xref: MA:0000016 xref: MAT:0000026 xref: MESH:D009420 xref: MIAA:0000026 xref: NCIT:C12755 xref: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA xref: SCTID:278196006 xref: TAO:0000396 xref: UMLS:C0027763 {source="ncithesaurus:Nervous_System"} xref: VHOG:0000402 xref: WBbt:0005735 xref: Wikipedia:Nervous_system xref: XAO:0000177 xref: ZFA:0000396 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process relationship: composed_primarily_of CL:0002319 ! neural cell relationship: develops_from UBERON:0016880 ! future nervous system relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "nervous" xsd:string property_value: UBPROP:0000007 "neural" xsd:string [Term] id: UBERON:0001017 name: central nervous system namespace: uberon 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." [GO:0021551, http://www.frontiersinzoology.com/content/7/1/29, https://sourceforge.net/p/geneontology/ontology-requests/11422/] subset: cumbo subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cerebrospinal axis" NARROW [FMA:55675] synonym: "CNS" EXACT ABBREVIATION [] synonym: "neuraxis" RELATED [FMA:55675] synonym: "systema nervosum centrale" EXACT LATIN [FMA:55675, FMA:TA] xref: AAO:0000090 xref: BAMS:CNS xref: BILA:0000080 xref: BIRNLEX:1099 xref: BTO:0000227 xref: CALOHA:TS-0150 xref: EFO:0000908 xref: EHDAA2:0000225 xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 xref: FBbt:00005094 xref: FMA:55675 xref: GAID:570 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=854 xref: MA:0000167 xref: MAT:0000457 xref: MESH:D002490 xref: NCIT:C12438 xref: OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA xref: SCTID:278199004 xref: TAO:0000012 xref: UMLS:C0927232 {source="ncithesaurus:Central_Nervous_System"} xref: UMLS:C0927232 {source="BIRNLEX:1099"} xref: VHOG:0000293 xref: Wikipedia:Central_nervous_system xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7742", evidence="definitional"} ! neural tube relationship: develops_from UBERON:0016879 ! future central nervous system relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001021 name: nerve namespace: uberon 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." [FBbt:00005105, http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "nerves" EXACT PLURAL [TAO:0007009] synonym: "neural subtree" RELATED [FMA:65132] synonym: "peripheral nerve" EXACT [http://orcid.org/0000-0002-6601-2165] xref: AAO:0011070 xref: AEO:0000137 xref: BAMS:n xref: BIRNLEX:1615 xref: BSA:0000098 xref: BTO:0000925 xref: BTO:0001027 xref: CALOHA:TS-0772 xref: EHDAA2:0003137 xref: EHDAA:2851 xref: EHDAA:3776 xref: EHDAA:4657 xref: EMAPA:32808 xref: EMAPA:32815 xref: EV:0100371 xref: FBbt:00005105 xref: FMA:65132 xref: FMA:65239 xref: GAID:747 xref: GAID:758 xref: galen:Nerve xref: MA:0000217 xref: MA:0000228 xref: MESH:D010525 xref: NCIT:C12466 xref: NCIT:C12768 xref: NLX:147826 xref: OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA xref: SCTID:244457007 xref: SCTID:256864008 xref: TAO:0007009 xref: UMLS:C0027740 {source="ncithesaurus:Nerve"} xref: UMLS:C0031119 {source="ncithesaurus:Peripheral_Nerve"} xref: VHOG:0000901 xref: Wikipedia:Nervous_system xref: XAO:0000204 xref: XAO:0003047 xref: ZFA:0007009 is_a: UBERON:0000122 {source="FBbt"} ! neuron projection bundle relationship: has_developmental_contribution_from UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: UBPROP:0000001 "A portion of tissue which is a fasiculated group of axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007009", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000007 "nervous" xsd:string [Term] id: UBERON:0001032 name: sensory system namespace: uberon def: "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." [Wikipedia:Sensory_system] subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "organa sensuum" EXACT LATIN [FMA:75259, FMA:TA] synonym: "organa sensuum" RELATED LATIN [Wikipedia:Sensory_system] synonym: "sense organ subsystem" EXACT [] synonym: "sense organs" EXACT [FMA:75259] synonym: "sense organs set" EXACT [FMA:75259] synonym: "sensory organ system" RELATED [] synonym: "sensory subsystem" EXACT [] synonym: "sensory systems" EXACT PLURAL [TAO:0000282] synonym: "set of sense organs" RELATED [FMA:75259] xref: AAO:0000555 xref: BAMS:SEN xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 xref: FBbt:00007692 xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 xref: MIAA:0000031 xref: NLXANAT:090816 xref: TAO:0000282 xref: VHOG:0001674 xref: Wikipedia:Sensory_system xref: XAO:0003194 xref: ZFA:0000282 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: part_of UBERON:0004456 ! entire sense organ system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png xsd:anyURI property_value: UBPROP:0000003 "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string [Term] id: UBERON:0001041 name: foregut namespace: uberon def: "Anterior subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] subset: developmental_classification subset: pheno_slim subset: uberon_slim synonym: "praeenteron" RELATED LATIN [Wikipedia:Foregut] synonym: "proenteron" RELATED LATIN [Wikipedia:Foregut] xref: AAO:0011042 xref: BILA:0000085 xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 xref: FBbt:00005379 xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 xref: SCTID:361409009 xref: TGMA:0001014 xref: UMLS:C0231051 {source="ncithesaurus:Foregut"} xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png xsd:anyURI property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string property_value: UBPROP:0000001 "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." xsd:string {source="MP:0000474"} property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000285", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001042 name: chordate pharynx namespace: uberon def: "A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]." [http://www.feedexp.org] comment: Consider generalizing to deuterostome pharynx subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "pharynx" BROAD SENSU [FMA:46688] xref: AAO:0000967 xref: BTO:0001049 xref: CALOHA:TS-0785 xref: EFO:0000836 xref: EHDAA2:0001458 xref: EHDAA:2947 xref: EMAPA:16706 xref: EV:0100065 xref: FMA:46688 xref: GAID:155 xref: galen:Pharynx xref: MA:0000432 xref: MESH:A03.867 xref: NCIT:C12425 xref: OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA xref: SCTID:181211006 xref: TAO:0000056 xref: UMLS:C0031354 {source="ncithesaurus:Pharynx"} xref: VHOG:0000462 xref: Wikipedia:Pharynx xref: XAO:0003227 xref: ZFA:0000056 is_a: UBERON:0006562 ! pharynx relationship: continuous_with UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus relationship: develops_from UBERON:0009145 {source="EHDAA2"} ! pharyngeal region of foregut relationship: distally_connected_to UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus relationship: has_skeleton UBERON:0008895 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! splanchnocranium relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001004 ! respiratory system property_value: UBPROP:0000001 "A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]." xsd:string {source="MESH:A03.867"} property_value: UBPROP:0000001 "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000056", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} property_value: UBPROP:0000001 "The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000002 "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} property_value: UBPROP:0000002 "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} property_value: UBPROP:0000003 "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001043 name: esophagus namespace: uberon def: "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993)." [http://www.rivm.nl/interspeciesinfo/inter/oesophagus/, Wikipedia:Esophagus] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gullet" EXACT [] synonym: "oesophagus" EXACT [] xref: AAO:0000145 xref: ANISEED:1235301 xref: BTO:0000959 xref: CALOHA:TS-0700 xref: EFO:0000835 xref: EHDAA2:0001285 xref: EHDAA:2937 xref: EMAPA:16833 xref: EV:0100069 xref: FMA:7131 xref: GAID:291 xref: galen:Esophagus xref: MA:0000352 xref: MAT:0000048 xref: MESH:A03.365 xref: MIAA:0000048 xref: NCIT:C12389 xref: OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA xref: SCTID:181245004 xref: TAO:0000204 xref: UMLS:C0014876 {source="ncithesaurus:Esophagus"} xref: VHOG:0000450 xref: Wikipedia:Esophagus xref: XAO:0000127 xref: ZFA:0000204 is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0013765 ! digestive system element relationship: develops_from UBERON:0001041 ! foregut relationship: part_of UBERON:0004908 ! upper digestive tract relationship: proximally_connected_to UBERON:0001042 ! chordate pharynx property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg xsd:anyURI property_value: UBPROP:0000001 "Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000145", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000450", ontology="VHOG", source="DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "esophageal" xsd:string property_value: UBPROP:0000012 "esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001048 name: primordium namespace: uberon def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." [BTO:0001886, FB:DJS, FB:FBrf0089570, http://flybase.org/reports/FBrf0178740.html] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "bud" RELATED [] synonym: "future organ" RELATED [] synonym: "placode" RELATED [FBbt:00005495] synonym: "primordia" RELATED PLURAL [XAO:0003043] synonym: "rudiment" RELATED [] xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 xref: FBbt:00005495 xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 xref: UMLS:C0678727 {source="ncithesaurus:Primordium"} xref: Wikipedia:Primordium xref: XAO:0003043 is_a: UBERON:0005423 {source="EHDAA2"} ! developing anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism [Term] id: UBERON:0001049 name: neural tube namespace: uberon def: "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]." [Wikipedia:Neural_tube] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "neural primordium" RELATED [] synonym: "presumptive central nervous system" RELATED [] synonym: "tubus neuralis" RELATED LATIN [Wikipedia:Neural_tube] xref: AAO:0010617 xref: BTO:0001057 xref: CALOHA:TS-2371 xref: DHBA:10154 xref: EHDAA2:0001254 xref: EHDAA:2869 xref: EHDAA:908 xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1365 xref: MAT:0000069 xref: MIAA:0000069 xref: NCIT:C34226 xref: SCTID:362852000 xref: TAO:0001135 xref: UMLS:C0231024 {source="ncithesaurus:Neural_Tube"} xref: VHOG:0000307 xref: Wikipedia:Neural_tube xref: XAO:0003204 xref: ZFA:0001135 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: develops_from UBERON:0005068 ! neural rod property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} [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: upper_level xref: AAO:0010841 xref: AEO:0000000 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 xref: FBbt:10000000 xref: FBbt_root:00000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 xref: NCIT:C12219 xref: TAO:0100000 xref: TGMA:0001822 xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 is_a: BFO:0000004 ! independent continuant [Term] id: UBERON:0001068 name: skin of back namespace: uberon def: "A zone of skin that is part of a back [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "back skin" EXACT [] synonym: "back zone of skin" EXACT [OBOL:automatic] synonym: "skin, dorsal region" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "zone of skin of back" EXACT [OBOL:automatic] xref: EMAPA:36392 xref: FMA:10462 xref: FMA:22985 xref: MA:0000498 xref: SCTID:181492002 is_a: UBERON:0001085 {source="MA"} ! skin of trunk intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0011270 {source="MA"} ! dorsal trunk property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001070 name: external carotid artery namespace: uberon def: "A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]" [MGI:anna] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arteria carotis externa" RELATED LATIN [Wikipedia:External_carotid_artery] synonym: "external carotid" EXACT [AAO:0010218] xref: AAO:0010218 xref: AAO:0010416 xref: BTO:0004696 xref: EFO:0001953 xref: EHDAA2:0000461 xref: EMAPA:18611 xref: FMA:10635 xref: GAID:480 xref: MA:0001929 xref: MESH:D002342 xref: NCIT:C32551 xref: OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA xref: SCTID:362044002 xref: UMLS:C0007275 {source="ncithesaurus:External_Carotid_Artery"} xref: VHOG:0000265 xref: Wikipedia:External_carotid_artery xref: XAO:0000345 is_a: UBERON:0005396 {source="MA"} ! carotid artery segment is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: branching_part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches relationship: develops_from UBERON:0001530 {source="EHDAA2"} ! common carotid artery plus branches relationship: part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif xsd:anyURI property_value: seeAlso https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 xsd:anyURI property_value: UBPROP:0000008 "not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO" xsd:string [Term] id: UBERON:0001071 name: superficial cervical artery namespace: uberon def: "It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery." [Wikipedia:Superficial_part_of_transverse_cervical_artery] comment: The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] subset: uberon_slim synonym: "superficial branch of transverse cervical artery" EXACT [Wikipedia:Superficial_part_of_transverse_cervical_artery] xref: EMAPA:37117 {source="MA:th"} xref: FMA:10665 xref: MA:0002052 xref: NCIT:C53005 xref: SCTID:161746006 xref: UMLS:C0226271 {source="ncithesaurus:Superficial_Cervical_Artery"} xref: Wikipedia:Superficial_part_of_transverse_cervical_artery is_a: UBERON:0012320 ! cervical artery intersection_of: UBERON:0012320 ! cervical artery intersection_of: part_of UBERON:0035549 ! vasculature of integument relationship: part_of UBERON:0035549 ! vasculature of integument [Term] id: UBERON:0001074 name: pericardial cavity namespace: uberon def: "A potential space between the visceral and parietal layers of the pericardium." [Wikipedia:Pericardium] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cavitas pericardiaca" RELATED LATIN [Wikipedia:Pericardial_cavity] synonym: "cavity of pericardial sac" EXACT [] synonym: "pericardial space" EXACT [Wikipedia:Pericardial_cavity] xref: BSA:0000091 xref: EHDAA2:0001434 xref: EMAPA:16131 xref: EMAPA:16132 xref: FMA:11350 xref: galen:PericardialSpace xref: MA:0000053 xref: NCIT:C38662 xref: SCTID:362027001 xref: TAO:0002220 xref: UMLS:C0225972 {source="ncithesaurus:Pericardial_Cavity"} xref: VHOG:0000556 xref: Wikipedia:Pericardial_cavity xref: ZFA:0001655 is_a: UBERON:0002323 {source="MA"} ! coelemic cavity lumen is_a: UBERON:0035809 ! serous cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002406 ! pericardial sac relationship: contains UBERON:0002409 ! pericardial fluid relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom relationship: luminal_space_of UBERON:0002406 ! pericardial sac relationship: part_of UBERON:0002406 {source="FMA"} ! pericardial sac relationship: surrounded_by UBERON:0002357 ! serous pericardium property_value: RO:0002175 NCBITaxon:7718 {source="PMID:20959416"} property_value: UBPROP:0000001 "Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002220", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000556", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0001081 name: endocardium of ventricle namespace: uberon def: "Endocardium that is part of the cardiac ventricle." [ZFIN:curator] subset: pheno_slim subset: vertebrate_core synonym: "cardiac ventricle endocardium" EXACT [OBOL:automatic] synonym: "endocardium of cardiac ventricle" EXACT [OBOL:automatic] synonym: "endocardium of heart ventricle" EXACT [OBOL:automatic] synonym: "endocardium of lower chamber of heart" EXACT [OBOL:automatic] synonym: "endocardium of ventricle of heart" EXACT [OBOL:automatic] synonym: "heart ventricle endocardium" EXACT [OBOL:automatic] synonym: "lower chamber of heart endocardium" EXACT [OBOL:automatic] synonym: "ventricle endocardial tissue" RELATED [VHOG:0000607] synonym: "ventricle endocardium" EXACT [] synonym: "ventricle of heart endocardium" EXACT [OBOL:automatic] synonym: "ventricular endocardium" EXACT [] xref: EMAPA:32747 xref: FMA:12148 xref: MA:0000079 xref: SCTID:192172004 xref: TAO:0002247 xref: VHOG:0000607 xref: ZFA:0001615 is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0002165 ! endocardium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall [Term] id: UBERON:0001082 name: epicardium of ventricle namespace: uberon def: "An epicardial layer that lines a cardiac ventricle" [http://orcid.org/0000-0002-6601-2165] subset: vertebrate_core synonym: "cardiac ventricle epicardium" EXACT [OBOL:automatic] synonym: "ventricular epicardium" EXACT [] xref: FMA:12150 xref: TAO:0005058 xref: ZFA:0005058 is_a: UBERON:0002348 ! epicardium intersection_of: UBERON:0002348 ! epicardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle property_value: UBPROP:0000001 "The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005058", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001083 name: myocardium of ventricle namespace: uberon def: "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer." [ZFIN:curator] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "ventricle cardiac muscle" RELATED [VHOG:0000604] synonym: "ventricle myocardium" EXACT [] synonym: "ventricular myocardium" EXACT [] xref: EFO:0003088 xref: EMAPA:32748 xref: FMA:12151 xref: MA:0000082 xref: SCTID:192084000 xref: TAO:0005061 xref: VHOG:0000604 xref: ZFA:0005061 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall property_value: UBPROP:0000001 "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005061", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000604", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001084 name: skin of head namespace: uberon def: "A zone of skin that is part of a head [Automatically generated definition]." [OBOL:automatic] synonym: "adult head zone of skin" EXACT [OBOL:automatic] synonym: "head skin" EXACT [] synonym: "head zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of adult head" EXACT [OBOL:automatic] synonym: "zone of skin of head" EXACT [OBOL:automatic] xref: FMA:12166 xref: FMA:24756 xref: MA:0000582 xref: NCIT:C52757 xref: SCTID:181484006 xref: UMLS:C0205029 {source="ncithesaurus:Head_Skin"} is_a: UBERON:0012180 ! head or neck skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001085 name: skin of trunk namespace: uberon def: "A zone of skin that is part of a trunk [Automatically generated definition]." [OBOL:automatic] synonym: "torso zone of skin" EXACT [OBOL:automatic] synonym: "trunk skin" EXACT [] synonym: "trunk zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of torso" EXACT [OBOL:automatic] synonym: "zone of skin of trunk" EXACT [OBOL:automatic] xref: EMAPA:37278 {source="MA:th"} xref: FMA:12167 xref: FMA:23093 xref: MA:0000517 xref: NCIT:C12295 xref: SCTID:181489001 xref: UMLS:C0205031 {source="ncithesaurus:Skin_of_the_Trunk"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001090 name: synovial fluid namespace: uberon def: "Joint fluid is a transudate of plasma that is actively secreted by synovial cells." [https://www.ncbi.nlm.nih.gov/books/NBK274/] subset: uberon_slim subset: vertebrate_core synonym: "joint fluid" EXACT [https://www.ncbi.nlm.nih.gov/books/NBK274/] xref: BTO:0001339 xref: CALOHA:TS-0996 xref: ENVO:02000039 xref: FMA:12277 xref: GAID:265 xref: galen:SynovialFluid xref: MA:0002544 xref: MESH:D013582 xref: NCIT:C33718 xref: TAO:0005154 xref: UMLS:C0039097 {source="ncithesaurus:Synovial_Fluid"} xref: Wikipedia:Synovial_fluid xref: ZFA:0005154 is_a: UBERON:0007779 ! transudate is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland intersection_of: UBERON:0007779 ! transudate intersection_of: produced_by CL:0000214 ! synovial cell relationship: has_part CHEBI:16336 ! hyaluronic acid relationship: located_in UBERON:0007617 ! synovial cavity of joint relationship: produced_by CL:0000214 ! synovial cell property_value: UBPROP:0000001 "Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005154", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000009 "It provides nutrients and lubrication for articular cartilage" xsd:string property_value: UBPROP:0000010 "The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma" xsd:string [Term] id: UBERON:0001096 name: wall of esophagus namespace: uberon def: "An anatomical wall that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "anatomical wall of esophagus" EXACT [OBOL:automatic] synonym: "anatomical wall of gullet" EXACT [OBOL:automatic] synonym: "anatomical wall of oesophagus" EXACT [OBOL:automatic] synonym: "esophageal wall" EXACT [] synonym: "esophagus anatomical wall" EXACT [OBOL:automatic] synonym: "esophagus wall" EXACT [] synonym: "gullet anatomical wall" EXACT [OBOL:automatic] synonym: "gullet wall" EXACT [OBOL:automatic] synonym: "oesophagus anatomical wall" EXACT [OBOL:automatic] synonym: "oesophagus wall" EXACT [OBOL:automatic] synonym: "wall of gullet" EXACT [OBOL:automatic] synonym: "wall of oesophagus" EXACT [OBOL:automatic] xref: EMAPA:35326 xref: FMA:12611 xref: MA:0002691 is_a: UBERON:0000328 ! gut wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus [Term] id: UBERON:0001133 name: cardiac muscle tissue namespace: uberon alt_id: UBERON:0007096 def: "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." [ZFA:0005280] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cardiac muscle" EXACT [] synonym: "cardiac muscle muscle tissue" EXACT [OBOL:automatic] synonym: "cardiac muscle textus muscularis" EXACT [OBOL:automatic] synonym: "cardiac musculature" RELATED [BILA:0000134] synonym: "heart muscle muscle tissue" EXACT [OBOL:automatic] synonym: "heart muscle textus muscularis" EXACT [OBOL:automatic] synonym: "heart myocardium muscle tissue" EXACT [OBOL:automatic] synonym: "heart myocardium textus muscularis" EXACT [OBOL:automatic] synonym: "muscle of heart muscle tissue" EXACT [OBOL:automatic] synonym: "muscle of heart textus muscularis" EXACT [OBOL:automatic] synonym: "muscle tissue of cardiac muscle" EXACT [OBOL:automatic] synonym: "muscle tissue of heart muscle" EXACT [OBOL:automatic] synonym: "muscle tissue of heart myocardium" EXACT [OBOL:automatic] synonym: "muscle tissue of muscle of heart" EXACT [OBOL:automatic] synonym: "muscle tissue of myocardium" EXACT [OBOL:automatic] synonym: "myocardium muscle tissue" EXACT [OBOL:automatic] synonym: "myocardium textus muscularis" EXACT [OBOL:automatic] synonym: "textus muscularis of cardiac muscle" EXACT [OBOL:automatic] synonym: "textus muscularis of heart muscle" EXACT [OBOL:automatic] synonym: "textus muscularis of heart myocardium" EXACT [OBOL:automatic] synonym: "textus muscularis of muscle of heart" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium" EXACT [OBOL:automatic] xref: AAO:0010245 xref: AEO:0000142 xref: BILA:0000134 xref: BTO:0000199 xref: CALOHA:TS-0440 xref: EHDAA2:0003142 xref: EMAPA:32688 xref: FMA:14068 xref: galen:CardiacMuscle xref: galen:CardiacMuscleTissue xref: ncithesaurus:Heart_Muscle xref: TAO:0005280 xref: Wikipedia:Cardiac_muscle xref: ZFA:0005280 is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000746 ! cardiac muscle cell disjoint_from: UBERON:0001134 ! skeletal muscle tissue relationship: composed_primarily_of CL:0000746 ! cardiac muscle cell relationship: has_part CL:0000746 ! cardiac muscle cell relationship: part_of UBERON:0000948 {source="ZFA"} ! heart property_value: editor_note "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string [Term] id: UBERON:0001134 name: skeletal muscle tissue namespace: uberon def: "Muscle tissue that consists primarily of skeletal muscle fibers." [https://github.com/obophenotype/uberon/issues/324] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "skeletal muscle" BROAD [] synonym: "skeletal muscle system" RELATED [BTO:0001103] synonym: "somatic muscle" RELATED [BTO:0001103] xref: EMAPA:32716 xref: FMA:14069 xref: MA:0002439 xref: NCIT:C13050 xref: SCTID:426215008 xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"} xref: Wikipedia:Skeletal_striated_muscle is_a: UBERON:0002036 ! striated muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: composed_primarily_of CL:0008002 ! skeletal muscle fiber relationship: composed_primarily_of CL:0008002 ! skeletal muscle fiber relationship: develops_from UBERON:0003082 ! myotome relationship: part_of UBERON:0014892 ! skeletal muscle organ property_value: depicted:by Skeletal:muscle.jpg xsd:anyURI property_value: editor_note "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/dosumis property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/mellybelly property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/RDruzinsky property_value: UBPROP:0000001 "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {external_class="FMA:14069", ontology="FMA"} property_value: UBPROP:0000003 "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000319", ontology="VHOG", source="PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001135 name: smooth muscle tissue namespace: uberon def: "Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]." [GO:0006939, Wikipedia:Smooth_muscle_tissue] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "involuntary muscle" EXACT [] synonym: "non-striated muscle" EXACT [] synonym: "smooth muscle" EXACT [] synonym: "textus muscularis levis; textus muscularis nonstriatus" RELATED LATIN [Wikipedia:Smooth_muscle_tissue] synonym: "textus muscularis nonstriatus" EXACT LATIN [FMA:14070, FMA:TA] synonym: "visceral muscle" NARROW SENSU [] synonym: "visceral muscle tissue" NARROW SENSU [] xref: AAO:0010244 xref: AEO:0000141 xref: BTO:0001260 xref: CALOHA:TS-0943 xref: EFO:0000889 xref: EHDAA2:0003141 xref: EMAPA:32717 xref: EV:0100378 xref: FBbt:00003525 xref: FMA:14070 xref: GAID:167 xref: galen:SmoothMuscle xref: galen:SmoothMuscleTissue xref: MA:0000166 xref: MAT:0000303 xref: MESH:D009130 xref: MIAA:0000303 xref: NCIT:C12437 xref: OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA xref: TAO:0005274 xref: UMLS:C1267092 {source="ncithesaurus:Smooth_Muscle_Tissue"} xref: VHOG:0001246 xref: WBbt:0005781 xref: Wikipedia:Smooth_muscle_tissue xref: XAO:0000175 xref: ZFA:0005274 is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: has_part CL:0000192 ! smooth muscle cell disjoint_from: UBERON:0002036 ! striated muscle tissue relationship: composed_primarily_of CL:0000192 ! smooth muscle cell relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber property_value: depicted:by Glatte:Muskelzellen.jpg xsd:anyURI property_value: UBPROP:0000001 "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} property_value: UBPROP:0000003 "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001246", ontology="VHOG", source="DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000013 "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." xsd:string [Term] id: UBERON:0001136 name: mesothelium namespace: uberon def: "Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri)." [FMA:14074, Wikipedia:Mesothelium] subset: uberon_slim xref: AEO:0000111 xref: BTO:0002422 xref: CALOHA:TS-1183 xref: EHDAA2_RETIRED:0003111 xref: EHDAA:2331 xref: EHDAA:2349 xref: EHDAA:295 xref: EHDAA:6073 xref: EHDAA:640 xref: EHDAA:646 xref: EMAPA:32856 xref: FMA:14074 xref: MA:0000565 xref: NCIT:C33105 xref: SCTID:361918002 xref: UMLS:C0086610 {source="ncithesaurus:Mesothelium"} xref: Wikipedia:Mesothelium is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000487 ! simple squamous epithelium intersection_of: develops_from UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000042 ! serous membrane relationship: composed_primarily_of CL:0000077 {source="FMA"} ! mesothelial cell relationship: part_of UBERON:0000042 ! serous membrane property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg xsd:anyURI [Term] id: UBERON:0001137 name: dorsum namespace: uberon def: "A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.." [BSPO:0000063, UBERONREF:0000006, Wikipedia:Dorsum_(anatomy)] subset: efo_slim subset: uberon_slim synonym: "back" EXACT [FMA:14181] synonym: "back of body proper" EXACT [FMA:14181] synonym: "dorsal part of organism" EXACT [] xref: BTO:0001713 xref: CALOHA:TS-2223 xref: EFO:0001405 xref: FMA:14181 xref: GAID:30 xref: galen:Back xref: MESH:A01.176 xref: NCIT:C13062 xref: OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG xsd:anyURI property_value: UBPROP:0000007 "dorsal" xsd:string property_value: UBPROP:0000008 "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" xsd:string [Term] id: UBERON:0001145 name: ovarian vein namespace: uberon def: "A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries." [Wikipedia:Ovarian_vein] subset: uberon_slim synonym: "female reproductive system gonad vein" EXACT [OBOL:automatic] synonym: "female reproductive system gonada vein" EXACT [OBOL:automatic] synonym: "gonad of female reproductive system vein" EXACT [OBOL:automatic] synonym: "gonada of female reproductive system vein" EXACT [OBOL:automatic] synonym: "ovary vein" EXACT [OBOL:automatic] synonym: "vein of female reproductive system gonad" EXACT [OBOL:automatic] synonym: "vein of female reproductive system gonada" EXACT [OBOL:automatic] synonym: "vein of gonad of female reproductive system" EXACT [OBOL:automatic] synonym: "vein of gonada of female reproductive system" EXACT [OBOL:automatic] synonym: "vein of ovary" EXACT [OBOL:automatic] synonym: "vena ovarica dextra" RELATED LATIN [Wikipedia:Ovarian_vein] synonym: "vena ovarica sinistra" RELATED LATIN [Wikipedia:Ovarian_vein] xref: EMAPA:18644 xref: FMA:14346 xref: MA:0002186 xref: NCIT:C53058 xref: OpenCyc:Mx4rvrST5ZwpEbGdrcN5Y29ycA xref: SCTID:278193003 xref: UMLS:C0226720 {source="ncithesaurus:Ovarian_Vein"} xref: Wikipedia:Ovarian_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0000992 ! ovary relationship: drains UBERON:0000992 ! ovary relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg xsd:anyURI [Term] id: UBERON:0001190 name: ovarian artery namespace: uberon def: "An artery that supplies an ovary." [OBOL:automatic] subset: uberon_slim synonym: "arteria ovarica" RELATED LATIN [Wikipedia:Ovarian_artery] synonym: "ovarian arterial tree" EXACT [] xref: EMAPA:18620 xref: FMA:14761 xref: MA:0002012 xref: NCIT:C33242 xref: OpenCyc:Mx4rwOa9PZwpEbGdrcN5Y29ycA xref: SCTID:244280002 xref: UMLS:C0226411 {source="ncithesaurus:Ovarian_Artery"} xref: Wikipedia:Ovarian_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0000992 ! ovary relationship: supplies UBERON:0000992 ! ovary property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png xsd:anyURI property_value: UBPROP:0000001 "In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]." xsd:string {source="Wikipedia:Ovarian_artery"} [Term] id: UBERON:0001271 name: pelvic girdle region namespace: uberon def: "The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions." [DOI:10.1002/dvdy.22617, FMA:16581, FMA:23217, https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion, https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: uberon_slim subset: vertebrate_core synonym: "girdle - pelvic" RELATED [] synonym: "pelvic girdle" RELATED INCONSISTENT [] xref: EMAPA:37862 {source="MA:th"} xref: FMA:16581 xref: NCIT:C33291 xref: SCTID:360010001 xref: UMLS:C0684083 {source="ncithesaurus:Pelvic_Girdle"} xref: VSAO:0000304 is_a: UBERON:0007823 ! appendage girdle region is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007823 ! appendage girdle region intersection_of: part_of UBERON:0010709 ! pelvic complex disjoint_from: UBERON:0007832 ! pelvic girdle skeleton relationship: has_skeleton UBERON:0007832 ! pelvic girdle skeleton relationship: in_lateral_side_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0010709 ! pelvic complex property_value: IAO:0000232 "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" xsd:string property_value: UBPROP:0000001 "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000304", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0001325 name: muscle of pelvis namespace: uberon def: "Muscle (organ) which is a part of the pelvis. Examples: levator ani," [FMA:19086] subset: pheno_slim subset: uberon_slim synonym: "muscle organ of pelvis" EXACT [OBOL:automatic] synonym: "pelvic muscle" EXACT [FMA:19086] synonym: "pelvis muscle" EXACT [] synonym: "pelvis muscle organ" EXACT [OBOL:automatic] xref: EMAPA:18184 xref: EMAPA:37481 {source="MA:th"} xref: FMA:19086 xref: MA:0000534 is_a: UBERON:0003833 {source="MA"} ! abdominal segment muscle is_a: UBERON:0005179 ! pelvic region element intersection_of: UBERON:0014892 {source="FMAdef"} ! skeletal muscle organ intersection_of: part_of UBERON:0002355 {source="FMAdef"} ! pelvic region of trunk [Term] id: UBERON:0001415 name: skin of pelvis namespace: uberon def: "A zone of skin that is part of a pelvis [Automatically generated definition]." [OBOL:automatic] synonym: "pelvic skin" EXACT [] synonym: "pelvis skin" EXACT [] synonym: "pelvis zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of pelvis" EXACT [OBOL:automatic] xref: EMAPA:37282 {source="MA:th"} xref: FMA:22984 xref: MA:0000546 xref: SCTID:181517009 is_a: UBERON:0003836 ! abdominal segment skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk [Term] id: UBERON:0001416 name: skin of abdomen namespace: uberon def: "A zone of skin that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] subset: efo_slim subset: pheno_slim synonym: "abdomen skin" EXACT [] synonym: "abdomen zone of skin" EXACT [OBOL:automatic] synonym: "abdominal skin" EXACT [] synonym: "skin of abdomen proper" EXACT [FMA:22988] synonym: "zone of skin of abdomen" EXACT [OBOL:automatic] xref: EFO:0000214 xref: FMA:22988 xref: FMA:23000 xref: MA:0000523 xref: NCIT:C52758 xref: SCTID:361707007 xref: UMLS:C0222166 {source="ncithesaurus:Abdominal_Skin"} is_a: UBERON:0003836 ! abdominal segment skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen [Term] id: UBERON:0001417 name: skin of neck namespace: uberon def: "A zone of skin that is part of a neck [Automatically generated definition]." [OBOL:automatic] synonym: "neck (volume) zone of skin" EXACT [OBOL:automatic] synonym: "neck skin" EXACT [] synonym: "neck zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of neck" EXACT [OBOL:automatic] synonym: "zone of skin of neck (volume)" EXACT [OBOL:automatic] xref: EMAPA:37277 {source="MA:th"} xref: FMA:23021 xref: FMA:23022 xref: MA:0000590 xref: NCIT:C52756 xref: SCTID:361705004 xref: UMLS:C0205030 {source="ncithesaurus:Neck_Skin"} is_a: UBERON:0012180 ! head or neck skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0001418 name: skin of thorax namespace: uberon def: "A zone of skin that is part of a thorax [Automatically generated definition]." [OBOL:automatic] synonym: "thoracic skin" EXACT [] synonym: "thorax skin" EXACT [] synonym: "thorax zone of skin" EXACT [OBOL:automatic] synonym: "upper body skin" RELATED [] synonym: "zone of skin of thorax" EXACT [OBOL:automatic] xref: EMAPA:37765 {source="MA:th"} xref: FMA:23028 xref: FMA:23029 xref: MA:0000564 xref: SCTID:281723000 is_a: UBERON:0001085 ! skin of trunk intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0001434 name: skeletal system namespace: uberon def: "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000027] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "set of all bones and joints" NARROW SENSU [] synonym: "skeleton system" EXACT [] synonym: "Skelettsystem" RELATED [BTO:0001486] xref: AAO:0000566 xref: BTO:0001486 xref: CALOHA:TS-1320 xref: EFO:0000806 xref: EHDAA2:0003168 xref: EMAPA:35773 xref: FMA:23881 xref: MA:0000018 xref: NCIT:C12788 xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA xref: TAO:0000434 xref: UMLS:C0037253 {source="ncithesaurus:Skeletal_System"} xref: VHOG:0001254 xref: VSAO:0000027 xref: XAO:0003060 xref: ZFA:0000434 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: has_part UBERON:0004288 ! skeleton intersection_of: has_part UBERON:0004770 ! articular system disjoint_from: UBERON:0001474 ! bone element disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system property_value: seeAlso https://github.com/obophenotype/uberon/wiki/The-skeletal-system xsd:anyURI property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "skeletal" xsd:string property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001444 name: subdivision of head namespace: uberon subset: non_informative synonym: "head region" RELATED [] synonym: "head subdivision" EXACT [] synonym: "region of head" RELATED [] xref: FMA:24218 xref: SCTID:123852005 xref: XAO:0000040 is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000033 ! head [Term] id: UBERON:0001456 name: face namespace: uberon def: "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc)." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "facia/facies" RELATED LATIN [Wikipedia:Face] synonym: "visage" RELATED [BTO:0003369] xref: BTO:0003369 xref: CALOHA:TS-2216 xref: EMAPA:32763 xref: FMA:24728 xref: GAID:64 xref: galen:Face xref: HAO:0000316 xref: MA:0002473 xref: MESH:D005145 xref: NCIT:C13071 xref: OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA xref: SCTID:302549007 xref: UMLS:C0015450 {source="ncithesaurus:Face"} xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head relationship: contributes_to_morphology_of UBERON:0000033 ! head relationship: has_part UBERON:0000165 ! mouth relationship: has_part UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! facial skeleton relationship: has_skeleton UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! facial skeleton property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg xsd:anyURI property_value: UBPROP:0000001 "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." xsd:string {source="FMA:24728"} property_value: UBPROP:0000001 "The area that extends from the median ocellus to the oral foramen[HAO]." xsd:string {source="HAO:0000316", source="http://api.hymao.org/api/ref/67791", taxon="NCBITaxon:7399"} property_value: UBPROP:0000007 "facial" xsd:string property_value: UBPROP:0000011 "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" xsd:string {source="vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf"} [Term] id: UBERON:0001458 name: skin of lip namespace: uberon def: "A zone of skin that is part of a lip [Automatically generated definition]." [OBOL:automatic] synonym: "lip skin" EXACT [] synonym: "lip zone of skin" EXACT [OBOL:automatic] synonym: "skin of lips" RELATED PLURAL [] synonym: "zone of skin of lip" EXACT [OBOL:automatic] xref: EMAPA:37643 {source="MA:th"} xref: FMA:24764 xref: MA:0001579 xref: NCIT:C12291 xref: SCTID:244092005 xref: UMLS:C0222101 {source="ncithesaurus:Skin_of_the_Lip"} is_a: UBERON:0001084 ! skin of head intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip [Term] id: UBERON:0001474 name: bone element namespace: uberon def: "Skeletal element that is composed of bone tissue." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/277, PSPUB:0000170, VSAO:0000057] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "bone" RELATED [AEO:0000082, BTO:0000140, MA:0001459, VHOG:0001190] synonym: "bone organ" EXACT [FMA:5018] synonym: "bones" RELATED PLURAL [ZFA:0001514] xref: AAO:0000047 xref: AEO:0000082 xref: BTO:0000140 xref: CALOHA:TS-0088 xref: EFO:0000298 xref: EHDAA2:0003082 xref: EMAPA:32782 xref: ENVO:00002039 xref: EV:0100140 xref: FMA:30317 xref: FMA:5018 xref: GAID:92 xref: galen:Bone xref: MA:0001459 xref: MAT:0000299 xref: MIAA:0000299 xref: NCIT:C12366 xref: OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA xref: SCTID:90780006 xref: TAO:0001514 xref: UMLS:C0262950 {source="ncithesaurus:Bone"} xref: VHOG:0001190 xref: VSAO:0000057 xref: Wikipedia:Bone xref: XAO:0000169 xref: ZFA:0001514 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: UBPROP:0000001 "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000001 "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} property_value: UBPROP:0000003 "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001484 name: articular capsule namespace: uberon def: "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." [Wikipedia:Articular_capsule] subset: organ_slim subset: uberon_slim synonym: "capsula articularis" EXACT LATIN [FMA:34836, FMA:TA] synonym: "capsulae articulares" RELATED LATIN [Wikipedia:Articular_capsule] synonym: "fibrous capsule of joint" EXACT [] synonym: "joint capsule" EXACT [] synonym: "joint fibrous capsule" EXACT [] xref: EMAPA:37621 {source="MA:th"} xref: FMA:34836 xref: GAID:263 xref: galen:JointCapsule xref: MA:0001519 xref: MESH:D017746 xref: NCIT:C32259 xref: NCIT:C84388 xref: SCTID:182238002 xref: UMLS:C0206207 {source="ncithesaurus:Joint_Capsule"} xref: Wikipedia:Articular_capsule is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000094 ! membrane organ intersection_of: UBERON:0000094 ! membrane organ intersection_of: has_part UBERON:0007616 ! layer of synovial tissue intersection_of: surrounds UBERON:0002217 ! synovial joint relationship: has_part UBERON:0007616 ! layer of synovial tissue relationship: surrounds UBERON:0002217 ! synovial joint property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png xsd:anyURI property_value: UBPROP:0000012 "check ncita" xsd:string {external_ontology="ncit"} [Term] id: UBERON:0001497 name: muscle of pelvic girdle namespace: uberon alt_id: UBERON:0003271 def: "Any muscle organ that is part of a pelvic girdle [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "girdle-pelvic muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of girdle-pelvic" EXACT [OBOL:automatic] synonym: "muscle organ of pelvic girdle" EXACT [OBOL:automatic] synonym: "muscle organ of pelvic girdle bone" EXACT [OBOL:automatic] synonym: "pelvic girdle muscle" EXACT [] synonym: "pelvic girdle muscle organ" EXACT [OBOL:automatic] synonym: "pelvic girdle skeletal muscle" EXACT [EMAPA:18185] xref: EHDAA:8326 xref: EMAPA:18184 xref: EMAPA:18185 xref: FMA:37367 xref: MA:0000537 xref: RETIRED_EHDAA2:0001430 is_a: UBERON:0001325 ! muscle of pelvis is_a: UBERON:0010890 ! pelvic complex muscle intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0004470 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! musculature of pelvic girdle property_value: UBPROP:0000012 "Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle." xsd:string {external_ontology="MA"} [Term] id: UBERON:0001514 name: descending aorta namespace: uberon def: "The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]." [GO:0035906, Wikipedia:Descending_aorta] subset: pheno_slim subset: uberon_slim synonym: "aorta descendens" RELATED LATIN [Wikipedia:Descending_aorta] synonym: "aorta descendens" RELATED [Wikipedia:Descending_aorta] synonym: "pars descendens aortae" EXACT [FMA:3784] synonym: "pars descendens aortae" RELATED LATIN [Wikipedia:Descending_aorta] xref: EMAPA:18606 xref: FMA:3784 xref: MA:0002571 xref: NCIT:C32455 xref: OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA xref: SCTID:261399002 xref: UMLS:C0011666 {source="ncithesaurus:Descending_Aorta"} xref: Wikipedia:Descending_aorta is_a: UBERON:0005800 {source="FMA"} ! section of aorta relationship: develops_from UBERON:0005805 {source="Wikipedia"} ! dorsal aorta relationship: has_developmental_contribution_from UBERON:0005613 ! left dorsal aorta relationship: has_developmental_contribution_from UBERON:0005622 ! right dorsal aorta property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg xsd:anyURI property_value: UBPROP:0000011 "results from fusion of left and right dorsal aortae" xsd:string [Term] id: UBERON:0001515 name: thoracic aorta namespace: uberon def: "the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest" [http://www.medterms.com, MP:0010468] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "aorta thoracalis" RELATED LATIN [Wikipedia:Thoracic_aorta] synonym: "aorta thoracica" EXACT LATIN [FMA:3786, FMA:TA] synonym: "pars thoracica aortae" RELATED LATIN [Wikipedia:Thoracic_aorta] synonym: "thoracic part of aorta" EXACT [] xref: BTO:0000157 xref: EFO:0002525 xref: EMAPA:18603 xref: FMA:3786 xref: GAID:471 xref: galen:ThoracicAorta xref: MA:0002569 xref: MESH:D001013 xref: NCIT:C33766 xref: OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA xref: SCTID:302510009 xref: UMLS:C1522460 {source="ncithesaurus:Thoracic_Aorta"} xref: Wikipedia:Thoracic_aorta is_a: UBERON:0005800 {source="FMA"} ! section of aorta intersection_of: UBERON:0005800 ! section of aorta intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: contributes_to_morphology_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000915 ! thoracic segment of trunk property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png xsd:anyURI [Term] id: UBERON:0001516 name: abdominal aorta namespace: uberon def: "Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]." [BTO:0002976, Wikipedia:Abdominal_aorta] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "abdominal part of aorta" EXACT [FMA:3789] synonym: "abdominal part of aorta" RELATED [BTO:0002976] synonym: "aorta abdominalis" RELATED [BTO:0002976] synonym: "aorta abdominalis" RELATED LATIN [Wikipedia:Abdominal_aorta] synonym: "descending abdominal aorta" EXACT [FMA:3789] synonym: "pars abdominalis aortae" EXACT [FMA:3789] synonym: "pars abdominalis aortae" RELATED LATIN [Wikipedia:Abdominal_aorta] synonym: "pars abdominalis aortae" RELATED [BTO:0002976] xref: BTO:0002976 xref: EFO:0002524 xref: EMAPA:17856 xref: FMA:3789 xref: GAID:470 xref: galen:AbdominalAorta xref: MA:0000474 xref: MESH:D001012 xref: NCIT:C32038 xref: OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA xref: SCTID:244231007 xref: UMLS:C0003484 {source="ncithesaurus:Abdominal_Aorta"} xref: Wikipedia:Abdominal_aorta is_a: UBERON:0005800 ! section of aorta relationship: contributes_to_morphology_of UBERON:0001514 ! descending aorta relationship: part_of UBERON:0001514 {source="FMA"} ! descending aorta property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png xsd:anyURI property_value: editor_note "Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates" xsd:string [Term] id: UBERON:0001530 name: common carotid artery plus branches namespace: uberon def: "A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]." [Wikipedia:Common_carotid_artery] subset: pheno_slim subset: uberon_slim synonym: "a. carotis communis" RELATED LATIN [Wikipedia:Common_carotid_artery] synonym: "carotid artery" BROAD [FMA:3939] synonym: "carotid artery system" EXACT [EHDAA2:0000217] synonym: "common carotid artery" EXACT INCONSISTENT [FMA:3939] synonym: "trunk of common carotid tree" EXACT [FMA:3939] xref: CALOHA:TS-0116 xref: EHDAA2:0000217 xref: EHDAA:7331 xref: EMAPA:17855 xref: FMA:3939 xref: GAID:479 xref: MA:0001926 xref: MESH:D017536 xref: NCIT:C32352 xref: SCTID:362041005 xref: UMLS:C0162859 {source="ncithesaurus:Common_Carotid_Artery"} xref: VHOG:0000272 xref: Wikipedia:Common_carotid_artery is_a: UBERON:0004573 {source="FMA"} ! systemic artery is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0004363 {source="Wikipedia"} ! pharyngeal arch artery relationship: existence_starts_during UBERON:0000068 ! embryo stage property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg xsd:anyURI property_value: editor_note "we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'" xsd:string property_value: IAO:0000232 "This class represents the adult and developing structures'" xsd:string property_value: UBPROP:0000011 "in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae" xsd:string [Term] id: UBERON:0001555 name: digestive tract namespace: uberon def: "A tube extending from the mouth to the anus." [https://github.com/geneontology/go-ontology/issues/7549, Wikipedia:Talk\:Human_gastrointestinal_tract] subset: uberon_slim subset: vertebrate_core synonym: "alimentary canal" NARROW [] synonym: "alimentary tract" NARROW [] synonym: "digestive canal" RELATED [BTO:0000058] synonym: "digestive tube" EXACT [] synonym: "enteric tract" EXACT [ZFA:0000112] synonym: "gut" BROAD [] synonym: "gut tube" RELATED [] xref: AAO:0010023 xref: BILA:0000083 xref: BTO:0000511 xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 xref: FBbt:00003125 xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 xref: NCIT:C34082 xref: OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA xref: TAO:0000112 xref: TGMA:0001819 xref: UMLS:C0017189 {source="ncithesaurus:Gastrointestinal_Tract"} xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000025 ! tube relationship: connects UBERON:0000165 ! mouth relationship: develops_from UBERON:0007026 ! presumptive gut relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string [Term] id: UBERON:0001558 name: lower respiratory tract namespace: uberon def: "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]" [http://orcid.org/0000-0002-6601-2165, Wikipedia:Lower_respiratory_tract] subset: pheno_slim subset: uberon_slim synonym: "lower respiratory system" EXACT [] xref: EHDAA2:0001036 xref: EMAPA:16738 xref: FMA:45662 xref: MA:0000435 xref: OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g xref: SCTID:281488008 xref: VHOG:0000382 xref: Wikipedia:Lower_respiratory_tract is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: has_part UBERON:0000170 ! pair of lungs property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg xsd:anyURI [Term] id: UBERON:0001586 name: internal jugular vein namespace: uberon def: "One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]." [Wikipedia:Internal_jugular_vein] subset: uberon_slim synonym: "internal jugular" EXACT [EHDAA2:0000877] synonym: "internal jugular venous tree" EXACT [] synonym: "vena jugularis interna" RELATED LATIN [Wikipedia:Internal_jugular_vein] xref: AAO:0010236 xref: EHDAA2:0000877 xref: EHDAA:5407 xref: EMAPA:17620 xref: FMA:4724 xref: galen:InternalJugularVein xref: MA:0002157 xref: NCIT:C32849 xref: OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0000878 xref: SCTID:181372005 xref: UMLS:C0226550 {source="ncithesaurus:Internal_Jugular_Vein"} xref: Wikipedia:Internal_jugular_vein xref: XAO:0000382 is_a: UBERON:0004711 ! jugular vein relationship: drains UBERON:0000955 ! brain relationship: drains UBERON:0001456 ! face property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png xsd:anyURI property_value: UBPROP:0000001 "Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010236", ontology="AAO", source="AAO:BJB"} [Term] id: UBERON:0001605 name: ciliary muscle namespace: uberon def: "The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]." [Wikipedia:Ciliary_muscle] subset: pheno_slim subset: uberon_slim synonym: "Bowman`s muscles" RELATED [BTO:0000654] synonym: "ciliaris" RELATED [Wikipedia:Ciliary_muscle] synonym: "musculus ciliaris" RELATED LATIN [Wikipedia:Ciliary_muscle] synonym: "musculus ciliarus" EXACT [BTO:0000654] xref: BTO:0000654 xref: EMAPA:35240 xref: FMA:49151 xref: MA:0001269 xref: NCIT:C32315 xref: SCTID:280862009 xref: UMLS:C0559230 {source="ncithesaurus:Ciliary_Muscle"} xref: Wikipedia:Ciliary_muscle is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png xsd:anyURI [Term] id: UBERON:0001606 name: muscle of iris namespace: uberon def: "." [Wikipedia:Iris_muscle] subset: uberon_slim synonym: "iris muscle" EXACT [] synonym: "iris muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of iris" EXACT [OBOL:automatic] xref: EMAPA:35448 xref: FMA:49154 xref: MA:0001287 xref: SCTID:280888007 xref: Wikipedia:Iris_muscle is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0001769 ! iris property_value: editor_note "revisit this, see issue #331" xsd:string property_value: UBPROP:0000008 "in aves, stromal mesenchymal cells may migrate to the iris and become skeletal" xsd:string property_value: UBPROP:0000008 "The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]" xsd:string [Term] id: UBERON:0001612 name: facial artery namespace: uberon def: "A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]." [Wikipedia:Facial_artery] subset: uberon_slim synonym: "arteria maxillaris externa" RELATED LATIN [Wikipedia:Facial_artery] synonym: "external maxillary artery" RELATED [] xref: EMAPA:19213 xref: FMA:49549 xref: MA:0001950 xref: NCIT:C32578 xref: OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA xref: SCTID:181328007 xref: UMLS:C0226109 {source="ncithesaurus:Facial_Artery"} xref: Wikipedia:Facial_artery is_a: UBERON:0035398 ! branch of external carotid artery intersection_of: UBERON:0001637 ! artery intersection_of: branching_part_of UBERON:0001070 ! external carotid artery intersection_of: supplies UBERON:0001456 ! face relationship: supplies UBERON:0001456 ! face property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png xsd:anyURI [Term] id: UBERON:0001616 name: maxillary artery namespace: uberon def: "An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]." [Wikipedia:Maxillary_artery] subset: uberon_slim synonym: "arteria maxillaris" RELATED LATIN [Wikipedia:Maxillary_artery] synonym: "internal maxillary artery" RELATED [] xref: EHDAA2:0001069 xref: EHDAA:7357 xref: EMAPA:17311 xref: FMA:49675 xref: GAID:498 xref: MA:0001919 xref: MESH:D008438 xref: NCIT:C34205 xref: OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA xref: SCTID:181326006 xref: UMLS:C0024949 {source="ncithesaurus:Maxillary_Artery"} xref: Wikipedia:Maxillary_artery is_a: UBERON:0001637 ! artery is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001637 ! artery intersection_of: directly_develops_from UBERON:0003118 ! pharyngeal arch artery 1 relationship: develops_from UBERON:0003118 ! pharyngeal arch artery 1 relationship: directly_develops_from UBERON:0003118 ! pharyngeal arch artery 1 property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png xsd:anyURI property_value: UBPROP:0000011 "...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries" xsd:string {source="http://download.videohelp.com/vitualis/med/Vascular_Devt.html"} [Term] id: UBERON:0001630 name: muscle organ namespace: uberon def: "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]." [GO:0007517] subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] xref: AAO:0011066 xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 xref: GAID:131 xref: galen:Muscle xref: MA:0000015 xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA xref: SCTID:71616004 xref: TAO:0005145 xref: VHOG:0001245 xref: XAO:0000172 xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue relationship: composed_primarily_of UBERON:0002385 ! muscle tissue relationship: part_of UBERON:0001015 ! musculature property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "muscular" xsd:string [Term] id: UBERON:0001637 name: artery namespace: uberon def: "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." [AEO:JB] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arterial subtree" EXACT [] synonym: "arterial system" RELATED [] synonym: "arterial tree organ part" EXACT [] synonym: "arterial vessel" RELATED [] synonym: "arteries" EXACT PLURAL [TAO:0000005] xref: AAO:0010211 xref: AEO:0000208 xref: BTO:0000573 xref: CALOHA:TS-0054 xref: EFO:0000814 xref: EHDAA2:0000143 xref: EHDAA2:0003253 xref: EMAPA:35147 xref: EV:0100026 xref: FMA:50720 xref: GAID:468 xref: galen:Artery xref: MA:0000064 xref: MAT:0000034 xref: MESH:D001158 xref: MIAA:0000034 xref: NCIT:C12372 xref: OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA xref: SCTID:362877004 xref: TAO:0000005 xref: UMLS:C0003842 {source="ncithesaurus:Artery"} xref: VHOG:0001251 xref: Wikipedia:Artery xref: XAO:0000114 xref: ZFA:0000005 is_a: UBERON:0003509 ! arterial blood vessel relationship: channels_from UBERON:0000948 ! heart property_value: editor_note "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010211", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001251", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "arterial" xsd:string property_value: UBPROP:0000202 FMA:63812 [Term] id: UBERON:0001638 name: vein namespace: uberon def: "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [Wikipedia:Vein] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "vascular element" RELATED [EMAPA:th] synonym: "vena" RELATED LATIN [Wikipedia:Vein] synonym: "venae" RELATED PLURAL [VHOG:0001743] synonym: "venous subtree" BROAD [] synonym: "venous tree organ part" EXACT [] synonym: "venous vessel" BROAD [] xref: AAO:0010212 xref: AEO:0000209 xref: BTO:0000234 xref: CALOHA:TS-1108 xref: EFO:0000816 xref: EHDAA2:0003254 xref: EMAPA:35906 xref: EV:0100031 xref: FMA:50723 xref: GAID:492 xref: galen:Vein xref: MA:0000067 xref: MAT:0000037 xref: MESH:D014680 xref: MIAA:0000037 xref: NCIT:C12814 xref: OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA xref: SCTID:181367001 xref: TAO:0000082 xref: UMLS:C0042449 {source="ncithesaurus:Vein"} xref: VHOG:0001743 xref: Wikipedia:Vein xref: XAO:0000115 xref: ZFA:0000082 is_a: UBERON:0003920 ! venous blood vessel intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg xsd:anyURI property_value: editor_note "TODO - check with MA - vein vs venous blood vessel" xsd:string property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010212", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001743", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "venous" xsd:string property_value: UBPROP:0000202 FMA:63814 [Term] id: UBERON:0001651 name: right pulmonary artery namespace: uberon def: "The pulmonary artery that supplies the right lung." [UBERON:cjm] subset: uberon_slim synonym: "arteria pulmonalis dextra" RELATED LATIN [Wikipedia:Right_pulmonary_artery] synonym: "right main pulmonary artery" EXACT [] synonym: "right pulmonary arterial tree" EXACT [] xref: EMAPA:37378 {source="MA:th"} xref: FMA:50872 xref: galen:RightPulmonaryArtery xref: MA:0002500 xref: NCIT:C33489 xref: SCTID:244235003 xref: UMLS:C0923924 {source="ncithesaurus:Right_Pulmonary_Artery"} xref: Wikipedia:Right_pulmonary_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0002167 ! right lung relationship: supplies UBERON:0002167 ! right lung property_value: depicted:by Alveoli:diagram.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png xsd:anyURI property_value: editor_note "TODO - add class 'pulmonary artery tree organ'" xsd:string [Term] id: UBERON:0001652 name: left pulmonary artery namespace: uberon def: "The pulmonary artery that supplies the left lung." [UBERON:cjm] subset: uberon_slim synonym: "arteria pulmonalis sinistra" RELATED LATIN [Wikipedia:Left_pulmonary_artery] synonym: "left main pulmonary artery" EXACT [] synonym: "left pulmonary arterial tree" EXACT [] xref: EMAPA:37097 {source="MA:th"} xref: FMA:50873 xref: galen:LeftPulmonaryArtery xref: MA:0002032 xref: NCIT:C32971 xref: SCTID:244234004 xref: UMLS:C0923925 {source="ncithesaurus:Left_Pulmonary_Artery"} xref: Wikipedia:Left_pulmonary_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0002168 ! left lung relationship: supplies UBERON:0002168 ! left lung property_value: depicted:by Alveoli:diagram.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png xsd:anyURI property_value: editor_note "TODO - add class 'pulmonary artery tree organ'" xsd:string [Term] id: UBERON:0001653 name: facial vein namespace: uberon def: "The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]." [Wikipedia:Facial_vein] subset: uberon_slim synonym: "anterior facial vein" RELATED INCONSISTENT [Wikipedia:Facial_vein] synonym: "face vein" EXACT [OBOL:automatic] synonym: "vein of face" EXACT [OBOL:automatic] synonym: "vena facialis anterior" RELATED LATIN [Wikipedia:Facial_vein] xref: AAO:0010513 xref: EMAPA:19220 xref: FMA:50874 xref: MA:0002115 xref: NCIT:C32579 xref: OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA xref: SCTID:181374006 xref: UMLS:C0226532 {source="ncithesaurus:Facial_Vein"} xref: Wikipedia:Facial_vein is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001586 ! internal jugular vein relationship: tributary_of UBERON:0001586 {source="FMA"} ! internal jugular vein property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png xsd:anyURI property_value: UBPROP:0000001 "Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010513", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000012 "MA and NCITA also has 'anterior facial vein'" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001676 name: occipital bone namespace: uberon def: "the bone at the lower, posterior part of the skull" [ISBN:0-683-40008-8, MP:0005269] subset: pheno_slim subset: uberon_slim synonym: "occipital complex" RELATED [http://palaeos.com/vertebrates/bones/braincase/occiput.html] synonym: "occipital squama" RELATED [] synonym: "os occipitale" RELATED LATIN [Wikipedia:Occipital_bone] xref: EMAPA:25112 xref: FMA:52735 xref: GAID:227 xref: MA:0001468 xref: MESH:D009777 xref: NCIT:C12757 xref: OpenCyc:Mx4rwQtsiZwpEbGdrcN5Y29ycA xref: SCTID:181796003 xref: UMLS:C0028784 {source="ncithesaurus:Occipital_Bone"} xref: Wikipedia:Occipital_bone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0011164 ! neurocranium bone relationship: develops_from UBERON:0003089 {source="PMID:11523816"} ! sclerotome relationship: only_in_taxon NCBITaxon:117570 {source="WP"} ! Teleostomi relationship: part_of UBERON:0005902 {source="FMA"} ! occipital region relationship: surrounds UBERON:0003687 ! foramen magnum property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png xsd:anyURI property_value: UBPROP:0000008 "formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII" xsd:string {source="PMID:11523816"} property_value: UBPROP:0000008 "fusion of basi-, exo- and supra-occipitals (and maybe tabular)" xsd:string {source="Kardong"} [Term] id: UBERON:0001703 name: neurocranium namespace: uberon def: "Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof." [PMID:11523816, TAO:MAH, Wikipedia:Neuroranium, ZFA:0001580] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "brain box" EXACT [] synonym: "brain case" RELATED [ZFA:0001580] synonym: "brain pan" RELATED [http://www.thefreedictionary.com/braincase] synonym: "braincase" RELATED [ZFA:0001580] xref: AAO:0010153 xref: EHDAA2:0000243 xref: EMAPA:17681 xref: FMA:53672 xref: MA:0000317 xref: SCTID:361731002 xref: TAO:0001580 xref: Wikipedia:Neuroranium xref: XAO:0003170 xref: ZFA:0001580 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull relationship: develops_from UBERON:0004761 ! cartilaginous neurocranium relationship: location_of UBERON:0000955 ! brain relationship: part_of UBERON:0003128 ! cranium relationship: protects UBERON:0000955 ! brain property_value: UBPROP:0000001 "Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001580", ontology="TAO", source="TAO:MAH"} property_value: UBPROP:0000007 "neurocranial" xsd:string property_value: UBPROP:0000010 "It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" xsd:string property_value: UBPROP:0000011 "The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]." xsd:string {source="WP"} property_value: UBPROP:0000012 "It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ..." xsd:string {external_ontology="MA"} [Term] id: UBERON:0001708 name: jaw skeleton namespace: uberon def: "Subdivision of skeleton which includes upper and lower jaw skeletons." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Jaw] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "anterior splanchnocranium" RELATED [] synonym: "jaw" EXACT [MA:0001905] synonym: "jaw cartilage" EXACT [ZFA:0001227] synonym: "jaws" RELATED [] synonym: "mandibular arch" RELATED [TAO:0001227] synonym: "mandibular arch skeleton" EXACT [ZFA:0001227] synonym: "oral jaw skeleton" RELATED [] synonym: "pharyngeal arch 1 skeleton" RELATED [] synonym: "visceral arch 1" RELATED [] xref: AAO:0000988 xref: BTO:0001749 xref: EMAPA:35455 xref: FMA:54396 xref: GAID:214 xref: galen:Jaw xref: MA:0001905 xref: MESH:D007568 xref: NCIT:C48821 xref: OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA xref: SCTID:181811001 xref: TAO:0001227 xref: UMLS:C0022359 {source="ncithesaurus:Jaw"} xref: Wikipedia:Jaw xref: ZFA:0001227 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0011595 ! jaw region relationship: capable_of NBO:0000073 ! chewing relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0011156 {source="cjm"} ! facial skeleton relationship: part_of UBERON:0011595 ! jaw region relationship: skeleton_of UBERON:0011595 ! jaw region property_value: editor_note "TODO - move ZFA:0001227 (it is the entire jaw skeleton)." xsd:string property_value: UBPROP:0000001 "Skeletal and cartilage elements of the first pharyngeal arch.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001227", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000011 "There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983)." xsd:string property_value: UBPROP:0000012 "in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001710 name: lower jaw region namespace: uberon def: "Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]." [Wikipedia:Lower_jaw] comment: See notes for jaw w.r.t skeletal element vs subdivision of head subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "lower part of mouth" RELATED [] synonym: "mandibular part of mouth" EXACT [FMA:59398] synonym: "mandibular series" RELATED [] xref: AAO:0000272 xref: EFO:0003660 xref: EHDAA2:0001018 xref: EHDAA:7995 xref: EMAPA:17906 xref: FMA:59398 xref: MESH:D008334 xref: ncithesaurus:Lower_Jaw xref: SCTID:362637005 xref: VHOG:0000453 xref: Wikipedia:Lower_jaw is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000475 ! organism subdivision intersection_of: has_skeleton UBERON:0003278 ! skeleton of lower jaw relationship: develops_from UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! mandibular prominence relationship: has_skeleton UBERON:0003278 ! skeleton of lower jaw relationship: part_of UBERON:0011595 ! jaw region property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png xsd:anyURI property_value: UBPROP:0000001 "Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000272", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000453", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "Note isa/partof difference MA/FMA" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001731 name: cavity of pharynx namespace: uberon def: "A anatomical space that is enclosed by a pharynx." [OBOL:automatic] synonym: "cavitas pharyngealis" RELATED LATIN [] synonym: "cavitas pharyngis" RELATED [BTO:0002097] synonym: "lumen of pharynx" EXACT [] synonym: "pharyngeal cavity" EXACT [] xref: AAO:0010435 xref: BSA:0000113 xref: BTO:0002097 xref: EMAPA:18381 xref: FMA:54935 xref: SCTID:180543003 xref: XAO:0000105 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0006562 ! pharynx relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut relationship: luminal_space_of UBERON:0006562 ! pharynx relationship: part_of UBERON:0006562 ! pharynx property_value: UBPROP:0000008 "See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship" xsd:string property_value: UBPROP:0000011 "TOODO check" xsd:string [Term] id: UBERON:0001766 name: anterior chamber of eyeball namespace: uberon def: "the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens" [MESH:A09.371.060.067, MP:0005205] subset: pheno_slim synonym: "anterior chamber" EXACT [HP:0000593, MP:0010709] synonym: "anterior chamber of eye" EXACT [] synonym: "camera anterior" EXACT [] synonym: "camera anterior bulbi" RELATED [BTO:0002084] synonym: "camera anterior bulbi oculi" RELATED LATIN [Wikipedia:Anterior_chamber_of_eyeball] synonym: "camera oculi anterior" RELATED [BTO:0002084] synonym: "eye anterior chamber" EXACT [] xref: BTO:0002084 xref: EHDAA2:0000129 xref: EHDAA:9033 xref: EMAPA:18231 xref: FMA:58078 xref: GAID:889 xref: MA:0000262 xref: MESH:D000867 xref: NCIT:C12667 xref: SCTID:181160009 xref: UMLS:C0003151 {source="ncithesaurus:Anterior_Chamber_of_the_Eye"} xref: VHOG:0001431 xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: UBPROP:0000001 "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001431", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/anterior+chamber"} property_value: UBPROP:0000012 "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0001768 name: uvea namespace: uberon def: "the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]." [MP:0005197, Wikipedia:Uvea] subset: pheno_slim subset: uberon_slim synonym: "pars iridica retinae" RELATED [Wikipedia:Uvea] synonym: "tunica vasculatis oculi" RELATED [Wikipedia:Uvea] synonym: "tunica vasculosa bulbi" RELATED LATIN [Wikipedia:Uvea] synonym: "tunica vasculosa of eyeball" EXACT [FMA:58103] synonym: "uvea" EXACT [FMA:58103] synonym: "uveal tract" EXACT [FMA:58103] synonym: "vascular layer of eyeball" RELATED [FMA:58103] xref: CALOHA:TS-2228 xref: EMAPA:35901 xref: FMA:58103 xref: GAID:912 xref: MA:0002480 xref: MESH:D014602 xref: NCIT:C12811 xref: SCTID:280648000 xref: UMLS:C0042160 {source="ncithesaurus:Uvea"} xref: Wikipedia:Uvea is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png xsd:anyURI property_value: editor_note "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} property_value: UBPROP:0000007 "uveal" xsd:string [Term] id: UBERON:0001769 name: iris namespace: uberon def: "the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye" [ISBN:0-683-40008-8, MP:0001322] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "anterior uvea" RELATED [] synonym: "irides" RELATED PLURAL [] synonym: "irises" RELATED PLURAL [VHOG:0000101] xref: AAO:0010347 xref: BTO:0000653 xref: CALOHA:TS-0491 xref: EFO:0004245 xref: EMAPA:19154 xref: EV:0100345 xref: FMA:58235 xref: GAID:917 xref: MA:0000273 xref: MESH:D007498 xref: NCIT:C12737 xref: OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA xref: SCTID:181164000 xref: TAO:0001238 xref: UMLS:C0022077 {source="ncithesaurus:Iris"} xref: VHOG:0000101 xref: Wikipedia:Iris_(anatomy) xref: XAO:0000185 xref: ZFA:0001238 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea relationship: develops_from UBERON:0004128 {source="XAO"} ! optic vesicle relationship: part_of UBERON:0011892 ! anterior uvea property_value: UBPROP:0000001 "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "iridial" xsd:string property_value: UBPROP:0000008 "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" xsd:string [Term] id: UBERON:0001772 name: corneal epithelium namespace: uberon def: "the smooth stratified squamous epithelium that covers the outer surface of the cornea" [MESH:A09.371.060.217.325, MGI:smb, MP:0006000] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "anterior corneal epithelium" EXACT [] synonym: "anterior endothelium of cornea" RELATED [BTO:0000287] synonym: "cornea epithelial tissue" EXACT [OBOL:automatic] synonym: "cornea epithelium" EXACT [OBOL:automatic] synonym: "e. anterius corneae" RELATED LATIN [Wikipedia:Corneal_epithelium] synonym: "endothelium anterius corneae" RELATED [BTO:0000287] synonym: "endothelium camerae anterioris bulbi" RELATED [BTO:0000287] synonym: "endothelium corneale" RELATED [BTO:0000287] synonym: "epithelial tissue of cornea" EXACT [OBOL:automatic] synonym: "epithelium anterius (cornea)" EXACT [] synonym: "epithelium anterius corneae" EXACT LATIN [FMA:58263, FMA:TA] synonym: "epithelium corneæ anterior layer" EXACT [] synonym: "epithelium of cornea" EXACT [] synonym: "epithelium posterius corneae" RELATED [BTO:0000287] synonym: "external epithelium of cornea" EXACT [] xref: BTO:0000287 xref: CALOHA:TS-0173 xref: EFO:0001917 xref: EHDAA2:0000319 xref: EMAPA:17162 xref: FMA:58263 xref: GAID:895 xref: MA:0001243 xref: MESH:D019573 xref: NCIT:C12928 xref: SCTID:368825001 xref: TAO:0002187 xref: UMLS:C0459875 {source="ncithesaurus:Corneal_Epithelium"} xref: Wikipedia:Corneal_epithelium xref: ZFA:0001683 is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea relationship: contributes_to_morphology_of UBERON:0000964 ! cornea relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm relationship: part_of UBERON:0000964 ! cornea property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png xsd:anyURI property_value: UBPROP:0000001 "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002187", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} property_value: UBPROP:0000008 "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" xsd:string property_value: UBPROP:0000008 "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string [Term] id: UBERON:0001773 name: sclera namespace: uberon def: "Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]." [Wikipedia:Sclera, ZFIN:ZDB-PUB-050701-15] comment: Disease notes: implicated in rheumatoid arthritis. subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "scleral capsule" RELATED [] xref: AAO:0010354 xref: BTO:0001606 xref: EMAPA:19027 xref: EV:0100342 xref: FMA:58269 xref: GAID:911 xref: MA:0000280 xref: MESH:D012590 xref: NCIT:C12784 xref: OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA xref: SCTID:181163006 xref: UMLS:C0036410 {source="ncithesaurus:Sclera"} xref: VHOG:0001274 xref: Wikipedia:Sclera xref: XAO:0000183 xref: ZFA:0005563 is_a: UBERON:0000064 ! organ part is_a: UBERON:0010313 ! neural crest-derived structure relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme relationship: has_part CL:0000347 {source="ZFA"} ! scleral cell relationship: has_quality PATO:0000963 ! opaque relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: UBPROP:0000001 "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." xsd:string {source="Wikipedia:Sclera"} property_value: UBPROP:0000001 "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001274", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sclera"} property_value: UBPROP:0000007 "scleral" xsd:string property_value: UBPROP:0000008 "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" xsd:string property_value: UBPROP:0000010 "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." xsd:string property_value: UBPROP:0000011 "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." xsd:string property_value: UBPROP:0000011 "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." xsd:string [Term] id: UBERON:0001774 name: skeletal muscle of trunk namespace: uberon def: "A skeletal muscle organ that is part of the trunk region." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim subset: vertebrate_core synonym: "body musculature" EXACT [ZFA:0000473] synonym: "muscle of trunk" EXACT [FMA:58274] synonym: "muscle organ of torso" EXACT [OBOL:automatic] synonym: "muscle organ of trunk" EXACT [OBOL:automatic] synonym: "torso muscle organ" EXACT [OBOL:automatic] synonym: "trunk muscle" EXACT [] synonym: "trunk muscle organ" EXACT [OBOL:automatic] synonym: "trunk musculature" EXACT [] xref: AAO:0000611 xref: EMAPA:35888 xref: FMA:58274 xref: MA:0000514 xref: TAO:0000473 xref: XAO:0003230 xref: ZFA:0000473 is_a: UBERON:0005177 ! trunk region element is_a: UBERON:0014892 ! skeletal muscle organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0004479 {source="prolog"} ! musculature of trunk property_value: editor_note "Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'." xsd:string property_value: UBPROP:0000012 "Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here." xsd:string [Term] id: UBERON:0001775 name: ciliary body namespace: uberon def: "the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes" [ISBN:0-683-40008-8, MP:0005099, Wikipedia:Ciliary_body] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "anterior uvea" RELATED [] synonym: "ciliary bodies" RELATED PLURAL [VHOG:0000102] synonym: "corpus ciliare" RELATED LATIN [Wikipedia:Ciliary_body] synonym: "corpus ciliare" RELATED [Wikipedia:Ciliary_body] synonym: "ocular ciliary body" EXACT [] xref: AAO:0010341 xref: BTO:0000260 xref: CALOHA:TS-0694 xref: EMAPA:19065 xref: EV:0100346 xref: FMA:58295 xref: GAID:916 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1571 xref: MA:0000264 xref: MESH:D002924 xref: NCIT:C12345 xref: SCTID:263340007 xref: UMLS:C0008779 {source="ncithesaurus:Ciliary_Body"} xref: VHOG:0000102 xref: Wikipedia:Ciliary_body xref: XAO:0000186 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm relationship: has_part UBERON:0001605 ! ciliary muscle relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000102", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001776 name: optic choroid namespace: uberon def: "vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]." [Wikipedia:Choroid] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "chorioid" RELATED [BTO:0001829] synonym: "choroid" EXACT [MA:0000263] synonym: "choroid coat" EXACT [Wikipedia:Choroid] synonym: "choroidea" EXACT [Wikipedia:Choroid] synonym: "choroidea" RELATED LATIN [Wikipedia:Choroid] synonym: "eye choroid" EXACT [VHOG:0001568] synonym: "optic choroid" RELATED [ZFA:0005229] synonym: "posterior uvea" EXACT [Wikipedia:Uvea#Regions] xref: BTO:0001829 xref: CALOHA:TS-2054 xref: EMAPA:19077 xref: EV:0100347 xref: FMA:58298 xref: GAID:913 xref: MA:0000263 xref: MESH:D002829 xref: NCIT:C12344 xref: SCTID:181172003 xref: TAO:0005229 xref: UMLS:C0008520 {source="ncithesaurus:Choroid"} xref: VHOG:0001568 xref: Wikipedia:Choroid xref: ZFA:0005229 is_a: UBERON:0002203 ! vasculature of eye disjoint_from: UBERON:0011892 {source="lexical"} ! anterior uvea relationship: adjacent_to UBERON:0000966 ! retina relationship: adjacent_to UBERON:0001773 ! sclera relationship: adjacent_to UBERON:0011892 ! anterior uvea relationship: contributes_to_morphology_of UBERON:0001768 ! uvea relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: editor_note "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string property_value: UBPROP:0000007 "choroidal" xsd:string property_value: UBPROP:0000012 "MP treats posterior uvea and optic choroid as distinct" xsd:string {external_ontology="MP"} [Term] id: UBERON:0001777 name: substantia propria of cornea namespace: uberon def: "the lamellated connective tissue of the cornea between the Bowman and Descemet membranes" [ISBN:0-683-40008-8, MESH:A09.371.060.217.228, MP:0005300] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "corneal stroma" EXACT [MA:0001245] synonym: "stroma of cornea" EXACT [] synonym: "substantia propria" BROAD [] synonym: "substantia propria corneae" EXACT LATIN [FMA:58306, FMA:TA] xref: CALOHA:TS-1138 xref: EFO:0002514 xref: EMAPA:17602 xref: FMA:58306 xref: GAID:893 xref: MA:0001245 xref: MESH:D003319 xref: NCIT:C12699 xref: SCTID:362511000 xref: TAO:0002189 xref: UMLS:C0010040 {source="ncithesaurus:Corneal_Stroma"} xref: Wikipedia:Corneal_stroma xref: ZFA:0001685 is_a: UBERON:0003891 ! stroma is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0004367 ! Descemet's membrane relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea relationship: contributes_to_morphology_of UBERON:0000964 ! cornea relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest relationship: part_of UBERON:0000964 ! cornea property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png xsd:anyURI property_value: UBPROP:0000001 "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} [Term] id: UBERON:0001778 name: ciliary epithelium namespace: uberon def: "A double layer covering the ciliary body that produces aqueous humor." [Wikipedia:Ciliary_body#Ciliary_epithelium] synonym: "ciliary body epithelium" EXACT [FMA:58464] synonym: "epithelium of ciliary body" EXACT [FMA:58464] synonym: "ocular ciliary epithelium" EXACT [] xref: BTO:0001770 xref: CALOHA:TS-0695 xref: EMAPA:35239 xref: FMA:58464 xref: MA:0001238 xref: NCIT:C32314 xref: SCTID:280870004 xref: UMLS:C0459736 {source="ncithesaurus:Ciliary_Epithelium"} xref: Wikipedia:Ciliary_body#Ciliary_epithelium is_a: UBERON:0000488 {source="FMA"} ! atypical epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001775 ! ciliary body relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001775 {source="MA"} ! ciliary body relationship: produces UBERON:0001796 {source="Wikipedia"} ! aqueous humor of eyeball [Term] id: UBERON:0001779 name: iris stroma namespace: uberon def: "The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae." [http://www.drugs.com/dict/stroma-of-iris.html, Wikipedia:Iris_stroma] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "iridial stroma" EXACT [] synonym: "stroma of iris" EXACT [] xref: EMAPA:35451 xref: FMA:58526 xref: MA:0002777 xref: SCTID:280882008 xref: Wikipedia:Iris_stroma xref: ZFA:0005569 is_a: UBERON:0003891 ! stroma is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001769 ! iris relationship: contributes_to_morphology_of UBERON:0001769 ! iris relationship: part_of UBERON:0001769 ! iris property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png xsd:anyURI [Term] id: UBERON:0001781 name: layer of retina namespace: uberon def: "Any of the layers that make up the retina[MP]." [MP:0003727] subset: pheno_slim subset: vertebrate_core synonym: "retina layer" EXACT [] synonym: "retina neuronal layer" EXACT [MP:0006069] synonym: "retinal layer" EXACT [] synonym: "retinal neuronal layer" EXACT [MP:0006069] xref: AAO:0010353 xref: EMAPA:35742 xref: FMA:58617 xref: MA:0001319 xref: NCIT:C49328 xref: SCTID:280657006 xref: UMLS:C0459649 {source="ncithesaurus:Retina_Layer"} xref: XAO:0000266 is_a: UBERON:0022303 ! nervous system cell part layer relationship: contributes_to_morphology_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: UBPROP:0000012 "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001796 name: aqueous humor of eyeball namespace: uberon def: "A thick watery refractive medium that fills the space between the lens and the cornea[WP]." [Wikipedia:Aqueous_humor] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "aqueous humor" EXACT [] synonym: "aqueous humour" EXACT [EHDAA2:0000139] synonym: "humor aquosus" EXACT LATIN [FMA:58819, FMA:TA] xref: EHDAA2:0000139 xref: EHDAA:10196 xref: EMAPA:18232 xref: ENVO:02000024 xref: FMA:58819 xref: GAID:890 xref: MA:0001236 xref: MESH:D001082 xref: NCIT:C13190 xref: OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA xref: SCTID:280587006 xref: UMLS:C0003662 {source="ncithesaurus:Aqueous_Humor"} xref: VHOG:0000548 xref: Wikipedia:Aqueous_humor xref: ZFA:0005564 is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid relationship: contributes_to_morphology_of UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0001766 {notes="FMA def states A and P", notes="located_in in EHDAA2", source="VHOG"} ! anterior chamber of eyeball property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI property_value: UBPROP:0000001 "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aqueous+humour"} property_value: UBPROP:0000003 "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001801 name: anterior segment of eyeball namespace: uberon def: "any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)" [ISBN:0-683-40008-8, MESH:A09.371.060, MP:0005193] subset: pheno_slim subset: vertebrate_core synonym: "anterior eye segment" EXACT [] synonym: "anterior segment eye" EXACT [ZFA:0005566] synonym: "anterior segment of eye" EXACT [] synonym: "anterior segment of the eye" EXACT [] synonym: "eye anterior segment" EXACT [] synonym: "segmentum anterius (bulbus oculi)" EXACT [] synonym: "segmentum anterius bulbi oculi" RELATED LATIN [Wikipedia:Anterior_segment_of_eyeball] xref: EMAPA:36594 xref: FMA:58865 xref: MA:0002484 xref: MESH:D000869 xref: NCIT:C12668 xref: SCTID:280658001 xref: UMLS:C0003153 {source="ncithesaurus:Anterior_Eye_Segment"} xref: Wikipedia:Anterior_segment_of_eyeball xref: ZFA:0005566 is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: in_anterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png xsd:anyURI [Term] id: UBERON:0001802 name: posterior segment of eyeball namespace: uberon def: "any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)" [ISBN:0-683-40008-8, MP:0005195] subset: pheno_slim subset: vertebrate_core synonym: "eye posterior segment" EXACT [] synonym: "posterior eye segment" EXACT [] synonym: "posterior segment eye" EXACT [ZFA:0005567] synonym: "posterior segment of eye" EXACT [] synonym: "posterior segment of the eye" EXACT [] synonym: "segmentum posterius (bulbus oculi)" EXACT [] synonym: "segmentum posterius bulbi oculi" RELATED LATIN [Wikipedia:Posterior_segment_of_eyeball] xref: EMAPA:36595 xref: FMA:58868 xref: MA:0002485 xref: NCIT:C12906 xref: SCTID:280659009 xref: UMLS:C0278450 {source="ncithesaurus:Posterior_Eye_Segment"} xref: Wikipedia:Posterior_segment_of_eyeball xref: ZFA:0005567 is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: in_posterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xsd:anyURI [Term] id: UBERON:0001803 name: epithelium of lens namespace: uberon def: "A layer of epithelial cells that is part of the eye." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: vertebrate_core synonym: "epithelial tissue of eye lens" EXACT [OBOL:automatic] synonym: "epithelial tissue of lens" EXACT [OBOL:automatic] synonym: "epithelium lentis" EXACT LATIN [FMA:58871, FMA:TA] synonym: "epithelium of eye lens" EXACT [OBOL:automatic] synonym: "eye lens epithelial tissue" EXACT [OBOL:automatic] synonym: "eye lens epithelium" EXACT [OBOL:automatic] synonym: "lens epithelial tissue" EXACT [OBOL:automatic] synonym: "lens epithelium" EXACT [] xref: BTO:0001873 xref: CALOHA:TS-0543 xref: EMAPA:32871 xref: FMA:58871 xref: MA:0001301 xref: SCTID:362523006 xref: TAO:0001326 xref: Wikipedia:Lens_(anatomy)#Lens_Epithelium xref: XAO:0004094 xref: ZFA:0001326 is_a: UBERON:0000484 ! simple cuboidal epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000965 ! lens of camera-type eye relationship: contributes_to_morphology_of UBERON:0000965 ! lens of camera-type eye relationship: part_of UBERON:0000965 ! lens of camera-type eye property_value: IAO:0000232 "this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former" xsd:string [Term] id: UBERON:0001804 name: capsule of lens namespace: uberon def: "the elastic, clear, membrane-like structure, that is outer most layer of the lens" [MGI:smb, MP:0003236, PMID:15483628] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "capsula lentis" EXACT LATIN [] synonym: "lens capsule" EXACT [] xref: EHDAA2:0000977 xref: EMAPA:18237 xref: FMA:58881 xref: MA:0001300 xref: NCIT:C32975 xref: SCTID:244500004 xref: UMLS:C0229232 {source="ncithesaurus:Lens_Capsule"} xref: VHOG:0000550 xref: Wikipedia:Lens_(anatomy)#Lens_capsule xref: ZFA:0005574 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 ! acellular membrane is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000965 ! lens of camera-type eye relationship: bounding_layer_of UBERON:0000965 ! lens of camera-type eye relationship: develops_from UBERON:0005614 {source="EHDAA2"} ! lens anterior epithelium relationship: has_part CHEBI:35722 ! sulfated glycosaminoglycan relationship: has_part GO:0005587 ! collagen type IV trimer relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000965 ! lens of camera-type eye property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png xsd:anyURI property_value: UBPROP:0000001 "The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000550", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000550", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24", source="http://bgee.unil.ch/"} property_value: UBPROP:0000010 "synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens" xsd:string property_value: UBPROP:0000012 "FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001833 name: lip namespace: uberon def: "One of the two fleshy folds which surround the opening of the mouth." [http://www.medterms.com/script/main/art.asp?articlekey=9458, Wikipedia:Lip] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "labia oris" RELATED LATIN [Wikipedia:Lip] synonym: "lips" RELATED [] xref: BTO:0001647 xref: CALOHA:TS-0558 xref: EMAPA:32839 xref: FMA:59816 xref: GAID:76 xref: galen:Lip xref: MA:0000343 xref: MESH:D008046 xref: NCIT:C12220 xref: OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA xref: SCTID:181221003 xref: TAO:0007006 xref: UMLS:C0023759 {source="ncithesaurus:Lip"} xref: VHOG:0000677 xref: Wikipedia:Lip xref: ZFA:0007006 is_a: UBERON:0003102 {source="ZFA"} ! surface structure relationship: contributes_to_morphology_of UBERON:0000165 ! mouth relationship: part_of UBERON:0000165 {source="BTO", source="FMA-implicit", source="VHOG", source="ZFA"} ! mouth relationship: surrounds UBERON:0000166 {source="cjm"} ! oral opening property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg xsd:anyURI property_value: RO:0002161 NCBITaxon:8782 property_value: UBPROP:0000001 "Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007006", ontology="TAO", source="ZFIN:curator", source="http//:www.medterms.com/script/main/art.asp?articlekey=9458"} property_value: UBPROP:0000007 "labial" xsd:string [Term] id: UBERON:0001835 name: lower lip namespace: uberon alt_id: UBERON:0003392 def: "Lip that covers the lower portion of the mouth.[TAO]." [TAO:0002060, Wikipedia:Lower_lip] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "labium inferius oris" RELATED LATIN [Wikipedia:Lower_lip] synonym: "lower jaw lip" EXACT [https://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0001020 xref: EMAPA:17909 xref: FMA:59818 xref: MA:0000921 xref: NCIT:C94572 xref: OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA xref: SCTID:245777007 xref: TAO:0002060 xref: UMLS:C0458583 {source="ncithesaurus:Lower_Lip"} xref: Wikipedia:Lower_lip xref: ZFA:0005225 is_a: UBERON:0001833 ! lip is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001833 ! lip intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: develops_from UBERON:0011596 ! future lower lip relationship: part_of UBERON:0001710 ! lower jaw region property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg xsd:anyURI property_value: UBPROP:0000001 "Lip that covers the lower portion of the mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002060", ontology="TAO", source="TAO:wd"} [Term] id: UBERON:0001891 name: midbrain namespace: uberon def: "The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." [GO:0030901] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "MB" BROAD ABBREVIATION [BIRNLEX:1667, NIFSTD:NeuroNames_abbrevSource] synonym: "mesencephalon" RELATED LATIN [Wikipedia:Midbrain] xref: AAO:0010149 xref: BAMS:MES xref: BIRNLEX:1667 xref: BM:MB xref: BTO:0000138 xref: CALOHA:TS-0630 xref: DHBA:10648 xref: DMBA:16649 xref: EFO:0000919 xref: EHDAA2:0001162 xref: EHDAA:3694 xref: EMAPA:16974 xref: EV:0100242 xref: FMA:61993 xref: HBA:9001 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 {source="BIRNLEX:1667"} xref: MA:0000207 xref: MAT:0000106 xref: MBA:313 xref: MESH:D008636 xref: MIAA:0000106 xref: NCIT:C12510 xref: OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0001104 xref: SCTID:279099009 xref: TAO:0000128 xref: UMLS:C0025462 {source="ncithesaurus:Mesencephalon"} xref: UMLS:C0025462 {source="BIRNLEX:1667"} xref: VHOG:0000069 xref: Wikipedia:Midbrain xref: XAO:0000014 xref: ZFA:0000128 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: develops_from UBERON:0009616 ! presumptive midbrain relationship: has_developmental_contribution_from UBERON:0003849 {evidence="definitional"} ! mesencephalic neural crest relationship: immediate_transformation_of UBERON:0009616 {source="Bgee:AN"} ! presumptive midbrain property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG xsd:anyURI property_value: editor_note "developmental relationships need revised" xsd:string property_value: UBPROP:0000001 "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010149", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000128", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000069", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "mesencephalic" xsd:string property_value: UBPROP:0000012 "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" xsd:string {external_ontology="ABA"} [Term] id: UBERON:0001892 name: rhombomere namespace: uberon def: "A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]." [Wikipedia:Rhombomere, ZFIN:curator] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "future rhombencephalon" RELATED [MIAA:0000272] synonym: "hindbrain neuromere" EXACT [] synonym: "hindbrain neuromeres" EXACT PLURAL [DHBA:HNM] synonym: "hindbrain segment" BROAD [ZFA:0001064] synonym: "rhombomere" EXACT [] synonym: "rhombomeres" RELATED PLURAL [VHOG:0000672] synonym: "segment of hindbrain" BROAD [ZFA:0001064] xref: DHBA:12664 xref: EFO:0003617 xref: EMAPA:16148 xref: FMA:295666 xref: MAT:0000272 xref: MIAA:0000272 xref: RETIRED_EHDAA2:0000669 xref: TAO:0001064 xref: VHOG:0000672 xref: Wikipedia:Rhombomere xref: XAO:0004079 xref: ZFA:0001064 is_a: UBERON:0004731 ! neuromere intersection_of: UBERON:0004731 ! neuromere intersection_of: part_of UBERON:0007277 ! presumptive hindbrain relationship: part_of UBERON:0007277 ! presumptive hindbrain property_value: UBPROP:0000001 "A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001064", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000672", ontology="VHOG", source="DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "In human embryonic development, the rhombomeres are present by day 29" xsd:string property_value: UBPROP:0000012 "DHBA divides this into A(1-3),B(4),C(5-7) and D(8)" xsd:string [Term] id: UBERON:0001896 name: medulla oblongata namespace: uberon def: "Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]." [FMA:62004, GO:0021550, Wikipedia:Bone_marrow_of_ovary_oblongata] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "bulb" BROAD [] synonym: "bulbus" EXACT LATIN [FMA:62004, FMA:TA] synonym: "medulla" BROAD [ABA:MY] synonym: "medulla oblonzata" RELATED LATIN [Wikipedia:Medulla_oblongata] synonym: "metepencephalon" RELATED [FMA:62004] xref: AAO:0010486 xref: BAMS:Md xref: BAMS:MY xref: BIRNLEX:957 xref: BM:Me xref: BTO:0000041 xref: CALOHA:TS-0607 xref: DMBA:17352 xref: EFO:0000924 xref: EHDAA2:0001088 xref: EHDAA:7588 xref: EMAPA:17550 xref: EV:0100275 xref: FMA:62004 xref: GAID:590 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 {source="BIRNLEX:957"} xref: MA:0000206 xref: MAT:0000111 xref: MAT:0000367 xref: MBA:354 xref: MESH:D008526 xref: MIAA:0000111 xref: NCIT:C12442 xref: OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA xref: SCTID:279104005 xref: TAO:0000545 xref: UMLS:C0025148 {source="ncithesaurus:Medulla_Oblongata"} xref: UMLS:C0025148 {source="BIRNLEX:957"} xref: UMLS:C1269575 {source="BIRNLEX:957"} xref: VHOG:0000181 xref: Wikipedia:Bone_marrow_of_ovary_oblongata xref: XAO:0003100 xref: ZFA:0000545 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of GO:0002027 ! regulation of heart rate relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg xsd:anyURI property_value: UBPROP:0000001 "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010486", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001915 name: endothelium of capillary namespace: uberon def: "An endothelium that is part of a capillary [Automatically generated definition]." [OBOL:automatic] synonym: "blood capillary endothelium" EXACT [OBOL:automatic] synonym: "capillary endothelium" EXACT [] synonym: "capillary vessel endothelium" EXACT [OBOL:automatic] synonym: "endothelium of blood capillary" EXACT [OBOL:automatic] synonym: "endothelium of capillary vessel" EXACT [OBOL:automatic] xref: BTO:0004954 xref: CALOHA:TS-0112 xref: EMAPA:36292 xref: FMA:62114 xref: MA:0000711 xref: NCIT:C49215 xref: UMLS:C0006904 {source="ncithesaurus:Capillary_Endothelium"} is_a: UBERON:0004638 ! blood vessel endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001982 ! capillary relationship: part_of UBERON:0001982 ! capillary [Term] id: UBERON:0001916 name: endothelium of arteriole namespace: uberon def: "An endothelium that is part of an arteriole [Automatically generated definition]." [OBOL:automatic] synonym: "arteriole endothelium" EXACT [] xref: EMAPA:36286 xref: FMA:62115 xref: MA:0000705 xref: NCIT:C49192 xref: UMLS:C1179024 {source="ncithesaurus:Arteriole_Endothelium"} is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004700 ! arterial system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001980 ! arteriole relationship: part_of UBERON:0001980 ! arteriole [Term] id: UBERON:0001917 name: endothelium of artery namespace: uberon def: "An endothelium that is part of an artery [Automatically generated definition]." [OBOL:automatic] synonym: "arterial endothelium" EXACT [] synonym: "artery endothelium" EXACT [] xref: AAO:0011013 xref: BTO:0004757 xref: EMAPA:35148 xref: FMA:62116 xref: MA:0000707 xref: NCIT:C49194 xref: UMLS:C1179025 {source="ncithesaurus:Artery_Endothelium"} xref: VHOG:0001215 xref: XAO:0000357 is_a: UBERON:0003915 ! endothelial tube is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004700 ! arterial system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery property_value: UBPROP:0000001 "The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011013", ontology="AAO", source="XAO:curator"} property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001215", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001918 name: endothelium of venule namespace: uberon def: "An endothelium that is part of a venule [Automatically generated definition]." [OBOL:automatic] synonym: "venule endothelium" EXACT [] xref: EMAPA:36290 xref: FMA:62117 xref: MA:0000716 xref: NCIT:C49319 xref: UMLS:C1179026 {source="ncithesaurus:Venule_Endothelium"} is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004701 ! venous system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001979 ! venule relationship: part_of UBERON:0001979 ! venule [Term] id: UBERON:0001919 name: endothelium of vein namespace: uberon def: "An endothelium that is part of a vein [Automatically generated definition]." [OBOL:automatic] synonym: "vein endothelium" EXACT [] synonym: "veinous endothelium" RELATED [VHOG:0001216] synonym: "venous endothelium" EXACT [] xref: AAO:0011110 xref: BTO:0004756 xref: EMAPA:36288 xref: FMA:62118 xref: MA:0000712 xref: NCIT:C49317 xref: UMLS:C1179027 {source="ncithesaurus:Vein_Endothelium"} xref: VHOG:0001216 xref: XAO:0000358 is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004701 ! venous system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001216", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001943 name: midbrain tegmentum namespace: uberon def: "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]." [FMA:FMA, ISBN:0471888893, Wikipedia:Midbrain_tegmentum] comment: 'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "mesencephalic tegmentum" RELATED [VHOG:0001367] synonym: "MTg" BROAD ABBREVIATION [BIRNLEX:1200, NIFSTD:NeuroNames_abbrevSource] synonym: "tegmentum" BROAD [ISBN:0471888893] synonym: "tegmentum mesencephali" EXACT LATIN [Wikipedia:Midbrain_tegmentum] synonym: "tegmentum mesencephalicum" RELATED LATIN [NeuroNames:491] synonym: "tegmentum of midbrain" EXACT [] xref: BAMS:MTg xref: BIRNLEX:1200 xref: BTO:0003388 xref: DHBA:12195 xref: EFO:0000921 xref: EHDAA2:0004475 xref: EMAPA:18215 xref: FMA:62393 xref: HBA:9002 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 {source="BIRNLEX:1200"} xref: MA:0000212 xref: MAT:0000452 xref: SCTID:362392007 xref: TAO:0000160 xref: UMLS:C0039441 {source="BIRNLEX:1200"} xref: VHOG:0001367 xref: Wikipedia:Midbrain_tegmentum xref: XAO:0004271 xref: ZFA:0000160 is_a: UBERON:0002616 ! regional part of brain relationship: develops_from UBERON:0010285 {source="ZFA"} ! midbrain basal plate relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png xsd:anyURI property_value: UBPROP:0000003 "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001367", ontology="VHOG", source="DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001948 name: regional part of spinal cord namespace: uberon def: "A multi-tissue structure that is part of a spinal cord." [OBOL:automatic] subset: non_informative synonym: "spinal cord part" RELATED [] xref: BIRNLEX:1496 xref: NCIT:C33969 xref: SCTID:244437008 xref: UMLS:C1268166 {source="ncithesaurus:Spinal_Cord_Part"} is_a: UBERON:0000073 ! regional part of nervous system is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord [Term] id: UBERON:0001969 name: blood plasma namespace: uberon def: "The liquid component of blood, in which erythrocytes are suspended." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "blood plasm" EXACT [] synonym: "plasma" BROAD [MA:0002501] synonym: "portion of blood plasma" EXACT [] synonym: "portion of plasma" BROAD [FMA:62970] xref: BTO:0000131 xref: CALOHA:TS-0800 xref: EFO:0001905 xref: EMAPA:35690 xref: FMA:62970 xref: GAID:1178 xref: MA:0002501 xref: MAT:0000052 xref: MESH:D010949 xref: MIAA:0000052 xref: NCIT:C13356 xref: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood intersection_of: surrounds CL:0000232 ! erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood relationship: surrounds CL:0000232 ! erythrocyte [Term] id: UBERON:0001972 name: submucosa of esophagus namespace: uberon def: "A submucosa that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophageal submucosa" EXACT [] synonym: "esophagus submucosa" EXACT [] synonym: "gullet submucosa" EXACT [OBOL:automatic] synonym: "oesophagus submucosa" EXACT [OBOL:automatic] synonym: "submucosa of esophagus" EXACT [] synonym: "submucosa of gullet" EXACT [OBOL:automatic] synonym: "submucosa of oesophagus" EXACT [OBOL:automatic] synonym: "submucous layer of esophagus" RELATED [BTO:0002109] synonym: "tela submucosa (oesophagus)" EXACT LATIN [FMA:62997, FMA:TA] synonym: "tela submucosa esophagi" EXACT LATIN [BTO:0002109] synonym: "tela submucosa oesophageae" EXACT LATIN [FMA:62997, FMA:TA] synonym: "tela submucosa oesophagi" RELATED [BTO:0002109] synonym: "tela submucosa of esophagus" EXACT [] xref: BTO:0002109 xref: EMAPA:35325 xref: FMA:62997 xref: MA:0002724 xref: SCTID:362128009 is_a: UBERON:0018257 ! submucosa of digestive tract intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 ! wall of esophagus [Term] id: UBERON:0001974 name: lamina propria of esophagus namespace: uberon def: "A lamina propria that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophageal lamina propria" RELATED [EMAPA:26987] synonym: "esophagus lamina propria" EXACT [] synonym: "esophagus lamina propria mucosa" EXACT [OBOL:automatic] synonym: "esophagus lamina propria mucosae" EXACT [OBOL:automatic] synonym: "gullet lamina propria" EXACT [OBOL:automatic] synonym: "gullet lamina propria mucosa" EXACT [OBOL:automatic] synonym: "gullet lamina propria mucosae" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of esophagus" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of gullet" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of oesophagus" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of esophagus" EXACT [] synonym: "lamina propria mucosae of gullet" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of oesophagus" EXACT [OBOL:automatic] synonym: "lamina propria of gullet" EXACT [OBOL:automatic] synonym: "lamina propria of oesophagus" EXACT [OBOL:automatic] synonym: "oesophagus lamina propria" RELATED [] synonym: "oesophagus lamina propria mucosa" EXACT [OBOL:automatic] synonym: "oesophagus lamina propria mucosae" EXACT [OBOL:automatic] xref: EMAPA:26987 xref: FMA:63050 xref: MA:0001568 xref: NCIT:C49223 xref: UMLS:C1707949 {source="ncithesaurus:Esophageal_Lamina_Propria"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0002469 {source="FMA"} ! esophagus mucosa [Term] id: UBERON:0001975 name: serosa of esophagus namespace: uberon def: "A serous membrane that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophagus serosa" EXACT [] synonym: "esophagus serous membrane" EXACT [OBOL:automatic] synonym: "gullet serosa" EXACT [OBOL:automatic] synonym: "gullet serous membrane" EXACT [OBOL:automatic] synonym: "oesophagus serosa" RELATED [] synonym: "oesophagus serous membrane" EXACT [OBOL:automatic] synonym: "serosa of abdominal part of esophagus" EXACT [] synonym: "serosa of gullet" EXACT [OBOL:automatic] synonym: "serosa of oesophagus" EXACT [] synonym: "serous coat of oesophagus" EXACT [] synonym: "serous membrane of esophagus" EXACT [OBOL:automatic] synonym: "serous membrane of gullet" EXACT [OBOL:automatic] synonym: "serous membrane of oesophagus" EXACT [OBOL:automatic] synonym: "tunica serosa oesophageae" EXACT LATIN [FMA:63057, FMA:TA] xref: EMAPA:35322 xref: FMA:63057 xref: MA:0001571 is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 ! wall of esophagus [Term] id: UBERON:0001976 name: epithelium of esophagus namespace: uberon def: "the epithelial layer that lines the luminal space of the esophagus" [ISBN:0-683-40008-8, MP:0000468] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "epithelial tissue of esophagus" EXACT [OBOL:automatic] synonym: "epithelial tissue of gullet" EXACT [OBOL:automatic] synonym: "epithelial tissue of oesophagus" EXACT [OBOL:automatic] synonym: "epithelium of gullet" EXACT [OBOL:automatic] synonym: "epithelium of oesophagus" EXACT [OBOL:automatic] synonym: "esophageal epithelium" EXACT [] synonym: "esophagus epithelial tissue" EXACT [OBOL:automatic] synonym: "esophagus epithelium" EXACT [] synonym: "gullet epithelial tissue" EXACT [OBOL:automatic] synonym: "gullet epithelium" EXACT [OBOL:automatic] synonym: "oesophagus epithelial tissue" EXACT [OBOL:automatic] synonym: "oesophagus epithelium" RELATED [] xref: BTO:0001578 xref: CALOHA:TS-0698 xref: EFO:0003041 xref: EHDAA2:0001287 xref: EMAPA:16835 xref: FMA:63063 xref: MA:0001565 xref: NCIT:C49221 xref: TAO:0001499 xref: UMLS:C1179544 {source="ncithesaurus:Esophageal_Epithelium"} xref: ZFA:0001499 is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001043 ! esophagus relationship: contributes_to_morphology_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0002469 {source="FMA"} ! esophagus mucosa property_value: editor_note "TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar" xsd:string property_value: UBPROP:0000001 "Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001499", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001979 name: venule namespace: uberon def: "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins" [MESH:A07.231.432.952, MP:0004125] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "venula" RELATED LATIN [Wikipedia:Venule] xref: BTO:0002626 xref: EMAPA:35917 xref: FMA:63130 xref: MA:0000071 xref: MESH:A07.231.432.952 xref: NCIT:C12818 xref: SCTID:341687009 xref: TAO:0005315 xref: UMLS:C0042520 {source="ncithesaurus:Venule"} xref: VHOG:0001765 xref: Wikipedia:Venule xref: ZFA:0005315 is_a: UBERON:0003920 ! venous blood vessel relationship: connects UBERON:0001638 ! vein relationship: connects UBERON:0001982 ! capillary property_value: depicted:by Illu:capillary.jpg xsd:anyURI property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005315", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001980 name: arteriole namespace: uberon def: "The smallest division of the artery located between the muscular arteries and the capillaries[GO]." [GO:0014830] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arteriola" RELATED LATIN [Wikipedia:Arteriole] xref: AAO:0010253 xref: BTO:0001997 xref: EMAPA:35146 xref: FMA:63182 xref: MA:0000063 xref: MESH:D001160 xref: NCIT:C12672 xref: SCTID:337724002 xref: TAO:0002138 xref: UMLS:C0003847 {source="ncithesaurus:Arteriole"} xref: VHOG:0001763 xref: Wikipedia:Arteriole xref: ZFA:0005255 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: connects UBERON:0001637 ! artery intersection_of: connects UBERON:0001982 ! capillary relationship: connects UBERON:0001637 ! artery relationship: connects UBERON:0001982 ! capillary relationship: contributes_to_morphology_of UBERON:0001637 ! artery property_value: depicted:by Illu:capillary.jpg xsd:anyURI property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002138", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010253", ontology="AAO", source="AAO:BJB"} [Term] id: UBERON:0001981 name: blood vessel namespace: uberon def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "region of vascular tree organ" EXACT [FMA:50722] synonym: "vas sanguineum" RELATED LATIN [Wikipedia:Blood_vessel] synonym: "vascular element" BROAD [EMAPA:35993] synonym: "vascular tree organ region" EXACT [FMA:50722] xref: AAO:0011004 xref: AEO:0000207 xref: BTO:0001102 xref: CALOHA:TS-0080 xref: EFO:0000817 xref: EHDAA2:0003252 xref: EHDAA:240 xref: EMAPA:32743 xref: EMAPA:35993 xref: FMA:50722 xref: FMA:63183 xref: GAID:169 xref: MA:0000060 xref: MAT:0000393 xref: MESH:D001808 xref: NCIT:C12679 xref: NLXANAT:090901 xref: OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA xref: SCTID:361097006 xref: TAO:0002137 xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"} xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg xsd:anyURI property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001982 name: capillary namespace: uberon def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "blood capillary" EXACT [] synonym: "capillary vessel" EXACT [] xref: AAO:0010252 xref: BTO:0002045 xref: CALOHA:TS-2006 xref: EFO:0001906 xref: EMAPA:35198 xref: EV:0100035 xref: FMA:63194 xref: MA:0000065 xref: MESH:A07.231.432.410 xref: NCIT:C12685 xref: NLXANAT:090902 xref: OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA xref: TAO:0005250 xref: UMLS:C0935624 {source="ncithesaurus:Capillary"} xref: VHOG:0001253 xref: Wikipedia:Capillary xref: XAO:0000116 xref: ZFA:0005250 is_a: UBERON:0001981 {source="FMA", source="MA", source="XAO"} ! blood vessel is_a: UBERON:0010523 {source="ZFA"} ! microcirculatory vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: connects UBERON:0001979 ! venule intersection_of: connects UBERON:0001980 ! arteriole relationship: connects UBERON:0001979 ! venule relationship: connects UBERON:0001980 ! arteriole property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg xsd:anyURI property_value: editor_note "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string property_value: UBPROP:0000001 "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010252", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001253", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000010 "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" xsd:string [Term] id: UBERON:0001985 name: corneal endothelium namespace: uberon def: "A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]." [Wikipedia:Corneal_endothelium] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cornea endothelium" EXACT [OBOL:automatic] synonym: "endothelium of cornea" EXACT [OBOL:automatic] synonym: "epithelium posterius corneae" RELATED LATIN [Wikipedia:Corneal_endothelium] xref: CALOHA:TS-0172 xref: EMAPA:35935 xref: FMA:63882 xref: GAID:891 xref: MA:0001242 xref: MESH:D004728 xref: NCIT:C12707 xref: SCTID:368827009 xref: TAO:0002186 xref: UMLS:C0014259 {source="ncithesaurus:Corneal_Endothelium"} xref: Wikipedia:Corneal_endothelium xref: ZFA:0001687 is_a: UBERON:0001986 ! endothelium is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball relationship: contributes_to_morphology_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png xsd:anyURI [Term] id: UBERON:0001986 name: endothelium namespace: uberon def: "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]" [FMA:63916, https://github.com/obophenotype/uberon/issues/225, MESH:A10.272.491] comment: The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) subset: efo_slim subset: uberon_slim xref: BTO:0000393 xref: CALOHA:TS-0278 xref: EFO:0002548 xref: FMA:63916 xref: GAID:520 xref: galen:Endothelium xref: MESH:D004727 xref: NCIT:C12481 xref: SCTID:27168002 xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: composed_primarily_of CL:0000115 ! endothelial cell relationship: composed_primarily_of CL:0000115 ! endothelial cell relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: UBPROP:0000007 "endothelial" xsd:string [Term] id: UBERON:0002012 name: pulmonary artery namespace: uberon def: "An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Pulmonary_artery] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "arteria pulmonalis" RELATED LATIN [Wikipedia:Pulmonary_artery] synonym: "pulmonary arterial subtree" RELATED [FMA:66326] synonym: "pulmonary arterial tree" EXACT [FMA:66326] synonym: "pulmonary arterial tree organ part" EXACT [FMA:66326] synonym: "truncus pulmonalis" RELATED LATIN [Wikipedia:Pulmonary_artery] xref: AAO:0010221 xref: BTO:0000778 xref: CALOHA:TS-0839 xref: EFO:0001399 xref: EHDAA2:0001575 xref: EHDAA:4351 xref: EMAPA:17008 xref: FMA:66326 xref: GAID:505 xref: galen:PulmonaryArtery xref: MA:0002031 xref: MESH:D011651 xref: NCIT:C12774 xref: OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA xref: SCTID:181380003 xref: UMLS:C0034052 {source="ncithesaurus:Pulmonary_Artery"} xref: VHOG:0000982 xref: Wikipedia:Pulmonary_artery xref: XAO:0004162 is_a: UBERON:0001637 ! artery is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013768 ! great vessel of heart intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0008886 ! pulmonary vascular system intersection_of: supplies UBERON:0002048 ! lung disjoint_from: UBERON:0004573 ! systemic artery relationship: continuous_with UBERON:0002333 ! pulmonary trunk relationship: develops_from UBERON:0002061 {source="Wikipedia"} ! truncus arteriosus relationship: develops_from UBERON:0003123 {source="EHDAA2", source="XAO"} ! pharyngeal arch artery 6 relationship: develops_from UBERON:0005339 {source="EHDAA2"} ! outflow tract pulmonary component relationship: part_of UBERON:0008886 ! pulmonary vascular system relationship: supplies UBERON:0002048 ! lung property_value: depicted:by Alveoli:diagram.png xsd:anyURI property_value: UBPROP:0000001 "Major artery which supplies blood to the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010221", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000982", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+artery"} property_value: UBPROP:0000003 "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000982", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]" xsd:string [Term] id: UBERON:0002016 name: pulmonary vein namespace: uberon def: "Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]." [GO:0060577] subset: pheno_slim subset: uberon_slim synonym: "pulmonary venous tree organ part" EXACT [] synonym: "venae pulmonales" RELATED LATIN [Wikipedia:Pulmonary_vein] xref: AAO:0010521 xref: BTO:0001799 xref: CALOHA:TS-0840 xref: EHDAA2:0001579 xref: EHDAA:2629 xref: EMAPA:18645 xref: FMA:66643 xref: GAID:543 xref: galen:PulmonaryVein xref: MA:0002206 xref: MESH:D011667 xref: NCIT:C12776 xref: SCTID:430160002 xref: UMLS:C0034090 {source="ncithesaurus:Pulmonary_Vein"} xref: VHOG:0001133 xref: Wikipedia:Pulmonary_vein xref: XAO:0000394 is_a: UBERON:0001638 ! vein is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013768 ! great vessel of heart intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002048 ! lung relationship: develops_from UBERON:0002061 ! truncus arteriosus relationship: drains UBERON:0002048 ! lung relationship: part_of UBERON:0008886 ! pulmonary vascular system property_value: depicted:by Alveoli:diagram.png xsd:anyURI property_value: UBPROP:0000001 "Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010521", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001133", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+vein"} property_value: UBPROP:0000001 "the veins that return oxygenated blood from the lungs to the left atrium of the heart" xsd:string {source="MP:0002726,MGI:cwg"} property_value: UBPROP:0000003 "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001133", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: UBPROP:0000202 FMA:70827 [Term] id: UBERON:0002018 name: synovial membrane of synovial joint namespace: uberon def: "Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints)." [Wikipedia:Synovial_membrane] subset: efo_slim subset: uberon_slim synonym: "membrana synovialis (capsula articularis)" EXACT LATIN [FMA:9865, FMA:TA] synonym: "membrana synovialis capsulae articularis" EXACT LATIN [Wikipedia:Synovial_membrane] synonym: "stratum synoviale" EXACT LATIN [FMA:66762, FMA:TA] synonym: "stratum synoviale (capsula articularis)" EXACT LATIN [FMA:9865, FMA:TA] synonym: "synovial layer" BROAD [FMA:66762] synonym: "synovial layer of articular capsule of synovial joint" RELATED [FMA:9865] synonym: "synovial membrane" BROAD [AEO:0000181] synonym: "synovial membrane of articular capsule of synovial joint" RELATED [FMA:9865] synonym: "synovium" BROAD [BTO:0001823, VHOG:0001282] synonym: "synovium of articular capsule of synovial joint" RELATED [FMA:9865] xref: AEO:0000181 xref: BTO:0001823 xref: EFO:0001393 xref: EHDAA2_RETIRED:0003181 xref: EMAPA:37476 {source="MA:th"} xref: EV:0100143 xref: FMA:9865 xref: GAID:264 xref: galen:SynovialMembrane xref: MA:0000114 xref: MESH:D013583 xref: NCIT:C12473 xref: SCTID:361828005 xref: UMLS:C0039099 {source="ncithesaurus:Synovial_Membrane"} xref: VHOG:0001282 xref: Wikipedia:Synovial_membrane is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0006915 ! stratified squamous epithelium is_a: UBERON:0007616 {source="FMA"} ! layer of synovial tissue is_a: UBERON:0012275 ! meso-epithelium relationship: attaches_to UBERON:0001484 {source="GAID"} ! articular capsule relationship: has_part CL:0000214 ! synovial cell relationship: part_of UBERON:0002217 {source="EHDAA2"} ! synovial joint property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png xsd:anyURI property_value: UBPROP:0000003 "Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001282", ontology="VHOG", source="PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002020 name: gray matter namespace: uberon def: "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Gray_matter] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "gray mater" RELATED [ZFA:0001681] synonym: "gray matter" EXACT [] synonym: "gray matter of neuraxis" EXACT [FMA:67242] synonym: "grey matter" EXACT [] synonym: "grey matter of neuraxis" EXACT [] synonym: "grey substance" EXACT [] synonym: "grisea" RELATED LATIN [] synonym: "neuronal grey matter" EXACT [AEO:0001012] synonym: "substantia grisea" EXACT LATIN [FMA:67242, FMA:TA] xref: AEO:0001012 xref: EHDAA2:0003136 xref: EHDAA2_RETIRED:0004658 xref: EMAPA:37596 {source="MA:th"} xref: FMA:67242 xref: HBA:4006 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2869 xref: MA:0001112 xref: NCIT:C32695 xref: OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA xref: TAO:0002197 xref: UMLS:C0018220 {source="ncithesaurus:Gray_Matter"} xref: VHOG:0001768 xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: composed_primarily_of GO:0043025 ! neuronal cell body property_value: depicted:by Spinal:nerve.svg xsd:anyURI property_value: UBPROP:0000001 "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002197", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002028 name: hindbrain namespace: uberon def: "The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]." [Wikipedia:Rhombencephalon, ZFA:0000029, ZFIN:curator] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "rhombencephalon" RELATED [] xref: AAO:0010150 xref: BAMS:HB xref: BIRNLEX:942 xref: BTO:0000672 xref: CALOHA:TS-0457 xref: DHBA:10653 xref: DMBA:16808 xref: EFO:0000923 xref: EHDAA2:0000746 xref: EHDAA:3514 xref: EHDAA:6487 xref: EMAPA:16916 xref: FMA:67687 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 {source="BIRNLEX:942"} xref: MA:0000195 xref: MAT:0000107 xref: MBA:1065 xref: MESH:D012249 xref: MIAA:0000107 xref: NCIT:C40336 xref: SCTID:303456008 xref: TAO:0000029 xref: UMLS:C0035507 {source="ncithesaurus:Hind-Brain"} xref: UMLS:C0035507 {source="BIRNLEX:942"} xref: UMLS:C1522180 {source="BIRNLEX:942"} xref: VHOG:0000070 xref: Wikipedia:Rhombencephalon xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: develops_from UBERON:0007277 ! presumptive hindbrain relationship: immediate_transformation_of UBERON:0007277 {source="Bgee:AN"} ! presumptive hindbrain relationship: only_in_taxon NCBITaxon:89593 ! Craniata property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg xsd:anyURI property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} property_value: UBPROP:0000001 "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010150", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000002 "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO"} property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000070", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "rhombencephalic" xsd:string property_value: UBPROP:0000012 "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" xsd:string {external_ontology="MA"} [Term] id: UBERON:0002036 name: striated muscle tissue namespace: uberon def: "Muscle tissue that contains fibers that are divided by transverse bands into striations." [CL:0000737, GOC:dph, GOC:mtg_muscle] subset: pheno_slim subset: uberon_slim synonym: "striated muscle" EXACT [] xref: AAO:0010762 xref: AEO:0000140 xref: CALOHA:TS-2047 xref: EHDAA2:0003140 xref: EMAPA:36390 xref: FMA:67905 xref: galen:StriatedMuscle xref: MA:0002438 xref: NCIT:C12436 xref: OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA xref: UMLS:C1331262 {source="ncithesaurus:Striated_Muscle_Tissue"} xref: WBbt:0005779 xref: Wikipedia:Striated_muscle is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: composed_primarily_of CL:0000737 ! striated muscle cell relationship: composed_primarily_of CL:0000737 ! striated muscle cell property_value: UBPROP:0000001 "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010762", ontology="AAO", source="AAO:CAM"} [Term] id: UBERON:0002040 name: bronchial artery namespace: uberon def: "A systemic artery that supplies the lung with with oxygenated blood." [UBERON:cjm, Wikipedia:Bronchial_artery] comment: Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. subset: uberon_slim synonym: "arteriae bronchiales" RELATED LATIN [Wikipedia:Bronchial_artery] synonym: "bronchial arterial tree" EXACT [] synonym: "rami bronchiales partis thoracicae aortae" RELATED LATIN [Wikipedia:Bronchial_artery] xref: EMAPA:18608 xref: FMA:68109 xref: GAID:477 xref: MA:0001923 xref: MESH:D001981 xref: NCIT:C32230 xref: OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg xref: SCTID:244247009 xref: UMLS:C0006257 {source="ncithesaurus:Bronchial_Artery"} xref: Wikipedia:Bronchial_artery is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0004573 ! systemic artery intersection_of: part_of UBERON:0004571 ! systemic arterial system intersection_of: supplies UBERON:0002048 ! lung relationship: supplies UBERON:0002048 ! lung property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png xsd:anyURI [Term] id: UBERON:0002048 name: lung namespace: uberon def: "Respiration organ that develops as an outpocketing of the esophagus." [http://orcid.org/0000-0002-6601-2165] comment: Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "pulmo" EXACT LATIN [] xref: AAO:0000275 xref: AAO:0010567 xref: BTO:0000763 xref: CALOHA:TS-0568 xref: EFO:0000934 xref: EHDAA2:0001042 xref: EHDAA:1554 xref: EHDAA:2205 xref: EMAPA:16728 xref: EV:0100042 xref: FMA:7195 xref: GAID:345 xref: galen:Lung xref: MA:0000415 xref: MAT:0000135 xref: MESH:D008168 xref: MIAA:0000135 xref: NCIT:C12468 xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA xref: SCTID:181216001 xref: UMLS:C0024109 {source="ncithesaurus:Lung"} xref: VHOG:0000310 xref: Wikipedia:Lung xref: XAO:0000119 is_a: UBERON:0000171 ! respiration organ is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0015212 ! lateral structure relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: develops_from UBERON:0000118 ! lung bud relationship: in_lateral_side_of UBERON:0000170 ! pair of lungs relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs property_value: RO:0002161 NCBITaxon:32443 {editor="BGEE:fb", source="https://github.com/obophenotype/uberon/issues/701"} property_value: RO:0002161 NCBITaxon:7777 {editor="BGEE:fb", source="https://github.com/obophenotype/uberon/issues/701"} property_value: seeAlso https://github.com/obophenotype/uberon/issues/701 xsd:anyURI property_value: UBPROP:0000001 "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010567", ontology="AAO", source="AAO:SBH"} property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000310", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "pulmonary" xsd:string property_value: UBPROP:0000008 "respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi" xsd:string [Term] id: UBERON:0002049 name: vasculature namespace: uberon def: "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face." [ZFA:0005249] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "vascular network" EXACT [FMA:69050] xref: BTO:0003718 xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: BFO:0000040 ! material entity is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg xsd:anyURI property_value: editor_note "see also: vascular system. Consider merging?" xsd:string property_value: UBPROP:0000007 "vascular" xsd:string [Term] id: UBERON:0002050 name: embryonic structure namespace: uberon def: "Anatomical structure that is part of an embryo." [BTO:0000174, ZFIN:curator] subset: efo_slim subset: inconsistent_with_fma subset: vertebrate_core synonym: "developing embryonic structure" EXACT [FBbt:00004208] synonym: "developing structure" RELATED [] synonym: "embryonale Struktur" RELATED [BTO:0000174] synonym: "embryonic anatomical structure" EXACT [RETIRED_EHDAA2:0003169] synonym: "embryonic structures" RELATED PLURAL [ZFA:0001105] xref: AAO:0000138 xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 xref: FBbt:00004208 xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 xref: NCIT:C13229 xref: RETIRED_EHDAA2:0003169 xref: SCTID:667009 xref: TAO:0001105 xref: UMLS:C0013948 {source="ncithesaurus:Embryonic_Structure"} xref: VSAO:0000178 xref: XAO:0003042 xref: ZFA:0001105 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002061 name: truncus arteriosus namespace: uberon def: "The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles." [Wikipedia:Truncus_arteriosus_(embryology)] subset: uberon_slim xref: EHDAA2:0004143 xref: EMAPA:35887 xref: FMA:70301 xref: GAID:554 xref: MA:0000103 xref: MESH:D014338 xref: NCIT:C34317 xref: OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw xref: SCTID:308828009 xref: UMLS:C1519589 {source="ncithesaurus:Trancus_Arteriosus"} xref: Wikipedia:Truncus_arteriosus_(embryology) is_a: UBERON:0001637 {source="EHDAA2"} ! artery is_a: UBERON:0002050 {source="FMA"} ! embryonic structure is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0005432 {source="EHDAA2"} ! aortic sac relationship: part_of UBERON:0004145 {source="MA"} ! outflow tract relationship: part_of UBERON:0005498 {source="EHDAA2"} ! primitive heart tube property_value: UBPROP:0000012 "assume spelling error for ncit" xsd:string {external_ontology="ncit"} [Term] id: UBERON:0002062 name: endocardial cushion namespace: uberon def: "The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]." [GO:0003197, Wikipedia:Atrioventricular_cushions, ZFIN:curator] comment: GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "atrioventricular canal cushion" RELATED [FMA:70302] synonym: "atrioventricular cushion" EXACT [Wikipedia:Endocardial_cushion] synonym: "AV cushion" EXACT [] synonym: "cardiac cushion" EXACT [PMID:15797462] synonym: "endocardial cushion tissue" EXACT [EHDAA2:0000434] synonym: "endocardial cushions" RELATED PLURAL [] xref: EHDAA2:0000434 xref: EHDAA2:0004028 xref: EHDAA:2586 xref: EMAPA:16696 xref: FMA:70302 xref: MA:0000078 xref: TAO:0001317 xref: VHOG:0000932 xref: Wikipedia:Atrioventricular_cushions xref: XAO:0004189 xref: ZFA:0001317 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005256 ! trunk mesenchyme is_a: UBERON:0009751 ! cardiac mesenchyme is_a: UBERON:0014387 ! mesenchyme derived from neural crest relationship: part_of UBERON:0002165 {source="ZFA"} ! endocardium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png xsd:anyURI property_value: UBPROP:0000001 "Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001317", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000002 "relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001317", ontology="TAO"} property_value: UBPROP:0000003 "(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000932", ontology="VHOG", source="DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002063 name: sinus venosus namespace: uberon def: "The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart." [PMID:20735616, Wikipedia:Sinus_venosus] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "inflow tract" BROAD [ZFA:0000154] synonym: "sinus venarum" RELATED [Wikipedia:Sinus_venosus] synonym: "sinus venosus cordis" RELATED LATIN [Wikipedia:Sinus_venosus] synonym: "venarum" RELATED [Wikipedia:Sinus_venosus] synonym: "venarum sinus" RELATED [Wikipedia:Sinus_venosus] synonym: "venosus" RELATED [Wikipedia:Sinus_venosus] xref: AAO:0010505 xref: EHDAA2:0001839 xref: EHDAA:480 xref: EMAPA:16237 xref: FMA:70303 xref: NCIT:C34299 xref: NCIT:C34300 xref: TAO:0000154 xref: UMLS:C0225857 {source="ncithesaurus:Sinus_Venarum"} xref: UMLS:C0231084 {source="ncithesaurus:Sinus_Venosus"} xref: VHOG:0000177 xref: Wikipedia:Sinus_venosus xref: ZFA:0000154 is_a: UBERON:0004151 ! cardiac chamber relationship: develops_from UBERON:0007278 ! presumptive sinus venosus relationship: immediate_transformation_of UBERON:0007278 {source="Bgee:AN"} ! presumptive sinus venosus relationship: part_of UBERON:0002350 {source="VHOG"} ! conducting system of heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png xsd:anyURI property_value: UBPROP:0000001 "Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000154", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010505", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000177", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]" xsd:string property_value: UBPROP:0000008 "In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu" xsd:string property_value: UBPROP:0000008 "In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract" xsd:string {source="ZFA:0000154"} [Term] id: UBERON:0002067 name: dermis namespace: uberon def: "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]." [Wikipedia:Dermis, ZFIN:curator] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "corium" RELATED [BTO:0000294] synonym: "corium" RELATED LATIN [Wikipedia:Dermis] synonym: "cutis" RELATED [BTO:0000294] synonym: "vertebrate dermis" EXACT [] xref: AAO:0000128 xref: BTO:0000294 xref: CALOHA:TS-2076 xref: EFO:0000953 xref: EMAPA:17527 xref: EV:0100154 xref: FMA:70323 xref: GAID:1321 xref: MA:0000152 xref: MAT:0000153 xref: MESH:D020405 xref: MIAA:0000153 xref: NCIT:C12701 xref: SCTID:361696001 xref: TAO:0001119 xref: UMLS:C0011646 {source="ncithesaurus:Dermis"} xref: VHOG:0000108 xref: Wikipedia:Dermis xref: XAO:0000217 xref: ZFA:0001119 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013754 ! integumentary system layer relationship: composed_primarily_of UBERON:0002384 ! connective tissue relationship: deep_to UBERON:0001003 ! skin epidermis relationship: develops_from UBERON:0010083 ! future dermis relationship: has_part GO:0071953 ! elastic fiber relationship: has_part UBERON:0011860 ! collection of collagen fibrils relationship: immediate_transformation_of UBERON:0010083 {evidence="definitional"} ! future dermis relationship: part_of UBERON:0002097 {source="FMA"} ! skin of body relationship: superficial_to UBERON:0002072 ! hypodermis property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg xsd:anyURI property_value: editor_note "Consider adding a layer-of-skin grouping class for all skin layers" xsd:string property_value: UBPROP:0000001 "A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001119", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000108", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "dermal" xsd:string [Term] id: UBERON:0002072 name: hypodermis namespace: uberon def: "Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]." [Wikipedia:Hypodermis] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "hypoderm" EXACT [] synonym: "sub-tegumental tissue" RELATED [BTO:0004525] synonym: "subcutaneous tissue" RELATED [Wikipedia:Hypodermis] synonym: "subcutis" RELATED [] synonym: "subtegumental tissue" RELATED [BTO:0004525] synonym: "superficial fascia" RELATED INCONSISTENT [] synonym: "tela subcutanea" RELATED LATIN [Wikipedia:Hypodermis] synonym: "vertebrate hypodermis" EXACT [] xref: BTO:0001314 xref: CALOHA:TS-2366 xref: EMAPA:37505 {source="MA:th"} xref: FMA:70544 xref: NCIT:C33645 xref: TAO:0001136 xref: UMLS:C0278403 {source="ncithesaurus:Subcutis"} xref: Wikipedia:Hypodermis xref: ZFA:0001136 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: composed_primarily_of UBERON:0001013 ! adipose tissue relationship: composed_primarily_of UBERON:0011825 {source="FMA-modified"} ! loose connective tissue relationship: deep_to UBERON:0002067 ! dermis relationship: part_of UBERON:0002199 {source="ZFA"} ! integument relationship: superficial_to UBERON:0001015 ! musculature property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg xsd:anyURI property_value: UBPROP:0000001 "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001136", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]." xsd:string {source="FMA:70544"} property_value: UBPROP:0000007 "hypodermal" xsd:string property_value: UBPROP:0000007 "subcutaneous" xsd:string property_value: UBPROP:0000007 "subcutaneus" xsd:string property_value: UBPROP:0000012 "BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument." xsd:string {external_ontology="BTO"} [Term] id: UBERON:0002075 name: viscus namespace: uberon def: "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen." [BTO:0001491, https://github.com/obophenotype/mouse-anatomy-ontology/issues/14, Wikipedia:Viscus] subset: organ_slim subset: pheno_slim subset: uberon_slim subset: upper_level synonym: "splanchnic tissue" RELATED [BTO:0001491] synonym: "viscera" RELATED [] synonym: "visceral organ" EXACT [RETIRED_EHDAA2:0002201] synonym: "visceral organ system" EXACT [MA:0000019] synonym: "visceral tissue" RELATED [BTO:0001491] xref: AAO:0010386 xref: BTO:0001491 xref: EHDAA:512 xref: EMAPA:16245 xref: FMA:7085 xref: MA:0000019 xref: MESH:D014781 xref: NCIT:C28287 xref: RETIRED_EHDAA2:0002201 xref: SCTID:118760003 xref: UMLS:C0042779 {source="ncithesaurus:Viscera"} xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen relationship: located_in UBERON:0002323 ! coelemic cavity lumen property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002078 name: right cardiac atrium namespace: uberon def: "A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Right_atrium] subset: pheno_slim subset: uberon_slim synonym: "atrium dextrum" RELATED LATIN [Wikipedia:Right_atrium] synonym: "cardiac right atrium" EXACT [] synonym: "heart right atrium" EXACT [MA:0000075] synonym: "right atrium" EXACT [VHOG:0000328] synonym: "right atrium of heart" EXACT [] synonym: "right cardiac atrium" EXACT [] xref: AAO:0010248 xref: BTO:0001703 xref: EHDAA2:0000290 xref: EMAPA:17321 xref: FMA:7096 xref: galen:RightAtrium xref: MA:0000075 xref: NCIT:C12868 xref: OpenCyc:Mx4runNcs6fqEdudWQACs5b6Bw xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw xref: SCTID:244383003 xref: UMLS:C0225844 {source="ncithesaurus:Right_Atrium"} xref: VHOG:0000328 xref: Wikipedia:Right_atrium xref: XAO:0003192 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber intersection_of: UBERON:0002081 ! cardiac atrium intersection_of: in_right_side_of UBERON:0000948 ! heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg xsd:anyURI property_value: UBPROP:0000001 "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" xsd:string {source="FMA:7096"} property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000328", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0002079 name: left cardiac atrium namespace: uberon def: "A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Left_atrium] subset: pheno_slim subset: uberon_slim synonym: "atrium sinistrum" EXACT LATIN [Wikipedia:Left_atrium] synonym: "cardiac left atrium" EXACT [] synonym: "heart left atrium" EXACT [MA:0000074] synonym: "left atrium" EXACT [VHOG:0000369] synonym: "left atrium of heart" EXACT [] synonym: "left cardiac atrium" EXACT [] xref: AAO:0010247 xref: BTO:0001702 xref: EHDAA2:0000275 xref: EMAPA:17315 xref: FMA:7097 xref: galen:LeftAtrium xref: MA:0000074 xref: NCIT:C12869 xref: OpenCyc:Mx4rkJN1AagEEdudWQACs5b6Bw xref: OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw xref: SCTID:244387002 xref: UMLS:C0225860 {source="ncithesaurus:Left_Atrium"} xref: VHOG:0000369 xref: Wikipedia:Left_atrium xref: XAO:0003191 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035553 ! left cardiac chamber intersection_of: UBERON:0002081 ! cardiac atrium intersection_of: in_left_side_of UBERON:0000948 ! heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg xsd:anyURI property_value: UBPROP:0000001 "Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]" xsd:string {source="FMA:7097"} property_value: UBPROP:0000001 "The chamber of the heart that receives blood from the lungs[XAO:EJS]." xsd:string {source="XAO:EJS"} property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000369", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0002080 name: heart right ventricle namespace: uberon def: "A cardiac ventricle that is in the right side of the heart." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "cardiac right ventricle" EXACT [] synonym: "right cardiac ventricle" RELATED [EMAPA:17340] synonym: "right ventricle" EXACT [FMA:7098] synonym: "right ventricle of heart" EXACT [] synonym: "ventriculus dexter" RELATED LATIN [Wikipedia:Right_ventricle] xref: BTO:0001630 xref: CALOHA:TS-0443 xref: EHDAA2:0000196 xref: EMAPA:17340 xref: FMA:7098 xref: galen:RightVentricle xref: MA:0000093 xref: NCIT:C12870 xref: OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA xref: SCTID:244384009 xref: UMLS:C0225883 {source="ncithesaurus:Right_Ventricle"} xref: VHOG:0000717 xref: Wikipedia:Right_ventricle is_a: UBERON:0002082 ! cardiac ventricle is_a: UBERON:0035554 ! right cardiac chamber intersection_of: UBERON:0002082 ! cardiac ventricle intersection_of: in_right_side_of UBERON:0000948 ! heart relationship: develops_from UBERON:0009889 {source="PMID:17276708"} ! secondary heart field relationship: has_developmental_contribution_from UBERON:0004706 {source="cjm"} ! bulbus cordis property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg xsd:anyURI property_value: UBPROP:0000001 "The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000717", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI property_value: UBPROP:0000008 "In mammals continuous with the pulmonary arteries" xsd:string [Term] id: UBERON:0002081 name: cardiac atrium namespace: uberon def: "Cardiac chamber in which blood enters the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Heart_atrium] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "atria" EXACT PLURAL [] synonym: "atrial tissue" RELATED [BTO:0000903] synonym: "atrium" EXACT [ZFA:0000471] synonym: "atrium of heart" EXACT [] synonym: "cardiac atria" EXACT PLURAL [] synonym: "heart atrium" EXACT [] xref: AAO:0010246 xref: BTO:0000903 xref: CALOHA:TS-0437 xref: EFO:0000277 xref: EHDAA2:0000154 xref: EHDAA:1265 xref: EMAPA:16688 xref: EV:0100019 xref: FMA:7099 xref: GAID:555 xref: galen:Atrium xref: MA:0000073 xref: MAT:0000496 xref: MESH:D006325 xref: NCIT:C12728 xref: SCTID:261405004 xref: TAO:0000471 xref: UMLS:C0018792 {source="ncithesaurus:Cardiac_Atrium"} xref: VHOG:0000175 xref: Wikipedia:Heart_atrium xref: ZFA:0000471 is_a: UBERON:0004151 ! cardiac chamber relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: develops_from UBERON:0010227 ! future cardiac atrium relationship: immediate_transformation_of UBERON:0010227 ! future cardiac atrium property_value: UBPROP:0000001 "One of four heart chambers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000471", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010246", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000175", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002082 name: cardiac ventricle namespace: uberon def: "Cardiac chamber through which blood leaves the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Ventricle_(heart)] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "heart ventricle" EXACT [] synonym: "lower chamber of heart" EXACT [] synonym: "ventricle" BROAD [] synonym: "ventricle of heart" EXACT [] xref: AAO:0010249 xref: BTO:0000862 xref: CALOHA:TS-0444 xref: EFO:0000317 xref: EHDAA2:0004164 xref: EHDAA:1912 xref: EMAPA:17331 xref: EV:0100020 xref: FMA:7100 xref: GAID:568 xref: galen:Ventricle xref: MA:0000091 xref: MAT:0000497 xref: MESH:D006352 xref: NCIT:C12730 xref: OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA xref: SCTID:277699000 xref: TAO:0000009 xref: UMLS:C0018827 {source="ncithesaurus:Cardiac_Ventricle"} xref: VHOG:0000435 xref: Wikipedia:Ventricle_(heart) xref: XAO:0003193 xref: ZFA:0000009 is_a: UBERON:0004151 ! cardiac chamber relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: develops_from UBERON:0006283 ! future cardiac ventricle relationship: immediate_transformation_of UBERON:0006283 {source="Bgee:AN"} ! future cardiac ventricle property_value: UBPROP:0000001 "A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010249", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "One of four heart chambers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000009", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000435", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002084 name: heart left ventricle namespace: uberon def: "A cardiac ventricle that is in the left side of the heart." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "cardiac left ventricle" EXACT [] synonym: "left cardiac ventricle" EXACT [] synonym: "left ventricle" EXACT [FMA:7101] synonym: "left ventricle of heart" EXACT [] synonym: "ventriculus sinister cordis" RELATED LATIN [Wikipedia:Left_ventricle] xref: BTO:0001629 xref: CALOHA:TS-0439 xref: EHDAA2:0002178 xref: EMAPA:17337 xref: FMA:7101 xref: galen:LeftVentricle xref: MA:0000092 xref: NCIT:C12871 xref: OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw xref: OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA xref: SCTID:244385005 xref: UMLS:C0225897 {source="ncithesaurus:Left_Ventricle"} xref: VHOG:0000718 xref: Wikipedia:Left_ventricle is_a: UBERON:0002082 ! cardiac ventricle is_a: UBERON:0035553 ! left cardiac chamber intersection_of: UBERON:0002082 ! cardiac ventricle intersection_of: in_left_side_of UBERON:0000948 ! heart relationship: continuous_with UBERON:0000947 ! aorta relationship: develops_from UBERON:0004140 {source="GO"} ! primary heart field property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg xsd:anyURI property_value: UBPROP:0000001 "Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000718", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000718", ontology="VHOG", source="DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI property_value: UBPROP:0000008 "In mammals continuous with aorta" xsd:string [Term] id: UBERON:0002085 name: interatrial septum namespace: uberon def: "A cardiac septum that divides the left and right atria of the heart." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "atrial septum" EXACT [] synonym: "atrium septum" EXACT [] synonym: "interatrial septal wall" EXACT [] xref: EHDAA2:0000838 xref: EHDAA:1896 xref: EMAPA:17011 xref: FMA:7108 xref: galen:InteratrialSeptum xref: MA:0000084 xref: NCIT:C32818 xref: OpenCyc:Mx4rpd49nLYEEduAAAACs2IKfQ xref: OpenCyc:Mx4rwGvku5wpEbGdrcN5Y29ycA xref: SCTID:362016003 xref: UMLS:C0225836 {source="ncithesaurus:Interatrial_Septum"} xref: VHOG:0000385 xref: Wikipedia:Interatrial_septum is_a: UBERON:0002099 ! cardiac septum intersection_of: UBERON:0002099 ! cardiac septum intersection_of: adjacent_to UBERON:0002078 ! right cardiac atrium intersection_of: adjacent_to UBERON:0002079 ! left cardiac atrium relationship: adjacent_to UBERON:0002078 ! right cardiac atrium relationship: adjacent_to UBERON:0002079 ! left cardiac atrium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png xsd:anyURI property_value: UBPROP:0000001 "The partition separating the right and left atria of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000385", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/interatrial+septum"} property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000385", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002090 name: postcranial axial skeleton namespace: uberon def: "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]." [https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957, https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834, ZFA:0000317] comment: previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "axial skeleton" BROAD [FMA:71221, https://github.com/obophenotype/uberon/wiki/The-axial-skeleton] synonym: "post-cranial axial skeleton" EXACT [] xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010912 ! subdivision of skeleton relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002091 name: appendicular skeleton namespace: uberon def: "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003, Wikipedia:Appendicular_skeleton] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "appendicular skeleton" EXACT [] synonym: "entire appendicular skeleton" EXACT [https://github.com/obophenotype/uberon/issues/59] synonym: "paired fin skeleton" NARROW SENSU [] synonym: "skeleton appendiculare" RELATED LATIN [Wikipedia:Appendicular_skeleton] xref: AAO:0000747 xref: EFO:0000951 xref: EMAPA:32729 xref: FMA:71222 xref: MA:0000290 xref: MAT:0000278 xref: MIAA:0000278 xref: NCIT:C49477 xref: SCTID:322050006 xref: UMLS:C0222646 {source="ncithesaurus:Appendicular_Skeleton"} xref: VHOG:0001666 xref: VSAO:0000076 xref: Wikipedia:Appendicular_skeleton xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0011249 ! appendicular skeletal system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton xsd:anyURI property_value: UBPROP:0000001 "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000076", ontology="VSAO", source="PSPUB:0000170", source="https://orcid.org/0000-0002-6601-2165"} property_value: UBPROP:0000001 "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000027", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000001 "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000747", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000012 "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002094 name: interventricular septum namespace: uberon def: "Cardiac septum which separates the right ventricle from the left ventricle.[FMA]" [FMA:7133] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "heart interventricular septum" EXACT [MA:0000085] synonym: "heart ventricular septum" EXACT [MA:0000085] synonym: "interventricular septum of heart" RELATED [BTO:0002483] synonym: "interventriculare cordis" RELATED [BTO:0002483] synonym: "intraventricular septum" RELATED [Wikipedia:Interventricular_septum] synonym: "s. interventriculare cordis" RELATED LATIN [Wikipedia:Interventricular_septum] synonym: "septum inferius" RELATED [Wikipedia:Interventricular_septum] synonym: "septum membranaceum" RELATED [Wikipedia:Interventricular_septum] synonym: "ventricle septum" RELATED [] synonym: "ventricular septum" RELATED [MA:0000085, Wikipedia:Interventricular_septum] xref: BTO:0002483 xref: EFO:0001956 xref: EHDAA:2603 xref: EMAPA:17333 xref: FMA:7133 xref: galen:InterventricularSeptum xref: MA:0000085 xref: NCIT:C32874 xref: OpenCyc:Mx4rwA7lp5wpEbGdrcN5Y29ycA xref: SCTID:362019005 xref: UMLS:C0225870 {source="ncithesaurus:Interventricular_Septum"} xref: VHOG:0000386 xref: Wikipedia:Interventricular_septum is_a: UBERON:0002099 ! cardiac septum intersection_of: UBERON:0002099 ! cardiac septum intersection_of: adjacent_to UBERON:0002080 ! heart right ventricle intersection_of: adjacent_to UBERON:0002084 ! heart left ventricle relationship: adjacent_to UBERON:0002080 ! heart right ventricle relationship: adjacent_to UBERON:0002084 ! heart left ventricle property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png xsd:anyURI property_value: UBPROP:0000001 "The partition separating the right and left ventricles of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000386", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/interventricular+septum"} property_value: UBPROP:0000003 "The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000386", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430", source="http://bgee.unil.ch/"} property_value: UBPROP:0000011 "involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)" xsd:string {source="ISBN:0124020607"} [Term] id: UBERON:0002097 name: skin of body namespace: uberon def: "The organ covering the body that consists of the dermis and epidermis." [UBERON:cjm] subset: efo_slim subset: major_organ subset: pheno_slim subset: uberon_slim synonym: "entire integument" RELATED [] synonym: "entire skin" EXACT [] synonym: "integument" RELATED [] synonym: "integumental organ" RELATED [] synonym: "pelt" RELATED [] synonym: "skin" RELATED [] synonym: "skin organ" EXACT [] xref: BTO:0001253 xref: CALOHA:TS-0934 xref: EFO:0000962 xref: EHDAA2:0001844 xref: EMAPA:17525 xref: FMA:7163 xref: galen:Skin xref: MESH:D012867 xref: MFMO:0000099 xref: NCIT:C12470 xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA xref: SCTID:181469002 xref: UMLS:C1123023 {source="ncithesaurus:Skin"} xref: Wikipedia:Skin xref: XAO:0000023 is_a: UBERON:0000062 ! organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: composed_primarily_of UBERON:0000014 ! zone of skin relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0002199 ! integument property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg xsd:anyURI property_value: IAO:0000232 "consider 'integumentary system' for invertebrates" xsd:string property_value: UBPROP:0000012 "MA uses the term skin to refer to what is called here: zone of skin" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002099 name: cardiac septum namespace: uberon def: "The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles." [MESH:A07.541.459] subset: pheno_slim subset: uberon_slim synonym: "cardiac septa" EXACT PLURAL [] synonym: "heart septa" EXACT PLURAL [] synonym: "heart septum" EXACT [] synonym: "septum of heart" EXACT [] synonym: "spiral septa" RELATED PLURAL [XAO:0004141] xref: EMAPA:35400 xref: FMA:7180 xref: GAID:562 xref: MA:0000083 xref: MESH:D006346 xref: NCIT:C49485 xref: SCTID:362014000 xref: UMLS:C0018819 {source="ncithesaurus:Heart_Septum"} is_a: UBERON:0003037 ! septum is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003037 ! septum intersection_of: part_of UBERON:0000948 ! heart relationship: adjacent_to UBERON:0004151 ! cardiac chamber relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart property_value: UBPROP:0000008 "'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'" xsd:string property_value: UBPROP:0000012 "in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this" xsd:string {external_ontology="GO"} [Term] id: UBERON:0002100 name: trunk namespace: uberon def: "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." [TAO:0001115, UBERONREF:0000006, Wikipedia:Torso] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "Rumpf" RELATED [BTO:0001493] synonym: "thoracolumbar region" EXACT [] synonym: "torso" EXACT [] synonym: "trunk region" EXACT [XAO:0000054] xref: AAO:0010339 xref: BILA:0000116 xref: BTO:0001493 xref: CALOHA:TS-1071 xref: EFO:0000966 xref: EMAPA:31857 xref: FMA:7181 xref: galen:Trunk xref: MA:0000004 xref: MAT:0000296 xref: MIAA:0000296 xref: NCIT:C33816 xref: OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA xref: SCTID:262225004 xref: TAO:0001115 xref: UMLS:C0460005 {source="ncithesaurus:Trunk"} xref: Wikipedia:Torso xref: XAO:0000054 xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: has_part UBERON:0000915 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! thoracic segment of trunk relationship: has_part UBERON:0000916 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! abdomen relationship: part_of UBERON:0013702 ! body proper property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002104 name: visual system namespace: uberon alt_id: UBERON:0007036 def: "The sensory system subserving the sense of vision." [NIFSTD:FMAID_7191] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "photosensory system" EXACT [BILA:0000140] synonym: "visual organ system" EXACT [] xref: AAO:0000632 xref: BILA:0000140 xref: EMAPA:36003 xref: FMA:7191 xref: http://uri.neuinfo.org/nif/nifstd/FMAID_7191 xref: MA:0002444 xref: NCIT:C12888 xref: OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA xref: SCTID:281831001 xref: TAO:0001127 xref: UMLS:C0587900 {source="ncithesaurus:Visual_System"} xref: Wikipedia:Visual_system xref: XAO:0003198 xref: ZFA:0001127 is_a: UBERON:0001032 ! sensory system relationship: capable_of GO:0007601 ! visual perception property_value: UBPROP:0000001 "The sensory system used for sight.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000632", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0002111 name: artery smooth muscle tissue namespace: uberon def: "A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]." [OBOL:automatic] synonym: "arterial smooth muscle" EXACT [BTO:0000087] synonym: "arterial smooth muscle cell" RELATED [BTO:0000087] synonym: "artery smooth muscle" EXACT [] synonym: "artery smooth muscle tissue" EXACT [] synonym: "smooth muscle of artery" EXACT [FMA:72024] xref: BTO:0000087 xref: CALOHA:TS-1198 xref: EMAPA:36285 xref: FMA:72024 xref: MA:0000708 xref: NCIT:C49195 xref: UMLS:C1706851 {source="ncithesaurus:Artery_Smooth_Muscle_Tissue"} is_a: UBERON:0004237 ! blood vessel smooth muscle is_a: UBERON:0004695 ! arterial system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery [Term] id: UBERON:0002112 name: smooth muscle of esophagus namespace: uberon def: "A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "esophageal smooth muscle" EXACT [] synonym: "esophagus involuntary muscle" EXACT [OBOL:automatic] synonym: "esophagus non-striated muscle" EXACT [OBOL:automatic] synonym: "esophagus smooth muscle" EXACT [] synonym: "esophagus smooth muscle tissue" EXACT [OBOL:automatic] synonym: "gullet involuntary muscle" EXACT [OBOL:automatic] synonym: "gullet non-striated muscle" EXACT [OBOL:automatic] synonym: "gullet smooth muscle" EXACT [OBOL:automatic] synonym: "gullet smooth muscle tissue" EXACT [OBOL:automatic] synonym: "involuntary muscle of esophagus" EXACT [OBOL:automatic] synonym: "involuntary muscle of gullet" EXACT [OBOL:automatic] synonym: "involuntary muscle of oesophagus" EXACT [OBOL:automatic] synonym: "non-striated muscle of esophagus" EXACT [OBOL:automatic] synonym: "non-striated muscle of gullet" EXACT [OBOL:automatic] synonym: "non-striated muscle of oesophagus" EXACT [OBOL:automatic] synonym: "oesophagus involuntary muscle" EXACT [OBOL:automatic] synonym: "oesophagus non-striated muscle" EXACT [OBOL:automatic] synonym: "oesophagus smooth muscle" RELATED [] synonym: "oesophagus smooth muscle tissue" EXACT [OBOL:automatic] synonym: "smooth muscle of gullet" EXACT [OBOL:automatic] synonym: "smooth muscle of oesophagus" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of esophagus" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of gullet" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of oesophagus" EXACT [OBOL:automatic] xref: EMAPA:35323 xref: FMA:72025 xref: MA:0001573 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001043 ! esophagus relationship: contributes_to_morphology_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0003832 ! esophagus muscle [Term] id: UBERON:0002118 name: right ovary namespace: uberon def: "An ovary that is part of a right side of organism [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37367 {source="MA:th"} xref: FMA:7213 xref: MA:0001705 xref: NCIT:C33487 xref: SCTID:280123002 xref: UMLS:C0227873 {source="ncithesaurus:Right_Ovary"} is_a: UBERON:0000992 ! ovary is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000992 ! ovary intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: in_right_side_of UBERON:0000468 ! multicellular organism property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0002119 name: left ovary namespace: uberon def: "An ovary that is part of a left side of organism [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37366 {source="MA:th"} xref: FMA:7214 xref: MA:0001704 xref: NCIT:C32969 xref: SCTID:280124008 xref: UMLS:C0227874 {source="ncithesaurus:Left_Ovary"} is_a: UBERON:0000992 ! ovary is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000992 ! ovary intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: in_left_side_of UBERON:0000468 ! multicellular organism property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI property_value: UBPROP:0000008 "In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" xsd:string {source="Wikipedia:Ovary#In_other_animals"} [Term] id: UBERON:0002165 name: endocardium namespace: uberon alt_id: UBERON:0006225 def: "The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]." [GO:0003157] comment: fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "endocardial lining" EXACT [EMAPA:32686] synonym: "endocardial tissue" EXACT [EMAPA:17868] synonym: "heart endocardial tissue" RELATED [VHOG:0000084] synonym: "heart endocardium" EXACT [] xref: AAO:0010408 xref: BTO:0000387 xref: CALOHA:TS-2075 xref: EFO:0000821 xref: EHDAA2:0004153 xref: EMAPA:17868 xref: EMAPA:32686 xref: EV:0100021 xref: FMA:7280 xref: GAID:550 xref: galen:Endocardium xref: MA:0000076 xref: MAT:0000455 xref: MESH:D004699 xref: NCIT:C13004 xref: OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw xref: SCTID:362013006 xref: TAO:0001320 xref: UMLS:C0014124 {source="ncithesaurus:Endocardium"} xref: VHOG:0000084 xref: Wikipedia:Endocardium xref: XAO:0000066 xref: ZFA:0001320 is_a: UBERON:0002523 ! tunica intima is_a: UBERON:0005983 ! heart layer relationship: develops_from UBERON:0007280 ! presumptive endocardium relationship: has_part UBERON:0005316 ! endocardial endothelium relationship: immediate_transformation_of UBERON:0007280 {source="Bgee:AN"} ! presumptive endocardium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png xsd:anyURI property_value: UBPROP:0000001 "Layer that lines the lumen of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001320", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010408", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber." xsd:string {source="FMA:7280"} [Term] id: UBERON:0002166 name: endocardium of atrium namespace: uberon def: "Endocardium that is part of the atrium." [ZFIN:curator] subset: pheno_slim subset: vertebrate_core synonym: "atrial endocardium" EXACT [] synonym: "atrium endocardial tissue" RELATED [VHOG:0000606] synonym: "atrium endocardium" EXACT [] synonym: "atrium of heart endocardium" EXACT [OBOL:automatic] synonym: "Cardiac atria endocardium" EXACT [OBOL:automatic] synonym: "cardiac atrium endocardium" EXACT [OBOL:automatic] synonym: "endocardium of atrium of heart" EXACT [OBOL:automatic] synonym: "endocardium of Cardiac atria" EXACT [OBOL:automatic] synonym: "endocardium of cardiac atrium" EXACT [OBOL:automatic] synonym: "endocardium of heart atrium" EXACT [OBOL:automatic] synonym: "heart atrium endocardium" EXACT [OBOL:automatic] xref: EMAPA:32745 xref: FMA:7284 xref: MA:0000077 xref: SCTID:192001005 xref: TAO:0002169 xref: VHOG:0000606 xref: ZFA:0001614 is_a: UBERON:0002165 ! endocardium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: contributes_to_morphology_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium [Term] id: UBERON:0002167 name: right lung namespace: uberon def: "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]" [FMA:FMA, Wikipedia:Right_lung] subset: pheno_slim subset: uberon_slim xref: EHDAA2:0001730 xref: EHDAA:4969 xref: EMAPA:17661 xref: FMA:7309 xref: MA:0000426 xref: NCIT:C33483 xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA xref: SCTID:361967000 xref: UMLS:C0225706 {source="ncithesaurus:Right_Lung"} xref: VHOG:0000301 xref: Wikipedia:Right_lung is_a: UBERON:0002048 ! lung intersection_of: UBERON:0002048 ! lung intersection_of: in_right_side_of UBERON:0000170 ! pair of lungs relationship: in_right_side_of UBERON:0000170 ! pair of lungs property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png xsd:anyURI property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000301", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210", source="http://bgee.unil.ch/"} property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0002168 name: left lung namespace: uberon def: "Lung which consists of the left upper lobe and left lower lobe.[FMA]" [FMA:FMA, Wikipedia:Left_lung] subset: pheno_slim subset: uberon_slim xref: EHDAA2:0000943 xref: EHDAA:4947 xref: EMAPA:17653 xref: FMA:7310 xref: MA:0000425 xref: NCIT:C32967 xref: OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA xref: SCTID:361982005 xref: UMLS:C0225730 {source="ncithesaurus:Left_Lung"} xref: VHOG:0000618 xref: Wikipedia:Left_lung is_a: UBERON:0002048 ! lung intersection_of: UBERON:0002048 ! lung intersection_of: in_left_side_of UBERON:0000170 ! pair of lungs relationship: in_left_side_of UBERON:0000170 ! pair of lungs property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png xsd:anyURI property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000618", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210", source="http://bgee.unil.ch/"} property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0002190 name: subcutaneous adipose tissue namespace: uberon alt_id: UBERON:0008875 def: "A portion of adipose tissue that is part of the hypodermis, beneath the dermis." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "fatty layer of subcutaneous tissue" EXACT [FMA:74315] synonym: "fatty layer of superficial fascia" RELATED [FMA:74315] synonym: "hypodermis fat layer" EXACT [MP:0011156] synonym: "panniculus adiposus" BROAD [MP:0011156] synonym: "panniculus adiposus (tela subcutanea)" EXACT LATIN [FMA:74315, FMA:TA] synonym: "panniculus adiposus telae subcutaneae" EXACT LATIN [FMA:74315, FMA:TA] synonym: "subcutaneous fat" RELATED [BTO:0004042] synonym: "subcutaneous fat layer" EXACT [MP:0011156] xref: BTO:0004042 xref: EMAPA:35829 xref: FMA:74315 xref: MA:0000473 is_a: UBERON:0001013 ! adipose tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001013 ! adipose tissue intersection_of: part_of UBERON:0002072 ! hypodermis relationship: contributes_to_morphology_of UBERON:0002072 ! hypodermis relationship: part_of UBERON:0002072 ! hypodermis property_value: UBPROP:0000001 "the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]" xsd:string {source="MP:0011156"} [Term] id: UBERON:0002193 name: hemolymphoid system namespace: uberon def: "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs." [http://orcid.org/0000-0002-6601-2165] synonym: "haemolymphoid system" RELATED [] synonym: "hematolymphoid system" EXACT [] synonym: "lymphomyeloid complex" EXACT [] xref: CALOHA:TS-2018 xref: EHDAA2:0004615 xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] id: UBERON:0002199 name: integument namespace: uberon def: "The dermis, epidermis and hypodermis." [Wikipedia:Integument] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "dermal system" RELATED [BTO:0000634] synonym: "dermis plus epidermis plus hypodermis" EXACT [] synonym: "dermoid system" RELATED [BTO:0000634] synonym: "integumentum commune" EXACT LATIN [FMA:74657, FMA:TA] synonym: "skin" RELATED [] synonym: "skin and subcutaneous tissue" EXACT [] synonym: "skin plus hypodermis" EXACT [] synonym: "tegument" RELATED [BTO:0000634] synonym: "the integument" EXACT [FMA:74657] synonym: "vertebrate integument" RELATED [] xref: AAO:0000239 xref: BTO:0000634 xref: EMAPA:37504 {source="MA:th"} xref: FMA:74657 xref: galen:Integument xref: TAO:0000368 xref: VSAO:0000029 xref: Wikipedia:Integument xref: ZFA:0000368 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: has_part UBERON:0002072 ! hypodermis relationship: has_part UBERON:0002097 ! skin of body relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002416 {source="FMA"} ! integumental system property_value: IAO:0000232 "in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition." xsd:string property_value: UBPROP:0000001 "Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000239", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "Surface structure that is the outer protective covering of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000029", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000001 "The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000368", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000007 "integumental" xsd:string property_value: UBPROP:0000007 "integumentary" xsd:string [Term] id: UBERON:0002200 name: vasculature of head namespace: uberon def: "Vasculature that is part of a head [Automatically generated definition]." [OBOL:automatic] subset: efo_slim subset: vertebrate_core synonym: "adult head vascular network" EXACT [OBOL:automatic] synonym: "adult head vasculature" EXACT [OBOL:automatic] synonym: "cranial vasculature" EXACT [] synonym: "head vascular network" EXACT [OBOL:automatic] synonym: "head vasculature" RELATED [] synonym: "vascular network of adult head" EXACT [OBOL:automatic] synonym: "vascular network of head" EXACT [OBOL:automatic] synonym: "vasculature of adult head" EXACT [OBOL:automatic] xref: EFO:0003656 xref: FMA:74710 xref: TAO:0001267 xref: XAO:0004152 xref: ZFA:0001267 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head [Term] id: UBERON:0002201 name: vasculature of trunk namespace: uberon def: "A vasculature that is part of a trunk [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "torso vascular network" EXACT [OBOL:automatic] synonym: "torso vasculature" EXACT [OBOL:automatic] synonym: "trunk vascular network" EXACT [OBOL:automatic] synonym: "trunk vasculature" EXACT [] synonym: "vascular network of torso" EXACT [OBOL:automatic] synonym: "vascular network of trunk" EXACT [OBOL:automatic] synonym: "vasculature of torso" EXACT [OBOL:automatic] xref: FMA:74712 xref: TAO:0005024 xref: ZFA:0005024 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0002203 name: vasculature of eye namespace: uberon def: "Vasculature that is part of the eye region." [https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726, OBOL:automatic] subset: pheno_slim subset: vertebrate_core synonym: "eye vascular network" EXACT [OBOL:automatic] synonym: "eye vasculature" RELATED [] synonym: "ocular blood vessel" EXACT [ZFA:0007057] synonym: "ocular vasculature" EXACT [] synonym: "optic vasculature" RELATED [] synonym: "vascular network of eye" EXACT [OBOL:automatic] xref: FMA:74743 xref: SCTID:123846009 xref: TAO:0007057 xref: ZFA:0007057 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme relationship: part_of UBERON:0000019 ! camera-type eye property_value: UBPROP:0000012 "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0002204 name: musculoskeletal system namespace: uberon def: "Anatomical system that consists of the muscular and skeletal systems." [https://github.com/obophenotype/uberon/issues/77, VSAO:0000031, VSAO:curator] subset: uberon_slim synonym: "musculo-skeletal system" EXACT [] xref: AAO:0010546 xref: CALOHA:TS-1311 xref: EMAPA:32714 xref: EV:0100139 xref: FMA:7482 xref: GAID:98 xref: MA:0002418 xref: MESH:D009141 xref: NCIT:C12754 xref: OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g xref: SCTID:278858007 xref: UMLS:C0026860 {source="ncithesaurus:Musculoskeletal_System"} xref: VHOG:0001275 xref: VSAO:0000031 xref: Wikipedia:Musculoskeletal_system xref: XAO:0000168 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0040011 ! locomotion relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "musculoskeletal" xsd:string [Term] id: UBERON:0002213 name: cartilaginous joint namespace: uberon def: "Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]" [FMA:FMA, Wikipedia:Cartilaginous_joint] subset: uberon_slim subset: vertebrate_core synonym: "articulatio cartilaginea" EXACT [] synonym: "junctura cartilaginea" RELATED LATIN [Wikipedia:Cartilaginous_joint] xref: EMAPA:36581 xref: FMA:7496 xref: MA:0000320 xref: SCTID:58442004 xref: TAO:0005155 xref: Wikipedia:Cartilaginous_joint xref: ZFA:0005155 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011134 {source="FMA"} ! nonsynovial joint intersection_of: UBERON:0011134 ! nonsynovial joint intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: composed_primarily_of UBERON:0002418 ! cartilage tissue [Term] id: UBERON:0002217 name: synovial joint namespace: uberon def: "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]" [FMA:7501, Wikipedia:Synovial_joint] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "articulatio synoviale" EXACT [] synonym: "diarthrodial joints" RELATED PLURAL [ZFA:0005153] synonym: "diarthroses" EXACT PLURAL [ZFA:0005153] synonym: "diarthrosis" EXACT [] synonym: "diarthrosis joint" EXACT [] xref: AEO:0000183 xref: CALOHA:TS-2138 xref: EHDAA2:0003183 xref: FMA:7501 xref: galen:SynovialJoint xref: MA:0000322 xref: NCIT:C32461 xref: OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA xref: SCTID:113234001 xref: TAO:0005153 xref: Wikipedia:Synovial_joint xref: ZFA:0005153 is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: surrounded_by UBERON:0001484 ! articular capsule disjoint_from: UBERON:0011134 ! nonsynovial joint relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: surrounded_by UBERON:0001484 ! articular capsule property_value: UBPROP:0000001 "Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005153", ontology="TAO", source="ZFIN:Curator"} [Term] id: UBERON:0002224 name: thoracic cavity namespace: uberon def: "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax." [UBERON:cjm, Wikipedia:Thoracic_cavity] subset: pheno_slim subset: uberon_slim synonym: "cavitas thoracis" EXACT LATIN [Wikipedia:Thoracic_cavity] synonym: "cavity of chest" EXACT [] synonym: "cavity of thorax" EXACT [] synonym: "chest cavity" EXACT [] synonym: "pectoral cavity" EXACT [] synonym: "space of thoracic compartment" EXACT [FMA:7565] synonym: "thoracic lumen" EXACT [] xref: EMAPA:36497 xref: FMA:7565 xref: GAID:93 xref: MA:0000032 xref: MESH:A01.911.800 xref: NCIT:C12905 xref: OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg xref: OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA xref: SCTID:243949006 xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg xsd:anyURI property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string [Term] id: UBERON:0002240 name: spinal cord namespace: uberon def: "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)" [BIRNLEX:1709] subset: cumbo subset: efo_slim subset: major_organ subset: organ_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cerebro-cerebellar fissure" RELATED [NeuroNames:22] synonym: "cerebrocerebellar fissure" RELATED [NeuroNames:22] synonym: "fissura cerebro-cerebellaris" RELATED LATIN [NeuroNames:22] synonym: "fissura cerebrocerebellaris" RELATED LATIN [NeuroNames:22] synonym: "medulla spinalis" RELATED LATIN [Wikipedia:Spinal_cord] synonym: "medulla spinalis" RELATED [BTO:0001279] synonym: "SpC" RELATED ABBREVIATION [] synonym: "spinal cord structure" RELATED [ZFA:0000075] synonym: "spinal medulla" RELATED [BTO:0001279] xref: AAO:0010151 xref: BAMS:SP xref: BAMS:Spinal xref: BIRNLEX:1709 xref: BM:SpC xref: BTO:0001279 xref: CALOHA:TS-0953 xref: DHBA:12890 xref: DMBA:17651 xref: EFO:0000110 xref: EHDAA2:0001255 xref: EHDAA:2863 xref: EMAPA:17577 xref: EV:0100316 xref: FMA:7647 xref: GAID:695 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 {source="BIRNLEX:1709"} xref: MA:0000216 xref: MAT:0000183 xref: MESH:D013116 xref: MIAA:0000183 xref: NCIT:C12464 xref: OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA xref: SCTID:180959008 xref: TAO:0000075 xref: UMLS:C0037925 {source="ncithesaurus:Spinal_Cord"} xref: UMLS:C0037925 {source="BIRNLEX:1709"} xref: VHOG:0000601 xref: Wikipedia:Spinal_cord xref: XAO:0000020 xref: ZFA:0000075 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0003076 ! posterior neural tube relationship: develops_from UBERON:0006241 ! future spinal cord relationship: has_developmental_contribution_from UBERON:0003853 {evidence="definitional"} ! spinal cord neural crest relationship: has_part CL:0005000 {source="ZFA"} ! spinal cord interneuron relationship: immediate_transformation_of UBERON:0006241 {evidence="definitional"} ! future spinal cord relationship: part_of UBERON:0001017 ! central nervous system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg xsd:anyURI property_value: editor_note "TODO - add superclass to unify with VNC?" xsd:string property_value: UBPROP:0000001 "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010151", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000601", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002241 name: chondrocranium namespace: uberon def: "Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]." [http://medical-dictionary.thefreedictionary.com/chondrocranium, Wikipedia:Chondrocranium] subset: vertebrate_core synonym: "calvarium" RELATED [MA:0000317] synonym: "neurocranium" RELATED INCONSISTENT [MA:0000317] xref: AAO:0010169 xref: EHDAA2:0000243 xref: EMAPA:17681 xref: TAO:0001424 xref: VHOG:0000288 xref: Wikipedia:Chondrocranium xref: ZFA:0001424 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system property_value: editor_note "we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)" xsd:string property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010169", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001424", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000007 "chondrocranial" xsd:string property_value: UBPROP:0000008 "covers the brain dorsally in chondrichthyans" xsd:string [Term] id: UBERON:0002298 name: brainstem namespace: uberon def: "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]." [ISBN:0471888893, MP:0005277, Wikipedia:Brainstem, ZFA:0001707] comment: 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "accessory medullary lamina of pallidum" RELATED [NeuroNames:236] synonym: "brain stem" EXACT [ABA:BS] synonym: "lamella pallidi incompleta" RELATED LATIN [NeuroNames:236] synonym: "lamina medullaris accessoria" RELATED LATIN [NeuroNames:236] synonym: "lamina medullaris incompleta pallidi" RELATED LATIN [NeuroNames:236] synonym: "lamina pallidi incompleta" RELATED LATIN [NeuroNames:236] synonym: "truncus encephali" EXACT LATIN [Wikipedia:Brainstem] synonym: "truncus encephalicus" RELATED LATIN [BTO:0000146] xref: BAMS:BS xref: BIRNLEX:1565 xref: BTO:0000146 xref: CALOHA:TS-0093 xref: EFO:0001962 xref: EMAPA:32678 xref: EV:0100241 xref: FMA:79876 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 {source="BIRNLEX:1565"} xref: MA:0000169 xref: MBA:343 xref: MESH:D001933 xref: NCIT:C12441 xref: SCTID:180925009 xref: TAO:0002156 xref: UMLS:C0006121 {source="BIRNLEX:1565"} xref: UMLS:C0006121 {source="ncithesaurus:Brain_Stem"} xref: VHOG:0001457 xref: Wikipedia:Brainstem xref: ZFA:0001707 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: continuous_with UBERON:0002240 ! spinal cord relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png xsd:anyURI property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002156", ontology="TAO", source="ISBN:3764351209"} property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." xsd:string {source="ZFA:0001707"} property_value: UBPROP:0000001 "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" xsd:string {source="MP:0005277"} [Term] id: UBERON:0002302 name: myocardium of atrium namespace: uberon def: "the atrial part of middle layer of the heart, comprised of involuntary muscle" [ISBN:0-683-40008-8, MP:0010493] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "atrial myocardium" EXACT [ZFA:0001374] synonym: "atrium cardiac muscle" RELATED [VHOG:0000602] synonym: "atrium myocardium" EXACT [] xref: EFO:0003087 xref: EMAPA:32746 xref: FMA:83509 xref: MA:0000081 xref: SCTID:191910002 xref: TAO:0001374 xref: VHOG:0000602 xref: ZFA:0001374 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: contributes_to_morphology_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000602", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002315 name: gray matter of spinal cord namespace: uberon def: "The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue." [MP:0008503] subset: pheno_slim synonym: "gray matter of spinal cord" EXACT [OBOL:automatic] synonym: "gray substance of spinal cord" EXACT [FMA:256580] synonym: "grey matter of spinal cord" EXACT [] synonym: "grey substance of spinal cord" EXACT [] synonym: "spinal cord gray matter" EXACT [OBOL:automatic] synonym: "spinal cord grey matter" EXACT [] synonym: "spinal cord grey substance" EXACT [OBOL:automatic] synonym: "substantia grisea medullae spinalis" EXACT LATIN [FMA:256580, FMA:TA] xref: BAMS:Scgrey xref: DHBA:146035048 xref: EMAPA:35792 xref: FMA:256580 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2619 xref: MA:0000002 xref: NCIT:C32696 xref: NLXANAT:100204 xref: SCTID:279441003 xref: UMLS:C0475853 {source="ncithesaurus:Gray_Matter_of_the_Spinal_Cord"} is_a: UBERON:0002020 ! gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0002240 ! spinal cord relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord [Term] id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] subset: uberon_slim subset: vertebrate_core synonym: "body cavity" BROAD [BTO:0001707] synonym: "celom" RELATED [BTO:0001707] synonym: "coelom" RELATED [] synonym: "coelome" RELATED [BTO:0001707] synonym: "coelomic cavity" EXACT [EHDAA2:0000267] synonym: "coelomic cavity lumen" EXACT [EHDAA2:0000267] synonym: "hemocoel" RELATED [FBbt:00005060] synonym: "main body cavity" EXACT [] synonym: "space of body compartment" EXACT [FMA:85006] synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 xref: FBbt:00005060 xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002553 ! anatomical cavity relationship: develops_from UBERON:0003886 ! future coelemic cavity lumen relationship: luminal_space_of UBERON:0011997 ! coelom relationship: part_of UBERON:0011997 ! coelom relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen property_value: editor_note "check the FMA placement here; ncit placement of body cavity here probably not correct" xsd:string property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string [Term] id: UBERON:0002324 name: muscle of back namespace: uberon def: "Any muscle organ that is part of a back [Automatically generated definition]." [OBOL:automatic] synonym: "back muscle" EXACT [] synonym: "back muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of back" EXACT [OBOL:automatic] xref: EMAPA:35161 xref: FMA:85216 xref: MA:0000496 is_a: UBERON:0001774 ! skeletal muscle of trunk is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0004469 {source="prolog"} ! musculature of back [Term] id: UBERON:0002328 name: notochord namespace: uberon def: "A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube." [http://tolweb.org/Chordata/2499, https://github.com/obophenotype/uberon/issues/25, https://github.com/obophenotype/uberon/issues/271, ISBN:0815318960, Wikipedia:Notochord] comment: The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "embryonic notocord" EXACT [] synonym: "notochorda" RELATED LATIN [Wikipedia:Notochord] synonym: "notocord" EXACT [ZFA:0000135] xref: AAO:0000327 xref: BTO:0001768 xref: CALOHA:TS-0690 xref: EHDAA2:0001277 xref: EHDAA:1241 xref: EHDAA:6021 xref: EMAPA:16191 xref: EV:0100002 xref: FMA:85521 xref: GAID:1311 xref: http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg xref: MAT:0000281 xref: MESH:A16.254.610 xref: NCIT:C12463 xref: SCTID:308820002 xref: TAO:0000135 xref: UMLS:C0028439 {source="ncithesaurus:Notochord"} xref: VHOG:0000199 xref: VSAO:0000032 xref: Wikipedia:Notochord xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate relationship: dorsal_to UBERON:0001555 ! digestive tract relationship: existence_starts_during UBERON:0000068 ! embryo stage relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein relationship: ventral_to UBERON:0001049 ! neural tube property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "notochordal" xsd:string property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string [Term] id: UBERON:0002329 name: somite namespace: uberon def: "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm." [DOI:10.1111/j.1439-0426.2012.01987.x, Wikipedia:Somite] comment: When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "epimere" RELATED [ISBN:0073040584] synonym: "epimere mesoderm" RELATED [] synonym: "epithelial somite" RELATED [https://github.com/obophenotype/uberon/wiki/The-neural-crest] synonym: "mesodermal cluster" BROAD [GO:0001756] synonym: "somites" RELATED PLURAL [] synonym: "somitic mesoderm" RELATED [] synonym: "somitus" RELATED LATIN [Wikipedia:Somite] xref: AAO:0010569 xref: AEO:0001015 xref: BTO:0001558 xref: EHDAA2:0003436 xref: EHDAA:366 xref: EHDAA:699 xref: EMAPA:31169 xref: FMA:85522 xref: GAID:1306 xref: MAT:0000068 xref: MESH:A16.254.425.660.750 xref: MIAA:0000068 xref: NCIT:C34302 xref: TAO:0000155 xref: UMLS:C0376449 {source="ncithesaurus:Somite"} xref: VHOG:0000191 xref: Wikipedia:Somite xref: XAO:0000058 xref: ZFA:0000155 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: editor_note "currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "somitic" xsd:string [Term] id: UBERON:0002330 name: exocrine system namespace: uberon def: "Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]." [Wikipedia:Exocrine_gland] subset: pheno_slim subset: uberon_slim synonym: "exocrine glandular system" EXACT [EHDAA2:0002225] xref: CALOHA:TS-2057 xref: EHDAA2:0002225 xref: EMAPA:35329 xref: FMA:85539 xref: MA:0002411 xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: composed_primarily_of UBERON:0002365 ! exocrine gland relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0002333 name: pulmonary trunk namespace: uberon def: "An arterial trunk which is continuous with the heart and branches into the pulmonary arteries." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "main pulmonary artery" RELATED [Wikipedia:Pulmonary_artery] synonym: "pulmonary artery (trunk)" EXACT [] synonym: "trunk of pulmonary arterial tree" EXACT [] xref: EHDAA2:0001576 xref: EHDAA:9831 xref: EMAPA:17015 xref: FMA:8612 xref: galen:PulmonaryTrunk xref: MA:0002033 xref: NCIT:C116918 xref: OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA xref: VHOG:0001134 is_a: UBERON:0001637 {source="MA"} ! artery relationship: continuous_with UBERON:0000948 ! heart relationship: part_of UBERON:0008886 ! pulmonary vascular system property_value: depicted:by Alveoli:diagram.png xsd:anyURI property_value: UBPROP:0000001 "An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001134", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+trunk"} property_value: UBPROP:0000003 "As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001134", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002342 name: neural crest namespace: uberon def: "A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]." [MP:0009846] comment: Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "crista neuralis" RELATED LATIN [Wikipedia:Neural_crest] synonym: "NC" EXACT ABBREVIATION [XAO:0000048] synonym: "neural crest material" RELATED [VHOG:0000057] xref: AAO:0010578 xref: BTO:0001764 xref: CALOHA:TS-0676 xref: EHDAA2:0004419 xref: EMAPA:32737 xref: FMA:86666 xref: GAID:1310 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1366 xref: MAT:0000066 xref: MESH:A16.254.600 xref: MIAA:0000066 xref: NCIT:C34222 xref: SCTID:361462002 xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png xsd:anyURI property_value: depicted:by Neural:Crest.png xsd:anyURI property_value: editor_note "consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002343 name: abdomen musculature namespace: uberon def: "Set of all muscles in abdomen." [OBOL:automatic] subset: pheno_slim subset: vertebrate_core synonym: "abdominal musculature" EXACT [] synonym: "muscle group of abdomen" EXACT [FMA:71294] synonym: "muscles of abdomen" EXACT [FMA:71294] synonym: "musculature of abdomen" EXACT [] synonym: "musculature of abdominal wall" EXACT [FMA:86917] synonym: "set of muscles of abdomen" EXACT [FMA:71294] xref: FMA:71294 xref: FMA:86917 xref: TAO:0001327 xref: ZFA:0001327 is_a: UBERON:0004479 ! musculature of trunk intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen property_value: IAO:0000232 "distinction between abdomen muscle and abdomen musculature" xsd:string [Term] id: UBERON:0002346 name: neurectoderm namespace: uberon def: "Embryonic ectoderm that gives rise to nervous tissue." [Wikipedia:Neuroectoderm] subset: uberon_slim subset: vertebrate_core synonym: "epithelium tubi neuralis; neuroectoderma" RELATED LATIN [Wikipedia:Neuroectoderm] synonym: "neuaral ectoderm" RELATED [] synonym: "neural ectoderm" EXACT [] synonym: "neuroectoderm" EXACT [] synonym: "presumptive central nervous system" RELATED [] synonym: "ventral neurogenic region" RELATED [VHOG:0000150] xref: AAO:0011074 xref: BILA:0000039 xref: CALOHA:TS-1212 xref: EHDAA2:0001248 xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 xref: FBbt:00001061 xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 xref: NCIT:C34228 xref: TAO:0001120 xref: UMLS:C1518271 {source="ncithesaurus:Neuroectoderm"} xref: VHOG:0000150 xref: Wikipedia:Neuroectoderm xref: XAO:0000042 xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell relationship: has_part CL:0000530 {source="ZFA"} ! primary neuron property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "neurectodermal" xsd:string property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002348 name: epicardium namespace: uberon def: "a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "heart epicardium" EXACT [] synonym: "pericardium visceral mesothelium" RELATED [EMAPA:16589] synonym: "visceral serous pericardium of heart" EXACT [FMA:9461] synonym: "visceral serous pericardium proper" EXACT [FMA:9461] xref: AAO:0010409 xref: EHDAA2:0002202 xref: FMA:9461 xref: galen:Epicardium xref: NCIT:C13164 xref: TAO:0005057 xref: UMLS:C0225968 {source="ncithesaurus:Epicardium"} xref: VHOG:0000119 xref: Wikipedia:Epicardium xref: XAO:0000316 xref: ZFA:0005057 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: attaches_to UBERON:0002349 {source="FMA"} ! myocardium relationship: develops_from UBERON:0004160 ! proepicardium relationship: part_of UBERON:0000948 {source="multiple"} ! heart relationship: part_of UBERON:0002425 {source="FMA-inferred"} ! visceral serous pericardium property_value: editor_note "TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer." xsd:string property_value: UBPROP:0000001 "External layer of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005057", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010409", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000009 "The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]" xsd:string [Term] id: UBERON:0002349 name: myocardium namespace: uberon def: "the middle layer of the heart, comprised mainly of striated cardiac muscle fibers" [ISBN:0-683-40008-8, MP:0005329] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cardiac muscle" RELATED [ZFA:0001319] synonym: "heart muscle" RELATED [ZFA:0001319] synonym: "heart muscle" RELATED [FMA:9462] synonym: "heart myocardium" EXACT [] synonym: "muscle of heart" EXACT [FMA:9462] xref: AAO:0010410 xref: BSA:0000089 xref: BTO:0000901 xref: CALOHA:TS-0440 xref: EFO:0000819 xref: EHDAA2:0004150 xref: EMAPA:32688 xref: EV:0100022 xref: FMA:9462 xref: GAID:173 xref: galen:Myocardium xref: MA:0000164 xref: MAT:0000453 xref: MESH:D009206 xref: NCIT:C12371 xref: OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw xref: RETIRED_EHDAA2:0001220 xref: SCTID:362012001 xref: TAO:0001319 xref: UMLS:C0027061 {source="ncithesaurus:Myocardium"} xref: VHOG:0000083 xref: Wikipedia:Myocardium xref: XAO:0000065 xref: ZFA:0001319 is_a: UBERON:0005983 ! heart layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0018260 ! layer of muscle tissue intersection_of: UBERON:0005983 ! heart layer intersection_of: composed_primarily_of UBERON:0001133 ! cardiac muscle tissue relationship: composed_primarily_of UBERON:0001133 ! cardiac muscle tissue relationship: has_part UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0000383 ! musculature of body property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg xsd:anyURI property_value: editor_note "TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium" xsd:string property_value: UBPROP:0000001 "Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000083", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000001 "The middle layer of the heart, consisting of cardiac muscle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010410", ontology="AAO", source="AAO:BJB"} property_value: UBPROP:0000007 "myocardial" xsd:string [Term] id: UBERON:0002350 name: conducting system of heart namespace: uberon def: "The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]" [GO:0003161] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "cardiac conducting system" EXACT [VHOG:0001271] synonym: "cardiac conduction system" EXACT [] synonym: "cardiac impulse conducting system" EXACT [GO:0003161] synonym: "cardionector" EXACT [] synonym: "central conduction system" RELATED [] synonym: "complexus stimulans cordis" EXACT LATIN [FMA:9476, FMA:TA] synonym: "heart conduction system" EXACT [GO:0003161] synonym: "impulse conducting system" EXACT [MA:0000094] synonym: "systema conducente cordis" EXACT LATIN [FMA:9476, FMA:TA] xref: EFO:0003909 xref: EHDAA2:0004185 xref: EMAPA:35428 xref: EV:0100025 xref: FMA:9476 xref: MA:0000094 xref: MESH:D006329 xref: SCTID:281489000 xref: TAO:0005063 xref: VHOG:0001271 xref: ZFA:0005063 is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium is_a: UBERON:0010131 {source="FMA"} ! conducting tissue of heart relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: has_part CL:0002068 {source="FMA"} ! Purkinje myocyte relationship: has_part CL:0002073 {source="FMA"} ! transitional myocyte relationship: has_part CL:0002074 {source="FMA"} ! myocardial endocrine cell relationship: has_part CL:1000409 {source="FMA"} ! myocyte of sinoatrial node relationship: has_part CL:1000410 {source="FMA"} ! myocyte of atrioventricular node property_value: editor_note "EHDAA2 divides the system from the tissue" xsd:string property_value: UBPROP:0000003 "The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001271", ontology="VHOG", source="DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002351 name: sinoatrial node namespace: uberon def: "The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]." [GO:0003163, Wikipedia:Sinoatrial_node] comment: WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cardiac pacemaker" EXACT [FMA:9477] synonym: "Koch's node" EXACT [FMA:9477] synonym: "node of Keith-Flack" EXACT [FMA:9477] synonym: "nodus sinuatrialis" EXACT LATIN [FMA:9477, FMA:TA] synonym: "nodus sinuatrialis" RELATED LATIN [Wikipedia:Sinoatrial_node] synonym: "SA nodal muscle tissue" EXACT [FMA:9477] synonym: "SA node" EXACT [FMA:9477] synonym: "sinoatrial node" EXACT [FMA:9477] synonym: "sinu-atrial node" EXACT [FMA:9477] synonym: "sinuatrial nodal muscle tissue" EXACT [FMA:9477] synonym: "sinuatrial node" EXACT [FMA:9477] synonym: "sinus node" EXACT [FMA:9477] synonym: "sinus node of Keith and Flack" EXACT [FMA:9477] xref: BTO:0004358 xref: EHDAA2:0004184 xref: EMAPA:35772 xref: FMA:9477 xref: GAID:561 xref: MA:0000097 xref: MESH:D012849 xref: NCIT:C33555 xref: OpenCyc:Mx4rOhejDGMcEd2AAABQjYGu0g xref: SCTID:277687007 xref: TAO:0005069 xref: UMLS:C0037189 {source="ncithesaurus:Sinoatrial_Node"} xref: Wikipedia:Sinoatrial_node xref: ZFA:0005069 is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart relationship: capable_of GO:0002027 ! regulation of heart rate relationship: capable_of_part_of GO:0060048 ! cardiac muscle contraction relationship: contributes_to_morphology_of UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0002350 {source="ZFA"} ! conducting system of heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg xsd:anyURI [Term] id: UBERON:0002352 name: atrioventricular node namespace: uberon def: "An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles." [UBERON:cjm, Wikipedia:Atrioventricular_node] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "A-V node" RELATED [EMAPA:35153] synonym: "Aschoff-Tawara node" EXACT [FMA:9478] synonym: "atrio-ventricular node" RELATED [EMAPA:35153] synonym: "atrioventricular nodal muscle tissue" EXACT [FMA:9478] synonym: "atriovetricular node" RELATED [TAO:0005070] synonym: "AV nodal muscle tissue" EXACT [FMA:9478] synonym: "AV node" EXACT [FMA:9478, MA:0000095] synonym: "downstream pacemaker" RELATED [ZFA:0005070] synonym: "node of Tawara" EXACT [FMA:9478] synonym: "nodus atrioventricularis" EXACT LATIN [FMA:TA] synonym: "nodus atrioventricularis" RELATED LATIN [Wikipedia:Atrioventricular_node] xref: BTO:0005689 xref: EFO:0000276 xref: EHDAA2:0004183 xref: EMAPA:35153 xref: FMA:9478 xref: GAID:558 xref: MA:0000095 xref: MAT:0000498 xref: MESH:D001283 xref: NCIT:C32161 xref: OpenCyc:Mx4rMfD91mMcEd2AAABQjYGu0g xref: SCTID:277688002 xref: TAO:0005070 xref: UMLS:C0004247 {source="ncithesaurus:Atrioventricular_Node"} xref: VHOG:0001474 xref: Wikipedia:Atrioventricular_node xref: ZFA:0005070 is_a: UBERON:0004491 ! cardiac muscle tissue of interatrial septum is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart relationship: connected_to UBERON:0002085 ! interatrial septum relationship: connected_to UBERON:0005979 ! crista terminalis relationship: contributes_to_morphology_of UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0002350 ! conducting system of heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png xsd:anyURI property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png xsd:anyURI property_value: UBPROP:0000003 "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001474", ontology="VHOG", source="DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002355 name: pelvic region of trunk namespace: uberon def: "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/720, Wikipedia:Pelvis] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "lesser pelvis" EXACT [FMA:9578] synonym: "pelvic region" EXACT [] synonym: "pelvis" EXACT [FMA:9578, MA:0000030] synonym: "pelvis region" EXACT [] synonym: "true pelvis" EXACT [FMA:9578] xref: BTO:0001006 xref: CALOHA:TS-2227 xref: EFO:0002805 xref: EMAPA:35931 xref: EV:0100012 xref: FMA:9578 xref: GAID:87 xref: galen:Pelvis xref: MA:0000030 xref: MESH:A01.673 xref: NCIT:C12767 xref: OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA xref: SCTID:229765004 xref: UMLS:C0030797 {source="ncithesaurus:Pelvis"} xref: Wikipedia:Pelvis is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0002417 ! abdominal segment of trunk property_value: UBPROP:0000007 "pelvic" xsd:string property_value: UBPROP:0000012 "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" xsd:string {external_ontology="MA"} [Term] id: UBERON:0002357 name: serous pericardium namespace: uberon def: "Serous membrane which is divided into parietal and visceral serous pericardium." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Serous_pericardium] subset: uberon_slim synonym: "pericardium serosum" RELATED LATIN [Wikipedia:Serous_pericardium] synonym: "serous portion of pericardium" EXACT [FMA:9582] xref: EMAPA:19030 xref: FMA:9582 xref: MA:0002739 xref: SCTID:243954002 xref: Wikipedia:Serous_pericardium is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000042 ! serous membrane relationship: attaches_to UBERON:0002359 {source="FMA"} ! fibrous pericardium relationship: has_part UBERON:0002408 ! parietal serous pericardium relationship: has_part UBERON:0002425 ! visceral serous pericardium relationship: part_of UBERON:0002406 {source="FMA"} ! pericardial sac [Term] id: UBERON:0002359 name: fibrous pericardium namespace: uberon def: "Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]" [FMA:9586] subset: organ_slim subset: uberon_slim synonym: "fibrous portion of pericardium" EXACT [] synonym: "pericardium fibrosum" RELATED LATIN [Wikipedia:Fibrous_pericardium] xref: EMAPA:19029 xref: FMA:9586 xref: MA:0002738 xref: SCTID:243953008 xref: Wikipedia:Fibrous_pericardium is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000094 {source="FMA"} ! membrane organ is_a: UBERON:0005181 ! thoracic segment organ relationship: composed_primarily_of UBERON:0006815 {source="WP"} ! areolar connective tissue relationship: continuous_with UBERON:0002408 ! parietal serous pericardium relationship: part_of UBERON:0002407 {source="FMA"} ! pericardium property_value: UBPROP:0000010 "most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]" xsd:string [Term] id: UBERON:0002365 name: exocrine gland namespace: uberon def: "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas" [Wikipedia:Exocrine_gland] subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "ducted gland" EXACT [AEO:0000097] synonym: "glandula exocrina" EXACT LATIN [Wikipedia:Exocrine_gland] xref: AEO:0000097 xref: BTO:0000765 xref: CALOHA:TS-2012 xref: EHDAA2:0003097 xref: EMAPA:35327 xref: FMA:9596 xref: GAID:34 xref: MA:0002564 xref: MESH:D005088 xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system relationship: has_part UBERON:0000058 ! duct relationship: part_of UBERON:0002330 ! exocrine system property_value: editor_note "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string [Term] id: UBERON:0002368 name: endocrine gland namespace: uberon def: "Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]." [Wikipedia:Endocrine_gland] subset: organ_slim subset: pheno_slim subset: uberon_slim synonym: "ductless gland" EXACT [AEO:0000098] synonym: "ductless gland" RELATED [Wikipedia:Ductless_gland] synonym: "glandula endocrina" EXACT [] synonym: "glandulae endocrinae" RELATED LATIN [Wikipedia:Endocrine_gland] xref: AEO:0000098 xref: BTO:0001488 xref: CALOHA:TS-1300 xref: EHDAA2:0003098 xref: EMAPA:35999 xref: FMA:9602 xref: GAID:335 xref: MA:0002563 xref: MESH:D004702 xref: NCIT:C12704 xref: OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA xref: SCTID:40818001 xref: UMLS:C0014133 {source="ncithesaurus:Endocrine_Gland"} xref: Wikipedia:Endocrine_gland is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0060986 ! endocrine hormone secretion relationship: part_of UBERON:0000949 ! endocrine system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png xsd:anyURI [Term] id: UBERON:0002371 name: bone marrow namespace: uberon def: "the soft tissue that fills the cavities of bones" [MGI:cwg, MP:0002397] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "medulla of bone" RELATED [BTO:0000141] synonym: "medulla ossea" EXACT LATIN [BTO:0000141, FMA:9608] synonym: "medulla ossium" EXACT LATIN [BTO:0000141, Wikipedia:Bone_marrow] synonym: "medullary bone" RELATED [] xref: AAO:0011007 xref: BTO:0000141 xref: BTO:0000829 xref: CALOHA:TS-0087 xref: EFO:0000868 xref: EMAPA:32760 xref: EV:0100046 xref: FMA:9608 xref: GAID:1287 xref: galen:BoneMarrow xref: MA:0000134 xref: MAT:0000084 xref: MESH:D001853 xref: MIAA:0000084 xref: NCIT:C12431 xref: OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA xref: SCTID:421320006 xref: UMLS:C0005953 {source="ncithesaurus:Bone_Marrow"} xref: VHOG:0001218 xref: Wikipedia:Bone_marrow xref: XAO:0000123 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: has_part UBERON:0012429 ! hematopoietic tissue intersection_of: part_of UBERON:0001474 ! bone element relationship: has_part CL:0002092 ! bone marrow cell relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg xsd:anyURI property_value: editor_note "consider placement of NCIT:C53466 medullary bone" xsd:string property_value: editor_note "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001218", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string [Term] id: UBERON:0002376 name: cranial muscle namespace: uberon alt_id: UBERON:0003899 def: "Any skeletal muscle that is part of the head region." [http://orcid.org/0000-0002-6601-2165] comment: defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "adult head muscle organ" NARROW [OBOL:automatic] synonym: "cephalic muscle" EXACT [ZFA:0001652] synonym: "cephalic musculature" EXACT [] synonym: "cranial muscle" RELATED [ZFA:0001652] synonym: "head muscle" EXACT [MA:0000578] synonym: "head muscle organ" EXACT [OBOL:automatic] synonym: "head muscles" RELATED [] synonym: "muscle of head" EXACT [FMA:9616] synonym: "muscle organ of adult head" EXACT [OBOL:automatic] synonym: "muscle organ of head" EXACT [OBOL:automatic] synonym: "musculus caput" EXACT [] xref: AAO:0000107 xref: BTO:0000021 xref: EFO:0003524 xref: EHDAA2:0000322 xref: EMAPA:18172 xref: FMA:9616 xref: MA:0000578 xref: SCTID:244718003 xref: ZFA:0001652 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010959 ! craniocervical muscle intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: attaches_to UBERON:0003129 ! skull intersection_of: part_of UBERON:0000033 ! head relationship: attaches_to UBERON:0003129 ! skull relationship: develops_from UBERON:0006904 {source="EHDAA2-abduced"} ! head mesenchyme from mesoderm relationship: has_developmental_contribution_from UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: part_of UBERON:0004461 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! skeletal musculature of head [Term] id: UBERON:0002377 name: muscle of neck namespace: uberon def: "Any muscle that is part of the cervical (neck) region." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "muscle organ of neck" EXACT [OBOL:automatic] synonym: "muscle organ of neck (volume)" EXACT [OBOL:automatic] synonym: "neck (volume) muscle organ" EXACT [OBOL:automatic] synonym: "neck muscle" EXACT [] synonym: "neck muscle organ" EXACT [OBOL:automatic] xref: EMAPA:36050 xref: FMA:9617 xref: GAID:149 xref: MA:0000587 xref: MESH:D009334 xref: NCIT:C33163 xref: UMLS:C0027532 {source="ncithesaurus:Neck_Muscle"} is_a: UBERON:0010959 ! craniocervical muscle intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0004465 {source="prolog"} ! musculature of neck [Term] id: UBERON:0002378 name: muscle of abdomen namespace: uberon def: "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis." [Wikipedia:Abdominal_muscle] subset: pheno_slim subset: uberon_slim synonym: "abdomen muscle" EXACT [] synonym: "abdomen muscle organ" EXACT [OBOL:automatic] synonym: "abdominal muscle" EXACT [] synonym: "abdominal wall muscle" EXACT [] synonym: "abdominal wall musculature" RELATED [EMAPA:35103] synonym: "muscle organ of abdomen" EXACT [OBOL:automatic] xref: BTO:0001261 xref: EMAPA:35103 xref: FMA:9620 xref: GAID:89 xref: MA:0000520 xref: MESH:D000009 xref: NCIT:C32040 xref: OpenCyc:Mx4rvlygNJwpEbGdrcN5Y29ycA xref: SCTID:361352008 xref: UMLS:C0000739 {source="ncithesaurus:Abdominal_Muscle"} xref: Wikipedia:Abdominal_muscle is_a: UBERON:0003833 ! abdominal segment muscle is_a: UBERON:0005172 ! abdomen element intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0002343 {source="prolog"} ! abdomen musculature relationship: part_of UBERON:0003697 ! abdominal wall [Term] id: UBERON:0002384 name: connective tissue namespace: uberon def: "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/23, PSPUB:0000170, VSAO:0000017] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "Bindegewebe" RELATED [BTO:0000421] synonym: "portion of connective tissue" EXACT [FMA:9640] synonym: "textus connectivus" EXACT [] xref: AAO:0000098 xref: BTO:0000421 xref: CALOHA:TS-2009 xref: EFO:0000952 xref: EMAPA:35251 xref: FMA:9640 xref: GAID:100 xref: galen:ConnectiveTissue xref: MA:0000011 xref: MAT:0000301 xref: MESH:D003238 xref: MIAA:0000301 xref: NCIT:C12374 xref: OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA xref: SCTID:361919005 xref: TAO:0001641 xref: UMLS:C0009780 {source="ncithesaurus:Connective_Tissue"} xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} [Term] id: UBERON:0002385 name: muscle tissue namespace: uberon def: "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." [GO:0060537, https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764, Wikipedia:Muscle_tissue] comment: Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. subset: uberon_slim synonym: "muscular tissue" EXACT SENSU [] synonym: "portion of muscle tissue" EXACT [FMA:9641] synonym: "textus muscularis" EXACT [] xref: AAO:0000306 xref: AEO:0000122 xref: CALOHA:TS-0642 xref: EHDAA2:0003122 xref: EMAPA:32715 xref: FMA:9641 xref: galen:MuscleTissue xref: MA:0002437 xref: MESH:D009132 xref: NCIT:C12435 xref: SCTID:91727004 xref: UMLS:C2328219 {source="ncithesaurus:Muscle_Tissue"} xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of CL:0000187 ! muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction relationship: composed_primarily_of CL:0000187 ! muscle cell relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} [Term] id: UBERON:0002390 name: hematopoietic system namespace: uberon def: "Anatomical system that is involved in the production of hematopoietic cells." [Wikipedia:Haematopoiesis] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "Blutbildungssystem" RELATED [BTO:0000570] synonym: "haematological system" EXACT [] synonym: "haematopoietic system" RELATED [] synonym: "haemopoietic system" EXACT [] synonym: "hematological system" RELATED [] synonym: "hematolymphoid system" RELATED [] synonym: "hemopoietic system" RELATED [] synonym: "organa haemopoietica" EXACT [] xref: AAO:0011002 xref: BTO:0000570 xref: CALOHA:TS-0449 xref: EFO:0000798 xref: EMAPA:35402 xref: EV:0100045 xref: FMA:9667 xref: GAID:1008 xref: MA:0002434 xref: MAT:0000022 xref: MESH:D006413 xref: MIAA:0000022 xref: NCIT:C12909 xref: SCTID:362587009 xref: TAO:0005023 xref: UMLS:C0018957 {source="ncithesaurus:Hematopoietic_System"} xref: VHOG:0001624 xref: Wikipedia:Haematopoiesis xref: XAO:0000122 xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000007 "hematopoietic" xsd:string property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} [Term] id: UBERON:0002405 name: immune system namespace: uberon def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." [Wikipedia:Immune_system] subset: pheno_slim subset: uberon_slim subset: vertebrate_core xref: AAO:0011003 xref: BILA:0000104 xref: BTO:0005810 xref: FMA:9825 xref: GAID:328 xref: MA:0002711 xref: MESH:D007107 xref: NCIT:C12735 xref: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA xref: SCTID:362590003 xref: TAO:0001159 xref: UMLS:C0020962 {source="ncithesaurus:Immune_System"} xref: VHOG:0001247 xref: Wikipedia:Immune_system xref: XAO:0003152 xref: ZFA:0001159 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0002376 ! immune system process relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: protects UBERON:0000468 ! multicellular organism property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001247", ontology="VHOG", source="PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002406 name: pericardial sac namespace: uberon def: "a double-walled sac containing the heart and the roots of the great vessels." [https://github.com/obophenotype/uberon/issues/86, Wikipedia:Pericardium] subset: uberon_slim subset: vertebrate_core synonym: "pericardium" RELATED [] xref: FMA:9868 xref: RETIRED_EHDAA2:0001443 xref: SCTID:361326002 xref: TAO:0000054 is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0005906 ! serous sac intersection_of: UBERON:0005906 ! serous sac intersection_of: has_part UBERON:0001074 ! pericardial cavity intersection_of: has_part UBERON:0002357 ! serous pericardium relationship: has_part UBERON:0001074 ! pericardial cavity relationship: has_part UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002407 ! pericardium relationship: surrounded_by UBERON:0002359 {source="FMA"} ! fibrous pericardium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png xsd:anyURI [Term] id: UBERON:0002407 name: pericardium namespace: uberon def: "The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Pericardium] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core xref: AAO:0010817 xref: BSA:0000090 xref: BTO:0000717 xref: CALOHA:TS-0761 xref: EFO:0000820 xref: EHDAA:5376 xref: EMAPA:16133 xref: EV:0100023 xref: FMA:9869 xref: GAID:569 xref: galen:Pericardium xref: MA:0000099 xref: MAT:0000454 xref: MESH:D010496 xref: NCIT:C13005 xref: OpenCyc:Mx4rvoCLgJwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0001443 xref: SCTID:181295003 xref: TAO:0000054 xref: UMLS:C0031050 {source="ncithesaurus:Pericardium"} xref: VHOG:0001280 xref: Wikipedia:Pericardium xref: XAO:0004182 xref: ZFA:0000054 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000481 ! multi-tissue structure relationship: has_part UBERON:0002359 ! fibrous pericardium relationship: has_part UBERON:0002406 ! pericardial sac relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: surrounds UBERON:0002349 ! myocardium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png xsd:anyURI property_value: UBPROP:0000001 "Peritoneum that surrounds the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010817", ontology="AAO", source="AAO:JMG"} property_value: UBPROP:0000007 "pericardial" xsd:string property_value: UBPROP:0000012 "In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity" xsd:string {external_ontology="FMA"} property_value: UBPROP:0000012 "this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)" xsd:string {external_ontology="ZFA"} property_value: UBPROP:0000012 "we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002408 name: parietal serous pericardium namespace: uberon def: "Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim synonym: "lamina parietalis (pericardii serosum)" EXACT [] synonym: "lamina parietalis pericardii" EXACT LATIN [FMA:9870, FMA:TA] synonym: "parietal layer of serous pericardium" EXACT [] synonym: "parietal pericardium" EXACT [VHOG:0000537] synonym: "pericardial sac" RELATED INCONSISTENT [DOI:10.5962/bhl.title.1013] xref: EHDAA:3422 xref: EHDAA:5378 xref: EMAPA:19031 xref: FMA:9870 xref: MA:0000483 xref: NCIT:C94500 xref: SCTID:243956000 xref: UMLS:C0225969 {source="ncithesaurus:Parietal_Pericardium"} xref: VHOG:0000537 xref: Wikipedia:Parietal_pericardium is_a: UBERON:0022351 ! parietal serous membrane intersection_of: UBERON:0022351 ! parietal serous membrane intersection_of: part_of UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002357 ! serous pericardium property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png xsd:anyURI [Term] id: UBERON:0002409 name: pericardial fluid namespace: uberon def: "Transudate contained in the pericardial cavity.[FMA]" [FMA:9887, Wikipedia:Pericardial_fluid] subset: uberon_slim xref: BTO:0001016 xref: FMA:9887 xref: MA:0002530 xref: Wikipedia:Pericardial_fluid is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland is_a: UBERON:0036217 ! coelomic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0002425 ! visceral serous pericardium relationship: located_in UBERON:0001074 ! pericardial cavity relationship: produced_by UBERON:0002425 ! visceral serous pericardium [Term] id: UBERON:0002416 name: integumental system namespace: uberon alt_id: UBERON:0007029 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." [CARO:0002001, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/29] subset: efo_slim subset: grouping_class subset: pheno_slim synonym: "body surface" RELATED [] synonym: "dermal system" RELATED [MIAA:0000033] synonym: "external covering of organism" RELATED [] synonym: "integumentary system" EXACT [FMA:72979] synonym: "integumentum commune" RELATED LATIN [Wikipedia:Integumentary_system] synonym: "organism surface" RELATED [EHDAA2:0003154] synonym: "surface" RELATED [BILA:0000118] xref: AEO:0000154 xref: BILA:0000118 xref: CALOHA:TS-1299 xref: CARO:0002001 xref: EFO:0000807 xref: EHDAA2:0000836 xref: EHDAA2_RETIRED:0003154 xref: EHDAA:6520 xref: EMAPA:17524 xref: EV:0100151 xref: FBbt:00004969 xref: FMA:72979 xref: galen:Surface xref: HAO:0000421 xref: MA:0000014 xref: MAT:0000033 xref: MESH:D034582 xref: MIAA:0000033 xref: NCIT:C12907 xref: SCTID:361692004 xref: TADS:0000108 xref: UMLS:C0037267 {source="ncithesaurus:Integumentary_System"} xref: VHOG:0000403 xref: Wikipedia:Integumentary_system xref: XAO:0000176 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0007376 ! outer epithelium relationship: surrounded_by UBERON:0013514 ! space surrounding organism property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/tfhayamizu property_value: UBPROP:0000003 "(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000403", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002417 name: abdominal segment of trunk namespace: uberon def: "The abdominal segment of the torso." [Wikipedia:Lumbar] synonym: "abdomen/pelvis/perineum" RELATED [MA:0000021] synonym: "lower body" RELATED [MA:0000021] synonym: "lower trunk" RELATED [FMA:259211] synonym: "lumbar region" RELATED [https://orcid.org/0000-0002-6601-2165] xref: EMAPA:35104 xref: FMA:259211 xref: MA:0000021 xref: SCTID:362875007 xref: Wikipedia:Lumbar is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis [Term] id: UBERON:0002418 name: cartilage tissue namespace: uberon def: "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/37, https://sourceforge.net/p/obo/vertebrate-skeletal-anatomy-vsao-term-requests/5, PSPUB:0000170, VSAO:0000040] comment: Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "cartilage" RELATED [] synonym: "cartilage tissue" EXACT [FMA:37377] synonym: "cartilages" RELATED [VHOG:0001207] synonym: "cartilaginous tissue" EXACT [] synonym: "chondrogenic tissue" EXACT [VSAO:0000040] synonym: "portion of cartilage tissue" RELATED [FMA:37377] xref: AAO:0000060 xref: AEO:0000087 xref: BTO:0000206 xref: EFO:0000949 xref: EHDAA2:0003087 xref: EMAPA:32730 xref: EV:0100141 xref: FMA:37377 xref: GAID:99 xref: galen:Cartilage xref: MA:0000104 xref: MAT:0000189 xref: MESH:D002356 xref: MIAA:0000189 xref: NCIT:C12373 xref: NCIT:C32268 xref: OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA xref: SCTID:309312004 xref: TAO:0001501 xref: UMLS:C0007301 {source="ncithesaurus:Cartilage"} xref: VHOG:0001207 xref: VSAO:0000040 xref: Wikipedia:Cartilage xref: XAO:0000170 xref: ZFA:0005622 is_a: UBERON:0004755 ! skeletal tissue disjoint_from: UBERON:0002481 {source="https://github.com/obophenotype/uberon/issues/117"} ! bone tissue relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: has_part CHEBI:18085 ! glycosaminoglycan relationship: has_part CL:0000138 ! chondrocyte relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg xsd:anyURI property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/mellybelly property_value: UBPROP:0000001 "A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000060", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000001 "Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001501", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000040", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000060", ontology="AAO"} property_value: UBPROP:0000003 "Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001207", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002419 name: skin gland namespace: uberon def: "A gland that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] subset: organ_slim synonym: "glandulae cutis" EXACT LATIN [FMA:71878, FMA:TA] synonym: "set of skin glands" RELATED [FMA:71878] synonym: "skin glands" RELATED PLURAL [] synonym: "skin glands set" RELATED PLURAL [] xref: EMAPA:35774 xref: FMA:71878 xref: MA:0000146 xref: SCTID:110485007 is_a: UBERON:0003297 ! gland of integumental system is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006003 ! integumentary adnexa intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body property_value: editor_note "check FMA, use plural for now as general class not there" xsd:string [Term] id: UBERON:0002424 name: oral epithelium namespace: uberon def: "An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues" [https://orcid.org/0000-0002-6601-2165] subset: vertebrate_core synonym: "epithelium of mucosa of mouth" EXACT [FMA:265152] synonym: "epithelium of oral mucosa" EXACT [FMA:265152] xref: AAO:0010357 xref: BTO:0001775 xref: CALOHA:TS-0715 xref: EHDAA2:0001325 xref: EHDAA:2187 xref: EMAPA:16839 xref: EMAPA:26942 xref: FMA:265152 xref: MA:0000344 xref: NCIT:C49595 xref: TAO:0000816 xref: UMLS:C1709332 {source="ncithesaurus:Oral_Cavity_Epithelium"} xref: VHOG:0000187 xref: XAO:0003201 xref: ZFA:0000816 is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003729 ! mouth mucosa relationship: adjacent_to UBERON:0000167 {source="AAO-modified"} ! oral cavity relationship: part_of UBERON:0003729 ! mouth mucosa property_value: editor_note "consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)" xsd:string property_value: UBPROP:0000001 "The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]." xsd:string {source="ZFA:0000816"} property_value: UBPROP:0000011 "the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme" xsd:string {source="PMID:16488870"} [Term] id: UBERON:0002425 name: visceral serous pericardium namespace: uberon def: "Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]." [Wikipedia:Visceral_pericardium] subset: pheno_slim subset: uberon_slim synonym: "epicardium" RELATED [MA:0000484] synonym: "lamina visceralis pericardii serosi" EXACT LATIN [Wikipedia:Epicardium] synonym: "pericardium visceral mesothelium" RELATED [EMAPA:16589] synonym: "serous visceral pericardium" EXACT [] synonym: "visceral lamina of serous pericardium" EXACT [] synonym: "visceral layer of serous pericardium" EXACT [] synonym: "visceral pericardium" EXACT [VHOG:0000538] xref: EMAPA:16589 xref: EMAPA:19032 xref: FMA:84882 xref: MA:0000484 xref: SCTID:243955001 xref: VHOG:0000538 xref: Wikipedia:Visceral_pericardium is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0022350 ! visceral serous membrane intersection_of: UBERON:0022350 ! visceral serous membrane intersection_of: part_of UBERON:0002357 ! serous pericardium relationship: attaches_to UBERON:0002349 {source="FMA"} ! myocardium relationship: contributes_to_morphology_of UBERON:0002407 ! pericardium relationship: has_part UBERON:0002348 {source="cjm"} ! epicardium relationship: part_of UBERON:0002357 ! serous pericardium [Term] id: UBERON:0002443 name: choroidal blood vessel namespace: uberon def: "A blood vessel that is part of a choroid [Automatically generated definition]." [OBOL:automatic] comment: cannot find singular in FMA, using Set class subset: pheno_slim synonym: "blood vessel of choroid" EXACT [OBOL:automatic] synonym: "blood vessel of choroid coat" EXACT [OBOL:automatic] synonym: "blood vessel of choroidea" EXACT [OBOL:automatic] synonym: "blood vessel of posterior uvea" EXACT [OBOL:automatic] synonym: "choroid blood vessel" EXACT [OBOL:automatic] synonym: "choroid blood vessels" EXACT [] synonym: "choroid blood vessels set" EXACT [] synonym: "choroid coat blood vessel" EXACT [OBOL:automatic] synonym: "choroidea blood vessel" EXACT [OBOL:automatic] synonym: "posterior uvea blood vessel" EXACT [OBOL:automatic] synonym: "set of choroid blood vessels" RELATED [FMA:76550] synonym: "vasa sanguinea choroideae" EXACT LATIN [FMA:76550, FMA:TA] xref: EMAPA:17828 xref: FMA:76550 xref: MA:0001237 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001776 ! optic choroid [Term] id: UBERON:0002458 name: spinal artery namespace: uberon def: "Arteries that supply the spinal cord." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Spinal_artery] subset: uberon_slim subset: vertebrate_core synonym: "spinal arteries" EXACT PLURAL [ZFA:0000682] xref: EHDAA2:0001890 xref: EHDAA:4355 xref: EMAPA:18241 xref: MA:0002043 xref: NCIT:C33587 xref: SCTID:244228006 xref: TAO:0000682 xref: UMLS:C0447043 {source="ncithesaurus:Spinal_Artery"} xref: Wikipedia:Spinal_artery xref: ZFA:0000682 is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0002240 ! spinal cord relationship: supplies UBERON:0002240 ! spinal cord [Term] id: UBERON:0002469 name: esophagus mucosa namespace: uberon alt_id: UBERON:0003345 def: "A mucosa that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophageal mucosa" EXACT [] synonym: "esophageal mucous membrane" EXACT [] synonym: "esophagus mucosa" EXACT [FMA:62996] synonym: "esophagus mucous membrane" EXACT [OBOL:automatic] synonym: "lamina muscularis mucosae oesophageae" EXACT LATIN [FMA:62996, FMA:TA] synonym: "mucosa of esophagus" EXACT [OBOL:automatic] synonym: "mucosa of oesophagus" EXACT [OBOL:automatic] synonym: "mucous membrane of esophagus" EXACT [] synonym: "mucous membrane of oesophagus" EXACT [FMA:62996] synonym: "muscularis mucosae of oesophagus" RELATED INCONSISTENT [FMA:62996] synonym: "oesophageal mucosa" EXACT [FMA:62996] synonym: "oesophagus mucosa" EXACT [] synonym: "oesophagus mucous membrane" EXACT [OBOL:automatic] synonym: "tunica mucosa esophagi" EXACT [] synonym: "tunica mucosa oesophageae" EXACT LATIN [FMA:62996, FMA:TA] synonym: "tunica mucosa oesophagi" EXACT [] synonym: "tunica mucosa oesophagi" RELATED [BTO:0002859] xref: BTO:0002859 xref: EMAPA:26981 xref: FMA:62996 xref: MA:0002680 xref: NCIT:C32538 xref: SCTID:362127004 xref: UMLS:C0227176 {source="ncithesaurus:Esophageal_Mucosa"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000344 ! mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 ! wall of esophagus [Term] id: UBERON:0002481 name: bone tissue namespace: uberon def: "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000047] subset: pheno_slim subset: uberon_slim synonym: "bone" RELATED [MESH:A02.835.232] synonym: "calcium tissue" EXACT [] synonym: "mineralized bone tissue" NARROW [XAO:0004040] synonym: "osseous tissue" EXACT [] synonym: "osteogenic tissue" EXACT [VSAO:curator] synonym: "portion of bone tissue" RELATED [FMA:224804] xref: CALOHA:TS-2011 xref: EMAPA:35179 xref: FMA:224804 xref: galen:BoneTissue xref: MA:0002780 xref: MESH:D001842 xref: NCIT:C13076 xref: UMLS:C0391978 {source="ncithesaurus:Bone_Tissue"} xref: VSAO:0000047 xref: Wikipedia:Bone_tissue xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string property_value: UBPROP:0000001 "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} [Term] id: UBERON:0002506 name: iris epithelium namespace: uberon def: "An epithelium that is part of a iris [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "epithelial tissue of iris" EXACT [OBOL:automatic] synonym: "epithelium of iris" EXACT [OBOL:automatic] synonym: "epithelium pigmentosum (iris)" EXACT [FMA:58517] synonym: "epithelium pigmentosum iridis" EXACT LATIN [FMA:58517, FMA:TA] synonym: "iris epithelial tissue" EXACT [OBOL:automatic] synonym: "iris epithelium" EXACT [FMA:58517] synonym: "iris pigmented epithelium" RELATED [MA:0002826] synonym: "pigmented epithelium of iris" EXACT [FMA:58517] xref: EMAPA:35447 xref: FMA:58517 xref: MA:0002826 is_a: UBERON:0000488 {source="FMA"} ! atypical epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001769 ! iris relationship: contributes_to_morphology_of UBERON:0001769 ! iris relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001769 {source="MA"} ! iris [Term] id: UBERON:0002513 name: endochondral bone namespace: uberon def: "Replacement bone that forms within cartilage." [GO:0001958, GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/54, VSAO:0000145] subset: uberon_slim subset: vertebrate_core synonym: "cartilaginous bone" RELATED [BTO:0002157] synonym: "endochondral bones" RELATED PLURAL [ZFA:0001591] synonym: "ossified chondrogenic bone" EXACT [VSAO:0000145] xref: AAO:0010776 xref: AEO:0000083 xref: BTO:0002157 xref: EHDAA2:0003083 xref: FMA:24321 xref: TAO:0001591 xref: VSAO:0000145 xref: XAO:0004018 xref: ZFA:0001591 is_a: UBERON:0001474 ! bone element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010363 {source="VSAO"} ! endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: develops_from UBERON:0005863 ! cartilaginous condensation relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:2001544 ! sublingual cartilage property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg xsd:anyURI property_value: editor_note "placement in this class to be inferred" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/mellybelly property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern xsd:anyURI property_value: UBPROP:0000001 "Replacement bone that forms within cartilage.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000145", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} property_value: UBPROP:0000012 "some structures, e.g. in ZFA are both intramembrane and endochondral" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0002514 name: intramembranous bone namespace: uberon def: "Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, https://github.com/obophenotype/uberon/issues/267, Wikipedia:Intramembranous_ossification] synonym: "intramembranous bones" RELATED PLURAL [ZFA:0001635] synonym: "membrane bone" RELATED [AEO:0000085] xref: EMAPA:36615 xref: TAO:0001644 xref: Wikipedia:Intramembranous_ossification xref: ZFA:0001635 is_a: UBERON:0001474 {source="VSAO"} ! bone element relationship: develops_from UBERON:0003104 ! mesenchyme relationship: output_of GO:0001957 ! intramembranous ossification property_value: UBPROP:0000001 "Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001644", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000005 "[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]" xsd:string {date_retrieved="2012-09-06", external_class="TAO:0001644", ontology="TAO", source="Curator"} [Term] id: UBERON:0002521 name: elastic tissue namespace: uberon def: "Connective tissue composed of elastic fibers." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "elastic connective tissue" EXACT [] synonym: "elastic fiber" NARROW [] synonym: "textus connectivus elasticus" EXACT LATIN [] xref: FMA:20113 xref: GAID:926 xref: MA:0002853 xref: MESH:D004547 xref: NCIT:C32495 xref: SCTID:27197004 xref: Wikipedia:Elastic_fiber is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: composed_primarily_of GO:0071953 ! elastic fiber relationship: composed_primarily_of GO:0071953 ! elastic fiber relationship: has_quality PATO:0001171 ! elastic property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png xsd:anyURI [Term] id: UBERON:0002522 name: tunica media namespace: uberon def: "The middle layer of an artery or vein. [WP,unvetted]." [Wikipedia:Tunica_media] comment: May be composed of smooth muscle and elastic tissue subset: uberon_slim synonym: "tunica media vasorum" RELATED LATIN [Wikipedia:Tunica_media] synonym: "tunica media vasorum" RELATED [BTO:0002011] xref: BTO:0002011 xref: EMAPA:36298 xref: FMA:55590 xref: GAID:170 xref: MA:0002855 xref: MESH:D017540 xref: NCIT:C33821 xref: SCTID:61695000 xref: UMLS:C0162867 {source="ncithesaurus:Tunica_Media"} xref: Wikipedia:Tunica_media is_a: UBERON:0004797 {source="MA"} ! blood vessel layer relationship: has_part UBERON:0002521 {source="cjm"} ! elastic tissue relationship: has_part UBERON:0004237 {source="cjm"} ! blood vessel smooth muscle relationship: surrounded_by UBERON:0005734 ! tunica adventitia of blood vessel property_value: depicted:by Illu:artery.jpg xsd:anyURI [Term] id: UBERON:0002523 name: tunica intima namespace: uberon def: "The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]." [ISBN:0073040584, NCIT:C33820, Wikipedia:Tunica_intima] subset: uberon_slim synonym: "Bichat's tunic" RELATED [BTO:0002012] synonym: "intima" RELATED [BTO:0002012] synonym: "tunica intima vasorum" RELATED [BTO:0002012] xref: BTO:0002012 xref: EMAPA:36297 xref: FMA:55589 xref: GAID:523 xref: MA:0002861 xref: MESH:D017539 xref: NCIT:C33820 xref: SCTID:8361002 xref: SCTID:87483006 xref: UMLS:C0162864 {source="ncithesaurus:Tunica_Intima"} xref: Wikipedia:Tunica_intima is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: adjacent_to UBERON:0010161 {source="ISBN:0073040584"} ! lumen of blood vessel relationship: has_part UBERON:0001986 ! endothelium relationship: surrounded_by UBERON:0002522 {notes="check for exceptions, e.g. capillaries"} ! tunica media property_value: depicted:by Illu:artery.jpg xsd:anyURI property_value: editor_note "the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure" xsd:string property_value: editor_note "the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts" xsd:string property_value: UBPROP:0000001 "The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]" xsd:string {ontology="Wikipedia", source="Wikipedia:Tunica_intima"} [Term] id: UBERON:0002530 name: gland namespace: uberon alt_id: UBERON:MIAA_0000021 def: "an organ that functions as a secretory or excretory organ" [MGI:csmith, MP:0002163] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "Druese" RELATED [BTO:0000522] synonym: "glandula" RELATED [BTO:0000522] synonym: "glandula" RELATED LATIN [Wikipedia:Gland] synonym: "glandular organ" EXACT [http://orcid.org/0000-0002-6601-2165] xref: AAO:0000212 xref: AEO:0000096 xref: BTO:0000522 xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 xref: EHDAA:4475 xref: EHDAA:6522 xref: EMAPA:18425 xref: FBbt:00100317 xref: FMA:7146 xref: FMA:86294 xref: galen:Gland xref: HAO:0000375 xref: MA:0003038 xref: MAT:0000021 xref: MIAA:0000021 xref: NCIT:C13319 xref: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA xref: SCTID:134358001 xref: UMLS:C1285092 {source="ncithesaurus:Gland"} xref: Wikipedia:Gland xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: produces UBERON:0000463 ! organism substance property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png xsd:anyURI property_value: UBPROP:0000007 "glandular" xsd:string [Term] id: UBERON:0002532 name: epiblast (generic) namespace: uberon def: "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]" [Wikipedia:Epiblast, ZFIN:curator] subset: early_development subset: grouping_class subset: uberon_slim subset: vertebrate_core synonym: "blastocyst" RELATED [] synonym: "ectoblast" RELATED [MP:0003886] synonym: "epiblast" EXACT [VHOG:0000243] synonym: "epiblastus" RELATED LATIN [Wikipedia:Epiblast] synonym: "primitive ectoderm" RELATED [VHOG:0000243] xref: BTO:0004593 xref: FMA:296704 xref: MAT:0000067 xref: MIAA:0000067 xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png xsd:anyURI property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002539 name: pharyngeal arch namespace: uberon def: "One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches." [http://orcid.org/0000-0002-6601-2165, PMID:16313389, ZFA:yb] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "arcus pharyngei" RELATED LATIN [Wikipedia:Pharyngeal_arch] synonym: "branchial arch" NARROW [BTO:0001785, MP:0002884] synonym: "pharyngeal arches" EXACT PLURAL [] synonym: "visceral arch" RELATED [] xref: AAO:0010359 xref: BTO:0001785 xref: EFO:0000959 xref: EHDAA:571 xref: EMAPA:16117 xref: FMA:293015 xref: GAID:1292 xref: MAT:0000242 xref: MESH:A16.254.160 xref: MIAA:0000242 xref: NCIT:C34249 xref: SCTID:308766004 xref: TAO:0001306 xref: UMLS:C0080322 {source="ncithesaurus:Pharyngeal_Arch"} xref: VHOG:0000155 xref: Wikipedia:Pharyngeal_arch xref: XAO:0000096 xref: ZFA:0001306 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: developmentally_induced_by UBERON:0007690 {source="PMID:16313389"} ! early pharyngeal endoderm relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0008814 ! pharyngeal arch system relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png xsd:anyURI property_value: UBPROP:0000001 "One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010359", ontology="AAO", source="NLM:branchial+arch"} property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000155", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000013 "Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering" xsd:string [Term] id: UBERON:0002546 name: cranial placode namespace: uberon def: "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic." [http://www.ncbi.nlm.nih.gov/books/NBK53175/, https://github.com/obophenotype/uberon/issues/135, https://github.com/seger/aao/issues/4, https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/] subset: efo_slim synonym: "cranial placodes" RELATED PLURAL [XAO:0000305] synonym: "ectodermal cranial placode" EXACT [UBERON:cjm] synonym: "ectodermal placode" BROAD INCONSISTENT [FMA:293966, PMID:22512454] synonym: "placode" BROAD [Wikipedia:Placode] xref: AAO:0010466 xref: EFO:0001650 xref: FMA:293966 xref: MAT:0000369 xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode relationship: only_in_taxon NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! Chordata relationship: part_of UBERON:0000033 ! head property_value: editor_note "Do not merge with neurogenic placode" xsd:string property_value: UBPROP:0000008 "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" xsd:string {source="PMID:11523831"} property_value: UBPROP:0000013 "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" xsd:string [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: EMAPA:37442 {source="MA:th"} xref: FMA:67552 xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space relationship: location_of UBERON:0000463 ! organism substance [Term] id: UBERON:0002616 name: regional part of brain namespace: uberon def: "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia." [BIRNLEX:1167] subset: non_informative synonym: "anatomical structure of brain" EXACT [OBOL:automatic] synonym: "biological structure of brain" EXACT [OBOL:automatic] synonym: "brain anatomical structure" EXACT [OBOL:automatic] synonym: "brain biological structure" EXACT [OBOL:automatic] synonym: "brain part" EXACT [] synonym: "neuraxis segment" EXACT [FMA:55676] synonym: "neuroanatomical region" EXACT [] synonym: "segment of brain" EXACT [BIRNLEX:1167] xref: BIRNLEX:1167 xref: FMA:55676 xref: NCIT:C13031 xref: SCTID:384763002 xref: UMLS:C0445620 {source="ncithesaurus:Brain_Part"} is_a: UBERON:0000073 ! regional part of nervous system is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0000955 ! brain relationship: composed_primarily_of UBERON:0003714 ! neural tissue relationship: part_of UBERON:0000955 ! brain [Term] id: UBERON:0003037 name: septum namespace: uberon def: "A wall, dividing a cavity or structure into smaller ones[WP]." [Wikipedia:Septum] comment: general anatomical term in FMA subset: pheno_slim synonym: "septa" EXACT PLURAL [] xref: AAO:0011127 xref: FMA:86461 xref: OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ xref: Wikipedia:Septum is_a: UBERON:0000061 ! anatomical structure relationship: located_in UBERON:0002553 ! anatomical cavity property_value: UBPROP:0000007 "septal" xsd:string [Term] id: UBERON:0003052 name: midbrain-hindbrain boundary namespace: uberon def: "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate." [GO:0021555] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "isthmic organizer territory" RELATED [XAO:0000016] synonym: "isthmo-cerebellar region" RELATED [VHOG:0000649] synonym: "isthmus" RELATED [] synonym: "isthmus/MHB" RELATED [Geisha:syn, NCBITaxon:8782] synonym: "MHB" EXACT [] synonym: "mid-hindbrain boundary" EXACT [] synonym: "mid-hindbrain junction" EXACT [] synonym: "midbrain hindbrain boundary" EXACT [] xref: AAO:0011064 xref: DMBA:16810 xref: EHDAA2:0004395 xref: EHDAA:5789 xref: EMAPA:32857 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2076 xref: NCIT:C93172 xref: TAO:0000042 xref: VHOG:0000649 xref: XAO:0000016 xref: ZFA:0000042 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: immediate_transformation_of UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0000955 {source="ZFA"} ! brain property_value: editor_note "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string property_value: UBPROP:0000003 "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000649", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003055 name: periderm namespace: uberon def: "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis." [ISBN:9780878932504] subset: pheno_slim subset: uberon_slim synonym: "epidermis epithelial layer" RELATED [] synonym: "epidermis outer layer" RELATED [] synonym: "epitrichium" RELATED [MP:0013530] synonym: "EVL" RELATED [ZFA:0001185] synonym: "periderm" RELATED [] synonym: "skin periderm" EXACT [EHDAA2:0001846] xref: EHDAA2:0001846 xref: EHDAA:6538 xref: FMA:295662 xref: NCIT:C34247 xref: TAO:0001185 xref: UMLS:C1518973 {source="ncithesaurus:Periderm"} xref: VHOG:0001680 xref: XAO:0000029 xref: ZFA:0001185 is_a: UBERON:0000487 {source="EHDAA2"} ! simple squamous epithelium is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0007383 {source="ZFA"} ! enveloping layer of ectoderm relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument property_value: UBPROP:0000001 "The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001185", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001185", ontology="TAO"} property_value: UBPROP:0000008 "In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]" xsd:string property_value: UBPROP:0000011 "In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis" xsd:string property_value: UBPROP:0000011 "Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)" xsd:string [Term] id: UBERON:0003056 name: pre-chordal neural plate namespace: uberon def: "The portion of neural plate anterior to the mid-hindbrain junction." [XB:curator] synonym: "anterior neural plate" RELATED [] xref: AAO:0011084 xref: TAO:0007016 xref: VHOG:0001200 xref: XAO:0000045 xref: ZFA:0007016 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: anterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0003075 ! neural plate property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001200", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003057 name: chordal neural plate namespace: uberon def: "The portion of neural plate posterior to the mid-hindbrain junction." [XB:curator] synonym: "posterior neural plate" RELATED [] xref: TAO:0007017 xref: VHOG:0001201 xref: XAO:0000046 xref: ZFA:0007017 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate relationship: posterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001201", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003059 name: presomitic mesoderm namespace: uberon def: "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." [ZFIN:curator] subset: efo_slim subset: pheno_slim synonym: "presumptive somite mesoderm" RELATED [] synonym: "PSM" RELATED [] synonym: "segmental plate" EXACT [] synonym: "somitogenic mesoderm" RELATED [] synonym: "somitomeric mesoderm" RELATED [GO:0002075] synonym: "unsegmented mesenchyme" RELATED [VHOG:0000559] synonym: "unsegmented paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] xref: AAO:0011086 xref: EFO:0001982 xref: EMAPA:16189 xref: EMAPA:16752 xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate relationship: develops_from UBERON:0007282 ! presumptive segmental plate relationship: has_potential_to_develop_into UBERON:0002329 ! somite relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003061 name: blood island namespace: uberon def: "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." [Wikipedia:Blood_island_of_umbilical_vesicle] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "blood islands" EXACT PLURAL [] synonym: "caudal hematopoietic tissue" RELATED [] synonym: "posterior blood island" RELATED [] synonym: "posterior ICM" RELATED [] synonym: "VBI" RELATED [] synonym: "ventral blood island" RELATED [] synonym: "ventral lateral plate mesoderm" BROAD [] xref: AAO:0011006 xref: EFO:0003489 xref: EHDAA:207 xref: NCIT:C34113 xref: TAO:0000094 xref: TE:E5.11.2.0.0.0.4 xref: UMLS:C1511224 {source="ncithesaurus:Blood_Island"} xref: VHOG:0000085 xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure relationship: contains_process GO:0001525 {source="ISBN:0073040584"} ! angiogenesis relationship: contains_process GO:0030097 {source="ISBN:0073040584"} ! hemopoiesis relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0003063 name: prechordal plate namespace: uberon alt_id: UBERON:0004881 def: "A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue" [ISBN:0838580343, MP:0004387] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "head mesenchyme" BROAD [XAO:0000079] synonym: "head mesoderm" BROAD [XAO:0000079] xref: AAO:0011085 xref: EHDAA2:0001493 xref: EHDAA:181 xref: FMA:295532 xref: TAO:0000060 xref: VHOG:0000086 xref: Wikipedia:Prechordal_plate xref: XAO:0000079 xref: ZFA:0000060 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0034878 ! prechordal mesoderm relationship: part_of UBERON:0003068 {source="ZFA"} ! axial mesoderm relationship: transformation_of UBERON:0034878 {todo="PMID:16313393"} ! prechordal mesoderm property_value: editor_note "TODO - check; developmental relationship to anterior hypoblast in ZFA?" xsd:string property_value: UBPROP:0000001 "Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000060", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003064 name: intermediate mesoderm namespace: uberon def: "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." [GOC:curators, Wikipedia:Intermediate_mesoderm] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "IM" RELATED [] synonym: "intermediate mesenchyme" RELATED [https://github.com/obophenotype/uberon/wiki/The-neural-crest] synonym: "intermediate plate" RELATED [EMAPA:16178] synonym: "intermediate plate mesoderm" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "mesenchyma intermedium" RELATED LATIN [Wikipedia:Intermediate_mesoderm] xref: AAO:0010575 xref: EMAPA:16056 xref: EMAPA:16178 xref: FMA:293147 xref: NCIT:C34193 xref: SCTID:361476001 xref: TAO:0001206 xref: UMLS:C1284010 {source="ncithesaurus:Intermediate_Mesoderm"} xref: VHOG:0000087 xref: Wikipedia:Intermediate_mesoderm xref: XAO:0000085 xref: ZFA:0001206 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: adjacent_to UBERON:0003077 ! paraxial mesoderm relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm relationship: develops_from UBERON:0000926 {source="XAO"} ! mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: UBPROP:0000001 "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010575", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000087", ontology="VHOG", source="Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0003068 name: axial mesoderm namespace: uberon def: "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GO:0048318, Wikipedia:Chordamesoderm] subset: efo_slim subset: uberon_slim synonym: "chordamesoderm" RELATED [Wikipedia:Chordamesoderm] xref: AAO:0011017 xref: EFO:0003647 xref: TAO:0001204 xref: VHOG:0000107 xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000926 ! mesoderm relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003071 name: eye primordium namespace: uberon alt_id: UBERON:0005060 def: "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles." [GO:0046619, ZFA:0000570] subset: efo_slim synonym: "eye anlage" RELATED [XAO:0000227] synonym: "eye field" RELATED [] synonym: "eye placode" EXACT [OBOL:automatic] synonym: "occular primordium" EXACT [] synonym: "ocular primordium" EXACT [] synonym: "optic field" RELATED [] synonym: "optic placode" EXACT [GO:0046619] synonym: "optic placode of camera-type eye" EXACT [GO:0046619, https://orcid.org/0000-0002-6601-2165] synonym: "optic placodes" RELATED PLURAL [] synonym: "optic primordium" EXACT [] xref: AAO:0011038 xref: EFO:0003541 xref: EHDAA2:0004431 xref: TAO:0000570 xref: XAO:0000227 xref: XAO:0004090 xref: ZFA:0000570 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0001048 ! primordium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0001048 ! primordium intersection_of: has_potential_to_develop_into UBERON:0000019 ! camera-type eye relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: has_potential_to_develop_into UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0003056 {source="PMID:16496288", source="XAO"} ! pre-chordal neural plate property_value: UBPROP:0000012 "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." xsd:string {external_ontology="GO"} [Term] id: UBERON:0003072 name: optic cup namespace: uberon def: "Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]." [MP:0004269, Wikipedia:Optic_cup_(embryology), ZFA:0001202] subset: pheno_slim subset: vertebrate_core synonym: "eye cup" RELATED [] synonym: "eyecup" RELATED [BTO:0005351] synonym: "ocular cup" RELATED [VHOG:0000167] synonym: "ophtalmic cup" RELATED [BTO:0005351] xref: BTO:0005351 xref: EHDAA2:0001303 xref: EHDAA:2912 xref: EMAPA:16674 xref: NCIT:C34233 xref: SCTID:308789007 xref: TAO:0001202 xref: UMLS:C0231109 {source="ncithesaurus:Optic_Cup"} xref: VHOG:0000167 xref: ZFA:0001202 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: developmentally_induced_by UBERON:0003073 ! lens placode relationship: develops_from UBERON:0004128 {source="ZFA"} ! optic vesicle relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003073 name: lens placode namespace: uberon def: "A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]." [Wikipedia:Lens_placode, ZFIN:curator] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "lens placodes" RELATED PLURAL [ZFA:0000122] synonym: "placoda lentis" RELATED LATIN [Wikipedia:Lens_placode] xref: AAO:0011055 xref: EFO:0003494 xref: EHDAA2:0000982 xref: EHDAA:2908 xref: EMAPA:16672 xref: FMA:296767 xref: NCIT:C34202 xref: TAO:0000122 xref: UMLS:C1517770 {source="ncithesaurus:Lens_Placodes"} xref: VHOG:0000166 xref: Wikipedia:Lens_placode xref: XAO:0000240 xref: ZFA:0000122 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010312 ! immature eye is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode intersection_of: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye relationship: developmentally_induced_by UBERON:0004128 ! optic vesicle relationship: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png xsd:anyURI property_value: UBPROP:0000001 "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000122", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: UBPROP:0000011 "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" xsd:string {source="NCBIBook:NBK53175"} [Term] id: UBERON:0003075 name: neural plate namespace: uberon def: "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]" [ISBN:0815318960, OMD:neural+plate, Wikipedia:Neural_plate, ZFIN:curator] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "lamina neuralis" RELATED LATIN [Wikipedia:Neural_plate] synonym: "presumptive central nervous system" RELATED [] xref: AAO:0011072 xref: BTO:0001765 xref: DHBA:10153 xref: DMBA:15565 xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1362 xref: NCIT:C34225 xref: RETIRED_EHDAA2:0001252 xref: TAO:0000132 xref: UMLS:C0920623 {source="ncithesaurus:Neural_Plate"} xref: VHOG:0000068 xref: Wikipedia:Neural_plate xref: XAO:0000249 xref: ZFA:0000132 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord relationship: develops_from UBERON:0007284 ! presumptive neural plate relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata property_value: depicted:by Neural:Crest.png xsd:anyURI property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003076 name: posterior neural tube namespace: uberon xref: AAO:0011082 xref: TAO:0007037 xref: VHOG:0001383 xref: XAO:0000250 xref: ZFA:0007037 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure disjoint_from: UBERON:0003080 {source="lexical"} ! anterior neural tube relationship: develops_from UBERON:0003057 ! chordal neural plate relationship: part_of UBERON:0001049 ! neural tube property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001383", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003077 name: paraxial mesoderm namespace: uberon def: "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]" [GO:0048339, https://github.com/obophenotype/uberon/issues/30] subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "mesoderma paraxiale" RELATED LATIN [Wikipedia:Paraxial_mesoderm] synonym: "paraxial mesenchyme" EXACT [https://github.com/obophenotype/uberon/issues/30, https://github.com/obophenotype/uberon/wiki/The-neural-crest, ZFA:0000255] synonym: "somitic mesoderm" EXACT [ISBN:9780878932504] xref: AAO:0010568 xref: EFO:0003515 xref: EMAPA:16183 xref: EMAPA:16751 xref: FMA:293145 xref: NCIT:C34244 xref: SCTID:361475002 xref: TAO:0000255 xref: UMLS:C1284009 {source="ncithesaurus:Paraxial_Mesoderm"} xref: VHOG:0000114 xref: Wikipedia:Paraxial_mesoderm xref: XAO:0000259 xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: develops_from UBERON:0007285 ! presumptive paraxial mesoderm relationship: existence_starts_during UBERON:0000109 ! gastrula stage relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm relationship: in_lateral_side_of UBERON:0000922 ! embryo property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0003080 name: anterior neural tube namespace: uberon xref: AAO:0011012 xref: TAO:0007038 xref: VHOG:0001384 xref: XAO:0000307 xref: ZFA:0007038 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: part_of UBERON:0001049 ! neural tube property_value: editor_note "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001384", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim synonym: "lateral mesoderm" EXACT [GO:0048368] synonym: "lateral plate" RELATED [] synonym: "lateral plate mesenchyme" RELATED [EHDAA2:0000919] synonym: "LPM" EXACT ABBREVIATION [ZFA:0000121] synonym: "mesoderma laminae lateralis" RELATED LATIN [Wikipedia:Lateral_plate_mesoderm] xref: AAO:0010574 xref: EHDAA2:0000919 xref: EHDAA:379 xref: EMAPA:16179 xref: FMA:293149 xref: NCIT:C34199 xref: SCTID:361477005 xref: TAO:0000121 xref: UMLS:C1517749 {source="ncithesaurus:Lateral_Mesoderm"} xref: VHOG:0000118 xref: Wikipedia:Lateral_plate_mesoderm xref: XAO:0000311 xref: ZFA:0000121 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: surrounds UBERON:0003887 ! intraembryonic coelom property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xsd:anyURI property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0003082 name: myotome namespace: uberon def: "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells." [AEO:0001018] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle plate" RELATED [] synonym: "myomere" RELATED [] synonym: "myomeres" EXACT PLURAL [TAO:0001056] synonym: "myotome region" RELATED [] synonym: "myotomes" RELATED [] synonym: "myotomus" RELATED LATIN [Wikipedia:Myotome] xref: AAO:0011067 xref: AEO:0001018 xref: BTO:0000742 xref: EHDAA2_RETIRED:0003431 xref: EHDAA:1721 xref: EHDAA:1727 xref: EHDAA:1733 xref: EHDAA:1739 xref: EMAPA:32841 xref: FMA:295658 xref: NCIT:C34214 xref: SCTID:344535001 xref: TAO:0001056 xref: UMLS:C1513802 {source="ncithesaurus:Myotome_Region"} xref: VHOG:0001244 xref: Wikipedia:Myotome xref: XAO:0000315 xref: ZFA:0001056 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure relationship: contributes_to_morphology_of UBERON:0001630 ! muscle organ relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png xsd:anyURI property_value: editor_note "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string property_value: UBPROP:0000001 "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001056", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001244", ontology="VHOG", source="DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003084 name: heart primordium namespace: uberon def: "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone." [ZFIN:curator] subset: uberon_slim synonym: "cardiac field" RELATED [ZFA:0000028] synonym: "fused heart primordium" RELATED [] xref: AAO:0011044 xref: BTO:0001887 xref: NCIT:C34276 xref: TAO:0000028 xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001048 {source="Obol"} ! primordium relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm relationship: develops_from UBERON:0004140 ! primary heart field relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system property_value: editor_note "should probably be merged with heart rudiment." xsd:string property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} [Term] id: UBERON:0003089 name: sclerotome namespace: uberon def: "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [https://github.com/obophenotype/uberon/issues/316, Wikipedia:Sclerotome, XB:curator] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "sclerotomes" EXACT PLURAL [TAO:0001080] synonym: "sclerotomus" RELATED LATIN [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 xref: NCIT:C34287 xref: TAO:0001080 xref: UMLS:C0183176 {source="ncithesaurus:Sclerotome"} xref: VHOG:0000680 xref: Wikipedia:Sclerotome xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png xsd:anyURI property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} [Term] id: UBERON:0003099 name: cranial neural crest namespace: uberon def: "neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage." [MGI:anna] subset: efo_slim subset: uberon_slim subset: vertebrate_core synonym: "cephalic neural crest" EXACT [EMAPA:16091] synonym: "CNC" EXACT ABBREVIATION [XAO:0001001] synonym: "cranial NCC population" EXACT [] synonym: "crista neuralis cranialis" RELATED LATIN [Wikipedia:Cranial_neural_crest] synonym: "head crest" RELATED [] synonym: "head NCC population" EXACT [] synonym: "head neural crest" RELATED [] xref: AAO:0010580 xref: EFO:0003645 xref: EHDAA2:0004420 xref: EMAPA:16091 xref: TAO:0001194 xref: VHOG:0000063 xref: Wikipedia:Cranial_neural_crest xref: XAO:0001001 xref: ZFA:0001194 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0002342 ! neural crest property_value: UBPROP:0000001 "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010580", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "Neural crest that is part of the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001194", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000063", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003100 name: female organism namespace: uberon def: "Gonochoristic organism that can produce female gametes." [CARO:0000028] subset: pheno_slim subset: vertebrate_core synonym: "female" RELATED [TAO:0000303] synonym: "female human body" NARROW SENSU [FMA:67812] xref: AAO:0010030 xref: BILA:0000028 xref: CARO:0000028 xref: FBbt:00007011 xref: FMA:67812 xref: HAO:0000028 xref: SCTID:362608006 xref: TAO:0000303 xref: TGMA:0001839 xref: XAO:0003005 xref: ZFA:0000303 is_a: UBERON:0000468 ! multicellular organism [Term] id: UBERON:0003102 name: surface structure namespace: uberon def: "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/24] subset: upper_level synonym: "anatomical surface feature" EXACT [EHDAA2:0003010] synonym: "surface feature" RELATED [] synonym: "surface region" RELATED [] synonym: "surface structures" RELATED PLURAL [ZFA:0000292] xref: AAO:0010337 xref: AEO_RETIRED:0000010 xref: EHDAA2_RETIRED:0003010 xref: galen:SurfaceRegion xref: TAO:0000292 xref: VSAO:0000001 xref: Wikipedia:Surface_structure xref: XAO:0003028 xref: ZFA:0000292 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure relationship: adjacent_to UBERON:0013514 ! space surrounding organism relationship: part_of UBERON:0002416 ! integumental system property_value: editor_note "consider obsoleting. See issue/1305" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul property_value: UBPROP:0000001 "Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000292", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0003103 name: compound organ namespace: uberon def: "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [CARO:0000024] subset: organ_slim subset: upper_level synonym: "organ" RELATED [] xref: AAO:0010015 xref: AEO:0000024 xref: BILA:0000024 xref: CARO:0000024 xref: EHDAA2:0003024 xref: HAO:0000024 xref: TADS:0000598 xref: TAO:0000496 xref: TGMA:0001837 xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 name: mesenchyme namespace: uberon def: "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme." [https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up, https://en.wikipedia.org/wiki/Mesenchyme, https://github.com/obophenotype/uberon/issues/1641] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "mesenchyma" RELATED LATIN [Wikipedia:Mesenchyme] synonym: "mesenchymal tissue" EXACT [] synonym: "mesenchyme tissue" EXACT [] synonym: "portion of mesenchymal tissue" EXACT [] synonym: "portion of mesenchyme tissue" EXACT [] xref: AAO:0010427 xref: AEO:0000145 xref: BTO:0001393 xref: CALOHA:TS-0620 xref: EHDAA2:0003145 xref: EV:0100007 xref: NCIT:C13301 xref: TAO:0000393 xref: UMLS:C0162415 {source="ncithesaurus:Mesenchyme"} xref: VHOG:0000170 xref: Wikipedia:Mesenchyme xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell relationship: composed_primarily_of CL:0008019 ! mesenchymal cell relationship: functionally_related_to GO:0032502 ! developmental process relationship: has_developmental_contribution_from UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! mesoderm relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg xsd:anyURI property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000007 "mesenchymal" xsd:string [Term] id: UBERON:0003113 name: dermatocranium namespace: uberon def: "Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]." [Wikipedia:Skull_roof, ZFA:0000863] synonym: "dendrocranium" EXACT [TAO:0000863] synonym: "dermal bone cranium" RELATED [ZFA:0000863] synonym: "dermal part of skull" RELATED [] synonym: "dermal skull bones" RELATED [] synonym: "dermal skull roof" NARROW [PMID:11523816, Wikipedia:Skull_roof] synonym: "dermatocranial cover" NARROW [] synonym: "exocranium" EXACT [UBERONREF:0000007] synonym: "roof of skull" NARROW [Wikipedia:Skull_roof] synonym: "roofing bones of the skull" RELATED [Wikipedia:Skull_roof] synonym: "skull exoskeleton" RELATED [] synonym: "skull roof" NARROW [PMID:11523816, Wikipedia:Skull_roof] xref: AAO:0010154 xref: TAO:0000863 xref: VHOG:0001665 xref: Wikipedia:Skull_roof xref: XAO:0003169 xref: ZFA:0000863 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0010364 ! dermal skeleton property_value: editor_note "wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007" xsd:string property_value: RO:0002161 NCBITaxon:7777 {source="ISBN:0073040584"} property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000863", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010154", ontology="AAO", source="AAO:BJB"} [Term] id: UBERON:0003117 name: pharyngeal arch 6 namespace: uberon alt_id: UBERON:0004349 def: "The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles" [MP:0006347] subset: pheno_slim synonym: "6th arch" EXACT [EHDAA2:0004075] synonym: "6th pharyngeal arch" RELATED [VHOG:0001205] synonym: "6th visceral arch" RELATED [VHOG:0001205] synonym: "branchial arch 4" RELATED SENSU [AAO:0010368, ZFA:0001609] synonym: "fourth branchial arch" RELATED SENSU [] synonym: "gill arch 4" EXACT [ZFA:0001609] synonym: "sixth branchial arch" EXACT [] synonym: "sixth pharyngeal arch" RELATED [VHOG:0001205] synonym: "sixth visceral arch" RELATED [XAO:0000453] synonym: "visceral arch 6" EXACT [ZFA:0001609] xref: AAO:0010368 xref: EHDAA2:0004075 xref: EMAPA:32766 xref: FMA:293047 xref: SCTID:308772004 xref: TAO:0001601 xref: VHOG:0001205 xref: XAO:0000453 xref: ZFA:0001609 is_a: UBERON:0002539 ! pharyngeal arch property_value: UBPROP:0000001 "The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010368", ontology="AAO", source="ISBN:0-02-377110-0"} property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001205", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000103 "6" xsd:nonNegativeInteger [Term] id: UBERON:0003118 name: pharyngeal arch artery 1 namespace: uberon alt_id: UBERON:0004371 def: "The vessels formed within the first pair of branchial arches in embryogenesis" [MP:0010355] subset: pheno_slim subset: vertebrate_core synonym: "1st aortic arch artery" RELATED [EMAPA:16685] synonym: "1st arch artery" EXACT [EMAPA:16685] synonym: "1st branchial arch artery" RELATED [EMAPA:16685] synonym: "1st pharyngeal arch artery" RELATED [EMAPA:16685] synonym: "AA1" EXACT [ZFA:0005005] synonym: "aortic arch 1" EXACT [ZFA:0005005] synonym: "first aortic arch" EXACT [XAO:0000342] synonym: "first arch artery" RELATED [EMAPA:16685] synonym: "first branchial arch artery" EXACT [] synonym: "mandibular aortic arch" EXACT [ZFA:0005005] xref: AAO:0010415 xref: EHDAA2:0000007 xref: EMAPA:16202 xref: EMAPA:16685 xref: SCTID:308774003 xref: TAO:0005005 xref: VHOG:0000149 xref: XAO:0000342 xref: ZFA:0005005 is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0004362 ! pharyngeal arch 1 relationship: contributes_to_morphology_of UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0004362 ! pharyngeal arch 1 property_value: UBPROP:0000008 "Disappears early in development in tetrapods" xsd:string property_value: UBPROP:0000012 "ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0003123 name: pharyngeal arch artery 6 namespace: uberon alt_id: UBERON:0004351 def: "The vessels formed within the sixth pair of branchial arches in embryogenesis" [MP:0006355] subset: pheno_slim subset: vertebrate_core synonym: "6th aortic arch artery" RELATED [EMAPA:17005] synonym: "6th arch artery" EXACT [EMAPA:17005] synonym: "6th branchial arch artery" RELATED [EMAPA:17005] synonym: "6th pharyngeal arch artery" RELATED [EMAPA:17005] synonym: "AA6" EXACT [ZFA:0005016] synonym: "aortic arch 6" EXACT [ZFA:0005016] synonym: "pulmonary arch" RELATED [ISBN:0073040584] synonym: "sixth aortic arch" EXACT [XAO:0000353] synonym: "sixth branchial arch artery" EXACT [] xref: AAO:0010422 xref: EHDAA2:0000102 xref: EMAPA:17005 xref: SCTID:308779008 xref: TAO:0005016 xref: VHOG:0000144 xref: Wikipedia:Aortic_arches#Arch_6 xref: XAO:0000353 xref: ZFA:0005016 is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0003117 ! pharyngeal arch 6 relationship: part_of UBERON:0003117 ! pharyngeal arch 6 property_value: UBPROP:0000001 "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005016", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010422", ontology="AAO", source="ISBN:0-02-377110-0"} property_value: UBPROP:0000001 "The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]." xsd:string {source="Wikipedia:Aortic_arches#Arch_6"} property_value: UBPROP:0000011 "the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} [Term] id: UBERON:0003128 name: cranium namespace: uberon def: "Upper portion of the skull that excludes the mandible (when present in the organism)." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Cranium_(anatomy)] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "bones of cranium" EXACT [FMA:71325] synonym: "calvarium" RELATED [BTO:0001328] synonym: "epicranial plate" RELATED [] synonym: "ossa cranii" EXACT LATIN [FMA:71325, FMA:TA] synonym: "set of bones of cranium" EXACT [FMA:71325] synonym: "skeletal system of head" RELATED [] synonym: "skull minus mandible" EXACT [] synonym: "upper part of skull" EXACT [] xref: BTO:0001328 xref: EFO:0000831 xref: EHDAA:6029 xref: EMAPA:17680 xref: FMA:71325 xref: MA:0000316 xref: MAT:0000340 xref: MIAA:0000340 xref: OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA xref: SCTID:181889008 xref: VHOG:0000334 xref: Wikipedia:Cranium_(anatomy) is_a: UBERON:0000075 {source="FMA-inferred"} ! subdivision of skeletal system relationship: part_of UBERON:0003129 ! skull property_value: UBPROP:0000007 "cranial" xsd:string property_value: UBPROP:0000012 "the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium" xsd:string {external_ontology="FMA"} property_value: UBPROP:0000013 "The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" xsd:string {source="WP"} [Term] id: UBERON:0003129 name: skull namespace: uberon def: "Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]." [http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376, PMID:11523816, Wikipedia:Skull] subset: pheno_slim subset: uberon_slim synonym: "cranial skeleton" RELATED [] synonym: "skeletal system of head" RELATED [] xref: BTO:0001295 xref: CALOHA:TS-2344 xref: EHDAA2:0000325 xref: EMAPA:17680 xref: FMA:46565 xref: GAID:82 xref: galen:Skull xref: MESH:D012886 xref: NCIT:C12789 xref: OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA xref: SCTID:110530005 xref: UMLS:C0037303 {source="ncithesaurus:Skull"} xref: Wikipedia:Skull xref: WikipediaCategory:Skull is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0003128 ! cranium relationship: has_part UBERON:0003278 ! skeleton of lower jaw relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0010323 ! cranial skeletal system property_value: RO:0002175 NCBITaxon:7762 property_value: UBPROP:0000012 "in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible." xsd:string {external_ontology="FMA"} property_value: UBPROP:0000012 "in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton" xsd:string property_value: UBPROP:0000013 "A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates" xsd:string {source="WP"} [Term] id: UBERON:0003133 name: reproductive organ namespace: uberon def: "An organ involved in reproduction" [UBERON:xp] subset: functional_classification subset: organ_slim subset: pheno_slim synonym: "genital organ" EXACT [] synonym: "genitalia" RELATED PLURAL [] synonym: "reproductive system organ" EXACT [] synonym: "sex organ" EXACT [] xref: EMAPA:17381 xref: EMAPA:37731 {source="MA:th"} xref: MA:0001752 xref: MESH:D005835 xref: NCIT:C25177 xref: OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA xref: SCTID:128181006 xref: TGMA:0000591 xref: UMLS:C0017420 {source="ncithesaurus:Genitalia"} xref: WBbt:0008422 is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0000003 ! reproduction relationship: capable_of GO:0000003 ! reproduction property_value: UBPROP:0000012 "GO uses genitalia for the singular organ" xsd:string {external_ontology="GO"} [Term] id: UBERON:0003134 name: female reproductive organ namespace: uberon def: "A female organ involved in reproduction" [UBERON:xp] subset: organ_slim subset: pheno_slim synonym: "female organism reproductive organ" EXACT [OBOL:automatic] synonym: "female organism reproductive structure" EXACT [OBOL:automatic] synonym: "female organism reproductive system organ" EXACT [OBOL:automatic] synonym: "female organism sex organ" EXACT [OBOL:automatic] synonym: "female reproductive gland/organ" EXACT [MA:0000544] synonym: "female reproductive system organ" EXACT [] synonym: "female sex organ" EXACT [] synonym: "reproductive organ of female organism" EXACT [OBOL:automatic] synonym: "reproductive structure of female organism" EXACT [OBOL:automatic] synonym: "reproductive system organ of female organism" EXACT [OBOL:automatic] synonym: "sex organ of female organism" EXACT [OBOL:automatic] xref: EMAPA:28540 xref: MA:0000544 is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0000474 ! female reproductive system [Term] id: UBERON:0003218 name: ovary septum namespace: uberon def: "Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]." [GO:0080126] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003037 ! septum intersection_of: UBERON:0003037 ! septum intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary [Term] id: UBERON:0003236 name: epithelium of lower jaw namespace: uberon def: "An epithelium that is part of a lower jaw [Automatically generated definition]." [OBOL:automatic] synonym: "epithelial tissue of lower jaw" EXACT [OBOL:automatic] synonym: "epithelial tissue of ventral mandibular arch" EXACT [OBOL:automatic] synonym: "epithelium of ventral mandibular arch" EXACT [OBOL:automatic] synonym: "lower jaw epithelial tissue" EXACT [OBOL:automatic] synonym: "lower jaw epithelium" EXACT [OBOL:automatic] synonym: "ventral mandibular arch epithelial tissue" EXACT [OBOL:automatic] synonym: "ventral mandibular arch epithelium" EXACT [OBOL:automatic] xref: EHDAA2:0001019 xref: EHDAA:7999 xref: EMAPA:35516 xref: VHOG:0000802 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0035037 ! jaw epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0001710 ! lower jaw region [Term] id: UBERON:0003258 name: endoderm of foregut namespace: uberon def: "An endoderm that is part of a foregut [Automatically generated definition]." [OBOL:automatic] synonym: "foregut endoderm" EXACT [OBOL:automatic] xref: EHDAA2:0004568 xref: EHDAA:524 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0015833 ! foregut epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001041 ! foregut property_value: editor_note "TODO - check" xsd:string [Term] id: UBERON:0003269 name: skeletal muscle tissue of eye namespace: uberon def: "A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]." [OBOL:automatic] synonym: "eye skeletal muscle" EXACT [OBOL:automatic] synonym: "eye skeletal muscle group" RELATED [EHDAA2:0000486] synonym: "eye skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of eye" EXACT [OBOL:automatic] xref: EHDAA2:0000486 xref: EHDAA:2923 xref: EMAPA:17844 is_a: UBERON:0001134 ! skeletal muscle tissue is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye [Term] id: UBERON:0003278 name: skeleton of lower jaw namespace: uberon def: "A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "lower jaw" BROAD [MA:0001906] synonym: "lower jaw" BROAD [ZFA:0001273] synonym: "lower jaw skeleton" EXACT [AAO:0000274] synonym: "mandible" BROAD [ZFA:0001273] synonym: "mandibles" RELATED PLURAL [TAO:0001273] synonym: "mandibular series" RELATED [ZFA:0001273] xref: AAO:0000274 xref: EHDAA2:0004606 xref: EHDAA:8005 xref: EMAPA:17906 xref: EMAPA:17910 xref: FMA:54398 xref: MA:0001906 xref: TAO:0001273 xref: VHOG:0000428 xref: XAO:0003084 xref: ZFA:0001273 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0001708 ! jaw skeleton relationship: part_of UBERON:0001710 {source="EHDAA2"} ! lower jaw region relationship: skeleton_of UBERON:0001710 ! lower jaw region property_value: UBPROP:0000001 "The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001273", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000428", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003294 name: gland of foregut namespace: uberon def: "A gland that is part of a foregut [Automatically generated definition]." [OBOL:automatic] synonym: "foregut gland" EXACT [OBOL:automatic] xref: EHDAA2:0000567 xref: EHDAA:950 xref: EMAPA:16557 xref: VHOG:0000650 is_a: UBERON:0003408 ! gland of digestive tract intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001041 ! foregut relationship: part_of UBERON:0001041 ! foregut [Term] id: UBERON:0003295 name: pharyngeal gland namespace: uberon def: "Racemose mucous glands beneath the mucous membrane of the pharynx." [http://www.biology-online.org/dictionary/] subset: organ_slim synonym: "glandulae pharyngeae" RELATED [BTO:0004849] synonym: "pharynx gland" EXACT [EHDAA2:0001461] xref: BTO:0004849 xref: EHDAA2:0001461 xref: EHDAA:2967 xref: FMA:55075 is_a: UBERON:0003408 ! gland of digestive tract is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 {source="BTO"} ! chordate pharynx [Term] id: UBERON:0003297 name: gland of integumental system namespace: uberon def: "A gland that is part of a integumental system [Automatically generated definition]." [OBOL:automatic] synonym: "integumental gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "integumental system gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "integumentary gland" EXACT [http://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0000837 xref: EHDAA:6522 xref: EMAPA:17758 xref: MA:0000144 xref: VHOG:0000654 is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002416 ! integumental system relationship: part_of UBERON:0002416 ! integumental system [Term] id: UBERON:0003304 name: mesoderm blood island namespace: uberon alt_id: UBERON:0003305 def: "A blood island that is part of a mesoderm." [OBOL:automatic] synonym: "mesenchyme blood island" RELATED [OBOL:automatic] synonym: "mesoderm blood islands" EXACT PLURAL [EHDAA2:0003241] xref: EHDAA2:0003241 xref: EHDAA:170 xref: EMAPA:16115 is_a: UBERON:0003061 ! blood island is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0003061 ! blood island intersection_of: part_of UBERON:0000926 ! mesoderm relationship: part_of UBERON:0000926 ! mesoderm relationship: part_of UBERON:0007798 {source="EHDAA2"} ! vascular system property_value: UBPROP:0000012 "in EHDAA2, gives rise to blood and dorsal aorta" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0003314 name: eye mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing camera-type eye." [OBOL:automatic] synonym: "mesenchyme of eye" EXACT [OBOL:automatic] xref: EHDAA2:0000485 xref: EHDAA:2910 xref: EMAPA:16673 xref: VHOG:0001084 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0009891 ! facial mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: develops_from UBERON:0009920 {source="EHDAA2"} ! optic neural crest relationship: part_of UBERON:0000019 ! camera-type eye property_value: editor_note "TODO - change mesenchyme relationships to precursor_of" xsd:string [Term] id: UBERON:0003315 name: mesenchyme of ovary namespace: uberon def: "Mesenchyme that is part of a developing ovary [Automatically generated definition]." [OBOL:automatic] synonym: "female reproductive system gonad mesenchyme" EXACT [OBOL:automatic] synonym: "female reproductive system gonada mesenchyme" EXACT [OBOL:automatic] synonym: "gonad of female reproductive system mesenchyme" EXACT [OBOL:automatic] synonym: "gonada of female reproductive system mesenchyme" EXACT [OBOL:automatic] synonym: "mesenchyme of female reproductive system gonad" EXACT [OBOL:automatic] synonym: "mesenchyme of female reproductive system gonada" EXACT [OBOL:automatic] synonym: "mesenchyme of gonad of female reproductive system" EXACT [OBOL:automatic] synonym: "mesenchyme of gonada of female reproductive system" EXACT [OBOL:automatic] synonym: "ovary mesenchyme" EXACT [OBOL:automatic] xref: EHDAA2:0001362 xref: EHDAA:8128 xref: VHOG:0001441 is_a: UBERON:0003855 ! gonad mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary [Term] id: UBERON:0003324 name: mesenchyme of lower jaw namespace: uberon def: "Mesenchyme that is part of a developing lower jaw [Automatically generated definition]." [OBOL:automatic] synonym: "lower jaw mesenchyme" EXACT [OBOL:automatic] synonym: "mesenchyme of ventral mandibular arch" EXACT [OBOL:automatic] synonym: "ventral mandibular arch mesenchyme" EXACT [OBOL:automatic] xref: EHDAA2:0001024 xref: EHDAA:8003 xref: EMAPA:17916 xref: VHOG:0001069 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034995 ! jaw mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: develops_from UBERON:0006905 {source="EHDAA2"} ! mandibular process mesenchyme relationship: part_of UBERON:0001710 ! lower jaw region [Term] id: UBERON:0003343 name: mucosa of oral region namespace: uberon def: "A mucosa that is part of a oral opening [Automatically generated definition]." [OBOL:automatic] synonym: "mucosa of oral opening" EXACT [OBOL:automatic] synonym: "mucosa of oral part of face" EXACT [OBOL:automatic] synonym: "mucosa of organ of oral opening" EXACT [OBOL:automatic] synonym: "mucosa of organ of oral part of face" EXACT [OBOL:automatic] synonym: "mucosa of organ of oral region" EXACT [OBOL:automatic] synonym: "mucosa of organ of subdivision of mouth" EXACT [OBOL:automatic] synonym: "mucosa of subdivision of mouth" EXACT [OBOL:automatic] synonym: "mucous membrane of oral opening" EXACT [OBOL:automatic] synonym: "mucous membrane of oral part of face" EXACT [OBOL:automatic] synonym: "mucous membrane of oral region" EXACT [OBOL:automatic] synonym: "mucous membrane of subdivision of mouth" EXACT [OBOL:automatic] synonym: "oral opening mucosa" EXACT [OBOL:automatic] synonym: "oral opening mucosa of organ" EXACT [OBOL:automatic] synonym: "oral opening mucous membrane" EXACT [OBOL:automatic] synonym: "oral opening organ mucosa" EXACT [OBOL:automatic] synonym: "oral part of face mucosa" EXACT [OBOL:automatic] synonym: "oral part of face mucosa of organ" EXACT [OBOL:automatic] synonym: "oral part of face mucous membrane" EXACT [OBOL:automatic] synonym: "oral part of face organ mucosa" EXACT [OBOL:automatic] synonym: "oral region mucosa" EXACT [OBOL:automatic] synonym: "oral region mucosa of organ" EXACT [OBOL:automatic] synonym: "oral region mucous membrane" EXACT [OBOL:automatic] synonym: "oral region organ mucosa" EXACT [OBOL:automatic] synonym: "organ mucosa of oral opening" EXACT [OBOL:automatic] synonym: "organ mucosa of oral part of face" EXACT [OBOL:automatic] synonym: "organ mucosa of oral region" EXACT [OBOL:automatic] synonym: "organ mucosa of subdivision of mouth" EXACT [OBOL:automatic] synonym: "subdivision of mouth mucosa" EXACT [OBOL:automatic] synonym: "subdivision of mouth mucosa of organ" EXACT [OBOL:automatic] synonym: "subdivision of mouth mucous membrane" EXACT [OBOL:automatic] synonym: "subdivision of mouth organ mucosa" EXACT [OBOL:automatic] xref: EMAPA:26937 xref: SCTID:362083000 is_a: UBERON:0003729 ! mouth mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000166 ! oral opening relationship: part_of UBERON:0000166 ! oral opening [Term] id: UBERON:0003350 name: epithelium of mucosa namespace: uberon def: "A layer of epithelial cells on the surface of the mucosa." [BTO:0003752] comment: lies on top of lamina propria synonym: "lamina epithelialis mucosa" RELATED [BTO:0003752] synonym: "lamina epithelialis mucosae" RELATED [BTO:0003752] xref: BTO:0003752 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000344 ! mucosa relationship: part_of UBERON:0000344 ! mucosa [Term] id: UBERON:0003351 name: pharyngeal epithelium namespace: uberon def: "An epithelium that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "epithelial tissue of pharynx" EXACT [OBOL:automatic] synonym: "epithelium of pharynx" EXACT [OBOL:automatic] synonym: "pharynx epithelial tissue" EXACT [OBOL:automatic] synonym: "pharynx epithelium" EXACT [OBOL:automatic] xref: BSA:0000112 xref: BTO:0005240 xref: EMAPA:16708 xref: MA:0002725 xref: RETIRED_EHDAA2:0001460 xref: TAO:0001174 xref: XAO:0003202 xref: ZFA:0001174 is_a: UBERON:0003929 ! digestive tract epithelium is_a: UBERON:0004807 ! respiratory system epithelium is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: develops_from UBERON:0007690 {source="ZFA"} ! early pharyngeal endoderm relationship: part_of UBERON:0001042 {source="ZFA"} ! chordate pharynx property_value: UBPROP:0000001 "Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001174", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0003364 name: epithelium of right lung namespace: uberon def: "An epithelium that is part of a right lung [Automatically generated definition]." [OBOL:automatic] synonym: "epithelial tissue of right lung" EXACT [OBOL:automatic] synonym: "right lung epithelial tissue" EXACT [OBOL:automatic] synonym: "right lung epithelium" EXACT [OBOL:automatic] xref: EMAPA:17663 xref: MA:0003132 is_a: UBERON:0000115 ! lung epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002167 ! right lung relationship: part_of UBERON:0002167 ! right lung [Term] id: UBERON:0003365 name: epithelium of left lung namespace: uberon def: "An epithelium that is part of a left lung [Automatically generated definition]." [OBOL:automatic] synonym: "epithelial tissue of left lung" EXACT [OBOL:automatic] synonym: "left lung epithelial tissue" EXACT [OBOL:automatic] synonym: "left lung epithelium" EXACT [OBOL:automatic] xref: EMAPA:17655 xref: MA:0003131 is_a: UBERON:0000115 ! lung epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002168 ! left lung relationship: part_of UBERON:0002168 ! left lung [Term] id: UBERON:0003371 name: pelvic appendage bud ectoderm namespace: uberon alt_id: UBERON:0005232 def: "An unilaminar epithelium that surrounds a pelvic appendage bud." [OBOL:automatic] synonym: "hindlimb bud ectoderm" NARROW SENSU [EMAPA:16780] synonym: "hindlimb bud ectoderm" NARROW SENSU [] synonym: "hindlimb ectoderm" EXACT [VHOG:0001048] synonym: "hindlimb ectoderm" NARROW SENSU [VHOG:0001048] synonym: "leg ectoderm" RELATED [OBOL:automatic] synonym: "lower limb bud ectoderm" NARROW SENSU [EHDAA2:0001034] synonym: "pelvic fin bud ectoderm" NARROW SENSU [] xref: EHDAA2:0001034 xref: EMAPA:16780 xref: VHOG:0001048 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: bounding_layer_of UBERON:0005420 ! pelvic appendage bud relationship: bounding_layer_of UBERON:0005420 ! pelvic appendage bud relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0005420 ! pelvic appendage bud [Term] id: UBERON:0003379 name: cardiac muscle of right atrium namespace: uberon def: "A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac muscle of cardiac right atrium" EXACT [OBOL:automatic] synonym: "cardiac muscle of heart right atrium" EXACT [OBOL:automatic] synonym: "cardiac muscle tissue of heart right atrium" EXACT [OBOL:automatic] synonym: "cardiac muscle tissue of right atrium" EXACT [OBOL:automatic] synonym: "cardiac muscle tissue of right atrium of heart" EXACT [OBOL:automatic] synonym: "myocardium of right atrium" EXACT [] synonym: "right atrium heart muscle" EXACT [EHDAA2:0004155] synonym: "right atrium myocardium" EXACT [VHOG:0001227] synonym: "textus muscularis of myocardium of right atrium" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium of right atrium of heart" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium of right cardiac atrium" EXACT [OBOL:automatic] xref: EHDAA2:0004155 xref: EMAPA:17326 xref: FMA:7282 xref: SCTID:362018002 xref: VHOG:0001227 is_a: UBERON:0004490 ! cardiac muscle tissue of atrium intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0002078 ! right cardiac atrium [Term] id: UBERON:0003380 name: cardiac muscle of left atrium namespace: uberon def: "A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac left atrium cardiac muscle" EXACT [OBOL:automatic] synonym: "cardiac left atrium cardiac muscle tissue" EXACT [OBOL:automatic] synonym: "cardiac muscle of cardiac left atrium" EXACT [OBOL:automatic] synonym: "cardiac muscle of heart left atrium" EXACT [OBOL:automatic] synonym: "cardiac muscle of left atrium of heart" EXACT [OBOL:automatic] synonym: "left atrium heart muscle" EXACT [EHDAA2:0004154] synonym: "left atrium myocardium" EXACT [VHOG:0001225] synonym: "myocardium of left atrium" EXACT [] synonym: "textus muscularis of myocardium of cardiac left atrium" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium of heart left atrium" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium of left atrium" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium of left atrium of heart" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium of left cardiac atrium" EXACT [OBOL:automatic] xref: EHDAA2:0004154 xref: EMAPA:17320 xref: FMA:7285 xref: SCTID:189936008 xref: VHOG:0001225 is_a: UBERON:0004490 ! cardiac muscle tissue of atrium intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002079 ! left cardiac atrium relationship: part_of UBERON:0002079 ! left cardiac atrium [Term] id: UBERON:0003381 name: cardiac muscle of right ventricle namespace: uberon def: "A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac muscle tissue of right ventricle" EXACT [FMA:83452] synonym: "right ventricle cardiac muscle" RELATED [VHOG:0001236] synonym: "right ventricular cardiac muscle tissue" EXACT [GO:0003221] xref: EMAPA:17342 xref: FMA:83452 xref: VHOG:0001236 is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: part_of UBERON:0002080 ! heart right ventricle [Term] id: UBERON:0003382 name: cardiac muscle of left ventricle namespace: uberon def: "A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac muscle tissue of left ventricle" EXACT [FMA:83453] synonym: "left ventricle cardiac muscle" RELATED [VHOG:0001234] synonym: "left ventricular cardiac muscle tissue" EXACT [GO:0003220] xref: EMAPA:17339 xref: FMA:83453 xref: VHOG:0001234 is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0002084 ! heart left ventricle [Term] id: UBERON:0003383 name: cardiac muscle tissue of interventricular septum namespace: uberon def: "A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac muscle of interventricular septum" EXACT [] synonym: "cardiac muscle tissue of interventricular septum" EXACT [FMA:84084] synonym: "interventricular septum cardiac muscle" EXACT [VHOG:0000999] synonym: "interventricular septum heart muscle" EXACT [EHDAA2:0004158] synonym: "interventricular septum muscle" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "interventricular septum myocardium" EXACT [VHOG:0000999] xref: EHDAA2:0004158 xref: EMAPA:17335 xref: FMA:84084 xref: VHOG:0000999 is_a: UBERON:0004492 ! cardiac muscle tissue of cardiac septum is_a: UBERON:0004667 ! interventricular septum muscular part intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002094 ! interventricular septum [Term] id: UBERON:0003384 name: skeletal muscle tissue of pharynx namespace: uberon def: "A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] synonym: "pharynx skeletal muscle" EXACT [OBOL:automatic] synonym: "pharynx skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of pharynx" EXACT [OBOL:automatic] xref: EMAPA:18963 is_a: UBERON:0004830 ! respiratory system skeletal muscle intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx [Term] id: UBERON:0003386 name: smooth muscle of eye namespace: uberon def: "any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi" [MGI:cwg, MP:0005247] subset: pheno_slim synonym: "ocular smooth muscle" EXACT [MA:0001268] xref: EMAPA:18807 xref: MA:0001268 is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: part_of UBERON:0000019 ! camera-type eye property_value: editor_note "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string [Term] id: UBERON:0003388 name: mesothelium of pericardial cavity namespace: uberon def: "A mesothelium that is part of a pericardium [Automatically generated definition]." [OBOL:automatic] synonym: "cavity of pericardial sac meso-epithelium" EXACT [OBOL:automatic] synonym: "cavity of pericardial sac mesothelium" EXACT [OBOL:automatic] synonym: "meso-epithelium of cavity of pericardial sac" EXACT [OBOL:automatic] synonym: "meso-epithelium of pericardial cavity" EXACT [OBOL:automatic] synonym: "mesothelium of cavity of pericardial sac" EXACT [OBOL:automatic] synonym: "pericardial cavity meso-epithelium" EXACT [OBOL:automatic] synonym: "pericardial cavity mesothelium" EXACT [OBOL:automatic] xref: RETIRED_EHDAA2:0001436 is_a: UBERON:0001136 ! mesothelium intersection_of: UBERON:0001136 ! mesothelium intersection_of: part_of UBERON:0002407 ! pericardium relationship: part_of UBERON:0002407 ! pericardium [Term] id: UBERON:0003406 name: cartilage of respiratory system namespace: uberon def: "A cartilage element that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius cartilage" EXACT [OBOL:automatic] synonym: "cartilage of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "respiratory system cartilage" EXACT [OBOL:automatic] xref: EMAPA:18694 xref: MA:0001818 is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003408 name: gland of digestive tract namespace: uberon def: "A gland that is part of a digestive tract [Automatically generated definition]." [OBOL:automatic] synonym: "digestive tract gland" EXACT [OBOL:automatic] synonym: "gland of digestive tract" EXACT [OBOL:automatic] synonym: "gland of lower gastrointestinal tract" EXACT [OBOL:automatic] synonym: "gut gland" EXACT [MA:0003202] synonym: "lower gastrointestinal tract gland" EXACT [OBOL:automatic] xref: EMAPA:18815 xref: MA:0003202 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002530 ! gland is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0003412 name: pelvic appendage bud mesenchyme namespace: uberon def: "Mesenchyme that is part of a pelvic appendage bud." [OBOL:automatic] synonym: "hindlimb bud mesenchyme" NARROW SENSU [EMAPA:16781] synonym: "leg mesenchyme" EXACT [OBOL:automatic] synonym: "lower limb bud mesenchyme" EXACT [EHDAA2:0001035] synonym: "mesoderm pelvic fin bud" NARROW SENSU [ZFA:0001386] synonym: "pelvic fin bud mesenchyme" NARROW SENSU [] xref: EHDAA2:0001035 xref: EMAPA:16781 xref: TAO:0001386 xref: ZFA:0001386 is_a: UBERON:0010329 ! paired limb/fin bud mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005420 ! pelvic appendage bud relationship: develops_from UBERON:0005730 ! pelvic appendage field relationship: part_of UBERON:0005420 ! pelvic appendage bud property_value: UBPROP:0000001 "Mesoderm part of pelvic fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001386", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0003426 name: dermis adipose tissue namespace: uberon def: "An adipose tissue that is part of a dermis [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "adipose tissue of dermis" EXACT [OBOL:automatic] synonym: "dermis fat tissue" EXACT [OBOL:automatic] synonym: "dermis fatty tissue" EXACT [OBOL:automatic] synonym: "fat tissue of dermis" EXACT [OBOL:automatic] synonym: "fatty tissue of dermis" EXACT [OBOL:automatic] xref: MA:0000798 is_a: UBERON:0001013 ! adipose tissue is_a: UBERON:0003585 ! dermis connective tissue intersection_of: UBERON:0001013 ! adipose tissue intersection_of: part_of UBERON:0002067 ! dermis [Term] id: UBERON:0003429 name: abdomen nerve namespace: uberon def: "A nerve that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] synonym: "nerve of abdomen" EXACT [OBOL:automatic] xref: MA:0000521 is_a: UBERON:0003825 ! nerve of abdominal segment intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen [Term] id: UBERON:0003430 name: neck nerve namespace: uberon def: "A nerve that is part of a neck [Automatically generated definition]." [OBOL:automatic] synonym: "neck (volume) nerve" EXACT [OBOL:automatic] synonym: "nerve of neck" EXACT [OBOL:automatic] synonym: "nerve of neck (volume)" EXACT [OBOL:automatic] xref: EMAPA:37263 {source="MA:th"} xref: MA:0000588 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0003439 name: nerve of trunk region namespace: uberon def: "A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk)." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class subset: non_informative synonym: "nerve of torso" EXACT [OBOL:automatic] synonym: "nerve of trunk" EXACT [OBOL:automatic] synonym: "torso nerve" EXACT [OBOL:automatic] synonym: "trunk nerve" RELATED [MA:0000515] xref: EMAPA:37264 {source="MA:th"} xref: MA:0000515 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0003443 name: thoracic cavity nerve namespace: uberon def: "A nerve that is located in a thoracic cavity [Automatically generated definition]." [OBOL:automatic] synonym: "cavity of chest nerve" EXACT [OBOL:automatic] synonym: "cavity of thorax nerve" EXACT [OBOL:automatic] synonym: "chest cavity nerve" EXACT [OBOL:automatic] synonym: "nerve of cavity of chest" EXACT [OBOL:automatic] synonym: "nerve of cavity of thorax" EXACT [OBOL:automatic] synonym: "nerve of chest cavity" EXACT [OBOL:automatic] synonym: "nerve of pectoral cavity" EXACT [OBOL:automatic] synonym: "nerve of thoracic cavity" EXACT [OBOL:automatic] synonym: "pectoral cavity nerve" EXACT [OBOL:automatic] xref: EMAPA:37267 {source="MA:th"} xref: MA:0000556 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: located_in UBERON:0002224 ! thoracic cavity relationship: located_in UBERON:0002224 ! thoracic cavity property_value: editor_note "consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve" xsd:string [Term] id: UBERON:0003444 name: pelvis nerve namespace: uberon def: "A nerve that is part of a pelvis [Automatically generated definition]." [OBOL:automatic] synonym: "nerve of pelvis" EXACT [OBOL:automatic] xref: EMAPA:37269 {source="MA:th"} xref: MA:0000542 is_a: UBERON:0003825 ! nerve of abdominal segment intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk [Term] id: UBERON:0003457 name: head bone namespace: uberon def: "A bone that is part of a head [Automatically generated definition]." [OBOL:automatic] comment: Different sources vary regarding which bones are craniofacial; e.g. hyoid bone subset: pheno_slim synonym: "adult head bone" EXACT [OBOL:automatic] synonym: "adult head bone organ" EXACT [OBOL:automatic] synonym: "bone of adult head" EXACT [OBOL:automatic] synonym: "bone of head" EXACT [OBOL:automatic] synonym: "bone organ of adult head" EXACT [OBOL:automatic] synonym: "bone organ of head" EXACT [OBOL:automatic] synonym: "craniofacial bone" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "head bone organ" EXACT [OBOL:automatic] xref: EMAPA:35996 xref: MA:0000576 xref: SCTID:118646007 is_a: UBERON:0007914 ! bone of craniocervical region intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head [Term] id: UBERON:0003458 name: neck bone namespace: uberon def: "A bone that is part of a neck [Automatically generated definition]." [OBOL:automatic] synonym: "bone of neck" EXACT [OBOL:automatic] synonym: "bone of neck (volume)" EXACT [OBOL:automatic] synonym: "bone organ of neck" EXACT [OBOL:automatic] synonym: "bone organ of neck (volume)" EXACT [OBOL:automatic] synonym: "neck (volume) bone" EXACT [OBOL:automatic] synonym: "neck (volume) bone organ" EXACT [OBOL:automatic] synonym: "neck bone organ" EXACT [OBOL:automatic] xref: EMAPA:37246 {source="MA:th"} xref: MA:0000584 xref: OpenCyc:Mx4rvnpJSJwpEbGdrcN5Y29ycA is_a: UBERON:0007914 ! bone of craniocervical region intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0003462 name: facial bone namespace: uberon def: "A bone that is part of a facial skeleton [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "bone of facial skeleton" EXACT [OBOL:automatic] synonym: "bone of viscerocranium" RELATED [OBOL:automatic] synonym: "facial bone" EXACT [EMAPA:19019] synonym: "facial skeleton bone" EXACT [OBOL:automatic] synonym: "viscerocranium bone" RELATED [OBOL:automatic] xref: EMAPA:19019 xref: EMAPA:35924 xref: MA:0001482 xref: MA:0003159 xref: NCIT:C63706 xref: SCTID:181799005 xref: UMLS:C0015455 {source="ncithesaurus:Facial_Bone"} is_a: UBERON:0003457 ! head bone is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0011156 ! facial skeleton relationship: part_of UBERON:0011156 {source="MA"} ! facial skeleton property_value: editor_note "test whether 'facial bone' is an exact synonym" xsd:string [Term] id: UBERON:0003463 name: trunk bone namespace: uberon def: "A bone that is part of a trunk [Automatically generated definition]." [OBOL:automatic] synonym: "bone of torso" EXACT [OBOL:automatic] synonym: "bone of trunk" EXACT [OBOL:automatic] synonym: "bone organ of torso" EXACT [OBOL:automatic] synonym: "bone organ of trunk" EXACT [OBOL:automatic] synonym: "torso bone" EXACT [OBOL:automatic] synonym: "torso bone organ" EXACT [OBOL:automatic] synonym: "trunk bone organ" EXACT [OBOL:automatic] xref: EMAPA:36583 xref: MA:0000512 xref: SCTID:427358002 is_a: UBERON:0001474 ! bone element is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0003469 name: respiratory system artery namespace: uberon def: "An artery that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37569 {source="MA:th"} xref: MA:0001804 is_a: UBERON:0001637 ! artery is_a: UBERON:0003643 ! respiratory system arterial blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003471 name: artery of lower lip namespace: uberon def: "The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery." [Wikipedia:Inferior_labial_artery] synonym: "arteria labialis inferior" EXACT LATIN [Wikipedia:Inferior_labial_artery] synonym: "inferior labial artery" EXACT [FMA:49567] synonym: "inferior labial branch of facial artery" EXACT [FMA:49567] synonym: "ramus labialis inferior (arteria facialis)" EXACT [FMA:TA] synonym: "ramus labialis inferior arteriae facialis" EXACT LATIN [Wikipedia:Inferior_labial_artery] xref: EMAPA:37429 {source="MA:th"} xref: FMA:49567 xref: MA:0001916 xref: SCTID:145036002 xref: Wikipedia:Inferior_labial_artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0004573 ! systemic artery is_a: UBERON:0009657 ! artery of lip is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0001835 ! lower lip relationship: branching_part_of UBERON:0001612 {source="FMA"} ! facial artery relationship: part_of UBERON:0001612 ! facial artery relationship: supplies UBERON:0001835 ! lower lip [Term] id: UBERON:0003473 name: thoracic cavity artery namespace: uberon def: "An artery that is part of a thoracic cavity[cjm]." [https://sourceforge.net/tracker/index.php?func=detail&aid=3317815&group_id=76834&atid=1205376] synonym: "thoracic artery" RELATED [MESH:A07.231.114.891] xref: EMAPA:37241 {source="MA:th"} xref: MA:0001902 xref: MESH:D013895 is_a: UBERON:0001637 ! artery is_a: UBERON:0003519 ! thoracic cavity blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: located_in UBERON:0002224 ! thoracic cavity property_value: UBPROP:0000012 "in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity" xsd:string {external_ontology="MA"} [Term] id: UBERON:0003476 name: respiratory system venous blood vessel namespace: uberon def: "A vein that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius vein" EXACT [OBOL:automatic] synonym: "respiratory system vein" EXACT [OBOL:automatic] synonym: "vein of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "vein of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37584 {source="MA:th"} xref: MA:0001809 xref: MA:0001810 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001004 ! respiratory system relationship: drains UBERON:0001004 ! respiratory system [Term] id: UBERON:0003478 name: vein of lower lip namespace: uberon def: "The inferior labial vein is the vein receiving blood from the lower lip." [Wikipedia:Inferior_labial_vein] synonym: "inferior labial vein" EXACT [FMA:52541] synonym: "lower lip vein" EXACT [OBOL:automatic] synonym: "vena labialis inferior" EXACT LATIN [] synonym: "venae labiales inferiores" RELATED LATIN [Wikipedia:Inferior_labial_vein] xref: EMAPA:37202 {source="MA:th"} xref: FMA:52541 xref: MA:0002253 xref: SCTID:422955002 xref: Wikipedia:Inferior_labial_vein is_a: UBERON:0013136 ! vein of lip intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001835 ! lower lip relationship: drains UBERON:0001835 ! lower lip property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png xsd:anyURI [Term] id: UBERON:0003479 name: thoracic cavity vein namespace: uberon def: "A vein that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] synonym: "cavity of chest vein" EXACT [OBOL:automatic] synonym: "cavity of thorax vein" EXACT [OBOL:automatic] synonym: "chest cavity vein" EXACT [OBOL:automatic] synonym: "pectoral cavity vein" EXACT [OBOL:automatic] synonym: "vein of cavity of chest" EXACT [OBOL:automatic] synonym: "vein of cavity of thorax" EXACT [OBOL:automatic] synonym: "vein of chest cavity" EXACT [OBOL:automatic] synonym: "vein of pectoral cavity" EXACT [OBOL:automatic] synonym: "vein of thoracic cavity" EXACT [OBOL:automatic] xref: EMAPA:37242 {source="MA:th"} xref: MA:0001903 is_a: UBERON:0001638 ! vein is_a: UBERON:0003519 ! thoracic cavity blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: located_in UBERON:0002224 ! thoracic cavity [Term] id: UBERON:0003489 name: respiratory system capillary endothelium namespace: uberon def: "An endothelium of capillary that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius blood capillary endothelium" EXACT [OBOL:automatic] synonym: "apparatus respiratorius capillary endothelium" EXACT [OBOL:automatic] synonym: "apparatus respiratorius capillary vessel endothelium" EXACT [OBOL:automatic] synonym: "apparatus respiratorius endothelium of blood capillary" EXACT [OBOL:automatic] synonym: "apparatus respiratorius endothelium of capillary" EXACT [OBOL:automatic] synonym: "apparatus respiratorius endothelium of capillary vessel" EXACT [OBOL:automatic] synonym: "blood capillary endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "blood capillary endothelium of respiratory system" EXACT [OBOL:automatic] synonym: "capillary endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "capillary endothelium of respiratory system" EXACT [OBOL:automatic] synonym: "capillary vessel endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "capillary vessel endothelium of respiratory system" EXACT [OBOL:automatic] synonym: "endothelium of blood capillary of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "endothelium of blood capillary of respiratory system" EXACT [OBOL:automatic] synonym: "endothelium of capillary of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "endothelium of capillary of respiratory system" EXACT [OBOL:automatic] synonym: "endothelium of capillary vessel of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "endothelium of capillary vessel of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system blood capillary endothelium" EXACT [OBOL:automatic] synonym: "respiratory system capillary vessel endothelium" EXACT [OBOL:automatic] synonym: "respiratory system endothelium of blood capillary" EXACT [OBOL:automatic] synonym: "respiratory system endothelium of capillary" EXACT [OBOL:automatic] synonym: "respiratory system endothelium of capillary vessel" EXACT [OBOL:automatic] xref: EMAPA:37575 {source="MA:th"} xref: MA:0001808 is_a: UBERON:0001915 ! endothelium of capillary is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0001915 ! endothelium of capillary intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003526 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system capillary [Term] id: UBERON:0003494 name: respiratory system venule namespace: uberon def: "A venule that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius venule" EXACT [OBOL:automatic] synonym: "venule of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "venule of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37587 {source="MA:th"} xref: MA:0001813 is_a: UBERON:0001979 ! venule is_a: UBERON:0003504 ! respiratory system blood vessel intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003495 name: respiratory system arteriole namespace: uberon def: "An arteriole that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37568 {source="MA:th"} xref: MA:0001803 is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003643 ! respiratory system arterial blood vessel intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003469 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system artery [Term] id: UBERON:0003496 name: head blood vessel namespace: uberon def: "A blood vessel that is part of a head [Automatically generated definition]." [OBOL:automatic] synonym: "adult head blood vessel" EXACT [OBOL:automatic] synonym: "blood vessel of adult head" EXACT [OBOL:automatic] synonym: "blood vessel of head" EXACT [OBOL:automatic] xref: EMAPA:36610 xref: MA:0000575 xref: SCTID:127865000 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0011362 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! cranial blood vasculature [Term] id: UBERON:0003497 name: abdomen blood vessel namespace: uberon def: "A blood vessel that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of abdomen" EXACT [OBOL:automatic] xref: MA:0000518 is_a: UBERON:0003835 ! abdominal segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen property_value: seeAlso UBERON:0012254 xsd:string {notes="abdominal aorta artery"} [Term] id: UBERON:0003498 name: heart blood vessel namespace: uberon def: "A blood vessel that is part of a heart [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "blood vessel of heart" EXACT [OBOL:automatic] synonym: "cardiac blood vessel" RELATED [EMAPA:35397] xref: EMAPA:35397 xref: MA:0002483 is_a: UBERON:0003834 ! thoracic segment blood vessel is_a: UBERON:0005985 ! coronary vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0018674 ! heart vasculature [Term] id: UBERON:0003499 name: brain blood vessel namespace: uberon def: "A blood vessel that is part of a brain [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "blood vessel of brain" EXACT [OBOL:automatic] xref: EMAPA:35182 xref: MA:0002769 is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0008998 ! vasculature of brain [Term] id: UBERON:0003500 name: corneal blood vessel namespace: uberon def: "A blood vessel that is part of a cornea [Automatically generated definition]." [https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/index.php?func=detail&aid=3564332&group_id=36855&atid=440764] synonym: "blood vessel of cornea" EXACT [OBOL:automatic] synonym: "cornea blood vessel" EXACT [OBOL:automatic] xref: EMAPA:36611 xref: MA:0001241 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea property_value: editor_note "follow up on tracker item" xsd:string property_value: RO:0002175 NCBITaxon:9775 {source="PMID:17051153"} [Term] id: UBERON:0003501 name: retina blood vessel namespace: uberon def: "A blood vessel that is part of a retina [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "blood vessel of inner layer of eyeball" EXACT [OBOL:automatic] synonym: "blood vessel of retina" EXACT [OBOL:automatic] synonym: "blood vessel of tunica interna of eyeball" EXACT [OBOL:automatic] synonym: "inner layer of eyeball blood vessel" EXACT [OBOL:automatic] synonym: "retinal blood vessel" EXACT [OBOL:automatic] synonym: "tunica interna of eyeball blood vessel" EXACT [OBOL:automatic] xref: EMAPA:36520 xref: GAID:509 xref: MA:0001317 xref: MESH:D012171 xref: SCTID:280692003 xref: XAO:0004153 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000966 ! retina relationship: contributes_to_morphology_of UBERON:0000966 ! retina relationship: part_of UBERON:0004864 ! vasculature of retina [Term] id: UBERON:0003502 name: neck blood vessel namespace: uberon def: "A blood vessel that is part of a neck [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of neck" EXACT [OBOL:automatic] synonym: "blood vessel of neck (volume)" EXACT [OBOL:automatic] synonym: "neck (volume) blood vessel" EXACT [OBOL:automatic] xref: EMAPA:37236 {source="MA:th"} xref: MA:0000583 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0003504 name: respiratory system blood vessel namespace: uberon def: "A blood vessel that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius blood vessel" EXACT [OBOL:automatic] synonym: "blood vessel of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "blood vessel of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:35731 xref: EMAPA:35995 xref: MA:0001799 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003509 name: arterial blood vessel namespace: uberon def: "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." [https://orcid.org/0000-0002-6601-2165] comment: only in MA - supertype of artery, arteriole, aorta. subset: pheno_slim xref: EMAPA:35144 xref: MA:0000061 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004572 ! arterial system relationship: part_of UBERON:0004572 ! arterial system [Term] id: UBERON:0003511 name: iris blood vessel namespace: uberon def: "A blood vessel that is part of a iris [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "blood vessel of iris" EXACT [OBOL:automatic] xref: EMAPA:37387 {source="MA:th"} xref: MA:0001290 xref: ZFA:0005568 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0004118 ! vasculature of iris [Term] id: UBERON:0003512 name: lung blood vessel namespace: uberon def: "A blood vessel that is part of a lung [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "blood vessel of lung" EXACT [OBOL:automatic] synonym: "pulmonary vascular element" RELATED [EMAPA:32867] xref: EMAPA:32867 xref: MA:0002457 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003504 ! respiratory system blood vessel is_a: UBERON:0003834 ! thoracic segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002048 ! lung relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: UBERON:0003513 name: trunk blood vessel namespace: uberon def: "A blood vessel that is part of a trunk [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of torso" EXACT [OBOL:automatic] synonym: "blood vessel of trunk" EXACT [OBOL:automatic] synonym: "torso blood vessel" EXACT [OBOL:automatic] xref: EMAPA:37237 {source="MA:th"} xref: MA:0000511 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0003519 name: thoracic cavity blood vessel namespace: uberon def: "A blood vessel that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of cavity of chest" EXACT [OBOL:automatic] synonym: "blood vessel of cavity of thorax" EXACT [OBOL:automatic] synonym: "blood vessel of chest cavity" EXACT [OBOL:automatic] synonym: "blood vessel of pectoral cavity" EXACT [OBOL:automatic] synonym: "blood vessel of thoracic cavity" EXACT [OBOL:automatic] synonym: "cavity of chest blood vessel" EXACT [OBOL:automatic] synonym: "cavity of thorax blood vessel" EXACT [OBOL:automatic] synonym: "chest cavity blood vessel" EXACT [OBOL:automatic] synonym: "pectoral cavity blood vessel" EXACT [OBOL:automatic] xref: EMAPA:37240 {source="MA:th"} xref: MA:0000554 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: located_in UBERON:0002224 ! thoracic cavity relationship: located_in UBERON:0002224 ! thoracic cavity [Term] id: UBERON:0003520 name: pelvis blood vessel namespace: uberon def: "A blood vessel that is part of a pelvis [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of pelvis" EXACT [OBOL:automatic] xref: EMAPA:37244 {source="MA:th"} xref: MA:0000531 is_a: UBERON:0003835 ! abdominal segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk [Term] id: UBERON:0003526 name: respiratory system capillary namespace: uberon def: "A capillary that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius blood capillary" EXACT [OBOL:automatic] synonym: "apparatus respiratorius capillary" EXACT [OBOL:automatic] synonym: "apparatus respiratorius capillary vessel" EXACT [OBOL:automatic] synonym: "blood capillary of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "blood capillary of respiratory system" EXACT [OBOL:automatic] synonym: "capillary of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "capillary of respiratory system" EXACT [OBOL:automatic] synonym: "capillary vessel of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "capillary vessel of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system blood capillary" EXACT [OBOL:automatic] synonym: "respiratory system capillary vessel" EXACT [OBOL:automatic] xref: EMAPA:37574 {source="MA:th"} xref: MA:0001807 is_a: UBERON:0001982 ! capillary is_a: UBERON:0003504 ! respiratory system blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003528 name: brain gray matter namespace: uberon def: "A gray matter that is part of a brain [Automatically generated definition]." [OBOL:automatic] synonym: "brain grey matter" EXACT [MA:0000810] synonym: "brain grey substance" EXACT [OBOL:automatic] synonym: "gray matter of brain" EXACT [OBOL:automatic] synonym: "grey matter of brain" EXACT [OBOL:automatic] synonym: "grey substance of brain" EXACT [OBOL:automatic] xref: EMAPA:35184 xref: MA:0000810 xref: NCIT:C49333 xref: UMLS:C1707348 {source="ncithesaurus:Cerebral_Gray_Matter"} is_a: UBERON:0002020 ! gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain [Term] id: UBERON:0003566 name: head connective tissue namespace: uberon def: "A portion of connective tissue that is part of a head [Automatically generated definition]." [OBOL:automatic] synonym: "adult head connective tissue" EXACT [OBOL:automatic] synonym: "adult head portion of connective tissue" EXACT [OBOL:automatic] synonym: "adult head textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of adult head" EXACT [OBOL:automatic] synonym: "connective tissue of head" EXACT [OBOL:automatic] synonym: "head portion of connective tissue" EXACT [OBOL:automatic] synonym: "head textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of adult head" EXACT [OBOL:automatic] synonym: "portion of connective tissue of head" EXACT [OBOL:automatic] synonym: "textus connectivus of adult head" EXACT [OBOL:automatic] synonym: "textus connectivus of head" EXACT [OBOL:automatic] xref: EMAPA:16098 xref: MA:0000577 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000033 ! head relationship: develops_from UBERON:0005253 ! head mesenchyme relationship: part_of UBERON:0000033 ! head relationship: transformation_of UBERON:0005253 ! head mesenchyme [Term] id: UBERON:0003567 name: abdomen connective tissue namespace: uberon def: "A portion of connective tissue that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] synonym: "abdomen portion of connective tissue" EXACT [OBOL:automatic] synonym: "abdomen textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of abdomen" EXACT [OBOL:automatic] synonym: "portion of connective tissue of abdomen" EXACT [OBOL:automatic] synonym: "textus connectivus of abdomen" EXACT [OBOL:automatic] xref: MA:0000519 is_a: UBERON:0003838 ! abdominal segment connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen [Term] id: UBERON:0003568 name: neck connective tissue namespace: uberon def: "A portion of connective tissue that is part of a neck [Automatically generated definition]." [OBOL:automatic] synonym: "connective tissue of neck" EXACT [OBOL:automatic] synonym: "connective tissue of neck (volume)" EXACT [OBOL:automatic] synonym: "neck (volume) connective tissue" EXACT [OBOL:automatic] synonym: "neck (volume) portion of connective tissue" EXACT [OBOL:automatic] synonym: "neck (volume) textus connectivus" EXACT [OBOL:automatic] synonym: "neck portion of connective tissue" EXACT [OBOL:automatic] synonym: "neck textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of neck" EXACT [OBOL:automatic] synonym: "portion of connective tissue of neck (volume)" EXACT [OBOL:automatic] synonym: "textus connectivus of neck" EXACT [OBOL:automatic] synonym: "textus connectivus of neck (volume)" EXACT [OBOL:automatic] xref: EMAPA:37250 {source="MA:th"} xref: MA:0000585 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0003570 name: respiratory system connective tissue namespace: uberon def: "A portion of connective tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius connective tissue" EXACT [OBOL:automatic] synonym: "apparatus respiratorius portion of connective tissue" EXACT [OBOL:automatic] synonym: "apparatus respiratorius textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "connective tissue of respiratory system" EXACT [OBOL:automatic] synonym: "portion of connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "portion of connective tissue of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system portion of connective tissue" EXACT [OBOL:automatic] synonym: "respiratory system textus connectivus" EXACT [OBOL:automatic] synonym: "textus connectivus of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "textus connectivus of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:35968 xref: EMAPA:35977 xref: MA:0001814 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003580 name: lower respiratory tract connective tissue namespace: uberon def: "A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] synonym: "connective tissue of lower respiratory tract" EXACT [OBOL:automatic] synonym: "lower respiratory tract portion of connective tissue" EXACT [OBOL:automatic] synonym: "lower respiratory tract textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of lower respiratory tract" EXACT [OBOL:automatic] synonym: "textus connectivus of lower respiratory tract" EXACT [OBOL:automatic] xref: EMAPA:37548 {source="MA:th"} xref: MA:0002409 is_a: UBERON:0003570 ! respiratory system connective tissue is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract [Term] id: UBERON:0003585 name: dermis connective tissue namespace: uberon def: "A portion of connective tissue that is part of a dermis [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "connective tissue of dermis" EXACT [OBOL:automatic] synonym: "dermis portion of connective tissue" EXACT [OBOL:automatic] synonym: "dermis textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of dermis" EXACT [OBOL:automatic] synonym: "textus connectivus of dermis" EXACT [OBOL:automatic] xref: EMAPA:36509 xref: MA:0000799 is_a: UBERON:0002384 ! connective tissue is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002067 ! dermis relationship: develops_from UBERON:0004016 ! dermatome relationship: part_of UBERON:0002067 ! dermis [Term] id: UBERON:0003586 name: trunk connective tissue namespace: uberon def: "A portion of connective tissue that is part of a trunk [Automatically generated definition]." [OBOL:automatic] synonym: "connective tissue of torso" EXACT [OBOL:automatic] synonym: "connective tissue of trunk" EXACT [OBOL:automatic] synonym: "portion of connective tissue of torso" EXACT [OBOL:automatic] synonym: "portion of connective tissue of trunk" EXACT [OBOL:automatic] synonym: "textus connectivus of torso" EXACT [OBOL:automatic] synonym: "textus connectivus of trunk" EXACT [OBOL:automatic] synonym: "torso connective tissue" EXACT [OBOL:automatic] synonym: "torso portion of connective tissue" EXACT [OBOL:automatic] synonym: "torso textus connectivus" EXACT [OBOL:automatic] synonym: "trunk portion of connective tissue" EXACT [OBOL:automatic] synonym: "trunk textus connectivus" EXACT [OBOL:automatic] xref: EMAPA:37252 {source="MA:th"} xref: MA:0000513 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0003593 name: thoracic cavity connective tissue namespace: uberon def: "A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] synonym: "cavity of chest connective tissue" EXACT [OBOL:automatic] synonym: "cavity of chest portion of connective tissue" EXACT [OBOL:automatic] synonym: "cavity of chest textus connectivus" EXACT [OBOL:automatic] synonym: "cavity of thorax connective tissue" EXACT [OBOL:automatic] synonym: "cavity of thorax portion of connective tissue" EXACT [OBOL:automatic] synonym: "cavity of thorax textus connectivus" EXACT [OBOL:automatic] synonym: "chest cavity connective tissue" EXACT [OBOL:automatic] synonym: "chest cavity portion of connective tissue" EXACT [OBOL:automatic] synonym: "chest cavity textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of cavity of chest" EXACT [OBOL:automatic] synonym: "connective tissue of cavity of thorax" EXACT [OBOL:automatic] synonym: "connective tissue of chest cavity" EXACT [OBOL:automatic] synonym: "connective tissue of pectoral cavity" EXACT [OBOL:automatic] synonym: "connective tissue of thoracic cavity" EXACT [OBOL:automatic] synonym: "pectoral cavity connective tissue" EXACT [OBOL:automatic] synonym: "pectoral cavity portion of connective tissue" EXACT [OBOL:automatic] synonym: "pectoral cavity textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of cavity of chest" EXACT [OBOL:automatic] synonym: "portion of connective tissue of cavity of thorax" EXACT [OBOL:automatic] synonym: "portion of connective tissue of chest cavity" EXACT [OBOL:automatic] synonym: "portion of connective tissue of pectoral cavity" EXACT [OBOL:automatic] synonym: "portion of connective tissue of thoracic cavity" EXACT [OBOL:automatic] synonym: "textus connectivus of cavity of chest" EXACT [OBOL:automatic] synonym: "textus connectivus of cavity of thorax" EXACT [OBOL:automatic] synonym: "textus connectivus of chest cavity" EXACT [OBOL:automatic] synonym: "textus connectivus of pectoral cavity" EXACT [OBOL:automatic] synonym: "textus connectivus of thoracic cavity" EXACT [OBOL:automatic] synonym: "thoracic cavity portion of connective tissue" EXACT [OBOL:automatic] synonym: "thoracic cavity textus connectivus" EXACT [OBOL:automatic] xref: EMAPA:37255 {source="MA:th"} xref: MA:0000555 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: located_in UBERON:0002224 ! thoracic cavity relationship: located_in UBERON:0002224 ! thoracic cavity [Term] id: UBERON:0003594 name: pelvis connective tissue namespace: uberon def: "A portion of connective tissue that is part of a pelvis [Automatically generated definition]." [OBOL:automatic] synonym: "connective tissue of pelvis" EXACT [OBOL:automatic] synonym: "pelvis portion of connective tissue" EXACT [OBOL:automatic] synonym: "pelvis textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of pelvis" EXACT [OBOL:automatic] synonym: "textus connectivus of pelvis" EXACT [OBOL:automatic] xref: EMAPA:37257 {source="MA:th"} xref: MA:0000533 is_a: UBERON:0003838 ! abdominal segment connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk [Term] id: UBERON:0003601 name: neck cartilage namespace: uberon def: "A cartilage that is part of a neck [Automatically generated definition]." [OBOL:automatic] synonym: "cartilage of neck" EXACT [OBOL:automatic] synonym: "cartilage of neck (volume)" EXACT [OBOL:automatic] synonym: "neck (volume) cartilage" EXACT [OBOL:automatic] xref: EMAPA:37251 {source="MA:th"} xref: MA:0000586 is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0003603 name: lower respiratory tract cartilage namespace: uberon def: "A cartilage that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] synonym: "cartilage of lower respiratory tract" EXACT [OBOL:automatic] xref: EMAPA:37547 {source="MA:th"} xref: MA:0001819 xref: NCIT:C49256 xref: UMLS:C1708759 {source="ncithesaurus:Lower_Respiratory_Tract_Cartilage"} is_a: UBERON:0003406 ! cartilage of respiratory system is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract [Term] id: UBERON:0003605 name: eye skin gland namespace: uberon def: "A skin gland that is part of a camera-type eye [Automatically generated definition]." [OBOL:automatic] subset: organ_slim synonym: "camera-type eye skin gland" EXACT [OBOL:automatic] synonym: "camera-type eye skin glands" EXACT [OBOL:automatic] synonym: "camera-type eye skin glands set" EXACT [OBOL:automatic] synonym: "skin gland of camera-type eye" EXACT [OBOL:automatic] synonym: "skin gland of vertebrate eye" EXACT [OBOL:automatic] synonym: "skin glands of camera-type eye" EXACT [OBOL:automatic] synonym: "skin glands of vertebrate eye" EXACT [OBOL:automatic] synonym: "skin glands set of camera-type eye" EXACT [OBOL:automatic] synonym: "skin glands set of vertebrate eye" EXACT [OBOL:automatic] synonym: "vertebrate eye skin gland" EXACT [OBOL:automatic] synonym: "vertebrate eye skin glands" EXACT [OBOL:automatic] synonym: "vertebrate eye skin glands set" EXACT [OBOL:automatic] xref: EMAPA:37530 {source="MA:th"} xref: MA:0002451 is_a: UBERON:0002419 ! skin gland is_a: UBERON:0004859 ! eye gland is_a: UBERON:0015152 ! gland of ocular region intersection_of: UBERON:0002419 ! skin gland intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye [Term] id: UBERON:0003609 name: aorta elastic tissue namespace: uberon def: "The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall." [MP:0009862] subset: pheno_slim synonym: "adult aorta elastic connective tissue" EXACT [OBOL:automatic] synonym: "adult aorta elastic tissue" EXACT [OBOL:automatic] synonym: "adult aorta textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "aorta elastic connective tissue" EXACT [OBOL:automatic] synonym: "aorta elastic lamina" EXACT [MP:0009862] synonym: "aorta elastic laminae" EXACT PLURAL [MP:0009862] synonym: "aorta textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "dorsal aorta elastic connective tissue" EXACT [OBOL:automatic] synonym: "dorsal aorta elastic tissue" EXACT [OBOL:automatic] synonym: "dorsal aorta textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "elastic connective tissue of adult aorta" EXACT [OBOL:automatic] synonym: "elastic connective tissue of aorta" EXACT [OBOL:automatic] synonym: "elastic connective tissue of dorsal aorta" EXACT [OBOL:automatic] synonym: "elastic connective tissue of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "elastic tissue of adult aorta" EXACT [OBOL:automatic] synonym: "elastic tissue of aorta" EXACT [OBOL:automatic] synonym: "elastic tissue of dorsal aorta" EXACT [OBOL:automatic] synonym: "elastic tissue of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of adult aorta" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of aorta" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of dorsal aorta" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "trunk of aortic tree elastic connective tissue" EXACT [OBOL:automatic] synonym: "trunk of aortic tree elastic tissue" EXACT [OBOL:automatic] synonym: "trunk of aortic tree textus connectivus elasticus" EXACT [OBOL:automatic] xref: MA:0002859 is_a: UBERON:0003614 ! blood vessel elastic tissue intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta [Term] id: UBERON:0003610 name: heart elastic tissue namespace: uberon def: "The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers." [MP:0009863] subset: pheno_slim synonym: "cardiac elastic tissue" EXACT [MP:0009863] synonym: "elastic connective tissue of heart" EXACT [OBOL:automatic] synonym: "elastic tissue of heart" EXACT [OBOL:automatic] synonym: "heart elastic connective tissue" EXACT [OBOL:automatic] synonym: "heart textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of heart" EXACT [OBOL:automatic] xref: MA:0002858 is_a: UBERON:0003613 ! cardiovascular system elastic tissue is_a: UBERON:0003837 ! thoracic segment connective tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart [Term] id: UBERON:0003611 name: respiratory system elastic tissue namespace: uberon def: "An elastic tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius elastic connective tissue" EXACT [OBOL:automatic] synonym: "apparatus respiratorius elastic tissue" EXACT [OBOL:automatic] synonym: "apparatus respiratorius textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "elastic connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "elastic connective tissue of respiratory system" EXACT [OBOL:automatic] synonym: "elastic tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "elastic tissue of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system elastic connective tissue" EXACT [OBOL:automatic] synonym: "respiratory system textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37579 {source="MA:th"} xref: MA:0001820 is_a: UBERON:0002521 ! elastic tissue is_a: UBERON:0003570 ! respiratory system connective tissue intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0004777 ! respiratory system submucosa [Term] id: UBERON:0003613 name: cardiovascular system elastic tissue namespace: uberon def: "An elastic tissue that is part of a circulatory system [Automatically generated definition]." [OBOL:automatic] synonym: "cardiovascular system elastic connective tissue" EXACT [OBOL:automatic] synonym: "cardiovascular system textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "circulatory system elastic connective tissue" EXACT [OBOL:automatic] synonym: "circulatory system elastic tissue" EXACT [OBOL:automatic] synonym: "circulatory system textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "elastic connective tissue of cardiovascular system" EXACT [OBOL:automatic] synonym: "elastic connective tissue of circulatory system" EXACT [OBOL:automatic] synonym: "elastic tissue of cardiovascular system" EXACT [OBOL:automatic] synonym: "elastic tissue of circulatory system" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of cardiovascular system" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of circulatory system" EXACT [OBOL:automatic] xref: MA:0002857 is_a: UBERON:0002521 ! elastic tissue intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0001009 ! circulatory system relationship: part_of UBERON:0004535 ! cardiovascular system [Term] id: UBERON:0003614 name: blood vessel elastic tissue namespace: uberon def: "Elastic tissue layer that lines a blood vessel layer." [http://orcid.org/0000-0002-6601-2165, https://sourceforge.net/p/obo/mammalian-phenotype-requests/2026/] subset: pheno_slim synonym: "blood vessel elastic connective tissue" EXACT [OBOL:automatic] synonym: "blood vessel textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "elastic connective tissue of blood vessel" EXACT [OBOL:automatic] synonym: "elastic lamina" BROAD [MP:0006083] synonym: "elastic laminae" BROAD PLURAL [MP:0006083] synonym: "elastic tissue of blood vessel" EXACT [OBOL:automatic] synonym: "textus connectivus elasticus of blood vessel" EXACT [OBOL:automatic] synonym: "vascular elastic lamina" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "vascular elastic laminae" EXACT PLURAL [http://orcid.org/0000-0002-6601-2165] synonym: "vascular elastic tissue" EXACT [MP:0006083] xref: EMAPA:36300 xref: MA:0002856 is_a: UBERON:0003613 ! cardiovascular system elastic tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel [Term] id: UBERON:0003615 name: lung elastic tissue namespace: uberon def: "Elastic tissue that is part of a lung [Automatically generated definition]." [OBOL:automatic] synonym: "elastic connective tissue of lung" EXACT [OBOL:automatic] synonym: "elastic tissue of lung" EXACT [OBOL:automatic] synonym: "lung elastic connective tissue" EXACT [OBOL:automatic] synonym: "lung textus connectivus elasticus" EXACT [OBOL:automatic] synonym: "pulmonary elastic fiber" NARROW [http://orcid.org/0000-0002-6601-2165] synonym: "textus connectivus elasticus of lung" EXACT [OBOL:automatic] xref: MA:0002860 is_a: UBERON:0000114 ! lung connective tissue is_a: UBERON:0003611 ! respiratory system elastic tissue intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0002048 ! lung [Term] id: UBERON:0003618 name: aorta tunica media namespace: uberon def: "The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers." [MP:0009873] subset: pheno_slim synonym: "adult aorta tunica media" EXACT [OBOL:automatic] synonym: "dorsal aorta tunica media" EXACT [OBOL:automatic] synonym: "trunk of aortic tree tunica media" EXACT [OBOL:automatic] synonym: "tunica media of adult aorta" EXACT [OBOL:automatic] synonym: "tunica media of aorta" EXACT [OBOL:automatic] synonym: "tunica media of dorsal aorta" EXACT [OBOL:automatic] synonym: "tunica media of trunk of aortic tree" EXACT [OBOL:automatic] xref: EMAPA:35138 xref: FMA:74433 xref: MA:0002903 xref: SCTID:48467007 is_a: UBERON:0002522 ! tunica media intersection_of: UBERON:0002522 ! tunica media intersection_of: part_of UBERON:0000947 ! aorta relationship: contributes_to_morphology_of UBERON:0004663 ! aorta wall relationship: part_of UBERON:0004663 ! aorta wall [Term] id: UBERON:0003619 name: aorta tunica intima namespace: uberon def: "The innermost layer of the aorta, containing the endothelium and an inner elastic membrane." [MP:0009872] subset: pheno_slim synonym: "adult aorta tunica intima" EXACT [OBOL:automatic] synonym: "dorsal aorta tunica intima" EXACT [OBOL:automatic] synonym: "trunk of aortic tree tunica intima" EXACT [OBOL:automatic] synonym: "tunica intima of adult aorta" EXACT [OBOL:automatic] synonym: "tunica intima of aorta" EXACT [OBOL:automatic] synonym: "tunica intima of dorsal aorta" EXACT [OBOL:automatic] synonym: "tunica intima of trunk of aortic tree" EXACT [OBOL:automatic] xref: BTO:0005553 xref: EMAPA:35137 xref: FMA:74419 xref: MA:0002904 xref: SCTID:362031007 is_a: UBERON:0002523 ! tunica intima is_a: UBERON:0004797 ! blood vessel layer intersection_of: UBERON:0002523 ! tunica intima intersection_of: part_of UBERON:0000947 ! aorta relationship: contributes_to_morphology_of UBERON:0004663 ! aorta wall relationship: part_of UBERON:0004663 ! aorta wall [Term] id: UBERON:0003643 name: respiratory system arterial blood vessel namespace: uberon def: "An arterial blood vessel that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37565 {source="MA:th"} xref: MA:0001800 is_a: UBERON:0003504 ! respiratory system blood vessel is_a: UBERON:0003509 ! arterial blood vessel intersection_of: UBERON:0003509 ! arterial blood vessel intersection_of: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003684 name: abdominal cavity namespace: uberon def: "The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity)." [UBERON:cjm] subset: efo_slim synonym: "cavitas abdominis" RELATED LATIN [Wikipedia:Abdominal_cavity] synonym: "cavitas abdominis" RELATED [GAID:17] synonym: "cavity of abdominal compartment" EXACT [FMA:12266] synonym: "cavity of compartment of abdomen" EXACT [FMA:12266] synonym: "space of abdominal compartment" EXACT [FMA:12266] xref: EFO:0000213 xref: EMAPA:36505 xref: FMA:12266 xref: GAID:17 xref: galen:AbdominalCavity xref: MA:0003057 xref: MESH:A01.047.025 xref: NCIT:C12664 xref: OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA xref: SCTID:361294009 xref: UMLS:C0230168 {source="ncithesaurus:Abdominal_Cavity"} xref: Wikipedia:Abdominal_cavity is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0000916 ! abdomen intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen relationship: luminal_space_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0035819 ! abdominopelvic cavity property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg xsd:anyURI property_value: UBPROP:0000012 "in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003687 name: foramen magnum namespace: uberon def: "In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]." [Wikipedia:Foramen_magnum] comment: Design pattern notes: check whether this fits the foramen design pattern subset: pheno_slim subset: vertebrate_core xref: AAO:0010826 xref: EMAPA:37868 {source="MA:th"} xref: FMA:75306 xref: GAID:228 xref: MESH:D005539 xref: NCIT:C12495 xref: OpenCyc:Mx4rwOm-FpwpEbGdrcN5Y29ycA xref: SCTID:244679008 xref: TAO:0002045 xref: UMLS:C0016519 {source="ncithesaurus:Foramen_Magnum"} xref: Wikipedia:Foramen_magnum xref: ZFA:0005387 is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull intersection_of: conduit_for UBERON:0001896 ! medulla oblongata relationship: conduit_for UBERON:0001896 ! medulla oblongata relationship: located_in UBERON:0001676 ! occipital bone property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png xsd:anyURI property_value: UBPROP:0000001 "Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002045", ontology="TAO", source="TAO:wd"} [Term] id: UBERON:0003697 name: abdominal wall namespace: uberon def: "The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles." [ncithesaurus:Abdominal_Wall] subset: pheno_slim synonym: "abdominal wall proper" RELATED [FMA:10429] synonym: "layers of the abdominal wall" RELATED [Wikipedia:Abdominal_wall] synonym: "paries abdominalis" EXACT [Wikipedia:Abdominal_wall] synonym: "paries abdominalis" RELATED LATIN [Wikipedia:Abdominal_wall] synonym: "wall of abdomen" EXACT [FMA:259054] synonym: "wall of abdomen proper" EXACT [FMA:10429] xref: EMAPA:37064 {source="MA:th"} xref: FMA:10429 xref: FMA:259054 xref: GAID:26 xref: MESH:A01.047.050 xref: NCIT:C77608 xref: SCTID:181613000 xref: UMLS:C0836916 {source="ncithesaurus:Abdominal_Wall"} xref: Wikipedia:Abdominal_wall is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg xsd:anyURI [Term] id: UBERON:0003714 name: neural tissue namespace: uberon def: "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature." [FMA:9642] synonym: "nerve tissue" EXACT [FMA:9642] synonym: "nervous tissue" EXACT [FMA:9642] synonym: "portion of neural tissue" EXACT [FMA:9642] xref: AAO:0000325 xref: AEO:0000123 xref: EHDAA2:0003123 xref: FMA:9642 xref: GAID:609 xref: MESH:D009417 xref: NCIT:C13052 xref: OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ xref: SCTID:91728009 xref: UMLS:C0027757 {source="ncithesaurus:Nervous_Tissue"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: has_part CL:0000125 ! glial cell intersection_of: has_part CL:0000540 ! neuron disjoint_from: UBERON:0004755 ! skeletal tissue relationship: has_part CL:0000125 ! glial cell relationship: has_part CL:0000540 ! neuron relationship: part_of UBERON:0001016 ! nervous system property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000325", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000012 "FMA definition includes vasculature" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003729 name: mouth mucosa namespace: uberon def: "A mucous membrane that lines the mouth." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "buccal mucosa" RELATED [GAID:951] synonym: "mouth mucosa" EXACT [FMA:59660] synonym: "mouth mucous membrane" EXACT [OBOL:accepted] synonym: "mouth organ mucosa" EXACT [OBOL:accepted] synonym: "mucosa of mouth" EXACT [OBOL:accepted] synonym: "mucosal lining of mouth" RELATED [MA:0002794] synonym: "mucous membrane of mouth" EXACT [FMA:59660] synonym: "oral mucosa" RELATED [GAID:951] synonym: "oral mucous membrane" EXACT [] synonym: "oral part of viscerocranial mucosa" EXACT [FMA:59660] synonym: "tunica mucosa oris" EXACT LATIN [FMA:59660, FMA:TA] synonym: "tunica mucosa oris" RELATED LATIN [Wikipedia:Oral_mucosa] xref: BTO:0002860 xref: CALOHA:TS-0716 xref: EMAPA:26937 xref: FMA:59660 xref: GAID:951 xref: MA:0002794 xref: MESH:D009061 xref: NCIT:C77637 xref: UMLS:C0026639 {source="ncithesaurus:Oral_Mucosa"} xref: Wikipedia:Oral_mucosa is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000344 ! mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000165 ! mouth relationship: bounding_layer_of UBERON:0000165 ! mouth relationship: continuous_with UBERON:0000355 ! pharyngeal mucosa relationship: continuous_with UBERON:0001458 ! skin of lip relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system relationship: part_of UBERON:0000165 ! mouth property_value: IAO:0000232 "this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)" xsd:string property_value: UBPROP:0000001 "the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]." xsd:string {source="Wikipedia:Oral_mucosa"} [Term] id: UBERON:0003824 name: nerve of thoracic segment namespace: uberon def: "A nerve that is part of a thorax [Automatically generated definition]." [OBOL:automatic] synonym: "nerve of thorax" EXACT [OBOL:automatic] synonym: "thoracic segment nerve" EXACT [MA:0000562] synonym: "thorax nerve" EXACT [OBOL:automatic] synonym: "upper body nerve" RELATED [MA:0000562] xref: EMAPA:37265 {source="MA:th"} xref: MA:0000562 xref: MESH:D013900 xref: SCTID:359876006 is_a: UBERON:0003439 ! nerve of trunk region intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0003825 name: nerve of abdominal segment namespace: uberon def: "A nerve that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] synonym: "abdominal segment nerve" EXACT [MA:0000528] xref: EMAPA:37061 {source="MA:th"} xref: MA:0000528 is_a: UBERON:0003439 ! nerve of trunk region intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0003827 name: thoracic segment bone namespace: uberon def: "A bone that is part of a thorax [Automatically generated definition]." [OBOL:automatic] synonym: "bone of thorax" EXACT [OBOL:automatic] synonym: "bone organ of thorax" EXACT [OBOL:automatic] synonym: "thorax bone" EXACT [OBOL:automatic] synonym: "thorax bone organ" EXACT [OBOL:automatic] synonym: "upper body bone" RELATED [MA:0000559] xref: EMAPA:37247 {source="MA:th"} xref: MA:0000559 xref: SCTID:426649006 is_a: UBERON:0003463 ! trunk bone is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0003828 name: abdominal segment bone namespace: uberon def: "A bone that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] synonym: "abdominal segment of trunk bone" EXACT [OBOL:automatic] synonym: "abdominal segment of trunk bone organ" EXACT [OBOL:automatic] synonym: "bone of abdominal segment of trunk" EXACT [OBOL:automatic] synonym: "bone organ of abdominal segment of trunk" EXACT [OBOL:automatic] xref: EMAPA:37058 {source="MA:th"} xref: MA:0000525 is_a: UBERON:0003463 ! trunk bone is_a: UBERON:0005173 ! abdominal segment element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0003830 name: thoracic segment muscle namespace: uberon def: "Any muscle organ that is part of a thorax [Automatically generated definition]." [OBOL:automatic] synonym: "muscle organ of thorax" EXACT [OBOL:automatic] synonym: "thorax muscle organ" EXACT [OBOL:automatic] synonym: "upper body muscle" RELATED [MA:0000561] xref: MA:0000561 is_a: UBERON:0001774 ! skeletal muscle of trunk is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0004464 {source="prolog"} ! musculature of thorax [Term] id: UBERON:0003831 name: respiratory system muscle namespace: uberon def: "Any muscle organ that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "muscle organ of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system muscle organ" EXACT [OBOL:automatic] xref: EMAPA:35733 xref: MA:0001828 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0003832 name: esophagus muscle namespace: uberon def: "Any muscle organ that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophageal muscle" EXACT [] synonym: "esophagus muscle organ" EXACT [OBOL:automatic] synonym: "gullet muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of esophagus" EXACT [OBOL:automatic] synonym: "muscle organ of gullet" EXACT [OBOL:automatic] synonym: "muscle organ of oesophagus" EXACT [OBOL:automatic] synonym: "oesophagus muscle organ" EXACT [OBOL:automatic] xref: EMAPA:26983 xref: MA:0002682 xref: SCTID:360961009 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 {source="MA"} ! wall of esophagus property_value: editor_note "merge muscle and muscle layer?" xsd:string [Term] id: UBERON:0003833 name: abdominal segment muscle namespace: uberon def: "A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] synonym: "abdominal segment of trunk muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of abdominal segment of trunk" EXACT [OBOL:automatic] xref: EMAPA:37060 {source="MA:th"} xref: MA:0000527 is_a: UBERON:0001774 ! skeletal muscle of trunk is_a: UBERON:0005173 ! abdominal segment element intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0003834 name: thoracic segment blood vessel namespace: uberon def: "A blood vessel that is part of a thorax [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of thorax" EXACT [OBOL:automatic] synonym: "thorax blood vessel" EXACT [OBOL:automatic] synonym: "upper body blood vessel" RELATED [MA:0000558] xref: EMAPA:37238 {source="MA:th"} xref: MA:0000558 is_a: UBERON:0003513 ! trunk blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0003835 name: abdominal segment blood vessel namespace: uberon def: "A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] synonym: "abdominal segment of trunk blood vessel" EXACT [OBOL:automatic] synonym: "blood vessel of abdominal segment of trunk" EXACT [OBOL:automatic] xref: EMAPA:37057 {source="MA:th"} xref: MA:0000524 is_a: UBERON:0003513 ! trunk blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0003836 name: abdominal segment skin namespace: uberon def: "A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] synonym: "abdominal segment of trunk skin" EXACT [OBOL:automatic] synonym: "skin of abdominal segment of trunk" EXACT [OBOL:automatic] xref: EMAPA:37063 {source="MA:th"} xref: FMA:264898 xref: MA:0000530 is_a: UBERON:0001085 ! skin of trunk intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0003837 name: thoracic segment connective tissue namespace: uberon def: "A portion of connective tissue that is part of a thorax [Automatically generated definition]." [OBOL:automatic] synonym: "connective tissue of thorax" EXACT [OBOL:automatic] synonym: "portion of connective tissue of thorax" EXACT [OBOL:automatic] synonym: "textus connectivus of thorax" EXACT [OBOL:automatic] synonym: "thorax connective tissue" EXACT [OBOL:automatic] synonym: "thorax portion of connective tissue" EXACT [OBOL:automatic] synonym: "thorax textus connectivus" EXACT [OBOL:automatic] synonym: "upper body connective tissue" RELATED [MA:0000560] xref: EMAPA:37253 {source="MA:th"} xref: MA:0000560 is_a: UBERON:0003586 ! trunk connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0003838 name: abdominal segment connective tissue namespace: uberon def: "A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] synonym: "abdominal segment of trunk connective tissue" EXACT [OBOL:automatic] synonym: "abdominal segment of trunk portion of connective tissue" EXACT [OBOL:automatic] synonym: "abdominal segment of trunk textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of abdominal segment of trunk" EXACT [OBOL:automatic] synonym: "portion of connective tissue of abdominal segment of trunk" EXACT [OBOL:automatic] synonym: "textus connectivus of abdominal segment of trunk" EXACT [OBOL:automatic] xref: EMAPA:37059 {source="MA:th"} xref: MA:0000526 is_a: UBERON:0003586 ! trunk connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0003842 name: neural tube lumen namespace: uberon alt_id: UBERON:0005713 def: "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] synonym: "cavity of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "central lumen" RELATED [] synonym: "lumen of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "neural lumen" RELATED [EHDAA:2889] synonym: "neural tube neural lumen" EXACT [EHDAA2:0001269] synonym: "neurocoel" RELATED [VHOG:0001119] synonym: "prosencoel" NARROW [] xref: AAO:0011073 xref: EHDAA2:0001269 xref: EHDAA:2889 xref: EHDAA:914 xref: EMAPA:16167 xref: VHOG:0001119 xref: XAO:0000252 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0001049 ! neural tube relationship: luminal_space_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001119", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003848 name: gonadal vein namespace: uberon def: "In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]." [Wikipedia:Gonadal_vein] synonym: "gonad vein" EXACT [OBOL:automatic] synonym: "gonada vein" EXACT [OBOL:automatic] synonym: "vein of gonad" EXACT [OBOL:automatic] synonym: "vein of gonada" EXACT [OBOL:automatic] xref: EHDAA2:0000719 xref: EHDAA:8703 xref: OpenCyc:Mx4rvlWYh5wpEbGdrcN5Y29ycA xref: SCTID:278192008 xref: VHOG:0001340 xref: Wikipedia:Gonadal_vein is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: attaches_to UBERON:0000991 ! gonad relationship: attaches_to UBERON:0000991 ! gonad property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png xsd:anyURI [Term] id: UBERON:0003849 name: mesencephalic neural crest namespace: uberon def: "A neural crest that has_potential_to_developmentally_contribute_to a midbrain." [OBOL:automatic] subset: efo_slim subset: vertebrate_core synonym: "mesencephalic neural crest" EXACT [ZFA:0000935] synonym: "neural crest midbrain" EXACT [ZFA:0000935] xref: EFO:0003591 xref: EHDAA2:0001101 xref: EHDAA:360 xref: TAO:0000935 xref: VHOG:0000796 xref: ZFA:0000935 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain relationship: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000796", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003852 name: rhombencephalon neural crest namespace: uberon def: "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain." [OBOL:automatic] subset: vertebrate_core synonym: "neural crest hindbrain" EXACT [ZFA:0007063] synonym: "rhombencephalic neural crest" EXACT [ZFA:0007063] synonym: "rhombomere neural crest" RELATED [EMAPA:35747] xref: EHDAA2:0001628 xref: EHDAA:362 xref: EMAPA:35747 xref: TAO:0007063 xref: VHOG:0001210 xref: ZFA:0007063 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain relationship: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain property_value: UBPROP:0000001 "Cranial neural crest that is part of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007063", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001210", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003853 name: spinal cord neural crest namespace: uberon def: "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord." [OBOL:automatic] synonym: "neural crest spinal cord" EXACT [VHOG:0001006] synonym: "spinal neural crest" RELATED [VHOG:0001006] xref: EHDAA:696 xref: EMAPA:16163 xref: EMAPA:16881 xref: VHOG:0001006 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord relationship: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001006", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003854 name: spinal cord neural plate namespace: uberon def: "A neural plate that develops_from a future spinal cord." [OBOL:automatic] synonym: "neural plate of spinal cord" EXACT [OBOL:automatic] xref: FMA:312957 xref: TAO:0007021 xref: VHOG:0000439 xref: ZFA:0007021 is_a: UBERON:0003075 ! neural plate intersection_of: UBERON:0003075 ! neural plate intersection_of: develops_from UBERON:0006241 ! future spinal cord relationship: develops_from UBERON:0006241 {source="ZFA"} ! future spinal cord property_value: UBPROP:0000001 "Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000439", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000439", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003855 name: gonad mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing gonad [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "gonada mesenchyme" EXACT [OBOL:automatic] synonym: "mesenchyme of gonad" EXACT [OBOL:automatic] synonym: "mesenchyme of gonada" EXACT [OBOL:automatic] xref: EHDAA:5012 xref: EMAPA:16858 xref: EMAPA:17385 xref: VHOG:0001090 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000991 ! gonad relationship: part_of UBERON:0000991 ! gonad [Term] id: UBERON:0003886 name: future coelemic cavity lumen namespace: uberon def: "An anatomical cavity that has the potential to develop into a coelemic cavity lumen." [OBOL:automatic] subset: grouping_class subset: non_informative synonym: "body cavity precursor" RELATED [] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen relationship: existence_ends_during UBERON:0000111 ! organogenesis stage relationship: existence_starts_during UBERON:0000109 ! gastrula stage relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm [Term] id: UBERON:0003887 name: intraembryonic coelom namespace: uberon def: "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom" [MGI:anna, MP:0012187] subset: pheno_slim synonym: "somatic coelom" EXACT [Wikipedia:Intraembryonic_coelom] xref: EHDAA:251 xref: EMAPA:16088 xref: NCIT:C34195 xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003891 name: stroma namespace: uberon def: "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "stromal connective tissue" RELATED [] xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part relationship: composed_primarily_of UBERON:0002384 ! connective tissue relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: UBPROP:0000007 "stromal" xsd:string [Term] id: UBERON:0003897 name: axial muscle namespace: uberon def: "One of the skeletal muscles of the head and neck, spine, and ribs." [HP:0003327] subset: pheno_slim xref: EHDAA:5982 xref: EMAPA:18167 xref: MA:0003153 xref: RETIRED_EHDAA2:0000160 xref: TAO:0001954 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0014892 ! skeletal muscle organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: attaches_to_part_of UBERON:0005944 ! axial skeleton plus cranial skeleton intersection_of: part_of UBERON:0013701 ! main body axis relationship: attaches_to_part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0013700 ! axial musculature [Term] id: UBERON:0003898 name: skeletal muscle tissue of trunk namespace: uberon def: "A portion of skeletal muscle tissue in the trunk." [http://orcid.org/0000-0002-6601-2165] synonym: "skeletal muscle of torso" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of torso" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of trunk" EXACT [OBOL:automatic] synonym: "torso skeletal muscle" EXACT [OBOL:automatic] synonym: "torso skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "trunk skeletal muscle" EXACT [OBOL:automatic] synonym: "trunk skeletal muscle tissue" EXACT [OBOL:automatic] xref: SCTID:244848007 is_a: UBERON:0001134 ! skeletal muscle tissue intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0004479 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! musculature of trunk relationship: part_of UBERON:0013700 ! axial musculature [Term] id: UBERON:0003902 name: retinal neural layer namespace: uberon def: "The part of the retina that contains neurons and photoreceptor cells[GO]." [GO:0003407] subset: pheno_slim subset: vertebrate_core synonym: "neural layer of retina" EXACT [FMA:58628] synonym: "neural retina" EXACT [XAO:0003216, ZFA:0000046] synonym: "neural retinal epithelium" RELATED [MA:000027] synonym: "neuroretina" EXACT [ZFA:0000046] synonym: "stratum nervosum (retina)" EXACT [FMA:58628] synonym: "stratum nervosum retinae" EXACT LATIN [FMA:58628, FMA:TA] xref: AAO:0011095 xref: BTO:0000929 xref: CALOHA:TS-0685 xref: EHDAA2:0001253 xref: EHDAA:4763 xref: EMAPA:17171 xref: EMAPA:18590 xref: FMA:58628 xref: MA:0000277 xref: NCIT:C33166 xref: TAO:0000046 xref: UMLS:C1518263 {source="ncithesaurus:Neural_Retina"} xref: VHOG:0000535 xref: XAO:0003216 xref: ZFA:0000046 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0001781 ! layer of retina intersection_of: UBERON:0001781 ! layer of retina intersection_of: immediate_transformation_of UBERON:0005425 ! presumptive neural retina relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle relationship: develops_from UBERON:0005425 ! presumptive neural retina relationship: has_part CL:0000210 ! photoreceptor cell relationship: immediate_transformation_of UBERON:0005425 {source="Bgee:AN"} ! presumptive neural retina property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000535", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003909 name: sinusoid namespace: uberon def: "small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]." [Wikipedia:Sinusoid_(blood_vessel)] subset: vertebrate_core synonym: "endothelium of irregular blood filled space" RELATED [] synonym: "sinusoidal blood vessel" EXACT [] synonym: "sinusoidal blood vessel endothelium" EXACT [ZFA:0005261] synonym: "sinusoidal capillary" RELATED [http://www.medilexicon.com/medicaldictionary.php?t=13986] synonym: "sinusoidal endothelium" RELATED [] xref: FMA:63131 xref: SCTID:340163004 xref: TAO:0005261 xref: Wikipedia:Sinusoid_(blood_vessel) xref: ZFA:0005261 is_a: UBERON:2005260 {source="Wikipedia", source="ZFA"} ! fenestrated capillary property_value: UBPROP:0000001 "Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005261", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000007 "sinusoidal" xsd:string property_value: UBPROP:0000012 "some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined)." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003914 name: epithelial tube namespace: uberon def: "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GO:0060562, PMID:12526790] synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 xref: FBbt:00007474 is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_quality PATO:0002299 ! tubular property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string [Term] id: UBERON:0003915 name: endothelial tube namespace: uberon def: "Any endothelium that has the quality of being cylindrical [Automatically generated definition]." [OBOL:automatic] is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003914 ! epithelial tube intersection_of: UBERON:0001986 ! endothelium intersection_of: has_quality PATO:0002299 ! tubular [Term] id: UBERON:0003920 name: venous blood vessel namespace: uberon def: "A blood vessel that carries blood from the capillaries toward the heart" [http://www.thefreedictionary.com/venous+blood+vessel] comment: Compare to: vein synonym: "segment of venous tree organ" EXACT [FMA:86188] synonym: "venous tree organ segment" EXACT [FMA:86188] xref: EMAPA:35932 xref: FMA:86188 xref: MA:0000066 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004582 ! venous system relationship: part_of UBERON:0004582 ! venous system [Term] id: UBERON:0003928 name: digestive system duct namespace: uberon def: "A duct that is part of a digestive system [Automatically generated definition]." [OBOL:automatic] synonym: "duct of digestive system" EXACT [OBOL:automatic] synonym: "duct of gastrointestinal system" EXACT [OBOL:automatic] synonym: "gastrointestinal system duct" EXACT [OBOL:automatic] xref: TAO:0005162 xref: ZFA:0005162 is_a: UBERON:0000058 ! duct intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0001007 ! digestive system relationship: part_of UBERON:0001007 ! digestive system [Term] id: UBERON:0003929 name: digestive tract epithelium namespace: uberon def: "An epithelium that lines the lumen of the digestive tract." [http://orcid.org/0000-0002-6601-2165] synonym: "alimentary tract epithelium" RELATED [OBOL:automatic] synonym: "digestive tract epithelial tissue" EXACT [OBOL:automatic] synonym: "epithelial tissue of digestive tract" EXACT [OBOL:automatic] synonym: "epithelial tissue of gut" EXACT [OBOL:automatic] synonym: "epithelium of digestive tract" EXACT [OBOL:automatic] synonym: "epithelium of gut" EXACT [OBOL:automatic] synonym: "gastrodermis" EXACT SENSU [BGEE:ANN, NCBITaxon:6073] synonym: "gut epithelial tissue" EXACT [OBOL:automatic] synonym: "gut epithelium" EXACT [EHDAA2:0004567, MA:0003201, ZFA:0005123] xref: BTO:0000956 xref: EHDAA2:0004567 xref: EMAPA:32928 xref: MA:0003201 xref: NCIT:C12963 xref: TAO:0005123 xref: UMLS:C0836205 {source="ncithesaurus:Gut_Epithelium"} xref: XAO:0003200 xref: ZFA:0005123 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract property_value: UBPROP:0000001 "Epithelium lining the lumen of the gut.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005123", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000008 "" xsd:string [Term] id: UBERON:0003932 name: cartilage element of chondrocranium namespace: uberon def: "A cartilage element of chondrocranium. Example: neurocranial trabecula." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "cartilage of chondrocranium" EXACT [OBOL:accepted] synonym: "cartilaginous element of chondrocranium" EXACT [OBOL:accepted] synonym: "chondrocranium cartilage" EXACT [ZFA:0001461] synonym: "neurocranium cartilage" EXACT [ZFA:0001461] xref: EFO:0003690 xref: TAO:0001461 xref: ZFA:0001461 is_a: UBERON:0003933 ! cranial cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002241 ! chondrocranium relationship: part_of UBERON:0002241 ! chondrocranium [Term] id: UBERON:0003933 name: cranial cartilage namespace: uberon def: "A cartilage element that is part of the cranial skeleton." [https://orcid.org/0000-0002-6601-2165, ZFA:0001458] synonym: "cartilage of cranium" EXACT [OBOL:automatic] synonym: "cranial cartilages" RELATED PLURAL [ZFA:0001458] synonym: "cranium cartilage" EXACT [OBOL:automatic] xref: TAO:0001458 xref: ZFA:0001458 is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0010323 ! cranial skeletal system relationship: part_of UBERON:0010323 ! cranial skeletal system property_value: UBPROP:0000001 "Cartilage which is part of the cranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001458", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0003937 name: reproductive gland namespace: uberon def: "Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction." [MP:0000653] subset: organ_slim subset: pheno_slim synonym: "genitalia gland" EXACT [OBOL:automatic] synonym: "gland of genitalia" EXACT [MP:0000653] synonym: "gland of reproductive system" EXACT [OBOL:automatic] synonym: "reproductive gland" EXACT [MA:0001751] synonym: "reproductive system gland" EXACT [OBOL:automatic] synonym: "sex gland" EXACT [MP:0000653] xref: MA:0001751 is_a: UBERON:0002530 ! gland is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000990 ! reproductive system [Term] id: UBERON:0003952 name: anterior stroma of cornea namespace: uberon def: "The anterior segment of the lamellated connective tissue layer of the cornea" [MP:0003093] subset: pheno_slim synonym: "anterior stroma" BROAD [MP:0003093] synonym: "cornea anterior stroma" EXACT [MP:0003093] xref: EMAPA:37414 {source="MA:th"} is_a: UBERON:0003566 ! head connective tissue is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: in_anterior_side_of UBERON:0001777 ! substantia propria of cornea disjoint_from: UBERON:0003953 {source="lexical"} ! posterior stroma of cornea relationship: contributes_to_morphology_of UBERON:0001777 ! substantia propria of cornea relationship: in_anterior_side_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea [Term] id: UBERON:0003953 name: posterior stroma of cornea namespace: uberon def: "The posterior segment of the lamellated connective tissue layer of the cornea" [MP:0003094] subset: pheno_slim synonym: "cornea posterior stroma" EXACT [MP:0003094] synonym: "posterior stroma" BROAD [MP:0003094] xref: EMAPA:37415 {source="MA:th"} is_a: UBERON:0003566 ! head connective tissue is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: in_posterior_side_of UBERON:0001777 ! substantia propria of cornea relationship: contributes_to_morphology_of UBERON:0001777 ! substantia propria of cornea relationship: in_posterior_side_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea [Term] id: UBERON:0003967 name: cutaneous elastic tissue namespace: uberon def: "The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity" [MP:0008418] subset: pheno_slim synonym: "cutaneous elastic fiber" NARROW [MP:0008418] synonym: "dermal elastic fiber" NARROW [MP:0008418] xref: EMAPA:37841 {source="MA:th"} is_a: UBERON:0002521 ! elastic tissue is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0000014 ! zone of skin relationship: contributes_to_morphology_of UBERON:0000014 ! zone of skin relationship: part_of UBERON:0000014 ! zone of skin [Term] id: UBERON:0004015 name: embryonic-extraembryonic boundary namespace: uberon def: "The connection between the embryo proper and extraembryonic tissues" [MP:0003890] subset: pheno_slim is_a: UBERON:0000015 ! non-material anatomical boundary intersection_of: UBERON:0000015 ! non-material anatomical boundary intersection_of: adjacent_to UBERON:0000478 ! extraembryonic structure intersection_of: adjacent_to UBERON:0002050 ! embryonic structure relationship: adjacent_to UBERON:0000478 ! extraembryonic structure relationship: adjacent_to UBERON:0002050 ! embryonic structure [Term] id: UBERON:0004016 name: dermatome namespace: uberon def: "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." [AEO:0001017, AEO:JB] subset: pheno_slim synonym: "cutis plate" EXACT [Wikipedia:Cutis_plate] synonym: "dermatomal mesenchyme" EXACT [Wikipedia:Cutis_plate] synonym: "epimere mesoderm" RELATED [] synonym: "mesenchyma dermatomiale" RELATED LATIN [Wikipedia:Dermatomal_mesenchyme] xref: AAO:0011028 xref: AEO:0001017 xref: EHDAA2_RETIRED:0003428 xref: EHDAA:1719 xref: EHDAA:1725 xref: EHDAA:1731 xref: EHDAA:1737 xref: EMAPA:32838 xref: FMA:295656 xref: NCIT:C61572 xref: UMLS:C0180383 {source="ncithesaurus:Dermatome"} xref: Wikipedia:Dermatome_(embryology) xref: XAO:0000220 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png xsd:anyURI property_value: UBPROP:0000013 "Not to be confused with 'dermatome segment of skin'." xsd:string [Term] id: UBERON:0004022 name: germinal neuroepithelium namespace: uberon def: "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells" [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0004261] subset: pheno_slim synonym: "germinal neuroepithelial layer" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "germinal neuroepithelium" EXACT [NCBIBook:NBK10047] synonym: "original neural tube" EXACT [NCBIBook:NBK10047] is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium disjoint_from: UBERON:0006934 ! sensory epithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen relationship: bounding_layer_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube property_value: UBPROP:0000011 "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" xsd:string [Term] id: UBERON:0004060 name: neural tube ventricular layer namespace: uberon def: "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium" [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009689] subset: pheno_slim synonym: "ependymal layer" BROAD [NCBIBook:NBK10047] synonym: "neural tube ependymal layer" EXACT [NCBIBook:NBK10047] synonym: "neural tube ependymal zone" NARROW [MP:0009689] synonym: "neural tube ventricular germinal zone" EXACT [NCBIBook:NBK10047] synonym: "neural tube ventricular zone" EXACT [MP:0009689] xref: EMAPA:17152 xref: EMAPA:35362 xref: EMAPA_RETIRED:16783 xref: MA:0003193 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen relationship: develops_from UBERON:0004022 ! germinal neuroepithelium relationship: immediate_transformation_of UBERON:0004022 {source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube property_value: editor_note "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string property_value: UBPROP:0000001 "The layer of undifferentiated, proliferating cells that line the neural tube lumen" xsd:string {source="MP:0009689"} [Term] id: UBERON:0004061 name: neural tube mantle layer namespace: uberon def: "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] subset: pheno_slim synonym: "future brain marginal layer" RELATED [EMAPA:35360] synonym: "neural tube intermediate zone" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] xref: EMAPA:17148 xref: EMAPA:35360 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1367 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034707 {source="NCBIBook:NBK10047"} ! differentiating neuroepithelium relationship: adjacent_to UBERON:0004060 ! neural tube ventricular layer relationship: adjacent_to UBERON:0004062 ! neural tube marginal layer relationship: develops_from UBERON:0004022 {notes="by division", source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube [Term] id: UBERON:0004062 name: neural tube marginal layer namespace: uberon def: "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter" [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009691] subset: pheno_slim synonym: "brain marginal zone" RELATED [] synonym: "neural tube marginal zone" EXACT [MP:0009691] xref: EMAPA:17151 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1368 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005162 ! multi cell part structure relationship: adjacent_to UBERON:0004061 ! neural tube mantle layer relationship: develops_from UBERON:0004061 {notes="forms from axons"} ! neural tube mantle layer relationship: part_of UBERON:0001049 ! neural tube [Term] id: UBERON:0004088 name: orbital region namespace: uberon def: "The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present" [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "content of orbital part of eye" EXACT [FMA:260119] synonym: "eye region" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "ocular and peri-ocular region" RELATED [] synonym: "ocular region" RELATED [] synonym: "orbital content" RELATED [FMA:260119] synonym: "orbital part of eye" RELATED [FMA:72951] synonym: "orbital part of face" EXACT [http://orcid.org/0000-0002-6601-2165] xref: FMA:260119 is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001456 ! face property_value: editor_note "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string property_value: UBPROP:0000012 "in HP covers eyelid, eyebrow." xsd:string {external_ontology="HP:0000284"} [Term] id: UBERON:0004111 name: anatomical conduit namespace: uberon def: "Any tube, opening or passage that connects two distinct anatomical spaces." [http://orcid.org/0000-0002-6601-2165] synonym: "foramen" NARROW [EHDAA2:0003080] synonym: "foramina" NARROW PLURAL [https://orcid.org/0000-0002-6601-2165] synonym: "opening" RELATED [] synonym: "ostia" RELATED PLURAL [] synonym: "ostium" RELATED [] xref: AEO:0000080 xref: EHDAA2:0003080 xref: FMA:242873 xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space relationship: conduit_for UBERON:0000061 ! anatomical structure relationship: connects UBERON:0000464 {minCardinality="2", maxCardinality="2"} ! anatomical space relationship: has_part UBERON:0013686 ! anatomical conduit space property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004118 name: vasculature of iris namespace: uberon def: "A vasculature that is part of a iris [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "iris blood vessels" EXACT [ZFA:0005568] synonym: "iris vascular network" EXACT [OBOL:automatic] synonym: "iris vasculature" EXACT [] synonym: "vascular network of iris" EXACT [OBOL:automatic] xref: ZFA:0005568 is_a: UBERON:0002203 ! vasculature of eye intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0001769 ! iris [Term] id: UBERON:0004119 name: endoderm-derived structure namespace: uberon def: "An anatomical structure that develops (entirely or partially) from the endoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000925 ! endoderm relationship: develops_from UBERON:0000925 ! endoderm property_value: IAO:0000232 "Grouping term for query purposes" xsd:string [Term] id: UBERON:0004120 name: mesoderm-derived structure namespace: uberon def: "An anatomical structure that develops (entirely or partially) from the mesoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] xref: FBbt:00025998 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000926 ! mesoderm relationship: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000232 "Grouping term for query purposes" xsd:string [Term] id: UBERON:0004121 name: ectoderm-derived structure namespace: uberon def: "An anatomical structure that develops (entirely or partially) from the ectoderm." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] xref: FBbt:00025990 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0000924 ! ectoderm relationship: develops_from UBERON:0000924 ! ectoderm property_value: IAO:0000232 "Grouping term for query purposes" xsd:string [Term] id: UBERON:0004128 name: optic vesicle namespace: uberon def: "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]." [GO:0003404, Wikipedia:Optic_vesicles] comment: Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] subset: pheno_slim subset: vertebrate_core synonym: "evagination" RELATED [] synonym: "eye vesicle" RELATED [XAO:0000228] synonym: "ocular vesicle" RELATED [VHOG:0000165] synonym: "optic vesicles" RELATED PLURAL [ZFA:0000050] xref: AAO:0011039 xref: EHDAA2:0001320 xref: EMAPA:16540 xref: FMA:293357 xref: NCIT:C34236 xref: SCTID:362864008 xref: TAO:0000050 xref: UMLS:C0231106 {source="ncithesaurus:Optic_Vesicle"} xref: VHOG:0000165 xref: Wikipedia:Optic_vesicles xref: XAO:0000228 xref: ZFA:0000050 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: developmentally_induced_by UBERON:0004880 ! chordamesoderm relationship: develops_from UBERON:0002346 {source="GO-def"} ! neurectoderm relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png xsd:anyURI property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004139 name: cardiogenic plate namespace: uberon def: "The first recognizable structure derived from the heart field" [GO:0003142] subset: pheno_slim synonym: "cardiac crescent" RELATED [EMAPA:16106] synonym: "cardiogenic crescent" RELATED [GO:0003142] synonym: "heart rudiment" RELATED [] synonym: "myocardial plate" EXACT [EHDAA2:0000215] xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0003084 ! heart primordium property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004140 name: primary heart field namespace: uberon def: "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle." [GO:0003138, GOC:mtg_heart, GOC:rl] synonym: "FHF" RELATED ABBREVIATION [XAO:0004185] synonym: "first heart field" EXACT [XAO:0004185] synonym: "heart field" RELATED [XAO:0004185] synonym: "PHF" RELATED ABBREVIATION [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="BGEE:ann"} ! cardiopharyngeal field property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 name: heart tube namespace: uberon def: "An epithelial tube that will give rise to the mature heart." [GO:0003143, GOC:mtg_heart] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "embryonic heart tube" EXACT [GO:0003143] synonym: "endocardial heart tube" EXACT [MP:0012700] synonym: "endocardial tube" EXACT [XAO:0000337] xref: AAO:0010411 xref: EFO:0003526 xref: EMAPA:32685 xref: NCIT:C34161 xref: TAO:0000360 xref: XAO:0000337 xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0005498 ! primitive heart tube relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} [Term] id: UBERON:0004142 name: outflow tract septum namespace: uberon def: "The outflow tract septum is a partition in the outflow tract" [GO:0003148] xref: XAO:0004141 is_a: UBERON:0002099 ! cardiac septum intersection_of: UBERON:0002099 ! cardiac septum intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract [Term] id: UBERON:0004145 name: outflow tract namespace: uberon def: "The outflow tract is the portion of the heart through which blood flows into the arteries" [GO:0003151] subset: pheno_slim synonym: "arterial (outflow) pole" RELATED [PMID:20735616] synonym: "cardiac outflow tract" EXACT [PMID:20735616] synonym: "heart outflow tract" EXACT [] xref: EHDAA2:0001351 xref: EHDAA:464 xref: EHDAA:798 xref: EMAPA:16346 xref: MA:0000100 xref: VHOG:0000670 xref: XAO:0004139 is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004120 ! mesoderm-derived structure relationship: channel_for UBERON:0000178 ! blood relationship: channels_from UBERON:0000948 ! heart relationship: channels_into UBERON:0001637 ! artery relationship: part_of UBERON:0000948 ! heart property_value: UBPROP:0000008 "Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]" xsd:string [Term] id: UBERON:0004148 name: cardiac vein namespace: uberon def: "Vein of heart that drains the myocardium" [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "cardiac vein" EXACT [FMA:12846] synonym: "coronary vein" EXACT [ZFA:0005814] synonym: "coronary vein" RELATED [Wikipedia:Coronary_circulation] synonym: "heart vein" EXACT [OBOL:automatic] synonym: "vein of heart" EXACT [OBOL:automatic] xref: EHDAA2:0004507 xref: EMAPA:37137 {source="MA:th"} xref: FMA:12846 xref: galen:CoronaryVein xref: NCIT:C12878 xref: NCIT:C12882 xref: SCTID:277726009 xref: UMLS:C0226654 {source="ncithesaurus:Cardiac_Vein"} xref: UMLS:C0226737 {source="ncithesaurus:Coronary_Vein"} xref: Wikipedia:Coronary_circulation xref: ZFA:0005814 is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0005194 ! thoracic vein is_a: UBERON:0013140 {source="FMA"} ! systemic vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0000948 ! heart relationship: drains UBERON:0002349 ! myocardium [Term] id: UBERON:0004151 name: cardiac chamber namespace: uberon def: "A cardiac chamber surrounds an enclosed cavity within the heart" [GO:0003205] comment: generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus synonym: "chamber of heart" EXACT [] synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] id: UBERON:0004160 name: proepicardium namespace: uberon def: "An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium" [GO:0003342, http://en.wiktionary.org/wiki/proepicardium] synonym: "proepicardial cluster" EXACT [ZFA:0005808] synonym: "proepicardial organ" EXACT [ZFIN:ZDB-PUB-080218-16] xref: EMAPA:36025 xref: ZFA:0005808 is_a: UBERON:0003104 ! mesenchyme relationship: part_of UBERON:0004161 {notes="todo check other taxa"} ! septum transversum relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system property_value: UBPROP:0000007 "propepicardial" xsd:string property_value: UBPROP:0000008 "Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]" xsd:string [Term] id: UBERON:0004161 name: septum transversum namespace: uberon def: "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]." [VHOG:0000019, Wikipedia:Septum_transversum] subset: pheno_slim synonym: "transverse septum" EXACT [https://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0001829 xref: EHDAA:736 xref: EMAPA:16318 xref: FMA:295593 xref: NCIT:C34296 xref: SCTID:308819008 xref: UMLS:C0231004 {source="ncithesaurus:Septum_Transversum"} xref: VHOG:0000019 xref: Wikipedia:Septum_transversum is_a: UBERON:0003104 ! mesenchyme relationship: located_in UBERON:0002323 ! coelemic cavity lumen relationship: part_of UBERON:0002100 ! trunk property_value: UBPROP:0000001 "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000019", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/transverse+septum"} property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000019", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} property_value: UBPROP:0000011 "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut." xsd:string property_value: UBPROP:0000012 "in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0004176 name: external genitalia namespace: uberon def: "The external genitalia are the outer sex organs, such as the penis or vulva in mammals" [GO:0035261] comment: TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 subset: organ_slim subset: pheno_slim synonym: "external genitalia" EXACT [] synonym: "external reproductive organ" RELATED [] synonym: "external sex organ" RELATED [] xref: FMA:45643 xref: SCTID:362207005 is_a: UBERON:0003133 ! reproductive organ [Term] id: UBERON:0004177 name: hemopoietic organ namespace: uberon def: "Organ that is part of the hematopoietic system." [GOC:Obol] subset: organ_slim subset: pheno_slim synonym: "haematological system organ" EXACT [OBOL:automatic] synonym: "haemopoietic system organ" EXACT [OBOL:automatic] synonym: "hematopoeitic or lymphoid organ" NARROW [] synonym: "hematopoeitic organ" EXACT [] synonym: "hematopoietic system organ" EXACT [OBOL:automatic] synonym: "lymph organ" NARROW [MA:0000747] synonym: "lymphoid organ" NARROW [BTO:0004605, FMA:7143] synonym: "organ of haematological system" EXACT [OBOL:automatic] synonym: "organ of haemopoietic system" EXACT [OBOL:automatic] synonym: "organ of hematopoietic system" EXACT [OBOL:automatic] synonym: "organ of organa haemopoietica" EXACT [OBOL:automatic] synonym: "organa haemopoietica organ" EXACT [OBOL:automatic] xref: BTO:0004605 xref: EMAPA:37665 {source="MA:th"} xref: FMA:7143 xref: MA:0000747 xref: SCTID:361338006 is_a: UBERON:0000062 ! organ is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002390 ! hematopoietic system property_value: editor_note "consider splitting out lymph organ, compare with lymph node" xsd:string property_value: UBPROP:0000001 "the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]." xsd:string {source="http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs"} property_value: UBPROP:0000012 "the FMA class 'lymphoid organ' is a general anatomical term" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004178 name: aorta smooth muscle tissue namespace: uberon def: "the nonstriated, involuntary muscle tissue located in the wall of the aorta" [MGI:csmith, MP:0009865] subset: efo_slim subset: pheno_slim synonym: "aorta non-striated muscle" EXACT [OBOL:automatic] synonym: "aorta smooth muscle" EXACT [OBOL:automatic] synonym: "aortic smooth muscle" EXACT [BTO:0001685] xref: BTO:0001685 xref: CALOHA:TS-0048 xref: EFO:0002775 xref: EMAPA:35135 xref: MA:0000702 xref: NCIT:C49191 xref: UMLS:C1706825 {source="ncithesaurus:Aorta_Smooth_Muscle_Tissue"} is_a: UBERON:0004237 ! blood vessel smooth muscle is_a: UBERON:0004695 ! arterial system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta [Term] id: UBERON:0004185 name: endodermal part of digestive tract namespace: uberon def: "A portions of the gut that is derived from endoderm." [GO:0061031] synonym: "endodermal gut" EXACT [] synonym: "gut endoderm" EXACT [EMAPA:32930] xref: EMAPA:32930 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0004215 name: back nerve namespace: uberon def: "A nerve that is part of a back [Automatically generated definition]." [OBOL:automatic] synonym: "nerve of back" EXACT [OBOL:automatic] xref: EMAPA:37268 {source="MA:th"} xref: MA:0000497 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0001137 ! dorsum [Term] id: UBERON:0004225 name: respiratory system smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "airway smooth muscle" RELATED [BTO:0001660] synonym: "airway smooth muscle cell" RELATED [BTO:0001660] synonym: "respiratory smooth muscle" EXACT [BTO:0001660] synonym: "smooth muscle of respiratory system" EXACT [OBOL:automatic] xref: BTO:0001660 xref: EMAPA:35734 xref: MA:0001830 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0004233 name: lower respiratory tract smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] synonym: "involuntary muscle of lower respiratory tract" EXACT [OBOL:automatic] synonym: "lower respiratory tract involuntary muscle" EXACT [OBOL:automatic] synonym: "lower respiratory tract non-striated muscle" EXACT [OBOL:automatic] synonym: "lower respiratory tract smooth muscle tissue" EXACT [OBOL:automatic] synonym: "non-striated muscle of lower respiratory tract" EXACT [OBOL:automatic] synonym: "smooth muscle of lower respiratory tract" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of lower respiratory tract" EXACT [OBOL:automatic] xref: EMAPA:35520 xref: MA:0002410 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004225 ! respiratory system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract [Term] id: UBERON:0004234 name: iris smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]." [OBOL:automatic] synonym: "involuntary muscle of iris" EXACT [OBOL:automatic] synonym: "iridial smooth muscle" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "iris involuntary muscle" EXACT [OBOL:automatic] synonym: "iris non-striated muscle" EXACT [OBOL:automatic] synonym: "iris smooth muscle tissue" EXACT [OBOL:automatic] synonym: "non-striated muscle of iris" EXACT [OBOL:automatic] synonym: "smooth muscle of iris" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of iris" EXACT [OBOL:automatic] xref: BTO:0000655 xref: EMAPA:35448 xref: FMA:312338 xref: MA:0001270 is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0001606 ! muscle of iris property_value: editor_note "see notes for muscle of iris." xsd:string [Term] id: UBERON:0004236 name: arteriole smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:36287 xref: FMA:312251 xref: MA:0000706 is_a: UBERON:0004237 ! blood vessel smooth muscle is_a: UBERON:0004695 ! arterial system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001980 ! arteriole relationship: part_of UBERON:0001980 ! arteriole [Term] id: UBERON:0004237 name: blood vessel smooth muscle namespace: uberon alt_id: UBERON:0010508 def: "smooth muscle found within, and composing the majority of the wall of blood vessels." [Wikipedia:Vascular_smooth_muscle] subset: pheno_slim synonym: "blood vessel involuntary muscle" EXACT [OBOL:automatic] synonym: "blood vessel non-striated muscle" EXACT [OBOL:automatic] synonym: "blood vessel smooth muscle tissue" EXACT [OBOL:automatic] synonym: "involuntary muscle of blood vessel" EXACT [OBOL:automatic] synonym: "non-striated muscle of blood vessel" EXACT [OBOL:automatic] synonym: "smooth muscle of blood vessel" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of blood vessel" EXACT [OBOL:automatic] synonym: "vascular smooth muscle" EXACT [ZFA:0005321] synonym: "vascular smooth muscle tissue" EXACT [] xref: BTO:0001431 xref: CALOHA:TS-1107 xref: EMAPA:35177 xref: MA:0000710 xref: MESH:D009131 xref: NCIT:C33853 xref: TAO:0005321 xref: UMLS:C1519956 {source="ncithesaurus:Vascular_Smooth_Muscle_Tissue"} xref: Wikipedia:Vascular_smooth_muscle xref: ZFA:0005321 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel property_value: UBPROP:0000009 "Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension." xsd:string [Term] id: UBERON:0004246 name: outflow tract smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]." [OBOL:automatic] synonym: "involuntary muscle of outflow tract" EXACT [OBOL:automatic] synonym: "non-striated muscle of outflow tract" EXACT [OBOL:automatic] synonym: "outflow tract involuntary muscle" EXACT [OBOL:automatic] synonym: "outflow tract non-striated muscle" EXACT [OBOL:automatic] synonym: "outflow tract smooth muscle tissue" EXACT [OBOL:automatic] synonym: "smooth muscle of outflow tract" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of outflow tract" EXACT [OBOL:automatic] xref: EMAPA:37708 {source="MA:th"} xref: MA:0000492 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract [Term] id: UBERON:0004247 name: bone of dorsum namespace: uberon def: "A bone that is part of the dorsal region of an animal." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "back bone" RELATED [MA:0000494] synonym: "bone of back" RELATED [OBOL:automatic] synonym: "dorsal region bone" RELATED [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:37248 {source="MA:th"} xref: MA:0000494 is_a: UBERON:0001474 ! bone element is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001137 ! dorsum property_value: IAO:0000232 "this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93" xsd:string property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern xsd:anyURI [Term] id: UBERON:0004253 name: skin muscle namespace: uberon alt_id: UBERON:0015797 def: "Any muscle organ that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] synonym: "integumental system muscle" EXACT [MA:0003139] synonym: "muscle of integumental system" EXACT [EMAPA:18187] synonym: "muscle organ of skin" EXACT [OBOL:automatic] synonym: "skin muscle organ" EXACT [OBOL:automatic] xref: EMAPA:18187 xref: EMAPA:35776 xref: MA:0002710 xref: MA:0003139 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0002416 ! integumental system relationship: located_in UBERON:0002097 ! skin of body relationship: part_of UBERON:0002416 ! integumental system property_value: editor_note "review as part of general integumentary system review - part of skin, or more generally, integumental system" xsd:string property_value: UBPROP:0000012 "in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only" xsd:string {external_ontology="MA"} [Term] id: UBERON:0004258 name: back blood vessel namespace: uberon def: "A blood vessel that is part of a back [Automatically generated definition]." [OBOL:automatic] synonym: "blood vessel of back" EXACT [OBOL:automatic] xref: EMAPA:37243 {source="MA:th"} xref: MA:0000493 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0001137 ! dorsum [Term] id: UBERON:0004265 name: outflow tract myocardium namespace: uberon def: "A myocardium that is part of a outflow tract [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac muscle of outflow tract" EXACT [OBOL:automatic] synonym: "heart muscle of outflow tract" EXACT [OBOL:automatic] synonym: "heart myocardium of outflow tract" EXACT [OBOL:automatic] synonym: "muscle of heart of outflow tract" EXACT [OBOL:automatic] synonym: "myocardium of outflow tract" EXACT [OBOL:automatic] synonym: "outflow tract cardiac muscle" EXACT [OBOL:automatic] synonym: "outflow tract heart muscle" EXACT [OBOL:automatic] synonym: "outflow tract heart myocardium" EXACT [OBOL:automatic] synonym: "outflow tract muscle of heart" EXACT [OBOL:automatic] xref: EHDAA2:0001358 xref: EMAPA:35623 xref: MA:0000489 xref: VHOG:0000603 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract property_value: UBPROP:0000003 "(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000603", ontology="VHOG", source="PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004267 name: back connective tissue namespace: uberon def: "A portion of connective tissue that is part of a back [Automatically generated definition]." [OBOL:automatic] synonym: "mesenchyne of back" RELATED [OBOL:automatic] xref: EMAPA:37256 {source="MA:th"} xref: MA:0000495 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0001137 ! dorsum [Term] id: UBERON:0004271 name: outflow tract pericardium namespace: uberon def: "A pericardium that is part of a outflow tract [Automatically generated definition]." [OBOL:automatic] synonym: "pericardium of outflow tract" EXACT [OBOL:automatic] xref: EMAPA:37707 {source="MA:th"} xref: MA:0000491 is_a: UBERON:0002407 ! pericardium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002407 ! pericardium intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract [Term] id: UBERON:0004277 name: eye muscle namespace: uberon def: "A muscle that is part of the eye region." [OBOL:automatic] subset: pheno_slim xref: AAO:0000156 xref: EMAPA:35335 xref: MA:0000271 xref: OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="MA"} ! camera-type eye [Term] id: UBERON:0004288 name: skeleton namespace: uberon def: "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." [VSAO:0000026] subset: efo_slim subset: pheno_slim subset: uberon_slim synonym: "set of all bones" EXACT [] synonym: "set of bones of body" EXACT [] xref: AEO:0000168 xref: EHDAA2:0001843 xref: EHDAA:5047 xref: EMAPA:17213 xref: FMA:23875 xref: GAID:177 xref: galen:Skeleton xref: MA:0003006 xref: MAT:0000032 xref: MESH:D012863 xref: MIAA:0000032 xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA xref: SCTID:361378004 xref: VSAO:0000026 xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system property_value: seeAlso https://github.com/obophenotype/uberon/wiki/The-skeletal-system xsd:anyURI property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004290 name: dermomyotome namespace: uberon def: "The bilaminar epithelium formed from the myotome and dermatome." [AEO:0000214] synonym: "dermamyotome" RELATED [VHOG:0000676] synonym: "dermomyotomes" RELATED PLURAL [VHOG:0000676] xref: AAO:0010572 xref: AEO:0000214 xref: EHDAA2:0003259 xref: EMAPA:31109 xref: FMA:295654 xref: NCIT:C34140 xref: TAO:0001513 xref: UMLS:C1511786 {source="ncithesaurus:Dermomyotome"} xref: VHOG:0000676 xref: ZFA:0001513 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000486 {source="AEO"} ! multilaminar epithelium is_a: UBERON:0016888 {source="AEO"} ! transitional anatomical structure relationship: develops_from UBERON:0002329 {source="EHDAA2", source="ZFA"} ! somite relationship: has_part CL:0000075 ! columnar/cuboidal epithelial cell property_value: UBPROP:0000001 "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." xsd:string {source="http://medical-dictionary.thefreedictionary.com/dermomyotome"} property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." xsd:string {source="http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768"} property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001513", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Portion of somites that gives rise to dermis and muscles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010572", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000003 "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000676", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004291 name: heart rudiment namespace: uberon def: "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube." [GO:0003313] synonym: "heart cone" EXACT [GO:0003313] synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0004139 ! cardiogenic plate property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0004292 name: cardiac skeleton namespace: uberon def: "Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart." [GO:0003204, Wikipedia:Cardiac_skeleton] synonym: "anulus fibrosus dexter cordis" RELATED LATIN [Wikipedia:Cardiac_skeleton] synonym: "anulus fibrosus sinister cordis" RELATED LATIN [Wikipedia:Cardiac_skeleton] synonym: "cardiac fibrous skeleton" EXACT [EMAPA:36645] synonym: "fibrous skeleton of heart" EXACT [] synonym: "heart fibrous skeleton" EXACT [GO:0003204] synonym: "skeleton of heart" EXACT [FMA:9496] synonym: "trigona fibrosa" RELATED LATIN [Wikipedia:Cardiac_skeleton] synonym: "trigonum fibrosum dextrum cordis" RELATED LATIN [Wikipedia:Cardiac_skeleton] synonym: "trigonum fibrosum sinistrum cordis" RELATED LATIN [Wikipedia:Cardiac_skeleton] xref: EMAPA:36645 xref: FMA:9496 xref: Wikipedia:Cardiac_skeleton is_a: UBERON:0003837 ! thoracic segment connective tissue is_a: UBERON:0004120 ! mesoderm-derived structure relationship: adjacent_to UBERON:0002081 ! cardiac atrium relationship: adjacent_to UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0000948 ! heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png xsd:anyURI property_value: UBPROP:0000009 "It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]" xsd:string [Term] id: UBERON:0004297 name: respiratory system blood vessel smooth muscle namespace: uberon def: "A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "smooth muscle tissue of blood vessel of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37573 {source="MA:th"} xref: MA:0001806 is_a: UBERON:0004225 ! respiratory system smooth muscle is_a: UBERON:0004237 ! blood vessel smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003504 ! respiratory system blood vessel relationship: part_of UBERON:0003504 ! respiratory system blood vessel [Term] id: UBERON:0004348 name: optic eminence namespace: uberon def: "The embryonic structure that gives rise to the corneal ectoderm" [MP:0006305] subset: pheno_slim xref: EHDAA:938 xref: EMAPA:16322 xref: RETIRED_EHDAA2:0001308 xref: VHOG:0001296 is_a: UBERON:0006598 ! presumptive structure relationship: has_potential_to_develop_into UBERON:0000964 ! cornea [Term] id: UBERON:0004356 name: apical ectodermal ridge namespace: uberon def: "multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]." [MP:0001676, Wikipedia:Apical_ectodermal_ridge] subset: pheno_slim synonym: "AER" RELATED [MP:0001676] synonym: "apical epidermal ridge" EXACT [XAO:0004121] synonym: "crista ectodermalis apicalis" RELATED LATIN [Wikipedia:Apical_ectodermal_ridge] xref: AAO:0010760 xref: EMAPA:32744 xref: NCIT:C34109 xref: TAO:0002146 xref: UMLS:C1516037 {source="ncithesaurus:Apical_Ectodermal_Ridge"} xref: Wikipedia:Apical_ectodermal_ridge xref: XAO:0004121 xref: ZFA:0001702 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0002050 ! embryonic structure relationship: capable_of GO:0010464 ! regulation of mesenchymal cell proliferation relationship: capable_of GO:0061037 ! negative regulation of cartilage development relationship: developmentally_induced_by UBERON:0003104 ! mesenchyme relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0004357 ! paired limb/fin bud relationship: produces PR:000007499 ! fibroblast growth factor 8 property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg xsd:anyURI property_value: IAO:0000232 "note that media, dorsal fins etc have AERs." xsd:string property_value: UBPROP:0000001 "Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010760", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "Proliferative region that is part of the developing fin fold or fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002146", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000002 "relationship loss: subclass proliferative region (TAO:0000098)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002146", ontology="TAO"} property_value: UBPROP:0000008 "The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold" xsd:string {source="PMID:20574421"} property_value: UBPROP:0000009 "maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop" xsd:string [Term] id: UBERON:0004357 name: paired limb/fin bud namespace: uberon def: "An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." [https://orcid.org/0000-0002-6601-2165, ISBN:9780878932504, MP:0005650] comment: Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] subset: homology_grouping synonym: "limb - fin bud" EXACT [VHOG:0001258] synonym: "paired appendage bud" EXACT [] synonym: "paired limb/fin bud" EXACT [VHOG:0001258] xref: VHOG:0001258 is_a: UBERON:0003102 ! surface structure is_a: UBERON:0006598 ! presumptive structure relationship: has_developmental_contribution_from UBERON:0005732 ! paired limb/fin field relationship: has_part UBERON:0004356 ! apical ectodermal ridge relationship: has_potential_to_develop_into UBERON:0004708 ! paired limb/fin property_value: UBPROP:0000003 "The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001258", ontology="VHOG", source="DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004362 name: pharyngeal arch 1 namespace: uberon def: "The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries" [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "1st arch" RELATED [EHDAA2:0000006] synonym: "1st pharyngeal arch" EXACT [] synonym: "1st visceral arch" RELATED [VHOG:0000296] synonym: "arcus pharyngeus primus" RELATED LATIN [Wikipedia:First_pharyngeal_arch] synonym: "branchial arch 1" EXACT SENSU [] synonym: "first branchial arch" EXACT SENSU [] synonym: "first pharyngeal arch" EXACT [] synonym: "first visceral arch" EXACT SENSU [] synonym: "mandibular arch" EXACT [] synonym: "visceral arch 1" EXACT SENSU [] xref: AAO:0010364 xref: CALOHA:TS-2089 xref: EHDAA2:0000006 xref: EHDAA:573 xref: EMAPA:16118 xref: FMA:293019 xref: MFMO:0000095 xref: NCIT:C34175 xref: SCTID:308767008 xref: TAO:0001595 xref: UMLS:C1517197 {source="ncithesaurus:First_Pharyngeal_Arch"} xref: VHOG:0000296 xref: Wikipedia:First_pharyngeal_arch xref: XAO:0000097 xref: ZFA:0001612 is_a: UBERON:0002539 ! pharyngeal arch property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png xsd:anyURI property_value: UBPROP:0000001 "the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery" xsd:string {source="MP:0006337,MGI:smb"} property_value: UBPROP:0000001 "The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010364", ontology="AAO", source="XAO:EJS"} property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000296", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: UBPROP:0000103 "1" xsd:nonNegativeInteger [Term] id: UBERON:0004363 name: pharyngeal arch artery namespace: uberon alt_id: UBERON:0004342 def: "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]" [MP:0002672] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "a. arcuum pharyngeorum" RELATED LATIN [Wikipedia:Aortic_arches] synonym: "aortic arch" EXACT [ZFA:0005004] synonym: "aortic arch artery" RELATED [EMAPA:16684] synonym: "aortic arches" EXACT PLURAL [ZFA:0005004] synonym: "arteriae arcuum pharyngeorum" RELATED LATIN [Wikipedia:Aortic_arches] synonym: "branchial aortic arches" EXACT PLURAL [ZFIN:ZDB-PUB-080512-6] synonym: "branchial aortic arches" RELATED PLURAL [ZFA:0005004, ZFIN:ZDB-PUB-080512-6] synonym: "branchial arch artery" EXACT [EMAPA:16684] synonym: "embryonic aortic arch artery" EXACT [EMAPA:16684, MP:0002672] synonym: "PAA" EXACT ABBREVIATION [MP:0002672] synonym: "pharyngeal arch arteries" RELATED PLURAL [] synonym: "pharyngeal arch artery" EXACT [MP:0002672] synonym: "pharyngeal arch artery" RELATED [VHOG:0000122] xref: AAO:0010414 xref: EFO:0003695 xref: EHDAA2:0000186 xref: EHDAA:398 xref: EHDAA:7327 xref: EMAPA:16684 xref: NCIT:C32123 xref: TAO:0005004 xref: UMLS:C0003489 {source="ncithesaurus:Aortic_Arch"} xref: VHOG:0000122 xref: Wikipedia:Aortic_arches xref: XAO:0000341 xref: ZFA:0005004 is_a: UBERON:0003469 ! respiratory system artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0002539 ! pharyngeal arch relationship: has_potential_to_develop_into UBERON:0001637 ! artery relationship: part_of UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0007303 {source="ZFA"} ! pharyngeal vasculature property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png xsd:anyURI property_value: editor_note "add specific artery derivatives" xsd:string property_value: IAO:0000232 "Do not confuse with arch of aorta." xsd:string property_value: UBPROP:0000001 "Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aortic+arches"} property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods" xsd:string property_value: UBPROP:0000011 "The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches" xsd:string [Term] id: UBERON:0004367 name: Descemet's membrane namespace: uberon def: "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]." [https://github.com/obophenotype/uberon/issues/15, MP:0004285] comment: The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed) subset: pheno_slim subset: vertebrate_core synonym: "Descemet membrane" EXACT [] synonym: "Descemet's posterior elastic lamina" EXACT [FMA:58309] synonym: "lamina limitans posterior" EXACT [FMA:58309] synonym: "lamina limitans posterior corneae" EXACT LATIN [FMA:58309, FMA:TA] synonym: "posterior limiting lamina" EXACT [MA:0001246] synonym: "posterior limiting lamina of cornea" EXACT [FMA:58309] synonym: "posterior limiting membrane" EXACT [ZFA:0001686] xref: EMAPA:18804 xref: FMA:58309 xref: GAID:894 xref: MA:0001246 xref: MESH:D003886 xref: NCIT:C32454 xref: SCTID:281076002 xref: TAO:0002157 xref: UMLS:C0011665 {source="ncithesaurus:Descemet_s_Membrane"} xref: Wikipedia:Descemet%27s_membrane xref: ZFA:0001686 is_a: UBERON:0005769 ! basement membrane of epithelium is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: adjacent_to UBERON:0001777 ! substantia propria of cornea intersection_of: adjacent_to UBERON:0001985 ! corneal endothelium intersection_of: part_of UBERON:0000964 ! cornea disjoint_from: UBERON:0004370 {source="lexical"} ! anterior limiting lamina of cornea relationship: adjacent_to UBERON:0001777 ! substantia propria of cornea relationship: adjacent_to UBERON:0001985 ! corneal endothelium relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000964 ! cornea relationship: produced_by UBERON:0001985 {source="Cline et al"} ! corneal endothelium property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/gkoutos property_value: seeAlso https://github.com/obophenotype/uberon/issues/15 xsd:anyURI property_value: UBPROP:0000001 "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" xsd:string {date_retrieved="2016-05-01", external_class="TAO:0002157", ontology="ZFIN", source="ORCiD:0000-0001-9114-8737", source="ZFIN:ZDB-PUB-061010-3"} [Term] id: UBERON:0004370 name: anterior limiting lamina of cornea namespace: uberon def: "A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane." [ncithesaurus:Bowman_s_Membrane] subset: pheno_slim subset: vertebrate_core synonym: "anterior elastic lamina" EXACT [ZFA:0001684] synonym: "anterior limiting lamina" EXACT [MA:0001240] synonym: "anterior limiting lamina of cornea" EXACT [FMA:58273] synonym: "anterior limiting membrane" RELATED [ZFA:0001684] synonym: "Bowman's anterior elastic lamina" EXACT [FMA:58273] synonym: "Bowman's layer" EXACT [FMA:58273] synonym: "Bowman's membrane" EXACT [FMA:58273] synonym: "lamina limitans anterior (cornea)" EXACT [FMA:58273] synonym: "lamina limitans anterior corneae" EXACT LATIN [FMA:58273, FMA:TA] synonym: "Reichert's membrane" RELATED DUBIOUS [http://sourceforge.net/tracker/?func=detail&aid=2956371&group_id=76834&atid=974957] xref: FMA:58273 xref: MA:0001240 xref: NCIT:C32226 xref: SCTID:281075003 xref: TAO:0002155 xref: UMLS:C0229127 {source="ncithesaurus:Bowman_s_Membrane"} xref: Wikipedia:Bowman%27s_membrane xref: ZFA:0001684 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0005769 ! basement membrane of epithelium is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: attaches_to UBERON:0001772 ! corneal epithelium intersection_of: part_of UBERON:0000964 ! cornea relationship: attaches_to UBERON:0001772 ! corneal epithelium relationship: part_of UBERON:0000964 ! cornea property_value: UBPROP:0000001 "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002155", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string [Term] id: UBERON:0004375 name: bone of free limb or fin namespace: uberon def: "A bone that is part of an appendage [Automatically generated definition]." [OBOL:automatic] subset: homology_grouping synonym: "appendage bone" EXACT [] synonym: "bone of appendage" EXACT [] synonym: "bone of free segment of appendicular skeleton" EXACT [] is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010740 ! bone of appendage girdle complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004708 ! paired limb/fin relationship: part_of UBERON:0011582 ! paired limb/fin skeleton [Term] id: UBERON:0004455 name: neurula embryo namespace: uberon alt_id: UBERON:0007013 def: "An embryo at the neurula stage." [http://orcid.org/0000-0002-6601-2165] synonym: "neurula" EXACT [BTO:0001766] xref: BILA:0000061 xref: BTO:0001766 xref: NCIT:C34229 xref: UMLS:C1518306 {source="ncithesaurus:Neurula"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_starts_and_ends_during UBERON:0000110 ! neurula stage relationship: develops_from UBERON:0004734 ! gastrula relationship: existence_starts_and_ends_during UBERON:0000110 ! neurula stage [Term] id: UBERON:0004456 name: entire sense organ system namespace: uberon def: "Sum of all sensory systems in an organism." [http://orcid.org/0000-0002-6601-2165] subset: uberon_slim synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system relationship: existence_ends_during UBERON:0000066 ! fully formed stage property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string [Term] id: UBERON:0004461 name: skeletal musculature of head namespace: uberon def: "Any collection of skeletal muscles that is part of a head [Automatically generated definition]." [OBOL:automatic] comment: This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376 subset: non_informative synonym: "head musculature" EXACT [FMA:71287] synonym: "muscle group of head" EXACT [FMA:71287] synonym: "muscles of head" EXACT [FMA:71287] synonym: "musculi capitis" EXACT LATIN [FMA:71287, FMA:TA] synonym: "set of muscles of head" EXACT [FMA:71287] xref: EMAPA:18171 xref: FMA:71287 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0008229 ! craniocervical region musculature intersection_of: UBERON:0001015 ! musculature intersection_of: attaches_to UBERON:0003129 ! skull intersection_of: part_of UBERON:0000033 ! head relationship: attaches_to UBERON:0003129 ! skull relationship: develops_from UBERON:0005253 ! head mesenchyme relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0013700 ! axial musculature property_value: seeAlso https://github.com/obophenotype/mouse-anatomy-ontology/issues/4 xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/issues/1405 xsd:anyURI [Term] id: UBERON:0004464 name: musculature of thorax namespace: uberon def: "Any collection of muscles that is part of a thorax [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "muscle group of thorax" EXACT [FMA:71293] synonym: "muscles of thorax" EXACT [FMA:71293] synonym: "musculi thoracis" EXACT LATIN [FMA:71293, FMA:TA] synonym: "set of muscles of thorax" EXACT [FMA:71293] synonym: "thoracic musculature" EXACT [FMA:71293] xref: BTO:0000508 xref: EMAPA:37260 {source="MA:th"} xref: FMA:71293 is_a: UBERON:0004479 ! musculature of trunk intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk property_value: UBPROP:0000012 "BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0004465 name: musculature of neck namespace: uberon def: "Any collection of muscles that is part of a neck [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "cervical muscles" EXACT [AAO:0000091] synonym: "muscle group of neck" EXACT [FMA:71290] synonym: "muscles of neck" EXACT [FMA:71290] synonym: "musculi cervicis" EXACT LATIN [FMA:71290, FMA:TA] synonym: "musculi colli" EXACT LATIN [FMA:71290, FMA:TA] synonym: "neck musculature" EXACT [FMA:71290] synonym: "set of muscles of neck" EXACT [FMA:71290] xref: AAO:0000091 xref: EMAPA:36050 xref: FMA:71290 xref: MESH:D009334 is_a: UBERON:0008229 ! craniocervical region musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck [Term] id: UBERON:0004469 name: musculature of back namespace: uberon def: "Any collection of muscles that is part of a back [Automatically generated definition]." [OBOL:automatic] synonym: "muscle group of back" EXACT [FMA:71291] synonym: "muscles of back" EXACT [FMA:71291] synonym: "musculi dorsi" EXACT LATIN [FMA:71291, FMA:TA] synonym: "set of muscles of back" EXACT [FMA:71291] xref: FMA:71291 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0001137 ! dorsum [Term] id: UBERON:0004470 name: musculature of pelvic girdle namespace: uberon alt_id: UBERON:0004485 alt_id: UBERON:0005633 def: "Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "muscle group of pelvic girdle" EXACT [FMA:50205] synonym: "muscle group of pelvis" EXACT [FMA:50248] synonym: "muscular system of pelvis" RELATED [FMA:50248] synonym: "pelvic girdle muscle system" EXACT [EHDAA2:0001429] synonym: "pelvic girdle muscles" EXACT [AAO:0000427] synonym: "pelvic girdle musculature" EXACT [FMA:50205] synonym: "set of muscles of pelvic girdle" EXACT [FMA:50205] synonym: "set of muscles of pelvis" RELATED [FMA:50248] xref: AAO:0000427 xref: EHDAA2:0001429 xref: EMAPA:18184 xref: FMA:50205 xref: FMA:50248 is_a: UBERON:0004479 ! musculature of trunk is_a: UBERON:0014792 ! musculature of pelvic complex intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0001271 ! pelvic girdle region property_value: UBPROP:0000012 "we merge two FMA classes here" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004473 name: musculature of face namespace: uberon def: "Any collection of muscles that is part of a face." [OBOL:automatic] subset: pheno_slim synonym: "entire facial musculature" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "facial muscles" EXACT [FMA:71288] synonym: "muscle group of face" EXACT [FMA:71288] synonym: "musculi faciei" EXACT LATIN [FMA:71288, FMA:TA] synonym: "set of facial muscles" RELATED [FMA:71288] synonym: "set of muscles of face" RELATED [FMA:71288] xref: FMA:71288 is_a: UBERON:0008229 ! craniocervical region musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001456 ! face property_value: editor_note "originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose" xsd:string [Term] id: UBERON:0004479 name: musculature of trunk namespace: uberon def: "Any collection of muscles that is part of a trunk [Automatically generated definition]." [OBOL:automatic] subset: efo_slim subset: pheno_slim synonym: "muscle group of trunk" EXACT [FMA:50187] synonym: "muscular system of trunk" RELATED [FMA:50187] synonym: "set of muscles of trunk" EXACT [FMA:50187] xref: AAO:0011572 xref: EFO:0003531 xref: FMA:50187 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk property_value: editor_note "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004490 name: cardiac muscle tissue of atrium namespace: uberon def: "A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]." [OBOL:automatic] synonym: "atrial cardiac muscle tissue" EXACT [GO:0055009] synonym: "atrial heart muscle" EXACT [GO:0055009] synonym: "atrial myocardium" RELATED [GO:0055009, GOC:mtg_heart] synonym: "cardiac atrium muscle" EXACT [GO:0055009] xref: FMA:7283 is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002302 ! myocardium of atrium property_value: UBPROP:0000012 "in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging." xsd:string {external_ontology="GO"} [Term] id: UBERON:0004491 name: cardiac muscle tissue of interatrial septum namespace: uberon def: "A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]." [OBOL:automatic] synonym: "interatrial septum cardiac muscle tissue" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "interatrial septum heart muscle" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "interatrial septum muscle" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "interatrial septum myocardium" EXACT [http://orcid.org/0000-0002-6601-2165] xref: FMA:84083 is_a: UBERON:0004492 ! cardiac muscle tissue of cardiac septum intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002085 ! interatrial septum relationship: part_of UBERON:0002085 ! interatrial septum [Term] id: UBERON:0004492 name: cardiac muscle tissue of cardiac septum namespace: uberon def: "A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac septum cardiac muscle tissue" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "cardiac septum heart muscle" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "cardiac septum muscle" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "cardiac septum myocardium" EXACT [http://orcid.org/0000-0002-6601-2165] xref: FMA:226279 is_a: UBERON:0001133 ! cardiac muscle tissue intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002099 ! cardiac septum relationship: part_of UBERON:0002099 ! cardiac septum [Term] id: UBERON:0004493 name: cardiac muscle tissue of myocardium namespace: uberon def: "A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim xref: EMAPA:32688 xref: FMA:261726 xref: MA:0002441 is_a: UBERON:0001133 ! cardiac muscle tissue intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002349 ! myocardium relationship: part_of UBERON:0002349 {source="MA"} ! myocardium property_value: editor_note "Note placement of MA class based on parthood relationship" xsd:string [Term] id: UBERON:0004521 name: vasculature of muscle organ namespace: uberon def: "A vasculature that is part of a muscle organ [Automatically generated definition]." [OBOL:automatic] synonym: "muscular organ vasculature" EXACT [FMA:87123] xref: FMA:87123 is_a: UBERON:0004522 ! vasculature of musculoskeletal system is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0001630 ! muscle organ [Term] id: UBERON:0004522 name: vasculature of musculoskeletal system namespace: uberon def: "A vasculature that is part of a musculoskeletal system [Automatically generated definition]." [OBOL:automatic] xref: FMA:239607 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002204 ! musculoskeletal system relationship: part_of UBERON:0002204 ! musculoskeletal system [Term] id: UBERON:0004535 name: cardiovascular system namespace: uberon def: "Anatomical system that has as its parts the heart and blood vessels." [BTO:0000088] subset: efo_slim subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "CV system" RELATED [BTO:0000088] synonym: "Herz und Gefaesssystem" RELATED [BTO:0000088] xref: AAO:0011001 xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 xref: MA:0000010 xref: MAT:0000016 xref: MESH:D002319 xref: MIAA:0000016 xref: NCIT:C12686 xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA xref: SCTID:278198007 xref: TAO:0000010 xref: UMLS:C0007226 {source="ncithesaurus:Cardiovascular_System"} xref: VHOG:0000302 xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart intersection_of: has_part UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004537 name: blood vasculature namespace: uberon def: "A vascular network consisting of blood vessels." [https://orcid.org/0000-0002-6601-2165] synonym: "blood system" RELATED [] synonym: "blood vascular network" EXACT [] synonym: "blood vessel system" RELATED [] synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel relationship: composed_primarily_of UBERON:0001981 ! blood vessel [Term] id: UBERON:0004548 name: left eye namespace: uberon def: "An eye that is part of a left side of organism [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "left eyeball" EXACT [FMA:12515] synonym: "left orbital part of face" NARROW [FMA:54450] synonym: "left orbital region" NARROW [FMA:54450] xref: EMAPA:37362 {source="MA:th"} xref: FMA:12515 xref: MA:0002949 xref: NCIT:C119334 xref: SCTID:362503005 is_a: UBERON:0000970 ! eye is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000970 ! eye intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: in_left_side_of UBERON:0000468 ! multicellular organism property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0004549 name: right eye namespace: uberon def: "An eye that is part of a right side of organism [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "right eyeball" EXACT [FMA:12514] synonym: "right orbital part of face" NARROW [FMA:54449] synonym: "right orbital region" NARROW [FMA:54449] xref: EMAPA:37363 {source="MA:th"} xref: FMA:12514 xref: MA:0002950 xref: NCIT:C119333 xref: SCTID:362502000 is_a: UBERON:0000970 ! eye is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000970 ! eye intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: in_right_side_of UBERON:0000468 ! multicellular organism property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0004571 name: systemic arterial system namespace: uberon def: "The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Systemic_circulation#Arteries] subset: pheno_slim synonym: "systemic arterial circulatory system" EXACT [FMA:45623] xref: FMA:45623 xref: Wikipedia:Systemic_circulation#Arteries is_a: UBERON:0007798 {source="MA-inferred"} ! vascular system relationship: part_of UBERON:0004572 ! arterial system [Term] id: UBERON:0004572 name: arterial system namespace: uberon def: "The part of the cardiovascular system consisting of all arteries." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim xref: BTO:0004690 xref: EHDAA2:0000143 xref: EHDAA:396 xref: EMAPA:16201 xref: EMAPA:16371 xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: has_member UBERON:0001637 ! artery property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000273", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004573 name: systemic artery namespace: uberon def: "An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Artery#Systemic_arteries] subset: pheno_slim synonym: "systemic arterial subtree" EXACT [FMA:66464] xref: EMAPA:37126 {source="MA:th"} xref: FMA:66464 xref: Wikipedia:Artery#Systemic_arteries is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0004571 ! systemic arterial system relationship: part_of UBERON:0004571 ! systemic arterial system [Term] id: UBERON:0004581 name: systemic venous system namespace: uberon def: "The part of the venous system that drains the general body tissues[Kardong]" [ISBN:0073040584, Wikipedia:Systemic_venous_system] synonym: "systemic venous circulatory system" EXACT [FMA:45626] xref: FMA:45626 xref: Wikipedia:Systemic_venous_system is_a: UBERON:0002049 ! vasculature relationship: part_of UBERON:0004582 ! venous system property_value: UBPROP:0000001 "In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]" xsd:string {source="Wikipedia:Systemic_venous_system"} property_value: UBPROP:0000001 "Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]" xsd:string {ontology="FMA", source="FMA:45626"} property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004582 name: venous system namespace: uberon def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [https://orcid.org/0000-0002-6601-2165] synonym: "vein system" EXACT [] xref: BTO:0004692 xref: EHDAA2:0002171 xref: EHDAA:486 xref: EMAPA:16240 xref: MA:0002720 xref: NCIT:C33858 xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: composed_primarily_of UBERON:0001638 ! vein property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004638 name: blood vessel endothelium namespace: uberon def: "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart" [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: vertebrate_core xref: BTO:0000766 xref: CALOHA:TS-2155 xref: EMAPA:35176 xref: MA:0000709 xref: NCIT:C53395 xref: TAO:0005257 xref: UMLS:C1706972 {source="ncithesaurus:Blood_Vessel_Endothelium"} xref: ZFA:0005257 is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel [Term] id: UBERON:0004663 name: aorta wall namespace: uberon def: "An anatomical wall that is part of an aorta, enclosing the luminal space." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "aortic wall" EXACT [FMA:14156] synonym: "wall of aorta" EXACT [FMA:14156] xref: EMAPA:35139 xref: FMA:14156 xref: MA:0002901 is_a: UBERON:0035965 ! wall of blood vessel intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000947 ! aorta relationship: contributes_to_morphology_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta [Term] id: UBERON:0004664 name: aorta tunica adventitia namespace: uberon def: "the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers" [ISBN:0-683-40008-8, MP:0009871] subset: pheno_slim synonym: "tunica adventitia of aorta" EXACT [FMA:14283] xref: EMAPA:35136 xref: FMA:14283 xref: MA:0002902 xref: SCTID:24996002 is_a: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: part_of UBERON:0000947 ! aorta relationship: contributes_to_morphology_of UBERON:0004663 ! aorta wall relationship: part_of UBERON:0004663 ! aorta wall [Term] id: UBERON:0004667 name: interventricular septum muscular part namespace: uberon alt_id: UBERON:0004144 def: "The muscular portion of the wall between the two lower chambers of the heart" [http://orcid.org/0000-0002-6601-2165, Wikipedia:Interventricular_septum#Portions] subset: pheno_slim synonym: "cardiac ventricular muscular septum" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "muscular interventricular septum" EXACT [FMA:7134] synonym: "muscular interventricular septum" RELATED [MA:0002940] synonym: "muscular part interventricular septum" EXACT [] synonym: "muscular part of interventricular septum" EXACT [FMA:7134] synonym: "muscular septum" BROAD [GO:0003150] synonym: "pars muscularis (septi interventricularis)" EXACT [FMA:7134] synonym: "pars muscularis septi interventricularis" EXACT LATIN [FMA:7134, FMA:TA] synonym: "septum membranaceum" EXACT LATIN [] synonym: "ventricular muscular septum" EXACT [] xref: EHDAA2:0000885 xref: EHDAA:2607 xref: EMAPA:18247 xref: FMA:7134 xref: MA:0002940 xref: RETIRED_EHDAA2:0000888 is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: contributes_to_morphology_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum property_value: UBPROP:0000001 "The muscular septum is the lower part of the ventricular septum[GO]" xsd:string {source="GO:0003150"} [Term] id: UBERON:0004688 name: costo-cervical trunk namespace: uberon def: "The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]." [Wikipedia:Costocervical_trunk] synonym: "costocervical trunk" EXACT [FMA:10636] synonym: "truncus costocervicalis" RELATED LATIN [Wikipedia:Costocervical_trunk] synonym: "trunk of costocervical artery" EXACT [FMA:10636] xref: EMAPA:37496 {source="MA:th"} xref: FMA:10636 xref: MA:0001939 xref: SCTID:244225009 xref: Wikipedia:Costocervical_trunk is_a: UBERON:0001637 ! artery property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png xsd:anyURI [Term] id: UBERON:0004695 name: arterial system smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:36503 xref: MA:0000704 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0004572 ! arterial system relationship: part_of UBERON:0004572 ! arterial system [Term] id: UBERON:0004696 name: venous system smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:36613 xref: MA:0000715 is_a: UBERON:0004237 ! blood vessel smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0004582 ! venous system relationship: part_of UBERON:0004237 ! blood vessel smooth muscle relationship: part_of UBERON:0004582 ! venous system [Term] id: UBERON:0004699 name: outflow tract endothelium namespace: uberon def: "An endothelium that is part of a outflow tract [Automatically generated definition]." [OBOL:automatic] xref: MA:0000490 xref: VHOG:0001524 is_a: UBERON:0008307 ! heart endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract property_value: UBPROP:0000003 "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001524", ontology="VHOG", source="DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004700 name: arterial system endothelium namespace: uberon def: "An endothelium that is part of an arterial system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:35145 xref: MA:0000703 xref: NCIT:C49329 xref: UMLS:C1706849 {source="ncithesaurus:Arterial_System_Endothelium"} is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004572 ! arterial system relationship: part_of UBERON:0004572 ! arterial system [Term] id: UBERON:0004701 name: venous system endothelium namespace: uberon def: "An endothelium that is part of a venous system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:35907 xref: MA:0000714 xref: NCIT:C49320 xref: UMLS:C1710626 {source="ncithesaurus:Venous_System_Endothelium"} is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004582 ! venous system relationship: part_of UBERON:0004582 ! venous system [Term] id: UBERON:0004702 name: respiratory system blood vessel endothelium namespace: uberon def: "A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:35732 xref: MA:0001805 is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004807 ! respiratory system epithelium intersection_of: UBERON:0004638 ! blood vessel endothelium intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003504 ! respiratory system blood vessel [Term] id: UBERON:0004706 name: bulbus cordis namespace: uberon def: "a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches" [ISBN:0-683-40008-8, MP:0010568] subset: pheno_slim subset: vertebrate_core synonym: "primitive right ventricle endocardium" EXACT [EHDAA2:0000197, JB:def] xref: EHDAA2:0000197 xref: EHDAA:438 xref: EHDAA:768 xref: EMAPA:16333 xref: FMA:70300 xref: NCIT:C34114 xref: SCTID:361525002 xref: UMLS:C1284055 {source="ncithesaurus:Bulbus_Cordis"} xref: Wikipedia:Bulbus_cordis is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000948 ! heart property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png xsd:anyURI property_value: editor_note "TODO - check relationship to bulbus arteriosus" xsd:string property_value: UBPROP:0000001 "A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000173", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0004708 name: paired limb/fin namespace: uberon alt_id: UBERON:0009872 def: "An appendage that is part of an appendage girdle complex." [https://github.com/geneontology/go-ontology/issues/9029, UBERON:cjm] subset: homology_grouping synonym: "girdle-associated appendage" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "jointed paired lateral appendage" NARROW [https://orcid.org/0000-0002-6601-2165] synonym: "limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "limb/fin" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "paired appendage" NARROW [VSAO:0000067] synonym: "pectoral or pelvic appendage" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "pelvic/pectoral appendage" EXACT [https://orcid.org/0000-0002-6601-2165] xref: VSAO:0000067 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000026 {source="VSAO"} ! appendage intersection_of: UBERON:0000026 ! appendage intersection_of: part_of UBERON:0010707 ! appendage girdle complex relationship: connected_to UBERON:0007823 ! appendage girdle region relationship: develops_from UBERON:0004357 {evidence="definitional"} ! paired limb/fin bud relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature relationship: has_part UBERON:0002049 ! vasculature relationship: has_skeleton UBERON:0011582 ! paired limb/fin skeleton relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010707 {source="VSAO"} ! appendage girdle complex property_value: IAO:0000232 "this class is the union of the classes limb, pectoral fin and pelvic fin." xsd:string [Term] id: UBERON:0004709 name: pelvic appendage namespace: uberon alt_id: UBERON:0009876 def: "Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues." [VSAO:0000150] subset: homology_grouping synonym: "hindlimb/pelvic fin" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "pelvic appendage" EXACT [VSAO:0000126] synonym: "pelvic limb/fin" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "posterior appendage" BROAD [] synonym: "posterior limb/fin" EXACT [] synonym: "posterior paired appendage" EXACT [VSAO:0000126] xref: VSAO:0000126 is_a: UBERON:0004708 ! paired limb/fin intersection_of: UBERON:0004708 ! paired limb/fin intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: connected_to UBERON:0001271 ! pelvic girdle region relationship: develops_from UBERON:0005420 {evidence="definitional"} ! pelvic appendage bud relationship: has_skeleton UBERON:0007273 ! pelvic appendage skeleton relationship: part_of UBERON:0010709 ! pelvic complex [Term] id: UBERON:0004711 name: jugular vein namespace: uberon def: "The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava." [Wikipedia:Jugular_vein] synonym: "jugular" RELATED [] synonym: "vena jugularis" RELATED [BTO:0001744] xref: BTO:0001744 xref: CALOHA:TS-0497 xref: EMAPA:18638 xref: GAID:536 xref: MA:0002154 xref: MESH:D007601 xref: NCIT:C12738 xref: SCTID:244403000 xref: UMLS:C0022427 {source="ncithesaurus:Jugular_Vein"} xref: Wikipedia:Jugular_vein is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: drains UBERON:0000033 ! head property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png xsd:anyURI [Term] id: UBERON:0004716 name: conceptus namespace: uberon def: "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." [BTO:0003834, Wikipedia:Conceptus] synonym: "embryo plus adnexa" EXACT [] xref: AEO:0000194 xref: BTO:0003834 xref: EHDAA2:0000001 xref: EHDAA2:0003235 xref: EMAPA:36040 xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure relationship: develops_from CL:0000365 ! animal zygote relationship: existence_ends_with UBERON:0000068 ! embryo stage relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004731 name: neuromere namespace: uberon def: "A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres)." [DOI:10.1016/j.tins.2013.06.004, https://github.com/obophenotype/uberon/issues/318] subset: pheno_slim synonym: "neural metamere" RELATED [] synonym: "neural segment" RELATED [] synonym: "neural tube metameric segment" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "neural tube segment" EXACT [] synonym: "neuromere" EXACT [] synonym: "neuromeres" EXACT PLURAL [TAO:0001328] xref: NLX:147842 xref: TAO:0001328 xref: Wikipedia:Neuromere xref: ZFA:0001328 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: part_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube property_value: editor_note "We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted" xsd:string property_value: UBPROP:0000001 "A metameric segment of the central nervous system.[ZFA]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001328", ontology="TAO", source="ZFIN:curator"} created_by: Melissa Haendel creation_date: 2009-06-18T09:00:04Z [Term] id: UBERON:0004732 name: segmental subdivision of nervous system namespace: uberon def: "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres." [FBbt:00005140, http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "neuromere" RELATED [FBbt:00005140] xref: FBbt:00005140 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000063 ! organ subunit intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system property_value: editor_note "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string [Term] id: UBERON:0004733 name: segmental subdivision of hindbrain namespace: uberon def: "An organ subunit that is part of a hindbrain [Automatically generated definition]." [OBOL:automatic] subset: non_informative synonym: "hindbrain segment" EXACT [FMA:61998] synonym: "segment of hindbrain" EXACT [FMA:61998] xref: FMA:61998 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004732 ! segmental subdivision of nervous system is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain [Term] id: UBERON:0004734 name: gastrula namespace: uberon alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "gastrula embryo" EXACT [BILA:0000060] synonym: "tri-laminar disc" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "tri-laminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar blastocyst" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar blastoderm" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar disc" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 xref: FBbt:00005317 xref: FMA:293108 xref: GAID:1302 xref: MESH:A16.254.412 xref: MIAA:0000179 xref: NCIT:C34057 xref: NCIT:C34058 xref: UMLS:C0017199 {source="ncithesaurus:Gastrula"} xref: UMLS:C1284022 {source="ncithesaurus:Trilaminar_Embryonic_Disc"} xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage relationship: develops_from UBERON:0000307 ! blastula relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} [Term] id: UBERON:0004755 name: skeletal tissue namespace: uberon def: "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/134, PSPUB:0000170, VSAO:0000015] comment: Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from xref: EMAPA:37744 {source="MA:th"} xref: MA:0003047 xref: SCTID:309311006 xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002384 {source="VSAO"} ! connective tissue relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell relationship: part_of UBERON:0004765 ! skeletal element property_value: UBPROP:0000001 "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} [Term] id: UBERON:0004756 name: dermal skeletal element namespace: uberon def: "dermis-derived entity that is made of skeletal tissue." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/206] synonym: "dermal element" EXACT [VSAO:curator] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004765 ! skeletal element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0004765 ! skeletal element intersection_of: develops_from UBERON:0002067 ! dermis intersection_of: has_part UBERON:0004755 ! skeletal tissue relationship: develops_from UBERON:0002067 ! dermis relationship: has_part UBERON:0004755 ! skeletal tissue [Term] id: UBERON:0004761 name: cartilaginous neurocranium namespace: uberon def: "The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]." [Wikipedia:Chondrocranium] synonym: "cartilaginous chondocranium" EXACT [] synonym: "cartilaginous skull" RELATED [] synonym: "cartiligionous skeletal structure of skull" EXACT [] synonym: "chondocranium" RELATED [Wikipedia:Chondrocranium] synonym: "embryonic chondocranium" RELATED [] synonym: "neurocranium" RELATED SENSU [] xref: AAO:0000094 xref: AAO:0010153 xref: EHDAA:6031 xref: FMA:76621 xref: NCIT:C34121 xref: SCTID:155540009 xref: UMLS:C1516496 {source="ncithesaurus:Chondrocranium"} xref: Wikipedia:Chondrocranium xref: XAO:0003059 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: develops_from UBERON:0009617 {source="PMC1571569"} ! head paraxial mesoderm relationship: has_part UBERON:0002418 ! cartilage tissue relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: UBPROP:0000012 "in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004764 name: intramembranous bone tissue namespace: uberon def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, Wikipedia:Intramembranous_ossification] xref: MA:0002837 xref: Wikipedia:Intramembranous_ossification is_a: UBERON:0002481 ! bone tissue intersection_of: UBERON:0002481 ! bone tissue intersection_of: output_of GO:0001957 ! intramembranous ossification relationship: develops_from UBERON:0003104 ! mesenchyme relationship: output_of GO:0001957 ! intramembranous ossification relationship: part_of UBERON:0002514 ! intramembranous bone property_value: UBPROP:0000012 "note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)" xsd:string {external_ontology="MA"} [Term] id: UBERON:0004765 name: skeletal element namespace: uberon def: "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." [https://orcid.org/0000-0002-6601-2165] subset: organ_slim subset: uberon_slim xref: AAO:0011129 xref: galen:SkeletalStructure xref: TAO:0001890 xref: VSAO:0000128 xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004766 name: cranial bone namespace: uberon def: "A bone that is part of a cranium." [UBERON:automatic] synonym: "cranium bone" EXACT [UBERON:automatic] xref: SCTID:181792001 is_a: UBERON:0003457 ! head bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003128 ! cranium relationship: part_of UBERON:0003128 ! cranium property_value: IAO:0000232 "here cranium = skull - mandible" xsd:string [Term] id: UBERON:0004768 name: bone of lower jaw namespace: uberon def: "Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular" [https://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "lower jaw bone" EXACT [] is_a: UBERON:0012360 ! bone of jaw intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0003278 ! skeleton of lower jaw property_value: editor_note "Do not manually classify under here - bones are automatically classified" xsd:string [Term] id: UBERON:0004770 name: articular system namespace: uberon def: "Anatomical system that consists of all the joints of the body." [VSAO:0000181] synonym: "joint system" EXACT [FMA:23878] synonym: "set of all joints" RELATED [] synonym: "set of all joints of body" EXACT [FMA:23878] synonym: "set of joints of body" RELATED [FMA:23878] xref: EMAPA:35150 xref: FMA:23878 xref: MA:0003007 xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: has_member UBERON:0000982 ! skeletal joint relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: functionally_related_to GO:0040011 ! locomotion relationship: has_member UBERON:0000982 ! skeletal joint relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system [Term] id: UBERON:0004777 name: respiratory system submucosa namespace: uberon def: "A submucosa that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius submucosa" EXACT [OBOL:automatic] synonym: "submucosa of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "submucosa of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37578 {source="MA:th"} xref: MA:0001822 is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003570 ! respiratory system connective tissue [Term] id: UBERON:0004779 name: respiratory system lamina propria namespace: uberon def: "A lamina propria that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius lamina propria" EXACT [OBOL:automatic] synonym: "apparatus respiratorius lamina propria mucosa" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of respiratory system" EXACT [OBOL:automatic] synonym: "lamina propria of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "lamina propria of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system lamina propria mucosa" EXACT [OBOL:automatic] xref: EMAPA:37576 {source="MA:th"} xref: MA:0001821 is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003570 ! respiratory system connective tissue relationship: part_of UBERON:0004785 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system mucosa [Term] id: UBERON:0004784 name: heart ventricle wall namespace: uberon def: "An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "anatomical wall of cardiac ventricle" EXACT [OBOL:automatic] synonym: "anatomical wall of heart ventricle" EXACT [OBOL:automatic] synonym: "anatomical wall of lower chamber of heart" EXACT [OBOL:automatic] synonym: "anatomical wall of ventricle of heart" EXACT [OBOL:automatic] synonym: "cardiac ventricle anatomical wall" EXACT [OBOL:automatic] synonym: "cardiac ventricle wall" EXACT [OBOL:automatic] synonym: "heart ventricle anatomical wall" EXACT [OBOL:automatic] synonym: "lower chamber of heart anatomical wall" EXACT [OBOL:automatic] synonym: "lower chamber of heart wall" EXACT [OBOL:automatic] synonym: "ventricle of heart anatomical wall" EXACT [OBOL:automatic] synonym: "ventricle of heart wall" EXACT [OBOL:automatic] synonym: "ventricular wall" EXACT [FMA:13884] synonym: "wall of cardiac ventricle" EXACT [OBOL:automatic] synonym: "wall of heart ventricle" EXACT [OBOL:automatic] synonym: "wall of lower chamber of heart" EXACT [OBOL:automatic] synonym: "wall of ventricle" RELATED [MA:0002791] synonym: "wall of ventricle of heart" EXACT [OBOL:automatic] xref: FMA:13884 xref: MA:0002791 xref: NCIT:C119295 is_a: UBERON:0037144 ! wall of heart intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle [Term] id: UBERON:0004785 name: respiratory system mucosa namespace: uberon def: "the mucous membrane lining the respiratory tract" [MESH:A04.760, MGI:cwg, MP:0002277] subset: pheno_slim synonym: "apparatus respiratorius mucosa" EXACT [OBOL:automatic] synonym: "apparatus respiratorius mucosa of organ" EXACT [OBOL:automatic] synonym: "apparatus respiratorius mucous membrane" EXACT [OBOL:automatic] synonym: "laryngeal mucous membrane" RELATED [EMAPA:18334] synonym: "mucosa of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "mucosa of organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "mucosa of organ of respiratory system" EXACT [OBOL:automatic] synonym: "mucosa of respiratory system" EXACT [OBOL:automatic] synonym: "mucous membrane of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "mucous membrane of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory mucosa" RELATED [BTO:0000973] synonym: "respiratory system mucosa of organ" EXACT [OBOL:automatic] synonym: "respiratory system mucous membrane" EXACT [OBOL:automatic] synonym: "respiratory tract mucosa" RELATED [] xref: BTO:0000973 xref: EMAPA:18334 xref: EMAPA:37577 {source="MA:th"} xref: FMA:302092 xref: GAID:304 xref: MA:0001827 xref: MESH:D020545 is_a: UBERON:0000344 ! mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system property_value: editor_note "TODO - split respiratory tract mucosa from respiratory system mucosa" xsd:string [Term] id: UBERON:0004794 name: esophagus secretion namespace: uberon def: "A secretion that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophageal secretion" EXACT [FMA:79662] synonym: "gullet secretion" EXACT [OBOL:automatic] synonym: "oesophagus secretion" EXACT [OBOL:automatic] synonym: "secretion of esophagus" EXACT [OBOL:automatic] synonym: "secretion of gullet" EXACT [OBOL:automatic] synonym: "secretion of oesophagus" EXACT [OBOL:automatic] xref: FMA:79662 xref: MA:0002514 xref: NCIT:C52555 xref: UMLS:C0227179 {source="ncithesaurus:Esophagus_Secretion"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000456 ! secretion of exocrine gland intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus [Term] id: UBERON:0004797 name: blood vessel layer namespace: uberon def: "Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:36296 xref: MA:0002854 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0035965 ! wall of blood vessel property_value: depicted:by Blood:vessels.svg xsd:anyURI [Term] id: UBERON:0004802 name: respiratory tract epithelium namespace: uberon def: "the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi" [ISBN:0-683-40008-8, MGI:anna, MP:0010942] subset: pheno_slim synonym: "airway epithelium" RELATED [BTO:0000419] synonym: "epithelial tissue of respiratory tract" EXACT [OBOL:automatic] synonym: "epithelium of respiratory tract" EXACT [OBOL:automatic] synonym: "respiratory epithelium" RELATED [BTO:0000419] synonym: "respiratory tract epithelial tissue" EXACT [OBOL:automatic] xref: BTO:0000419 xref: CALOHA:TS-0023 xref: EMAPA:32827 xref: MA:0001480 xref: SCTID:321764001 xref: VHOG:0000981 is_a: UBERON:0004807 ! respiratory system epithelium is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010499 ! pseudostratified ciliated columnar epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0000072 ! proximo-distal subdivision of respiratory tract [Term] id: UBERON:0004807 name: respiratory system epithelium namespace: uberon def: "An epithelium that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "apparatus respiratorius epithelial tissue" EXACT [OBOL:automatic] synonym: "apparatus respiratorius epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "epithelial tissue of respiratory system" EXACT [OBOL:automatic] synonym: "epithelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "epithelium of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system epithelial tissue" EXACT [OBOL:automatic] xref: CALOHA:TS-0023 xref: EMAPA:32826 xref: MA:0001823 xref: VHOG:0000981 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0004815 name: lower respiratory tract epithelium namespace: uberon def: "An epithelium that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] synonym: "epithelial tissue of lower respiratory tract" EXACT [OBOL:automatic] synonym: "epithelium of lower respiratory tract" EXACT [OBOL:automatic] synonym: "lower respiratory tract epithelial tissue" EXACT [OBOL:automatic] xref: EMAPA:37549 {source="MA:th"} xref: MA:0001481 is_a: UBERON:0004802 ! respiratory tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract [Term] id: UBERON:0004830 name: respiratory system skeletal muscle namespace: uberon def: "A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "respiratory system skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "skeletal muscle of respiratory system" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37583 {source="MA:th"} xref: MA:0001829 is_a: UBERON:0001134 ! skeletal muscle tissue intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0004831 name: esophagus skeletal muscle namespace: uberon def: "A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] comment: Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal synonym: "esophagus skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle of esophagus" EXACT [OBOL:automatic] xref: EMAPA:36523 xref: MA:0001572 is_a: UBERON:0003898 ! skeletal muscle tissue of trunk intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0003832 ! esophagus muscle [Term] id: UBERON:0004833 name: lip skeletal muscle namespace: uberon def: "A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]." [OBOL:automatic] synonym: "lip skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle of lip" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue of lip" EXACT [OBOL:automatic] xref: EMAPA:37642 {source="MA:th"} xref: MA:0001578 is_a: UBERON:0001134 ! skeletal muscle tissue intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip property_value: editor_note "this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips" xsd:string [Term] id: UBERON:0004848 name: respiratory system arterial endothelium namespace: uberon def: "An endothelium of artery that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius arterial endothelium" EXACT [OBOL:automatic] synonym: "apparatus respiratorius artery endothelium" EXACT [OBOL:automatic] synonym: "apparatus respiratorius endothelium of artery" EXACT [OBOL:automatic] synonym: "arterial endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "arterial endothelium of respiratory system" EXACT [OBOL:automatic] synonym: "artery endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "artery endothelium of respiratory system" EXACT [OBOL:automatic] synonym: "endothelium of artery of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "endothelium of artery of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system artery endothelium" EXACT [OBOL:automatic] synonym: "respiratory system endothelium of artery" EXACT [OBOL:automatic] xref: EMAPA:37566 {source="MA:th"} xref: MA:0001801 is_a: UBERON:0001917 ! endothelium of artery is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0001917 ! endothelium of artery intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003469 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system artery [Term] id: UBERON:0004849 name: respiratory system venous endothelium namespace: uberon def: "An endothelium of vein that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] synonym: "apparatus respiratorius endothelium of vein" EXACT [OBOL:automatic] synonym: "apparatus respiratorius vein endothelium" EXACT [OBOL:automatic] synonym: "apparatus respiratorius venous endothelium" EXACT [OBOL:automatic] synonym: "endothelium of vein of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "endothelium of vein of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system endothelium of vein" EXACT [OBOL:automatic] synonym: "respiratory system vein endothelium" EXACT [OBOL:automatic] synonym: "vein endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "vein endothelium of respiratory system" EXACT [OBOL:automatic] synonym: "venous endothelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "venous endothelium of respiratory system" EXACT [OBOL:automatic] xref: EMAPA:37585 {source="MA:th"} xref: MA:0001811 is_a: UBERON:0001919 ! endothelium of vein is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0001919 ! endothelium of vein intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003476 ! respiratory system venous blood vessel [Term] id: UBERON:0004851 name: aorta endothelium namespace: uberon def: "the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall" [MGI:csmith, MP:0009864] subset: efo_slim subset: pheno_slim synonym: "adult aorta endothelium" EXACT [OBOL:automatic] synonym: "aortic endothelium" RELATED [BTO:0000394] synonym: "endothelium of adult aorta" EXACT [OBOL:automatic] synonym: "endothelium of aorta" EXACT [OBOL:automatic] synonym: "endothelium of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "endothelium of trunk of systemic arterial tree" EXACT [OBOL:automatic] synonym: "trunk of aortic tree endothelium" EXACT [OBOL:automatic] synonym: "trunk of systemic arterial tree endothelium" EXACT [OBOL:automatic] xref: BTO:0000394 xref: CALOHA:TS-0047 xref: EFO:0002597 xref: EMAPA:35134 xref: MA:0000701 xref: NCIT:C49190 xref: UMLS:C1706824 {source="ncithesaurus:Aorta_Endothelium"} is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004700 ! arterial system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta [Term] id: UBERON:0004852 name: cardiovascular system endothelium namespace: uberon def: "An endothelium that is part of the cardiovascular system." [https://orcid.org/0000-0002-6601-2165] subset: vertebrate_core synonym: "endothelia" RELATED PLURAL [ZFA:0001639] synonym: "vascular endothelia" RELATED PLURAL [XAO:0000356] xref: BTO:0001853 xref: EMAPA:35201 xref: GAID:519 xref: MA:0000717 xref: MESH:D004730 xref: NCIT:C13053 xref: TAO:0002171 xref: UMLS:C0014261 {source="ncithesaurus:Vascular_Endothelium"} xref: VHOG:0001217 xref: XAO:0000356 xref: ZFA:0001639 is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system property_value: editor_note "consider merging with 'endothelium'" xsd:string property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004857 name: skeletal muscle connective tissue namespace: uberon def: "A connective tissue that surrounds a skeletal muscle tissue." [OBOL:automatic] synonym: "connective tissue of skeletal muscle" EXACT [OBOL:automatic] synonym: "connective tissue of skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "portion of connective tissue of skeletal muscle" EXACT [OBOL:automatic] synonym: "portion of connective tissue of skeletal muscle tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle interstitial tissue" RELATED [MA:0002868] synonym: "skeletal muscle interstitum" RELATED [MA:0002868] synonym: "skeletal muscle portion of connective tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle textus connectivus" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue connective tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue portion of connective tissue" EXACT [OBOL:automatic] synonym: "skeletal muscle tissue textus connectivus" EXACT [OBOL:automatic] synonym: "textus connectivus of skeletal muscle" EXACT [OBOL:automatic] synonym: "textus connectivus of skeletal muscle tissue" EXACT [OBOL:automatic] xref: EMAPA:37743 {source="MA:th"} xref: MA:0002868 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: surrounds UBERON:0001134 ! skeletal muscle tissue relationship: surrounds UBERON:0001134 ! skeletal muscle tissue [Term] id: UBERON:0004859 name: eye gland namespace: uberon def: "A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid." [http://orcid.org/0000-0002-6601-2165] comment: Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands subset: organ_slim synonym: "eye-associated gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "gland of eye" EXACT [OBOL:automatic] xref: EMAPA:35334 xref: MA:0000267 is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0000970 ! eye [Term] id: UBERON:0004864 name: vasculature of retina namespace: uberon def: "A vasculature that is part of a retina [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "retina vasculature" EXACT [GO:0061298] synonym: "retina vasculature of camera-type eye" EXACT [GO:0061298] synonym: "retinal blood vessels" EXACT [FMA:76552] synonym: "retinal blood vessels set" EXACT [FMA:76552] synonym: "retinal vasculature" EXACT [OBOL:automatic] synonym: "set of blood vessels of retina" EXACT [OBOL:automatic] synonym: "set of retinal blood vessels" EXACT [FMA:76552] synonym: "vasa sanguinea retinae" EXACT LATIN [FMA:76552, FMA:TA] xref: FMA:76552 xref: MESH:D012171 xref: XAO:0004153 is_a: UBERON:0002203 ! vasculature of eye is_a: UBERON:0036302 ! vasculature of central nervous system plus retina intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002161 NCBITaxon:8782 {source="PMID:21622558", source="PMID:2772405", submitter="michaelerice"} [Term] id: UBERON:0004872 name: splanchnic layer of lateral plate mesoderm namespace: uberon def: "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]." [Wikipedia:Lateral_plate_mesoderm#Division_into_layers] subset: pheno_slim synonym: "inner layer of lateral plate mesoderm" EXACT [] synonym: "splanchnic mesoderm" RELATED [ISBN:9780878932504] synonym: "visceral mesoderm" BROAD [BILA:0000044, http://www.drugs.com/dict/visceral-mesoderm.html, http://www.stedmans.com/] xref: AAO:0011102 xref: BILA:0000044 xref: FMA:295568 xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004873 name: splanchnopleure namespace: uberon def: "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]." [Wikipedia:Splanchnopleure] synonym: "ventral splanchnic mesoderm" RELATED [Wikipedia:Intraembryonic_coelom] xref: EHDAA2:0001903 xref: EHDAA:383 xref: EMAPA:16181 xref: FMA:295564 xref: NCIT:C34303 xref: UMLS:C1519472 {source="ncithesaurus:Splanchnopleure"} xref: VHOG:0000558 xref: Wikipedia:Splanchnopleure is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png xsd:anyURI property_value: editor_note "TODO - check relationship to LPM" xsd:string [Term] id: UBERON:0004874 name: somatopleure namespace: uberon def: "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]." [Wikipedia:Somatopleure] xref: EHDAA2:0001847 xref: EHDAA:381 xref: EMAPA:16180 xref: FMA:295566 xref: NCIT:C34301 xref: UMLS:C1519423 {source="ncithesaurus:Somatopleure"} xref: VHOG:0000557 xref: Wikipedia:Somatopleure is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png xsd:anyURI property_value: UBPROP:0000011 "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" xsd:string property_value: UBPROP:0000012 "sources differ as to whether this is part-of or develops-from the LPM" xsd:string [Term] id: UBERON:0004880 name: chordamesoderm namespace: uberon def: "The central region of trunk mesoderm. This tissue forms the notochord" [https://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: pheno_slim synonym: "axial chorda mesoderm" EXACT [ZFA:0000091] synonym: "chorda mesoderm" EXACT [] synonym: "dorsal mesoderm" EXACT [https://github.com/obophenotype/uberon/wiki/The-neural-crest] synonym: "presumptive notochord" EXACT [ZFA:0000091] xref: AAO:0000478 xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string [Term] id: UBERON:0004883 name: lung mesenchyme namespace: uberon def: "The mass of tissue made up of mesenchymal cells in the lung." [GO:0060484] subset: pheno_slim synonym: "lung-associated mesenchyme" EXACT [GO:0060484] synonym: "mesenchyme of lung" EXACT [OBOL:automatic] synonym: "pulmonary mesenchyme" EXACT [GO:0060484] xref: EMAPA:32866 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002048 ! lung relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: part_of UBERON:0002048 ! lung [Term] id: UBERON:0004905 name: articulation namespace: uberon def: "Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] xref: FBbt:00005811 is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system [Term] id: UBERON:0004906 name: ectodermal part of digestive tract namespace: uberon def: "A portion of the gut that is derived from ectoderm." [GO:0007439] synonym: "ectodermal gut" EXACT [] synonym: "gut ectoderm" EXACT [EMAPA:32930] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0004908 name: upper digestive tract namespace: uberon def: "The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum." [Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract] subset: uberon_slim synonym: "upper gastrointestinal tract" EXACT [] synonym: "upper GI tract" EXACT [] xref: FMA:49177 xref: galen:UpperGastrointestinalTract xref: NCIT:C33837 xref: SCTID:181244000 xref: UMLS:C0226874 {source="ncithesaurus:Upper_Gastrointestinal_Tract"} xref: Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract is_a: UBERON:0004921 ! subdivision of digestive tract relationship: develops_from UBERON:0001041 ! foregut property_value: UBPROP:0000012 "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004909 name: epithelium of gonad namespace: uberon def: "An epithelium surrounding a gonad." [OBOL:automatic] synonym: "gonad epithelium" EXACT [OBOL:automatic] synonym: "gonadal epithelium" EXACT [OBOL:automatic] synonym: "gonadal sheath" RELATED [FBbt:00004859] xref: EHDAA:4032 xref: EHDAA:5931 xref: FBbt:00004859 xref: NCIT:C32676 xref: UMLS:C1517534 {source="ncithesaurus:Germinal_Epithelium"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000991 ! gonad relationship: part_of UBERON:0000991 ! gonad property_value: editor_note "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string [Term] id: UBERON:0004911 name: epithelium of female gonad namespace: uberon def: "An epithelium surrounding an ovary." [OBOL:automatic] synonym: "ovarian epithelium" EXACT [OBOL:automatic] synonym: "ovarian sheath" NARROW SENSU [FBbt:00004896] synonym: "ovary epithelium" EXACT [OBOL:automatic] xref: BTO:0003661 xref: FBbt:00004896 is_a: UBERON:0004909 ! epithelium of gonad intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary property_value: editor_note "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string [Term] id: UBERON:0004921 name: subdivision of digestive tract namespace: uberon def: "A proximal-distal subdivision of the digestive tract." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "alimentary system subdivision" RELATED [FMA:71131] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] xref: FBbt:00100315 xref: FMA:71131 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract relationship: subdivision_of UBERON:0001555 ! digestive tract property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string [Term] id: UBERON:0004923 name: organ component layer namespace: uberon def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0002-6601-2165] subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall [Term] id: UBERON:0004924 name: submucosa of pharynx namespace: uberon def: "The tissue underlying the tunica mucosa of the pharynx." [BTO:0002113] synonym: "pharyngeal submucosa" EXACT [FMA:75144] synonym: "pharyngobasilar fascia" RELATED [] synonym: "pharynx submucosa" EXACT [OBOL:automatic] synonym: "submucous coat of pharynx" RELATED [BTO:0002113] synonym: "submucous layer of pharynx" RELATED [BTO:0002113] synonym: "tela submucosa pharyngea" EXACT LATIN [FMA:75144, FMA:TA] synonym: "tela submucosa pharyngis" EXACT LATIN [BTO:0002113] xref: BTO:0002113 xref: FMA:75144 xref: SCTID:19594009 is_a: UBERON:0004777 ! respiratory system submucosa is_a: UBERON:0018257 ! submucosa of digestive tract intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx [Term] id: UBERON:0005032 name: mucosa of lower lip namespace: uberon def: "A mucosa that is part of a lower lip [Automatically generated definition]." [OBOL:automatic] synonym: "lower labial mucosa" EXACT [UBERON:cjm] synonym: "lower lip mucosa" EXACT [OBOL:automatic] synonym: "lower lip mucosa of organ" EXACT [OBOL:automatic] synonym: "lower lip mucous membrane" EXACT [OBOL:automatic] synonym: "lower lip organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of organ of lower lip" EXACT [OBOL:automatic] synonym: "mucous membrane of lower lip" EXACT [OBOL:automatic] synonym: "organ mucosa of lower lip" EXACT [OBOL:automatic] xref: FMA:59833 xref: NCIT:C12225 xref: SCTID:362089001 xref: UMLS:C0226939 {source="ncithesaurus:Mucosa_of_the_Lower_Lip"} is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0036294 ! mucosa of lip intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001835 ! lower lip relationship: part_of UBERON:0001835 ! lower lip [Term] id: UBERON:0005056 name: external female genitalia namespace: uberon def: "An external genitalia that is part of a female reproductive system [Automatically generated definition]." [OBOL:automatic] comment: TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 subset: organ_slim subset: pheno_slim synonym: "external female genital organ" EXACT [BTO:0003100] synonym: "external genitalia of female reproductive system" EXACT [OBOL:automatic] synonym: "female external genitalia" EXACT [FMA:45649] synonym: "organa genitalia feminina externa" RELATED [BTO:0003100] xref: BTO:0003100 xref: EMAPA:30984 xref: FMA:45649 xref: galen:FemaleExternalGenitalia xref: SCTID:362234008 is_a: UBERON:0003134 ! female reproductive organ is_a: UBERON:0004176 ! external genitalia intersection_of: UBERON:0004176 ! external genitalia intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009196 ! indifferent external genitalia property_value: UBPROP:0000008 "in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]" xsd:string [Term] id: UBERON:0005057 name: immune organ namespace: uberon def: "An organ that is part of a immune system [Automatically generated definition]." [OBOL:automatic] subset: organ_slim subset: pheno_slim synonym: "immune system organ" EXACT [] is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002405 ! immune system relationship: part_of UBERON:0002405 ! immune system [Term] id: UBERON:0005058 name: hemolymphoid system gland namespace: uberon def: "A gland that is part of a hemolymphoid system [Automatically generated definition]." [OBOL:automatic] subset: organ_slim synonym: "haemolymphoid system gland" RELATED [EMAPA:18766] synonym: "hemopoietic or lymphoid gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "hemopoietic or lymphoid organ" BROAD [GO:0048534] xref: EMAPA:18766 xref: MA:0002962 is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system [Term] id: UBERON:0005061 name: neural groove namespace: uberon def: "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds." [GO:0001842, http://orcid.org/0000-0002-6601-2165, Wikipedia:Neural_groove] xref: AAO:0011071 xref: EMAPA:35594 xref: FMA:295624 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1363 xref: NCIT:C34224 xref: SCTID:361463007 xref: UMLS:C0814992 {source="ncithesaurus:Neural_Groove"} xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 name: neural fold namespace: uberon def: "One of the two elevated edges of the neural groove[GO,MP]." [GO:0001842, MP:0011256, Wikipedia:Neural_fold] subset: pheno_slim synonym: "medullary fold" EXACT [MP:0011256] xref: EHDAA2:0001249 xref: FMA:295618 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1364 xref: NCIT:C34223 xref: SCTID:361461009 xref: UMLS:C0814993 {source="ncithesaurus:Neural_Fold"} xref: Wikipedia:Neural_fold xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 name: neural rod namespace: uberon def: "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]." [GO:0014024, ZFA:0000133] subset: efo_slim synonym: "neural tube rod" RELATED [GO:0014027] xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system relationship: develops_from UBERON:0007135 ! neural keel property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005076 name: hindbrain-spinal cord boundary namespace: uberon def: "An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord." [OBOL:automatic] synonym: "hindbrain-spinal cord boundary region" EXACT [] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: adjacent_to UBERON:0002028 ! hindbrain intersection_of: adjacent_to UBERON:0002240 ! spinal cord relationship: adjacent_to UBERON:0002028 ! hindbrain relationship: adjacent_to UBERON:0002240 ! spinal cord relationship: part_of UBERON:0001017 ! central nervous system [Term] id: UBERON:0005082 name: tube lumen namespace: uberon def: "A hole in a tube[GO]." [GO:0060609] xref: AEO:0000078 xref: EHDAA2:0004618 xref: RETIRED_EHDAA2:0003078 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: surrounded_by UBERON:0000025 ! tube relationship: surrounded_by UBERON:0000025 ! tube [Term] id: UBERON:0005085 name: ectodermal placode namespace: uberon def: "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]" [GO:0060788] synonym: "epithelial placode" RELATED [AEO:0000112] xref: AEO:0000218 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001048 ! primordium is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000924 ! ectoderm property_value: editor_note "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string property_value: UBPROP:0000008 "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." xsd:string property_value: UBPROP:0000012 "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" xsd:string {external_ontology="GO", source="https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347"} [Term] id: UBERON:0005090 name: muscle structure namespace: uberon def: "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." [GO:0061061] synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] xref: EMAPA:32715 xref: FBbt:00005073 xref: FMA:30316 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string [Term] id: UBERON:0005092 name: right horn of sinus venosus namespace: uberon synonym: "sinus venosus right horn" EXACT [VHOG:0000489] xref: EHDAA2:0001841 xref: EHDAA:484 xref: EMAPA:16239 xref: FMA:70318 xref: VHOG:0000489 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 {source="FMA"} ! embryonic structure relationship: in_right_side_of UBERON:0002063 ! sinus venosus relationship: part_of UBERON:0002063 ! sinus venosus property_value: UBPROP:0000003 "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000489", ontology="VHOG", source="DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005153 name: epithelial bud namespace: uberon def: "A bud is a protrusion that forms from an epithelial sheet by localized folding." [GO:0060572] xref: BTO:0001639 is_a: UBERON:0005157 ! epithelial fold [Term] id: UBERON:0005156 name: reproductive structure namespace: uberon def: "Any anatomical structure that is part of the reproductive system." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "reproductive system element" EXACT [] synonym: "reproductive system structure" EXACT [] is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure intersection_of: part_of UBERON:0000990 ! reproductive system relationship: part_of UBERON:0000990 ! reproductive system [Term] id: UBERON:0005157 name: epithelial fold namespace: uberon def: "An epithelial sheet bent on a linear axis." [GO:0060571] is_a: UBERON:0000483 ! epithelium [Term] id: UBERON:0005162 name: multi cell part structure namespace: uberon def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [CARO:0001000] subset: upper_level synonym: "cell part cluster" RELATED [FMA:83115] synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 xref: FBbt:00007060 xref: FMA:83115 is_a: BFO:0000040 ! material entity is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: composed_primarily_of GO:0005575 ! cellular_component relationship: has_component GO:0044464 {minCardinality="2"} ! obsolete cell part property_value: UBPROP:0000012 "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" xsd:string {external_ontology="CARO", external_ontology="FMA"} [Term] id: UBERON:0005172 name: abdomen element namespace: uberon def: "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "abdomen organ" EXACT [MA:0000522] xref: MA:0000522 xref: SCTID:272631008 is_a: UBERON:0005173 ! abdominal segment element intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen [Term] id: UBERON:0005173 name: abdominal segment element namespace: uberon def: "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "abdominal segment organ" EXACT [MA:0000529] xref: EMAPA:37062 {source="MA:th"} xref: MA:0000529 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002417 ! abdominal segment of trunk relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0005174 name: dorsal region element namespace: uberon def: "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "back organ" EXACT [MA:0001901] synonym: "dorsal region organ" EXACT [] xref: EMAPA:37274 {source="MA:th"} xref: MA:0001901 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0001137 ! dorsum [Term] id: UBERON:0005177 name: trunk region element namespace: uberon def: "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." [http://orcid.org/0000-0002-6601-2165] subset: non_informative subset: organ_slim synonym: "trunk organ" EXACT [MA:0000516] xref: EMAPA:37270 {source="MA:th"} xref: MA:0000516 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0005178 name: thoracic cavity element namespace: uberon def: "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." [http://orcid.org/0000-0002-6601-2165] subset: non_informative subset: pheno_slim synonym: "thoracic cavity organ" EXACT [MA:0000557] xref: EMAPA:37273 {source="MA:th"} xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ intersection_of: located_in UBERON:0002224 ! thoracic cavity relationship: located_in UBERON:0002224 ! thoracic cavity [Term] id: UBERON:0005179 name: pelvic region element namespace: uberon def: "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis." [http://orcid.org/0000-0002-6601-2165] subset: non_informative subset: organ_slim subset: pheno_slim synonym: "pelvic element" EXACT [] synonym: "pelvis organ" EXACT [MA:0000543] synonym: "pelvis region organ" EXACT [] xref: EMAPA:37275 {source="MA:th"} xref: MA:0000543 is_a: UBERON:0005173 ! abdominal segment element intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk [Term] id: UBERON:0005181 name: thoracic segment organ namespace: uberon def: "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "upper body organ" RELATED [MA:0000563] xref: EMAPA:37271 {source="MA:th"} xref: MA:0000563 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0005194 name: thoracic vein namespace: uberon def: "A vein that is part of a thorax [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:37197 {source="MA:th"} xref: MA:0002235 xref: NCIT:C53142 xref: SCTID:281472008 xref: UMLS:C0226629 {source="ncithesaurus:Thoracic_Vein"} is_a: UBERON:0001638 ! vein is_a: UBERON:0003834 ! thoracic segment blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk [Term] id: UBERON:0005216 name: optic eminence surface ectoderm namespace: uberon def: "An external ectoderm that is part of a optic eminence [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:16539 xref: RETIRED_EHDAA2:0001311 xref: VHOG:0000520 is_a: UBERON:0000076 ! external ectoderm intersection_of: UBERON:0000076 ! external ectoderm intersection_of: part_of UBERON:0004348 ! optic eminence relationship: part_of UBERON:0005234 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! optic eminence ectoderm [Term] id: UBERON:0005234 name: optic eminence ectoderm namespace: uberon def: "An ectoderm that is part of a optic eminence [Automatically generated definition]." [OBOL:automatic] xref: EHDAA:940 xref: EMAPA:16539 xref: RETIRED_EHDAA2:0001309 xref: VHOG:0001105 is_a: UBERON:0000924 ! ectoderm intersection_of: UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0004348 ! optic eminence relationship: part_of UBERON:0004348 ! optic eminence [Term] id: UBERON:0005243 name: interventricular septum endocardium namespace: uberon def: "An endocardium that is part of a interventricular septum [Automatically generated definition]." [OBOL:automatic] synonym: "endocardium of interventricular septum" EXACT [FMA:83584] synonym: "interventricular septum endocardial tissue" RELATED [VHOG:0000615] xref: EHDAA2:0000886 xref: EHDAA2:0000887 xref: FMA:83584 xref: VHOG:0000615 is_a: UBERON:0002165 ! endocardium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum property_value: editor_note "TODO - split?" xsd:string [Term] id: UBERON:0005248 name: bulbus cordis myocardium namespace: uberon def: "A myocardium that is part of a bulbus cordis [Automatically generated definition]." [OBOL:automatic] synonym: "bulbus cordis cardiac muscle" RELATED [VHOG:0000609] xref: EMAPA:36488 xref: VHOG:0000609 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0004706 ! bulbus cordis relationship: part_of UBERON:0004706 ! bulbus cordis [Term] id: UBERON:0005250 name: stomatodeum gland namespace: uberon def: "A gland that is part of a stomodeum." [OBOL:automatic] subset: organ_slim synonym: "stomatodaeum gland" EXACT [VHOG:0000658] xref: VHOG:0000658 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000930 ! stomodeum relationship: part_of UBERON:0000930 ! stomodeum property_value: editor_note "check this" xsd:string [Term] id: UBERON:0005253 name: head mesenchyme namespace: uberon def: "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." [ISBN:0683400088, MP:0011260] subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "cephalic mesenchyme" EXACT [MP:0011260] synonym: "cranial mesenchyme" RELATED [MGI:anna] synonym: "desmocranium" RELATED PENDING_REVIEW [FMA:76622] xref: EFO:0003492 xref: EHDAA2:0000732 xref: EHDAA:179 xref: EMAPA:16098 xref: EMAPA_RETIRED:16269 xref: FMA:76622 xref: TAO:0000113 xref: VHOG:0000332 xref: ZFA:0000113 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme property_value: UBPROP:0000001 "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000113", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005256 name: trunk mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing trunk." [OBOL:automatic] subset: efo_slim subset: vertebrate_core synonym: "trunk and cervical mesenchyme" RELATED [EHDAA2:0002092] xref: EFO:0003485 xref: EHDAA2:0002092 xref: EHDAA:377 xref: EMAPA:16177 xref: TAO:0000081 xref: VHOG:0000281 xref: ZFA:0000081 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000922 ! embryo intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme [Term] id: UBERON:0005290 name: myelencephalon namespace: uberon def: "The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]." [BTO:0000758, Wikipedia:Myelencephalon] subset: uberon_slim synonym: "myelencephalon (medulla oblongata)" RELATED [DHBA:10662] xref: BTO:0000758 xref: CALOHA:TS-0607 xref: CALOHA:TS-2365 xref: DHBA:10662 xref: EHDAA2:0001207 xref: EHDAA:5526 xref: EMAPA:17082 xref: HBA:9512 xref: MA:0000205 xref: VHOG:0000456 xref: Wikipedia:Myelencephalon is_a: UBERON:0004733 ! segmental subdivision of hindbrain relationship: develops_from UBERON:0010096 ! future myelencephalon relationship: immediate_transformation_of UBERON:0010096 {evidence="definitional"} ! future myelencephalon property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg xsd:anyURI property_value: RO:0002174 NCBITaxon:7955 property_value: UBPROP:0000001 "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myelencephalon"} property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} property_value: UBPROP:0000013 "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" xsd:string [Term] id: UBERON:0005291 name: embryonic tissue namespace: uberon def: "A portion of tissue that is part of an embryo." [OBOL:automatic] subset: pheno_slim subset: upper_level synonym: "developing tissue" RELATED [] synonym: "portion of embryonic tissue" EXACT [OBOL:automatic] xref: CALOHA:TS-2100 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0002050 ! embryonic structure [Term] id: UBERON:0005292 name: extraembryonic tissue namespace: uberon def: "Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." [https://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "extra-embryonic tissue" EXACT [] xref: BTO:0003360 xref: CALOHA:TS-2119 xref: EFO:0001406 xref: MAT:0000061 xref: MIAA:0000061 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: part_of UBERON:0016887 ! entire extraembryonic component relationship: part_of UBERON:0016887 ! entire extraembryonic component [Term] id: UBERON:0005316 name: endocardial endothelium namespace: uberon def: "The endothelial lining of the endocardium." [UBERON:cjm] synonym: "endocardium endothelium" EXACT [FMA:83596] synonym: "endothelium of endocardium" EXACT [FMA:83596] xref: FMA:83596 is_a: UBERON:0008307 ! heart endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0002165 ! endocardium relationship: part_of UBERON:0002165 ! endocardium [Term] id: UBERON:0005317 name: pulmonary artery endothelium namespace: uberon def: "An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]." [GO:0061155] synonym: "pulmonary artery endothelial tube" EXACT [GO:0061155] xref: BTO:0000137 is_a: UBERON:0001917 ! endothelium of artery is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery [Term] id: UBERON:0005334 name: oral lamina propria namespace: uberon def: "A lamina propria that is part of a mucosa of oral region." [OBOL:automatic] synonym: "lamina propria of oral mucosa" EXACT [] xref: EMAPA:26947 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000030 ! lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0003343 ! mucosa of oral region relationship: part_of UBERON:0003343 ! mucosa of oral region [Term] id: UBERON:0005337 name: outflow tract of ventricle namespace: uberon def: "A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]." [Wikipedia:Ventricular_outflow_tract] synonym: "heart ventricle outflow tract" EXACT [MP:0010224] synonym: "outflow part of ventricle" EXACT [] synonym: "ventricular outflow tract" EXACT [Wikipedia:Ventricular_outflow_tract] xref: FMA:13225 xref: Wikipedia:Ventricular_outflow_tract xref: XAO:0004140 is_a: UBERON:0004145 ! outflow tract intersection_of: UBERON:0004145 ! outflow tract intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle [Term] id: UBERON:0005338 name: outflow tract aortic component namespace: uberon def: "An outflow tract that is part of a aorta." [OBOL:automatic] xref: EHDAA2:0001353 xref: EMAPA:17329 xref: MA:0000101 xref: VHOG:0001394 is_a: UBERON:0004145 ! outflow tract intersection_of: UBERON:0004145 ! outflow tract intersection_of: part_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta property_value: editor_note "merge with LVOT?" xsd:string [Term] id: UBERON:0005339 name: outflow tract pulmonary component namespace: uberon xref: EHDAA2:0001359 xref: EHDAA:4401 xref: EMAPA:17330 xref: MA:0000102 xref: VHOG:0001395 is_a: UBERON:0004145 ! outflow tract property_value: editor_note "merge with RVOT?" xsd:string [Term] id: UBERON:0005388 name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] xref: FBbt:00004200 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: composed_primarily_of CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye relationship: composed_primarily_of CL:0000210 ! photoreceptor cell relationship: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0001016 ! nervous system [Term] id: UBERON:0005389 name: transparent eye structure namespace: uberon def: "A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "lens" NARROW [] is_a: UBERON:0000061 ! anatomical structure relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000970 ! eye property_value: UBPROP:0000009 "directing or focusing light onto light receptors" xsd:string [Term] id: UBERON:0005396 name: carotid artery segment namespace: uberon def: "One of: the common carotid artery, or its branches, the external and internal carotid arteries." [https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764, Wikipedia:Carotid_artery] subset: efo_slim subset: grouping_class subset: pheno_slim subset: vertebrate_core synonym: "carotid" EXACT [AAO:0010217] synonym: "carotid artery" EXACT [MA:0001925] synonym: "common carotid arterial subdivision" RELATED [FMA:70504] synonym: "subdivision of common carotid artery" EXACT [FMA:70504] xref: AAO:0010217 xref: BTO:0000168 xref: CALOHA:TS-0116 xref: EFO:0000818 xref: EHDAA:6385 xref: EMAPA:18609 xref: EV:0100379 xref: FMA:70504 xref: GAID:478 xref: galen:CarotidArtery xref: MA:0001925 xref: MAT:0000501 xref: MESH:D002339 xref: NCIT:C12687 xref: OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA xref: SCTID:362040006 xref: SCTID:69105007 xref: TAO:0000097 xref: UMLS:C0007272 {source="ncithesaurus:Carotid_Artery"} xref: VHOG:0000266 xref: Wikipedia:Carotid_artery xref: ZFA:0000097 is_a: UBERON:0004573 {source="FMA"} ! systemic artery property_value: editor_note "This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries" xsd:string property_value: UBPROP:0000001 "Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000097", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005398 name: female reproductive gland namespace: uberon def: "A sex gland that is part of a female reproductive system." [OBOL:automatic] subset: organ_slim subset: pheno_slim xref: BTO:0000254 xref: MA:0000383 is_a: UBERON:0003937 ! reproductive gland intersection_of: UBERON:0003937 ! reproductive gland intersection_of: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003134 ! female reproductive organ [Term] id: UBERON:0005420 name: pelvic appendage bud namespace: uberon def: "A limb bud that develops into a hindlimb or pelvic fin." [OBOL:automatic] comment: at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future subset: efo_slim synonym: "hindlimb/pelvic fin bud" EXACT [VHOG:0001260] synonym: "pelvic fin bud" RELATED [TAO:0001384] synonym: "pelvic fin buds" RELATED PLURAL [ZFA:0001384] xref: EFO:0003469 xref: TAO:0001384 xref: VHOG:0001260 xref: ZFA:0001384 is_a: UBERON:0004357 ! paired limb/fin bud intersection_of: UBERON:0004357 ! paired limb/fin bud intersection_of: has_potential_to_develop_into UBERON:0004709 ! pelvic appendage intersection_of: part_of UBERON:0000154 ! posterior region of body relationship: has_developmental_contribution_from UBERON:0005730 ! pelvic appendage field relationship: has_potential_to_develop_into UBERON:0004709 ! pelvic appendage relationship: part_of UBERON:0000154 ! posterior region of body property_value: RO:0002161 NCBITaxon:31033 {source="PMID:15893975"} property_value: UBPROP:0000001 "Fin bud that develops into the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001384", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001260", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005422 name: pelvic appendage apical ectodermal ridge namespace: uberon def: "An apical ectodermal ridge that is part of a pelvic appendage bud." [OBOL:automatic] subset: efo_slim subset: vertebrate_core synonym: "AER hindlimb" RELATED [VHOG:0001066] synonym: "apical ectodermal ridge hind limb" NARROW [VHOG:0001066] synonym: "apical ectodermal ridge hindlimb" NARROW [VHOG:0001066] synonym: "apical ectodermal ridge pelvic fin bud" RELATED [TAO:0001385] synonym: "leg AER" RELATED [] synonym: "lower lmb bud apical ectodermal ridge" NARROW [EHDAA2:0003194] xref: EFO:0003681 xref: EHDAA2:0003194 xref: EMAPA:16892 xref: TAO:0001385 xref: VHOG:0001066 xref: ZFA:0001385 is_a: UBERON:0004356 ! apical ectodermal ridge intersection_of: UBERON:0004356 ! apical ectodermal ridge intersection_of: part_of UBERON:0005420 ! pelvic appendage bud relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm relationship: part_of UBERON:0005420 ! pelvic appendage bud property_value: UBPROP:0000001 "An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001066", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge"} property_value: UBPROP:0000001 "Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001385", ontology="TAO", source="ZIFIN:curator"} property_value: UBPROP:0000003 "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001066", ontology="VHOG", source="DOI:10.1111/j.1440-169X.2007.00942.x", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005423 name: developing anatomical structure namespace: uberon 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 relationship: capable_of GO:0032502 ! developmental process [Term] id: UBERON:0005425 name: presumptive neural retina namespace: uberon def: "Portion of tissue that is the inner layer of the optic cup and will become the neural retina." [ZFIN:curator] subset: vertebrate_core synonym: "future neural epithelium" RELATED [EMAPA:16675] synonym: "future neural layer" RELATED [EMAPA:16675] synonym: "future neural retina" EXACT [] synonym: "future NR" RELATED [] synonym: "future retinal neural layer" EXACT [] synonym: "inner layer optic cup" EXACT [ZFA:0001071] synonym: "optic cup inner layer" EXACT [EHDAA2:0001304] synonym: "presumptive retina" RELATED [TAO:0001071] synonym: "presumptive retinas" EXACT PLURAL [ZFA:0001071] xref: EHDAA2:0001304 xref: EMAPA:16675 xref: TAO:0001071 xref: VHOG:0000490 xref: ZFA:0001071 is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer relationship: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003072 ! optic cup property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000490", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005426 name: lens vesicle namespace: uberon def: "Portion of tissue that gives rise to the lens." [https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834, ZFIN:curator] subset: pheno_slim subset: vertebrate_core synonym: "hollow lens vesicle" NARROW SENSU [] synonym: "immature lens" RELATED [ZFA:0001679] synonym: "lens mass" RELATED [ZFA:0001679, ZFIN:ZDB-PUB-091023-49] synonym: "presumptive lens" RELATED [ZFA:0001679] synonym: "solid lens vesicle" NARROW SENSU [ZFA:0001679] xref: EHDAA2:0000983 xref: EHDAA:4737 xref: EMAPA:17163 xref: SCTID:361510002 xref: TAO:0002205 xref: VHOG:0001163 xref: ZFA:0001679 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0003073 ! lens placode property_value: UBPROP:0000001 "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lens+vesicle"} property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: UBPROP:0000011 "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" xsd:string {source="ZFA"} [Term] id: UBERON:0005427 name: corneal primordium namespace: uberon def: "Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea." [ZFIN:ZDB-PUB-061010-3] xref: TAO:0002188 xref: ZFA:0001688 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 {source="Obol"} ! primordium is_a: UBERON:0010312 ! immature eye is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0000019 {source="ZFA"} ! camera-type eye [Term] id: UBERON:0005428 name: vagal neural crest namespace: uberon def: "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]." [ZFIN:curator] subset: vertebrate_core synonym: "enteric neural crest" RELATED [] synonym: "post-otic neural crest" RELATED [ZFA:0000818] synonym: "VNC" EXACT ABBREVIATION [XAO:0004191] xref: EHDAA2:0002156 xref: EHDAA:669 xref: TAO:0000818 xref: VHOG:0001208 xref: XAO:0004191 xref: ZFA:0000818 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest property_value: UBPROP:0000001 "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000818", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001208", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)" xsd:string {source="filemaps.com"} [Term] id: UBERON:0005432 name: aortic sac namespace: uberon def: "The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates" [MP:0012510] subset: pheno_slim synonym: "saccus aorticus" EXACT LATIN [] xref: EHDAA2:0004145 xref: EHDAA:9826 xref: EMAPA:36461 xref: FMA:71008 xref: RETIRED_EHDAA2:0000133 xref: SCTID:361527005 is_a: UBERON:0001637 {source="EHDAA2"} ! artery is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0004363 {source="EHDAA2"} ! pharyngeal arch artery relationship: part_of UBERON:0004145 ! outflow tract property_value: UBPROP:0000001 "the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]." xsd:string {source="http://medical-dictionary.thefreedictionary.com/aortic+sac"} [Term] id: UBERON:0005496 name: neural tube lateral wall namespace: uberon def: "Portion of tissue on the side of the lumen of the neural tube." [ZFA:0001435] subset: vertebrate_core synonym: "lateral wall neural tube" EXACT [ZFA:0001435] xref: EHDAA2:0001257 xref: EHDAA:2873 xref: EHDAA:912 xref: EMAPA:16166 xref: TAO:0001435 xref: VHOG:0000513 xref: ZFA:0001435 is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001049 ! neural tube [Term] id: UBERON:0005498 name: primitive heart tube namespace: uberon def: "Multi-tissue structure that arises from the heart rudiment and will become the heart tube." [ZFA:0000149] subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 xref: EMAPA:16215 xref: FMA:321916 xref: SCTID:361522004 xref: TAO:0000149 xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:0005501 name: rhombomere lateral wall namespace: uberon def: "A neural tube lateral wall that is part of a rhombomere." [OBOL:automatic] synonym: "future hindbrain lateral wall" RELATED [EMAPA:35364] xref: EMAPA:32819 xref: EMAPA:35364 is_a: UBERON:0005496 ! neural tube lateral wall intersection_of: UBERON:0005496 ! neural tube lateral wall intersection_of: part_of UBERON:0001892 ! rhombomere relationship: part_of UBERON:0001892 ! rhombomere [Term] id: UBERON:0005564 name: gonad primordium namespace: uberon def: "Portion of tissue that gives rise to the immature gonad." [ZFA:0001262] subset: efo_slim subset: grouping_class subset: vertebrate_core synonym: "future gonad" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "gonadal primordium" EXACT [ZFA:0001262] synonym: "immature gonad" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "primitive gonad" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "undifferentiated gonad" EXACT [ZFA:0001262] xref: EFO:0003651 xref: EHDAA:5927 xref: EMAPA:17204 xref: RETIRED_EHDAA2:0002148 xref: TAO:0001262 xref: WBbt:0008366 xref: ZFA:0001262 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001048 {source="Obol"} ! primordium relationship: has_potential_to_develop_into UBERON:0000991 ! gonad relationship: located_in UBERON:0002323 {gci_relation="part_of", gci_filler="NCBITaxon:33511", notes="conservatively place at deuterostome, excluding acoelomates"} ! coelemic cavity lumen relationship: part_of UBERON:0000990 {source="ZFA"} ! reproductive system property_value: UBPROP:0000001 "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001262", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000008 "this is a very broad grouping class" xsd:string [Term] id: UBERON:0005594 name: head somite namespace: uberon def: "Somite located in the head region, caudal to the otic vesicle" [PMID:11830559] synonym: "cranial somite" RELATED [XAO:0000313] synonym: "occipital somite" EXACT [PMID:11830559, XAO:0000313] xref: EHDAA2:0003437 xref: EMAPA:16172 xref: XAO:0000313 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0002329 ! somite is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0002329 ! somite intersection_of: develops_from UBERON:0009617 ! head paraxial mesoderm relationship: develops_from UBERON:0009617 {source="EHDAA2"} ! head paraxial mesoderm relationship: part_of UBERON:0009617 {source="EHDAA2"} ! head paraxial mesoderm property_value: UBPROP:0000008 "in humans this includes somites 1-4" xsd:string property_value: UBPROP:0000011 "They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)" xsd:string {source="PMID:11830559"} property_value: UBPROP:0000012 "EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0005597 name: lung primordium namespace: uberon alt_id: UBERON:3010717 def: "A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum." [XAO:0001002] subset: efo_slim synonym: "lateral diverticula" RELATED [XAO:0001002] synonym: "lung diverticulum" RELATED [AAO:3010717] synonym: "lung endoderm" RELATED [EFO:0002578] xref: AAO:0011059 xref: EFO:0002578 xref: EMAPA:36007 xref: XAO:0001002 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001048 {source="XAO"} ! primordium relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut relationship: has_potential_to_develop_into UBERON:0000170 ! pair of lungs relationship: part_of UBERON:0008947 ! respiratory primordium [Term] id: UBERON:0005598 name: trunk somite namespace: uberon def: "A somite that is part of a trunk." [OBOL:automatic] xref: AAO:0010385 xref: EHDAA2:0003438 xref: EMAPA:16184 xref: XAO:0000314 is_a: UBERON:0002329 ! somite intersection_of: UBERON:0002329 ! somite intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0005613 name: left dorsal aorta namespace: uberon xref: EHDAA2:0000936 xref: EHDAA:404 xref: EMAPA:16205 xref: MA:0000478 xref: SCTID:361403005 xref: VHOG:0000484 is_a: UBERON:0000947 ! aorta is_a: UBERON:0003513 ! trunk blood vessel relationship: part_of UBERON:0005805 ! dorsal aorta property_value: UBPROP:0000003 "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000484", ontology="VHOG", source="ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "Contributes to the arch of aorta in humans" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} [Term] id: UBERON:0005614 name: lens anterior epithelium namespace: uberon def: "A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex." [http://orcid.org/0000-0002-6601-2165] synonym: "anterior epithelium of lens vesicle" RELATED [EMAPA:17304] synonym: "anterior surface of lens" RELATED [FMA:58889] synonym: "lens epithelium" BROAD [] synonym: "lens subcapsular epithelium" EXACT [http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm] synonym: "subcapsular lens epithelium" EXACT [FMA:70612] xref: EHDAA2:0000984 xref: EHDAA:9059 xref: EMAPA:17304 xref: EMAPA:17839 xref: FMA:70612 xref: MA:0001302 xref: NCIT:C33641 xref: RETIRED_EHDAA2:0000976 xref: SCTID:362521008 xref: UMLS:C1182652 {source="ncithesaurus:Subcapsular_Epithelium_of_the_Lens"} xref: VHOG:0001425 is_a: UBERON:0001803 ! epithelium of lens intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0001804 ! capsule of lens intersection_of: part_of UBERON:0000965 ! lens of camera-type eye relationship: adjacent_to UBERON:0000389 ! lens cortex relationship: adjacent_to UBERON:0001804 ! capsule of lens property_value: UBPROP:0000010 "Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm" xsd:string [Term] id: UBERON:0005622 name: right dorsal aorta namespace: uberon xref: EHDAA2:0001720 xref: EHDAA:406 xref: EMAPA:16206 xref: MA:0000479 xref: SCTID:361404004 xref: VHOG:0000485 is_a: UBERON:0000947 ! aorta is_a: UBERON:0003513 ! trunk blood vessel relationship: part_of UBERON:0005805 ! dorsal aorta property_value: UBPROP:0000003 "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000485", ontology="VHOG", source="ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572", source="http://bgee.unil.ch/"} property_value: UBPROP:0000008 "Normally regresses in humans" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} [Term] id: UBERON:0005638 name: anterior chamber epithelium namespace: uberon def: "An epithelium that is part of a anterior chamber of eyeball." [OBOL:automatic] xref: EHDAA2:0000130 is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0001766 ! anterior chamber of eyeball [Term] id: UBERON:0005656 name: lens vesicle epithelium namespace: uberon def: "An epithelium that is part of a lens vesicle." [OBOL:automatic] xref: EHDAA2:0000987 xref: EMAPA:17165 xref: VHOG:0000532 is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0005426 ! lens vesicle [Term] id: UBERON:0005672 name: right lung endothelium namespace: uberon def: "An endothelium that is part of a right lung." [OBOL:automatic] xref: EHDAA2:0001755 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003364 ! epithelium of right lung intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0002167 ! right lung [Term] id: UBERON:0005673 name: left lung endothelium namespace: uberon def: "An endothelium that is part of a left lung." [OBOL:automatic] xref: EHDAA2:0000961 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003365 ! epithelium of left lung intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0002168 ! left lung [Term] id: UBERON:0005688 name: lens vesicle cavity namespace: uberon def: "An anatomical cavity that is part of a lens vesicle." [OBOL:automatic] synonym: "cavity of lens" BROAD [] synonym: "cavity of lens vesicle" EXACT [EMAPA:17164] synonym: "lens cavity" BROAD [EHDAA2:0000986] xref: EHDAA2:0000986 xref: EMAPA:17164 xref: VHOG:0000531 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0005426 ! lens vesicle relationship: luminal_space_of UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0005426 ! lens vesicle property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000531", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005702 name: optic eminence mesenchyme namespace: uberon def: "Mesenchyme that is part of a optic eminence." [OBOL:automatic] xref: EHDAA:942 xref: EMAPA:16324 xref: RETIRED_EHDAA2:0001310 xref: VHOG:0001073 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0004348 ! optic eminence relationship: part_of UBERON:0004348 ! optic eminence [Term] id: UBERON:0005720 name: hindbrain venous system namespace: uberon def: "A venous system that is part of a hindbrain." [OBOL:automatic] synonym: "rhombencephalon venous system" RELATED [VHOG:0001322] xref: EHDAA2:0000776 xref: EMAPA:18632 xref: VHOG:0001322 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004582 ! venous system is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0004582 ! venous system intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain [Term] id: UBERON:0005730 name: pelvic appendage field namespace: uberon def: "A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme." [OBOL:automatic] synonym: "pelvic appendage field of lateral plate mesoderm" EXACT [] synonym: "pelvic fin field" NARROW SENSU [ZFA:0001454] xref: TAO:0001454 xref: ZFA:0001454 is_a: UBERON:0005732 ! paired limb/fin field is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005732 ! paired limb/fin field intersection_of: has_potential_to_develop_into UBERON:0003412 ! pelvic appendage bud mesenchyme relationship: has_potential_to_develop_into UBERON:0003412 ! pelvic appendage bud mesenchyme property_value: UBPROP:0000001 "Embryonic region that develops into the pelvic fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001454", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005732 name: paired limb/fin field namespace: uberon def: "A ring of cells capable of forming a limb or paired fin[Gilbert,modified]." [ISBN:9780878932504] subset: homology_grouping synonym: "limb/fin field of lateral plate mesoderm" EXACT [] synonym: "paired limb/fin field" EXACT [] is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage intersection_of: has_potential_to_developmentally_contribute_to UBERON:0004357 ! paired limb/fin bud relationship: has_potential_to_developmentally_contribute_to UBERON:0004357 ! paired limb/fin bud relationship: part_of UBERON:0003081 {source="ISBN:9780878932504", source="ZFA-inferred"} ! lateral plate mesoderm property_value: editor_note "we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this." xsd:string [Term] id: UBERON:0005734 name: tunica adventitia of blood vessel namespace: uberon def: "The outermost layer of a blood vessel, composed mainly of fibrous tissue." [ISBN:0073040584, Wikipedia:Tunica_externa_(vessels)] synonym: "adventitia externa" EXACT [Wikipedia:Tunica_externa_(vessels)] synonym: "external coat" RELATED [Wikipedia:Tunica_externa_(vessels)] synonym: "tunica adventitia" EXACT [Wikipedia:Tunica_externa_(vessels)] synonym: "tunica adventitia of vessel" EXACT [Wikipedia:Tunica_externa_(vessels)] synonym: "tunica adventitia vasorum" RELATED LATIN [Wikipedia:Tunica_externa_(vessels)] synonym: "tunica externa vasorum" RELATED LATIN [Wikipedia:Tunica_externa_(vessels)] xref: BTO:0002010 xref: EMAPA:36299 xref: NCIT:C33818 xref: SCTID:61066005 xref: UMLS:C0225342 {source="ncithesaurus:Tunica_Adventitia"} xref: Wikipedia:Tunica_externa_(vessels) is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer is_a: UBERON:0005742 ! adventitia relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue relationship: has_quality PATO:0002462 ! collagenous property_value: depicted:by Illu:artery.jpg xsd:anyURI property_value: editor_note "TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings" xsd:string property_value: UBPROP:0000001 "The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]." xsd:string {source="Wikipedia:Tunica_externa_(vessels)"} [Term] id: UBERON:0005740 name: tunica intima of artery namespace: uberon def: "A tunica intima that is part of a artery." [OBOL:automatic] synonym: "arterial intima" EXACT [EV:0100028] synonym: "tunica interna (intima)(arteriae)" EXACT [FMA:14272] xref: EMAPA:36293 xref: EV:0100028 xref: FMA:14272 xref: galen:IntimaOfArtery xref: SCTID:40022005 is_a: UBERON:0002523 ! tunica intima is_a: UBERON:0004797 ! blood vessel layer intersection_of: UBERON:0002523 ! tunica intima intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0000415 ! artery wall [Term] id: UBERON:0005742 name: adventitia namespace: uberon def: "An outermost connective tissue covering of an organ, vessel, or other structure[WP]." [Wikipedia:Adventitia] subset: grouping_class synonym: "tunica advetitia" NARROW [Wikipedia:Adventitia] synonym: "tunica externa" NARROW [FMA:45635] xref: BTO:0002010 xref: FMA:45635 xref: SCTID:30180000 xref: Wikipedia:Adventitia is_a: UBERON:0004923 ! organ component layer relationship: composed_primarily_of UBERON:0002384 ! connective tissue property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg xsd:anyURI [Term] id: UBERON:0005744 name: bone foramen namespace: uberon def: "Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves." [TAO:curator] subset: vertebrate_core synonym: "foramen" BROAD [ZFA:0005386] xref: AAO:0010438 xref: TAO:0001736 xref: VHOG:0001760 xref: ZFA:0005386 is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png xsd:anyURI property_value: UBPROP:0000012 "in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper)." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0005764 name: acellular membrane namespace: uberon def: "A acellular anatomical structure that is the bounding layer of a anatomical structure." [OBOL:automatic] xref: FMA:63871 is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0000061 ! anatomical structure [Term] id: UBERON:0005769 name: basement membrane of epithelium namespace: uberon def: "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Basement_membrane] synonym: "basement membrane" RELATED [FMA:63872] synonym: "basement membrane of connective tissue" EXACT [FMA:63872] synonym: "membrana basalis" EXACT LATIN [Wikipedia:Basement_membrane] xref: AAO:0010596 xref: FMA:63872 xref: GAID:915 xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005800 name: section of aorta namespace: uberon def: "Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle." [ncithesaurus:Aortic_Segment] synonym: "aortic section" EXACT [] synonym: "aortic segment" RELATED [FMA:13087] synonym: "portion of aorta" RELATED [] synonym: "segment of aorta" RELATED [FMA:13087] xref: FMA:13087 xref: NCIT:C34027 xref: SCTID:119203005 xref: UMLS:C0506947 {source="ncithesaurus:Aortic_Segment"} is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000947 ! aorta [Term] id: UBERON:0005805 name: dorsal aorta namespace: uberon def: "The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once." [GO:0035907, https://sourceforge.net/p/geneontology/ontology-requests/8525/] subset: vertebrate_core synonym: "aorta dorsalis" EXACT LATIN [XAO:0000051] synonym: "aortae dorsales" RELATED LATIN [Wikipedia:Dorsal_aorta] synonym: "DA" EXACT [ZFA:0000014] synonym: "dorsal aorta root" RELATED [VHOG:0000264] synonym: "dorsal aortae" RELATED PLURAL [Wikipedia:Dorsal_aorta] synonym: "dorsal aortic root" RELATED [VHOG:0000264] synonym: "dorsal aortæ" RELATED PLURAL [Wikipedia:Dorsal_aorta] xref: AAO:0011029 xref: BTO:0004673 xref: EHDAA:402 xref: EMAPA:18606 xref: SCTID:338637006 xref: TAO:0000014 xref: VHOG:0000264 xref: Wikipedia:Dorsal_aorta xref: XAO:0000051 xref: ZFA:0000014 is_a: UBERON:0000947 ! aorta is_a: UBERON:0003513 ! trunk blood vessel relationship: develops_from UBERON:0001917 ! endothelium of artery relationship: develops_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0002201 ! vasculature of trunk property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png xsd:anyURI property_value: UBPROP:0000001 "Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]." xsd:string {source="Wikipedia:Dorsal_aorta"} property_value: UBPROP:0000001 "Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000014", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch" xsd:string {source="BTO:0004673"} property_value: UBPROP:0000002 "relationship loss: part_of axial vasculature (TAO:0001073)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000014", ontology="TAO"} property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000264", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005856 name: developing mesenchymal condensation namespace: uberon def: "A delimited region of dense mesenchyme within looser mesenchyme." [AEO:0000148] synonym: "mesenchyme condensation" EXACT [EMAPA:25351] xref: AEO:0000148 xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell [Term] id: UBERON:0005863 name: cartilaginous condensation namespace: uberon def: "Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes." [GO:curator] synonym: "cartilage condensation" EXACT [EMAPA:25353] synonym: "cartilagenous condensation" EXACT [EHDAA2:0003147] synonym: "chondrogenic condensation" EXACT [VSAO:0000092] xref: AEO:0000147 xref: EHDAA2_RETIRED:0003147 xref: EMAPA:32731 xref: VSAO:0000092 xref: XAO:0004022 is_a: UBERON:0005856 {source="AEO"} ! developing mesenchymal condensation relationship: develops_from UBERON:0005866 ! pre-cartilage condensation relationship: part_of UBERON:0004288 {source="AEO"} ! skeleton property_value: UBPROP:0000012 "isa cell condensation in VSAO; has_part chondroblast in AEO" xsd:string {external_ontology="VSAO"} [Term] id: UBERON:0005865 name: pre-muscle condensation namespace: uberon alt_id: UBERON:0008714 synonym: "pre muscle mass" EXACT [] synonym: "premuscle mass" EXACT [] xref: AEO:0000149 xref: EHDAA2_RETIRED:0003149 is_a: UBERON:0005856 ! developing mesenchymal condensation intersection_of: UBERON:0005856 ! developing mesenchymal condensation intersection_of: composed_primarily_of CL:0000680 ! muscle precursor cell relationship: composed_primarily_of CL:0000680 ! muscle precursor cell relationship: has_part CL:0000680 {source="AEO"} ! muscle precursor cell relationship: has_potential_to_develop_into UBERON:0005090 ! muscle structure [Term] id: UBERON:0005866 name: pre-cartilage condensation namespace: uberon def: "A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts." [AEO:0000150, AEO:JB] synonym: "pre-chondrogenic condensation" EXACT [] synonym: "precartilage condensation" EXACT [] synonym: "precartilagenous condensation" EXACT [] synonym: "prechondrogenic condensation" EXACT [] xref: AEO:0000150 xref: EHDAA2:0003150 xref: EMAPA:32736 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005856 {source="AEO"} ! developing mesenchymal condensation relationship: has_potential_to_develop_into UBERON:0007844 ! cartilage element relationship: part_of UBERON:0004288 {source="AEO"} ! skeleton property_value: UBPROP:0000001 "A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage." xsd:string {source="http://dictionary.reference.com/browse/precartilage"} [Term] id: UBERON:0005867 name: mandibular prominence namespace: uberon def: "the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip" [ISBN:0-683-40008-8, MP:0010939] subset: pheno_slim synonym: "mandibular process" RELATED [Wikipedia:Mandibular_prominence] synonym: "mandibular swelling" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "prominentia mandibularis" RELATED LATIN [Wikipedia:Mandibular_prominence] xref: EHDAA2:0001061 xref: EHDAA:5871 xref: EMAPA:17355 xref: FMA:293051 xref: NCIT:C34204 xref: UMLS:C1512982 {source="ncithesaurus:Mandibular_Prominence"} xref: Wikipedia:Mandibular_prominence is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0012314 ! embryonic facial prominence relationship: develops_from UBERON:0007237 ! 1st arch mandibular component relationship: part_of UBERON:0000166 ! oral opening property_value: editor_note "check develops_from" xsd:string [Term] id: UBERON:0005902 name: occipital region namespace: uberon def: "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles." [TAO:0001414, UBERONREF:0000007] synonym: "back of head" RELATED [FMA:49187] synonym: "basicranial region" EXACT [ZFA:0001414] synonym: "occipital part of head" EXACT [FMA:49187] synonym: "occipital region of head" EXACT [FMA:49187] xref: AAO:0010199 xref: BTO:0004675 xref: FMA:49187 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2431 xref: SCTID:362618001 xref: TAO:0001414 xref: XAO:0003173 xref: ZFA:0001414 is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0003128 ! cranium property_value: editor_note "TODO - check" xsd:string property_value: UBPROP:0000001 "An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010199", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001414", ontology="TAO", source="TAO:MAH"} [Term] id: UBERON:0005906 name: serous sac namespace: uberon def: "Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]" [FMA:9689, https://github.com/obophenotype/uberon/issues/86] comment: See notes for serous membrane xref: EMAPA:16060 xref: FMA:9689 xref: MA:0000005 xref: SCTID:362890006 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall [Term] id: UBERON:0005911 name: endo-epithelium namespace: uberon def: "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]" [FMA:69065] synonym: "endoderm-derived epithelium" EXACT [] synonym: "endoepithelium" EXACT [] xref: FMA:69065 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000483 ! epithelium intersection_of: develops_from UBERON:0000925 ! endoderm [Term] id: UBERON:0005913 name: zone of bone organ namespace: uberon synonym: "bone organ zone" EXACT [FMA:10483] xref: FMA:10483 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: part_of UBERON:0001474 ! bone element [Term] id: UBERON:0005944 name: axial skeleton plus cranial skeleton namespace: uberon def: "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]." [FMA:71221, https://github.com/obophenotype/uberon/issues/44, https://github.com/obophenotype/uberon/wiki/The-axial-skeleton, VSAO:0000056, Wikipedia:Axial_skeleton] subset: pheno_slim subset: uberon_slim synonym: "skeleton axiale" RELATED LATIN [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 xref: UMLS:C0222645 {source="ncithesaurus:Axial_Skeleton"} xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010912 ! subdivision of skeleton relationship: connected_to UBERON:0002091 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! appendicular skeleton relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg xsd:anyURI property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0005946 name: outflow tract of atrium namespace: uberon def: "An outflow tract that is part of a cardiac atrium." [OBOL:automatic] synonym: "outflow part of atrium" EXACT [FMA:14141] xref: FMA:14141 is_a: UBERON:0004145 ! outflow tract intersection_of: UBERON:0004145 ! outflow tract intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: continuous_with UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002081 ! cardiac atrium [Term] id: UBERON:0005953 name: outflow part of right ventricle namespace: uberon def: "Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk" [MP:0010428] synonym: "arterial cone" RELATED [MP:0010428] synonym: "conus arteriosus" RELATED [MP:0010428] synonym: "conus arteriosus (infundibulum)" EXACT [FMA:7216] synonym: "infundibulum" BROAD [Wikipedia:Conus_arteriosus] synonym: "infundibulum of right ventricle" EXACT [FMA:7216] synonym: "infundibulum of right ventricle" EXACT [MP:0010428] synonym: "outflow tract of right ventricle" EXACT [FMA:7216] synonym: "pulmonary cone" RELATED [MP:0010428] synonym: "pulmonary conus" EXACT [FMA:7216] synonym: "pulmonary conus" RELATED [MP:0010428] synonym: "right ventricle pulmonary outflow tract" EXACT [MP:0010428] synonym: "right ventricular outflow tract" EXACT [MP:0010428] synonym: "RVOT" EXACT ABBREVIATION [MP:0010428] xref: EMAPA:37926 {source="MA:th"} xref: FMA:7216 xref: NCIT:C61368 xref: SCTID:244379003 xref: UMLS:C1881209 {source="ncithesaurus:Infundibulum"} is_a: UBERON:0005337 ! outflow tract of ventricle intersection_of: UBERON:0005337 ! outflow tract of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: continuous_with UBERON:0002333 ! pulmonary trunk relationship: develops_from UBERON:0009889 {source="PMID:17276708"} ! secondary heart field relationship: part_of UBERON:0002080 ! heart right ventricle [Term] id: UBERON:0005956 name: outflow part of left ventricle namespace: uberon def: "Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta." [MP:0010429] subset: pheno_slim synonym: "aortic vestibule" EXACT [MP:0010429] synonym: "aortic vestibule" EXACT [FMA:9473] synonym: "heart left ventricle outflow tract" EXACT [MP:0010429] synonym: "left ventricular outflow" EXACT [FMA:9473] synonym: "left ventricular outflow tract" EXACT [HP:0011103] synonym: "LVOT" EXACT ABBREVIATION [MP:0010429] synonym: "outflow tract of left ventricle" EXACT [FMA:9473] synonym: "Sibson vestibule" EXACT [MP:0010429] synonym: "vestibulum aortae" EXACT LATIN [FMA:9473, FMA:TA] xref: EMAPA:37925 {source="MA:th"} xref: FMA:9473 xref: SCTID:264070001 xref: Wikipedia:Aortic_vestibule is_a: UBERON:0005337 ! outflow tract of ventricle intersection_of: UBERON:0005337 ! outflow tract of ventricle intersection_of: part_of UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0002084 ! heart left ventricle [Term] id: UBERON:0005965 name: outflow part of right atrium namespace: uberon def: "Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]" [FMA:9550, FMA:FMA] synonym: "main part of right atrium" EXACT [FMA:9550] synonym: "outflow tract of right atrium" EXACT [FMA:9550] xref: FMA:9550 is_a: UBERON:0005946 ! outflow tract of atrium intersection_of: UBERON:0005946 ! outflow tract of atrium intersection_of: part_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0002078 ! right cardiac atrium [Term] id: UBERON:0005966 name: outflow part of left atrium namespace: uberon def: "An outflow tract of atrium that is part of a left atrium." [OBOL:automatic] synonym: "main part of left atrium" EXACT [FMA:9551] synonym: "outflow tract of left atrium" EXACT [FMA:9551] xref: FMA:9551 is_a: UBERON:0005946 ! outflow tract of atrium intersection_of: UBERON:0005946 ! outflow tract of atrium intersection_of: part_of UBERON:0002079 ! left cardiac atrium relationship: part_of UBERON:0002079 ! left cardiac atrium [Term] id: UBERON:0005979 name: crista terminalis namespace: uberon def: "The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium" [MP:0010495] subset: pheno_slim synonym: "crista terminalis atrii dextri" EXACT LATIN [FMA:9236, FMA:TA] synonym: "crista terminalis cordis" EXACT [FMA:9236] synonym: "crista terminalis of right atrium" EXACT [FMA:9236] xref: EMAPA:37837 {source="MA:th"} xref: FMA:9236 xref: SCTID:277693004 xref: Wikipedia:Crista_terminalis is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: contributes_to_morphology_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0002078 ! right cardiac atrium [Term] id: UBERON:0005983 name: heart layer namespace: uberon def: "The laminar structure of the heart" [MP:0010545] subset: non_informative subset: pheno_slim is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000948 ! heart relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart [Term] id: UBERON:0005985 name: coronary vessel namespace: uberon def: "Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation" [MP:0010551] subset: pheno_slim xref: MESH:D003331 xref: Wikipedia:Coronary_circulation is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000055 ! vessel intersection_of: part_of UBERON:0000948 ! heart relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart property_value: editor_note "TODO - change relation from part_of" xsd:string [Term] id: UBERON:0005989 name: atrioventricular septum namespace: uberon def: "The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve" [MP:0010592] subset: pheno_slim synonym: "membranous atrioventricular septum" EXACT [FMA:7136] xref: EMAPA:37431 {source="MA:th"} xref: FMA:7136 xref: SCTID:280151006 xref: Wikipedia:Atrioventricular_septum is_a: UBERON:0002099 ! cardiac septum is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002099 ! cardiac septum intersection_of: adjacent_to UBERON:0002078 ! right cardiac atrium intersection_of: adjacent_to UBERON:0002084 ! heart left ventricle relationship: adjacent_to UBERON:0002078 ! right cardiac atrium relationship: adjacent_to UBERON:0002084 ! heart left ventricle relationship: develops_from UBERON:0002062 {source="PMID:15797462", source="Wikipedia"} ! endocardial cushion [Term] id: UBERON:0006003 name: integumentary adnexa namespace: uberon def: "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers." [http://code.google.com/p/caro2/issues/detail?id=5, http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "adnexae cutis" RELATED LATIN [Wikipedia:Skin_appendage] synonym: "body hair or bristle" NARROW [GO:GO] synonym: "skin adnexa" RELATED [Wikipedia:Skin_appendage] synonym: "skin adnexal structure" RELATED [] synonym: "skin appendage" RELATED [Wikipedia:Skin_appendage] xref: EMAPA:37883 {source="MA:th"} xref: Wikipedia:Skin_appendage is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0002416 ! integumental system property_value: editor_note "add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis." xsd:string property_value: UBPROP:0000001 "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]" xsd:string {source="MP:0010678"} [Term] id: UBERON:0006056 name: posterior surface of head namespace: uberon is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: in_posterior_side_of UBERON:0000033 ! head relationship: in_posterior_side_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head [Term] id: UBERON:0006207 name: aortico-pulmonary spiral septum namespace: uberon alt_id: UBERON:0005999 def: "The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions." [MP:0010650, Wikipedia:Aorticopulmonary_septum] subset: emapa_ehdaa2 subset: pheno_slim synonym: "aortic septum" RELATED [Wikipedia:Aorticopulmonary_septum] synonym: "aortico-pulmonary septum" EXACT [Wikipedia:Aorticopulmonary_septum] synonym: "aorticopulmonary septum" EXACT [Wikipedia:Aorticopulmonary_septum] synonym: "septum aorticopulmonale" EXACT LATIN [Wikipedia:Aorticopulmonary_septum] synonym: "spiral septum" RELATED [Wikipedia:Aorticopulmonary_septum] xref: CALOHA:TS-2409 xref: EHDAA2:0000136 xref: EHDAA:2592 xref: EMAPA:16827 xref: VHOG:0000502 xref: Wikipedia:Aorticopulmonary_septum is_a: UBERON:0004142 ! outflow tract septum is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002099 ! cardiac septum intersection_of: adjacent_to UBERON:0002333 ! pulmonary trunk intersection_of: adjacent_to UBERON:0005805 ! dorsal aorta relationship: adjacent_to UBERON:0002333 ! pulmonary trunk relationship: adjacent_to UBERON:0005805 ! dorsal aorta relationship: develops_from UBERON:0000095 {source="PMID:6844926", source="Wikipedia"} ! cardiac neural crest property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png xsd:anyURI [Term] id: UBERON:0006211 name: buccopharyngeal membrane namespace: uberon def: "The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx." [MP:0012521] subset: emapa_ehdaa2 subset: pheno_slim synonym: "oral membrane" RELATED [MP:0012521] synonym: "oral plate" RELATED [MP:0012521] synonym: "oropharyngeal membrane" RELATED [Wikipedia:Buccopharyngeal_membrane] synonym: "pharyngeal membrane" RELATED INCONSISTENT [MP:0012521] xref: EHDAA2:0000189 xref: EHDAA:536 xref: EMAPA:16259 xref: FMA:313607 xref: SCTID:361412007 xref: VHOG:0000380 xref: Wikipedia:Buccopharyngeal_membrane is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003037 ! septum relationship: has_developmental_contribution_from UBERON:0000924 ! ectoderm relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0006264 {source="EHDAA2"} ! mouth-foregut junction property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png xsd:anyURI [Term] id: UBERON:0006218 name: common atrial chamber namespace: uberon subset: emapa_ehdaa2 xref: EHDAA:1267 xref: EMAPA:16342 xref: RETIRED_EHDAA2:0000268 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0002081 ! cardiac atrium [Term] id: UBERON:0006238 name: future brain namespace: uberon def: "The embryonic precursor of the brain." [NLX:94995] subset: cumbo subset: efo_slim subset: emapa_ehdaa2 subset: vertebrate_core synonym: "brain rudiment" EXACT [TAO:0000146] synonym: "embryonic brain" RELATED [BTO:0004726] synonym: "encephalon" NARROW [NLX:94995] synonym: "presumptive brain" EXACT [ZFA:0000146] xref: BAMS:Enc xref: BTO:0004726 xref: EFO:0003431 xref: EHDAA:300 xref: EHDAA:830 xref: EMAPA:16089 xref: FMA:312967 xref: RETIRED_EHDAA2:0000591 xref: TAO:0000146 xref: ZFA:0000146 is_a: UBERON:0006598 ! presumptive structure relationship: has_potential_to_develop_into UBERON:0000955 ! brain relationship: part_of UBERON:0002346 ! neurectoderm property_value: UBPROP:0000001 "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} [Term] id: UBERON:0006241 name: future spinal cord namespace: uberon subset: efo_slim subset: vertebrate_core synonym: "presumptive spinal cord" EXACT [ZFA:0000417] synonym: "presumptive spinal cord neural keel" EXACT [TAO:0000417] synonym: "presumptive spinal cord neural plate" EXACT [TAO:0000417] synonym: "presumptive spinal cord neural rod" EXACT [TAO:0000417] xref: EFO:0003438 xref: EHDAA2:0000674 xref: EHDAA:898 xref: EMAPA:16092 xref: EMAPA:16755 xref: TAO:0000417 xref: ZFA:0000417 is_a: UBERON:0006598 ! presumptive structure relationship: has_potential_to_develop_into UBERON:0001049 {source="EHDAA2"} ! neural tube relationship: has_potential_to_develop_into UBERON:0002240 ! spinal cord relationship: part_of UBERON:0001017 ! central nervous system [Term] id: UBERON:0006264 name: mouth-foregut junction namespace: uberon def: "An anatomical junctions that overlaps the mouth and foregut." [OBOL:automatic] subset: emapa_ehdaa2 xref: EHDAA:534 xref: EMAPA:16258 xref: RETIRED_EHDAA2:0001205 xref: VHOG:0000592 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0007651 ! anatomical junction relationship: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0006267 name: notochordal plate namespace: uberon def: "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord." [VHOG:0001212] subset: emapa_ehdaa2 xref: EHDAA2:0001278 xref: EHDAA:264 xref: EMAPA:16101 xref: NCIT:C34231 xref: UMLS:C1518429 {source="ncithesaurus:Notochordal_Plate"} xref: VHOG:0001212 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0006268 name: notochordal process namespace: uberon def: "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot" [http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm] comment: The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. subset: emapa_ehdaa2 synonym: "chordamesoderm" RELATED [] synonym: "presumptive notochord" RELATED [] xref: EHDAA2:0001279 xref: EHDAA:224 xref: EMAPA:16102 xref: FMA:293135 xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm relationship: only_in_taxon NCBITaxon:7711 ! Chordata [Term] id: UBERON:0006283 name: future cardiac ventricle namespace: uberon alt_id: UBERON:0010226 def: "Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle." [ZFA:0001719] comment: The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] synonym: "early heart ventricle" EXACT [] synonym: "embryonic heart ventricle" EXACT [] synonym: "embryonic ventricle" BROAD [] synonym: "future heart ventricle" EXACT [] synonym: "presumptive cardiac ventricle heart tube" EXACT [ZFA:0001719] synonym: "primitive ventricle" EXACT [EHDAA2:0001531] synonym: "primitive ventricle of heart" EXACT [EMAPA:16350] synonym: "primordial cardiac ventricle" EXACT [FMA:71006] synonym: "primordial ventricle" EXACT [FMA:71006] xref: EHDAA2:0001531 xref: EMAPA:16350 xref: FMA:71006 xref: NCIT:C34160 xref: SCTID:361524003 xref: TAO:0002231 xref: Wikipedia:Embryonic_ventricle xref: ZFA:0001719 is_a: UBERON:0006598 ! presumptive structure relationship: has_potential_to_develop_into UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube relationship: part_of UBERON:0005498 {source="EMAPA"} ! primitive heart tube [Term] id: UBERON:0006311 name: chamber of eyeball namespace: uberon def: "A segment of the eyeball that is filled with refractive media" [http://orcid.org/0000-0002-6601-2165] synonym: "chamber of eye" RELATED [BTO:0002085] synonym: "eye chamber" EXACT [MA:0002459] synonym: "eyeball chamber" EXACT [FMA:58071] xref: BTO:0002085 xref: EMAPA:37529 {source="MA:th"} xref: FMA:58071 xref: MA:0002459 xref: NCIT:C32301 xref: SCTID:280540004 xref: UMLS:C0459556 {source="ncithesaurus:Chamber_of_the_Eye"} is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000063 ! organ subunit intersection_of: location_of UBERON:0006312 ! ocular refractive media intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: location_of UBERON:0006312 ! ocular refractive media relationship: part_of UBERON:0000019 ! camera-type eye [Term] id: UBERON:0006312 name: ocular refractive media namespace: uberon def: "Body substance in a liquid or semi-solid state in the eyeball which serves to refract light." [http://orcid.org/0000-0002-6601-2165] xref: MA:0001911 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000463 ! organism substance relationship: part_of UBERON:0000019 ! camera-type eye property_value: UBPROP:0000009 "ocular refraction" xsd:string [Term] id: UBERON:0006314 name: bodily fluid namespace: uberon def: "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." [MESH:A12.207, Wikipedia:Body_fluid] subset: pheno_slim synonym: "body fluid" EXACT [GAID:266] synonym: "fluid" BROAD [] xref: BIRNLEX:20 xref: EMAPA:37441 {source="MA:th"} xref: FMA:280556 xref: GAID:266 xref: galen:BodyFluid xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: has_quality PATO:0001548 ! quality of a liquid relationship: has_quality PATO:0001548 ! quality of a liquid [Term] id: UBERON:0006347 name: communicating artery namespace: uberon def: "An artery that connects two larger arteries." [ncithesaurus:Communicating_Artery] comment: Grouping for anterior and posterior xref: EMAPA:18598 xref: MA:0001938 xref: NCIT:C52851 xref: UMLS:C1707451 {source="ncithesaurus:Communicating_Artery"} is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: connects UBERON:0001637 {minCardinality="2", maxCardinality="2"} ! artery relationship: connects UBERON:0001637 ! artery [Term] id: UBERON:0006535 name: skin secretion namespace: uberon def: "A portion of organism substance that secreted_by a zone of skin." [OBOL:automatic] synonym: "skin fluid" RELATED [] synonym: "skin fluid/secretion" EXACT [MA:0002537] synonym: "skin substance" RELATED [] xref: MA:0002537 is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0000014 ! zone of skin relationship: produced_by UBERON:0000014 ! zone of skin [Term] id: UBERON:0006537 name: female reproductive gland secretion namespace: uberon def: "A portion of organism substance that is secreted by a female reproductive gland." [UBERON:cjm] synonym: "female reproductive system fluid" RELATED [] synonym: "female reproductive system fluid/secretion" EXACT [MA:0002510] synonym: "female reproductive system secretion" RELATED [] xref: MA:0002510 is_a: UBERON:0022293 ! reproductive gland secretion intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0005398 ! female reproductive gland relationship: produced_by UBERON:0005398 ! female reproductive gland [Term] id: UBERON:0006538 name: respiratory system fluid/secretion namespace: uberon def: "A portion of organism substance that secreted_by a respiratory system." [OBOL:automatic] synonym: "respiratory system fluid" RELATED [] synonym: "respiratory system secretion" RELATED [] xref: EMAPA:36550 xref: MA:0002533 xref: NCIT:C13722 xref: UMLS:C1514899 {source="ncithesaurus:Respiratory_System_Fluid_or_Secretion"} is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0001004 ! respiratory system relationship: produced_by UBERON:0001004 ! respiratory system [Term] id: UBERON:0006562 name: pharynx namespace: uberon def: "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." [GO:0060465] subset: grouping_class subset: uberon_slim synonym: "anterior part of foregut" RELATED [] synonym: "pharyngeal tube" RELATED [] xref: FBbt:00005380 xref: MAT:0000049 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: IAO:0000232 "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string property_value: UBPROP:0000007 "branchial" xsd:string property_value: UBPROP:0000007 "pharyngeal" xsd:string [Term] id: UBERON:0006563 name: tunica media of pulmonary trunk namespace: uberon def: "Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]" [FMA:85030, FMA:FMA] xref: FMA:85030 is_a: UBERON:0007239 ! tunica media of artery intersection_of: UBERON:0002522 ! tunica media intersection_of: part_of UBERON:0002333 ! pulmonary trunk relationship: part_of UBERON:0002333 ! pulmonary trunk [Term] id: UBERON:0006566 name: left ventricle myocardium namespace: uberon def: "A myocardium that is part of a left ventricle of a heart." [http://orcid.org/0000-0002-6601-2165] synonym: "left ventricular myocardium" EXACT [FMA:9558] synonym: "myocardium of left ventricle" EXACT [FMA:9558] xref: EMAPA:17339 xref: FMA:9558 xref: MA:0002983 xref: SCTID:362021000 is_a: UBERON:0001083 ! myocardium of ventricle intersection_of: UBERON:0001083 ! myocardium of ventricle intersection_of: part_of UBERON:0002084 ! heart left ventricle relationship: continuous_with UBERON:0003618 ! aorta tunica media relationship: part_of UBERON:0002084 ! heart left ventricle property_value: UBPROP:0000001 "Myocardium of ventricle which is continuous with the tunica media of aorta." xsd:string {source="FMA:9558"} [Term] id: UBERON:0006567 name: right ventricle myocardium namespace: uberon def: "A myocardium that is part of a right ventricle of a heart." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "myocardium of right ventricle" EXACT [FMA:9535] synonym: "right ventricular myocardium" EXACT [FMA:9535] xref: EMAPA:17342 xref: FMA:9535 xref: MA:0002984 xref: SCTID:362020004 is_a: UBERON:0001083 ! myocardium of ventricle intersection_of: UBERON:0001083 ! myocardium of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: continuous_with UBERON:0006563 ! tunica media of pulmonary trunk relationship: part_of UBERON:0002080 ! heart right ventricle property_value: UBPROP:0000001 "Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk." xsd:string {source="FMA:9535"} [Term] id: UBERON:0006595 name: presumptive endoderm namespace: uberon def: "Presumptive structure of the blastula that will develop into endoderm." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim xref: AAO:0000471 xref: EFO:0003437 xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000307 ! blastula [Term] id: UBERON:0006596 name: presumptive blood namespace: uberon subset: efo_slim synonym: "future blood" EXACT [] xref: AAO:0000468 xref: EFO:0003439 xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood relationship: has_potential_to_develop_into UBERON:0000178 ! blood [Term] id: UBERON:0006598 name: presumptive structure namespace: uberon def: "Portion of embryonic tissue determined by fate mapping to become a structure." [GOC:CVS, GOC:YMB, ZFA:0001116] synonym: "future structure" EXACT [] synonym: "presumptive structures" EXACT [ZFA:0001116] xref: AAO:0000479 xref: TAO:0001116 xref: ZFA:0001116 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure property_value: editor_note "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 name: presumptive ectoderm namespace: uberon def: "Presumptive structure of the blastula that will develop into ectoderm." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "presumptive epidermis" RELATED [ZFA:0001376] xref: AAO:0000470 xref: EFO:0003466 xref: TAO:0001376 xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000307 ! blastula [Term] id: UBERON:0006603 name: presumptive mesoderm namespace: uberon def: "Presumptive structure of the blastula that will develop into mesoderm." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim xref: AAO:0000476 xref: EFO:0003467 xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000307 ! blastula [Term] id: UBERON:0006677 name: surface of epithelium namespace: uberon def: "An anatomical boundary that adjacent_to a epithelium." [OBOL:automatic] synonym: "epithelium surface" EXACT [FMA:70997] xref: FMA:70997 is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: bounding_layer_of UBERON:0000483 ! epithelium relationship: bounding_layer_of UBERON:0000483 ! epithelium relationship: part_of UBERON:0000483 ! epithelium [Term] id: UBERON:0006761 name: corneo-scleral junction namespace: uberon def: "the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm" [MP:0013477] comment: This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 subset: efo_slim subset: pheno_slim subset: vertebrate_core synonym: "cornea limbus" EXACT [] synonym: "corneal limbus" EXACT [GAID:896] synonym: "corneal limbus" EXACT [FMA:58342] synonym: "corneal-scleral limbus" EXACT [PMID:17051547] synonym: "corneoscleral junction" EXACT [GAID:896] synonym: "limbus corneae" EXACT LATIN [Wikipedia:Corneal_limbus] synonym: "limbus corneae" RELATED LATIN [Wikipedia:Corneal_limbus] synonym: "sclerocorneal junction" EXACT [FMA:58342] synonym: "sclerocorneal limbus" EXACT [GAID:896] xref: EFO:0001403 xref: EMAPA:37835 {source="MA:th"} xref: FMA:58342 xref: GAID:896 xref: MESH:D016850 xref: SCTID:63716004 xref: Wikipedia:Corneal_limbus xref: ZFA:0005570 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0000964 ! cornea intersection_of: connects UBERON:0001773 ! sclera relationship: connects UBERON:0000964 ! cornea relationship: connects UBERON:0001773 ! sclera relationship: part_of UBERON:0000019 ! camera-type eye property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png xsd:anyURI [Term] id: UBERON:0006815 name: areolar connective tissue namespace: uberon def: "Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand." [FMA:63897] synonym: "areolar tissue" RELATED [] synonym: "loose areolar connective tissue" EXACT [FMA:63897] synonym: "loose connective tissue" RELATED [AAO:0000027] xref: AAO:0000027 xref: FMA:63897 xref: SCTID:68477002 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: has_part CL:1000303 {source="FMA"} ! fibroblast of areolar connective tissue relationship: part_of UBERON:0000030 ! lamina propria relationship: protects UBERON:0000062 ! organ property_value: UBPROP:0000001 "Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000027", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000002 "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000027", ontology="AAO"} property_value: UBPROP:0000009 "cushions body organs" xsd:string {source="AAO"} [Term] id: UBERON:0006834 name: uterus or analog namespace: uberon def: "A subdivision of a the reproductive tract in a female organism that is the site of embryo development." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "uterus" BROAD SENSU [FBbt:00004924] xref: FBbt:00004924 xref: TADS:0000421 xref: WBbt:0006760 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: site_of GO:0009790 ! embryo development relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000474 ! female reproductive system relationship: site_of GO:0009790 ! embryo development [Term] id: UBERON:0006876 name: vasculature of organ namespace: uberon def: "A vasculature that is part of a organ." [OBOL:automatic] subset: non_informative synonym: "organ vasculature" EXACT [FMA:74612] synonym: "set of blood vessels of organ" EXACT [FMA:74612] xref: FMA:74612 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000062 ! organ relationship: part_of UBERON:0000062 ! organ [Term] id: UBERON:0006904 name: head mesenchyme from mesoderm namespace: uberon def: "A head mesenchyme that develops_from a mesoderm." [OBOL:automatic] subset: efo_slim subset: vertebrate_core synonym: "cranial mesoderm" RELATED [UBERON:0005280] synonym: "head mesenchyme derived from mesoderm" EXACT [] synonym: "head mesenchyme from head mesoderm" EXACT [EHDAA2:0001118] synonym: "head mesenchyme from mesoderm" EXACT [] synonym: "head mesoderm" RELATED [AAO:0011051, UBERON:0005280] synonym: "mesenchyme derived from head mesoderm" EXACT [EHDAA:1057] synonym: "mesenchyme from head mesoderm" EXACT [] xref: AAO:0011051 xref: EFO:0003337 xref: EFO:0003603 xref: EHDAA2:0001118 xref: EHDAA:655 xref: EMAPA:16099 xref: EMAPA_RETIRED:16270 xref: FMA:293859 xref: TAO:0000998 xref: VHOG:0000185 xref: XAO:0000053 xref: ZFA:0000998 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme intersection_of: UBERON:0005253 ! head mesenchyme intersection_of: develops_from UBERON:0000926 ! mesoderm relationship: develops_from UBERON:0003063 {source="EHDAA2", source="XAO"} ! prechordal plate property_value: editor_note "merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme" xsd:string [Term] id: UBERON:0006905 name: mandibular process mesenchyme namespace: uberon def: "Mesenchyme that is part of a mandibular prominence." [OBOL:automatic] synonym: "mesenchyme of mandibular process" EXACT [EMAPA:17357] synonym: "mesenchyme of mandibular prominence" EXACT [https://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0001062 xref: EHDAA:5861 xref: EHDAA:5873 xref: EMAPA:17357 is_a: UBERON:0005253 ! head mesenchyme is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005867 ! mandibular prominence relationship: part_of UBERON:0005867 ! mandibular prominence [Term] id: UBERON:0006909 name: lumen of digestive tract namespace: uberon def: "An anatomical space that surrounded_by a digestive tract." [OBOL:automatic] synonym: "digestive tract lumen" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "gut cavity" EXACT [BTO:0000349] synonym: "gut lumen" EXACT [FMA:45677] synonym: "lumen of alimentary tract" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "lumen of digestive tract" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "lumen of gut" EXACT [FMA:45677] xref: BTO:0000349 xref: EMAPA:32908 xref: FMA:45677 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0001555 ! digestive tract relationship: luminal_space_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0006913 name: lip epithelium namespace: uberon def: "An epithelium that is part of a lip." [OBOL:automatic] xref: BTO:0004468 xref: TAO:0005334 xref: ZFA:0005334 is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip property_value: UBPROP:0000001 "The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005334", ontology="TAO", source="ZFIN:ZDB-PUB-060921-12"} [Term] id: UBERON:0006914 name: squamous epithelium namespace: uberon def: "An epithelium characterised by its most superficial layer consisting of squamous epithelial cells." [Wikipedia:Squamous_epithelium] xref: BTO:0002072 xref: NCIT:C12848 xref: SCTID:40118003 xref: UMLS:C0221909 {source="ncithesaurus:Squamous_Epithelium"} xref: Wikipedia:Squamous_epithelium is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006915 name: stratified squamous epithelium namespace: uberon def: "Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]" [FMA:45563, Wikipedia:Stratified_squamous_epithelium] subset: pheno_slim synonym: "epithelium stratificatum squamosum" EXACT [FMA:45563] xref: FMA:45563 xref: NCIT:C13180 xref: UMLS:C0836131 {source="ncithesaurus:Stratified_Squamous_Epithelium"} xref: Wikipedia:Stratified_squamous_epithelium is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000486 ! multilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell [Term] id: UBERON:0006920 name: esophagus squamous epithelium namespace: uberon def: "A squamous epithelium that is part of a esophagus." [OBOL:automatic] subset: pheno_slim synonym: "esophageal squamous epithelium" RELATED [OBOL:automatic] synonym: "squamous epithelium of esophagus" RELATED [OBOL:automatic] synonym: "squamous oesophageal epithelium" RELATED [MA:0001567] xref: BTO:0003635 xref: CALOHA:TS-1250 xref: EMAPA:35324 xref: MA:0001567 xref: NCIT:C49222 xref: UMLS:C1707950 {source="ncithesaurus:Esophageal_Squamous_Epithelium"} is_a: UBERON:0001976 ! epithelium of esophagus is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0006914 ! squamous epithelium intersection_of: part_of UBERON:0001043 ! esophagus property_value: UBPROP:0000012 "MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass" xsd:string {external_ontology="MA"} [Term] id: UBERON:0006925 name: digestive system gland namespace: uberon def: "Any gland that is part of the digestive system." [UBERON:cjm] subset: organ_slim synonym: "digestive gland" RELATED [BTO:0000345] xref: AAO:0000130 xref: BTO:0000345 is_a: UBERON:0002368 ! endocrine gland is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0002368 ! endocrine gland intersection_of: part_of UBERON:0001007 ! digestive system [Term] id: UBERON:0006934 name: sensory epithelium namespace: uberon def: "Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue." [BTO:0000314] synonym: "neuroepithelium" RELATED INCONSISTENT [BTO:0000314] xref: CALOHA:TS-0682 xref: FMA:62410 xref: SCTID:309045006 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000488 ! atypical epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000098 ! sensory epithelial cell relationship: has_part CL:0000098 ! sensory epithelial cell relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: UBPROP:0000012 "note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0006960 name: ovary stroma namespace: uberon def: "The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis." [Wikipedia:Stroma_of_ovary] synonym: "interstitial tissue of ovary" EXACT [FMA:18626] synonym: "ovarian stroma" EXACT [FMA:18626] synonym: "ovary stroma" EXACT [MA:0002991] synonym: "stroma of the ovary" EXACT [Wikipedia:Stroma_of_ovary] synonym: "stroma ovarica" EXACT [FMA:18626] synonym: "stroma ovarii" RELATED LATIN [Wikipedia:Stroma_of_ovary] xref: CALOHA:TS-1246 xref: EMAPA:28880 xref: FMA:18626 xref: MA:0002991 xref: NCIT:C33638 xref: SCTID:259306002 xref: UMLS:C0737271 {source="ncithesaurus:Stroma_of_the_Ovarian_Cortex"} xref: Wikipedia:Stroma_of_ovary is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003891 ! stroma is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0000992 ! ovary relationship: has_part CL:0002095 {source="FMA"} ! hilus cell of ovary relationship: part_of UBERON:0000992 ! ovary [Term] id: UBERON:0006965 name: vascular cord namespace: uberon def: "The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]." [GO:0072360, ZFA:0005077] subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell relationship: part_of UBERON:0014903 ! primordial vasculature relationship: site_of GO:0048754 ! branching morphogenesis of an epithelial tube [Term] id: UBERON:0006966 name: coronary capillary namespace: uberon def: "A capillary that is part of the coronary system." [http://orcid.org/0000-0002-6601-2165] synonym: "heart capillary" EXACT [GO:0003248] xref: ZFA:0005813 is_a: UBERON:0001982 ! capillary is_a: UBERON:0003498 ! heart blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0000948 ! heart [Term] id: UBERON:0006984 name: anatomical surface namespace: uberon def: "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n" [CARO:0001002] comment: Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. subset: upper_level xref: BILA:0000010 xref: CARO:0001002 xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary [Term] id: UBERON:0007005 name: cardiogenic splanchnic mesoderm namespace: uberon def: "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]." [http://www.drugs.com/dict/cardiogenic-mesoderm.html, https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7, XAO:0000235] subset: efo_slim subset: pheno_slim synonym: "cardiac mesoderm" RELATED [XAO:0000235] synonym: "cardiogenic mesoderm" RELATED [http://www.drugs.com/dict/cardiogenic-mesoderm.html] synonym: "cardiogenic region" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "cardiogenic splanchnopleure" EXACT [EHDAA2:0000214] synonym: "heart primordia" RELATED [XAO:0000235] xref: AAO:0011021 xref: BILA:0000051 xref: EFO:0000315 xref: EHDAA2:0000214 xref: EHDAA:385 xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string property_value: editor_note "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 name: cleaving embryo namespace: uberon def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage relationship: existence_ends_with UBERON:0000107 ! cleavage stage relationship: existence_starts_with UBERON:0000107 ! cleavage stage [Term] id: UBERON:0007026 name: presumptive gut namespace: uberon synonym: "embryonic digestive tube" RELATED [] synonym: "future digestive tract" EXACT [] synonym: "future digestive tube" EXACT [] synonym: "future gut" EXACT [] synonym: "primitive gut" EXACT [] synonym: "primordial digestive tube" RELATED [] synonym: "primordial gut" RELATED [] xref: BILA:0000084 xref: NCIT:C34268 xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract relationship: existence_starts_during UBERON:0000109 ! gastrula stage relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} [Term] id: UBERON:0007098 name: mandibular neural crest namespace: uberon def: "Cranial neural crest that migrates into the mandibular arch." [ZFA:0007064] xref: TAO:0007064 xref: XAO:0000024 xref: ZFA:0007064 is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest relationship: part_of UBERON:0003852 {source="ZFA"} ! rhombencephalon neural crest [Term] id: UBERON:0007100 name: primary circulatory organ namespace: uberon def: "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]." [GO:0007507] comment: Gene notes: Bmp, Nkx, Gata subset: grouping_class synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: FBbt:00003154 xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation relationship: has_part CL:0002494 ! cardiocyte property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 name: neural keel namespace: uberon def: "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section." [ZFIN:ZDB-PUB-961014-576] subset: efo_slim synonym: "presumptive central nervous system" RELATED [ZFA:0000131] xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system relationship: develops_from UBERON:0003075 ! neural plate property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0007188 name: mesothelium of serous pericardium namespace: uberon def: "A mesothelium that is part of a serous pericardium." [OBOL:automatic] synonym: "mesothelium of pericardium" EXACT [FMA:18149] synonym: "pericardial mesothelium" EXACT [FMA:18149] synonym: "serous pericardium mesothelium" EXACT [FMA:18149] xref: BTO:0003157 xref: EMAPA:16133 xref: FMA:18149 xref: SCTID:67300002 is_a: UBERON:0003388 ! mesothelium of pericardial cavity intersection_of: UBERON:0001136 ! mesothelium intersection_of: part_of UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002357 ! serous pericardium [Term] id: UBERON:0007195 name: stroma of bone marrow namespace: uberon def: "The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis." [Wikipedia:Bone_marrow#Stroma] synonym: "bone marrow stroma" EXACT [FMA:21426] xref: CALOHA:TS-0085 xref: FMA:21426 xref: Wikipedia:Bone_marrow#Stroma is_a: UBERON:0003891 ! stroma is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0002371 ! bone marrow relationship: has_part CL:0002240 ! marrow fibroblast relationship: has_part UBERON:0000332 ! yellow bone marrow relationship: has_part UBERON:0003909 ! sinusoid relationship: part_of UBERON:0002371 ! bone marrow [Term] id: UBERON:0007213 name: mesenchyme derived from head neural crest namespace: uberon def: "Mesenchyme that develops_from a cranial neural crest." [OBOL:automatic] subset: efo_slim subset: vertebrate_core synonym: "head mesenchyme from cranial neural crest" EXACT [] synonym: "head mesenchyme from neural crest" EXACT [EHDAA2:0000735] synonym: "head neural crest derived mesenchyme" EXACT [] xref: EFO:0003572 xref: EHDAA2:0000735 xref: EMAPA:16169 xref: EMAPA:16271 xref: EMAPA_RETIRED:16271 xref: TAO:0000787 xref: ZFA:0000787 is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0003099 ! cranial neural crest relationship: develops_from UBERON:0003099 ! cranial neural crest [Term] id: UBERON:0007237 name: 1st arch mandibular component namespace: uberon synonym: "ventral mandibular arch" RELATED [VHOG:0000510] synonym: "ventral pharyngeal arch 1" EXACT [VHOG:0000510] synonym: "ventral visceral arch 1" RELATED [VHOG:0000510] xref: EHDAA2:0000031 xref: EHDAA:583 xref: EMAPA:16382 xref: VHOG:0000510 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0004362 {source="EHDAA2"} ! pharyngeal arch 1 property_value: editor_note "relationship to Meckel's cartilage to be added" xsd:string property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000510", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0007239 name: tunica media of artery namespace: uberon def: "A tunica media that is part of a artery." [OBOL:automatic] synonym: "arterial media" EXACT [EV:0100029] synonym: "tunica media (arteriae)" EXACT [FMA:14273] xref: EMAPA:36294 xref: EV:0100029 xref: FMA:14273 xref: NCIT:C49321 xref: SCTID:84300001 xref: UMLS:C1710627 {source="ncithesaurus:Venous_System_Smooth_Muscle_Tissue"} is_a: UBERON:0002522 ! tunica media intersection_of: UBERON:0002522 ! tunica media intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0000415 ! artery wall [Term] id: UBERON:0007240 name: tunica adventitia of artery namespace: uberon def: "A tunica adventitia that is part of a artery." [OBOL:automatic] synonym: "arterial adventitia" EXACT [EV:0100030] synonym: "tunica externa (adventitia)(arteriae)" EXACT [FMA:14274] xref: EMAPA:36295 xref: EV:0100030 xref: FMA:14274 xref: SCTID:113261001 is_a: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: part_of UBERON:0001637 ! artery relationship: has_part CL:1000306 {source="FMA"} ! fibroblast of tunica adventitia of artery relationship: part_of UBERON:0000415 ! artery wall [Term] id: UBERON:0007241 name: tunica adventitia of vein namespace: uberon def: "A tunica adventitia that is part of a vein." [OBOL:automatic] synonym: "tunica externa (adventitia)(venae)" EXACT [FMA:14355] synonym: "venous adventitia" EXACT [EV:0100034] xref: EMAPA:36310 xref: EV:0100034 xref: FMA:14355 xref: SCTID:13202006 is_a: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein [Term] id: UBERON:0007242 name: tunica intima of vein namespace: uberon def: "A tunica intima that is part of a vein." [OBOL:automatic] synonym: "tunica interna (intima)(venae)" EXACT [FMA:14353] synonym: "venous intima" EXACT [EV:0100032] xref: EMAPA:36308 xref: EV:0100032 xref: FMA:14353 xref: SCTID:2436009 is_a: UBERON:0002523 ! tunica intima is_a: UBERON:0004797 ! blood vessel layer intersection_of: UBERON:0002523 ! tunica intima intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein [Term] id: UBERON:0007243 name: tunica media of vein namespace: uberon def: "A tunica media that is part of a vein." [OBOL:automatic] synonym: "tunica media (venae)" EXACT [FMA:14354] synonym: "venous media" EXACT [EV:0100033] xref: EMAPA:36309 xref: EV:0100033 xref: FMA:14354 xref: SCTID:42049001 is_a: UBERON:0002522 ! tunica media intersection_of: UBERON:0002522 ! tunica media intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein [Term] id: UBERON:0007270 name: pelvic appendage musculature namespace: uberon def: "Any collection of muscles that is part of a pelvic appendage." [OBOL:automatic] synonym: "pelvic fin musculature" NARROW SENSU [ZFA:0000258] xref: TAO:0000258 xref: ZFA:0000258 is_a: UBERON:0007271 ! appendage musculature is_a: UBERON:0014792 ! musculature of pelvic complex intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0004709 ! pelvic appendage relationship: part_of UBERON:0004709 ! pelvic appendage property_value: editor_note "currently defined by location rather than attachment" xsd:string property_value: UBPROP:0000001 "Musculature that is part of the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000258", ontology="TAO", source="TAO:curator"} [Term] id: UBERON:0007271 name: appendage musculature namespace: uberon def: "Any collection of muscles that is part of an appendage." [OBOL:automatic] synonym: "fin musculature" NARROW SENSU [ZFA:0000207] xref: TAO:0000207 xref: ZFA:0000207 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000026 ! appendage relationship: part_of UBERON:0000026 ! appendage property_value: editor_note "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0007273 name: pelvic appendage skeleton namespace: uberon def: "The collection of all skeletal elements in a pelvic appendage region." [https://orcid.org/0000-0002-6601-2165] is_a: UBERON:0011582 ! paired limb/fin skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0004709 ! pelvic appendage relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004709 {source="VSAO"} ! pelvic appendage relationship: skeleton_of UBERON:0004709 ! pelvic appendage [Term] id: UBERON:0007277 name: presumptive hindbrain namespace: uberon def: "The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure." [Wikipedia:Rhombencephalon] subset: efo_slim synonym: "embryonic rhombencephalon" RELATED [CALOHA:TS-2118] synonym: "future hindbrain" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "presumptive rhombencephalon" EXACT [ZFA:0000569] synonym: "rhombencephalon" RELATED [EHDAA2:0001630] xref: BAMS:HB xref: CALOHA:TS-2118 xref: EFO:0003440 xref: EHDAA2:0001630 xref: FMA:295640 xref: TAO:0000569 xref: Wikipedia:Rhombencephalon xref: ZFA:0000569 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0002028 ! hindbrain relationship: develops_from UBERON:0003076 {source="XAO-abduced"} ! posterior neural tube relationship: has_developmental_contribution_from UBERON:0003852 {source="cjm"} ! rhombencephalon neural crest relationship: has_potential_to_develop_into UBERON:0002028 ! hindbrain relationship: part_of UBERON:0006238 ! future brain property_value: editor_note "TODO - unify naming conventions" xsd:string property_value: UBPROP:0000001 "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." xsd:string {source="NPX:PDR"} [Term] id: UBERON:0007278 name: presumptive sinus venosus namespace: uberon def: "Portion of tissue that is part of the heart tube and will become the sinus venosus." [ZFA:0001722] xref: TAO:0002234 xref: ZFA:0001722 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0002063 ! sinus venosus relationship: has_potential_to_develop_into UBERON:0002063 ! sinus venosus relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube [Term] id: UBERON:0007280 name: presumptive endocardium namespace: uberon def: "A presumptive structure that has the potential to develop into a endocardium." [OBOL:automatic] xref: TAO:0002233 xref: ZFA:0001724 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0002165 ! endocardium relationship: develops_from UBERON:0003084 ! heart primordium relationship: has_potential_to_develop_into UBERON:0002165 ! endocardium relationship: part_of UBERON:0005498 ! primitive heart tube property_value: UBPROP:0000001 "Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002233", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0007281 name: presumptive midbrain hindbrain boundary namespace: uberon def: "Embryonic structure that gives rise to the midbrain hindbrain boundary." [ZFA:0001187] subset: efo_slim synonym: "presumptive MHB" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "presumptive midbrain-hindbrain boundary" EXACT [ZFA:0001187] xref: EFO:0003446 xref: TAO:0001187 xref: XAO:0004086 xref: ZFA:0001187 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary relationship: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain [Term] id: UBERON:0007282 name: presumptive segmental plate namespace: uberon def: "A presumptive structure that has the potential to develop into a presomitic mesoderm." [OBOL:automatic] subset: efo_slim synonym: "presumptive segmental plates" RELATED PLURAL [ZFA:0000053] xref: EFO:0003421 xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm [Term] id: UBERON:0007284 name: presumptive neural plate namespace: uberon def: "A presumptive structure that has the potential to develop into a neural plate." [OBOL:automatic] subset: efo_slim synonym: "prospective neuroectoderm" EXACT [ZFA:0000063] synonym: "prospective vegetal ectoderm" EXACT [ZFA:0000063] xref: EFO:0003424 xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate relationship: develops_from UBERON:0002346 ! neurectoderm relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate relationship: part_of UBERON:0004734 ! gastrula property_value: editor_note "consider merging" xsd:string property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0007285 name: presumptive paraxial mesoderm namespace: uberon def: "The part of the blastula that has the potential to develop into a paraxial mesoderm." [https://github.com/obophenotype/uberon/issues/1277, UBERON:cjm] subset: efo_slim synonym: "future paraxial mesenchyme" EXACT [UBERON:cjm] synonym: "future paraxial mesoderm" EXACT [] xref: EFO:0003443 xref: TAO:0000591 xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula [Term] id: UBERON:0007301 name: appendage blood vessel namespace: uberon def: "A blood vessel that is part of a limb/fin." [OBOL:automatic] synonym: "fin blood vessel" NARROW SENSU [ZFA:0005299] synonym: "limb blood vessel" NARROW SENSU [] xref: TAO:0005299 xref: ZFA:0005299 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000026 ! appendage relationship: part_of UBERON:0007304 ! appendage vasculature [Term] id: UBERON:0007303 name: pharyngeal vasculature namespace: uberon def: "A vasculature that is part of a chordate pharynx." [OBOL:automatic] synonym: "branchial vasculature" EXACT [ZFA:0005003] xref: TAO:0005003 xref: ZFA:0005003 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx [Term] id: UBERON:0007304 name: appendage vasculature namespace: uberon def: "A vasculature that is part of a limb/fin." [OBOL:automatic] synonym: "fin vasculature" NARROW SENSU [ZFA:0005095] xref: TAO:0005095 xref: ZFA:0005095 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000026 ! appendage relationship: part_of UBERON:0000026 ! appendage [Term] id: UBERON:0007376 name: outer epithelium namespace: uberon def: "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]." [GO:0008544] subset: grouping_class synonym: "epidermis" EXACT [GO:0008544] synonym: "epidermis (sensu Metazoa)" EXACT [] synonym: "hypoderm" RELATED INCONSISTENT [BTO:0000313] synonym: "hypodermis" RELATED INCONSISTENT [GO:0008544, WBbt:0005733] synonym: "outer epidermal layer" EXACT [] synonym: "outer epithelial layer" EXACT [] xref: BSA:0000073 xref: BTO:0000313 xref: FBbt:00004993 xref: HAO:0000298 xref: TADS:0000109 xref: WBbt:0005733 xref: Wikipedia:Epidermis_(zoology) is_a: UBERON:0003102 ! surface structure is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000468 ! multicellular organism intersection_of: develops_from UBERON:0007383 ! enveloping layer of ectoderm relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: develops_from UBERON:0007383 ! enveloping layer of ectoderm property_value: editor_note "this grouping class exists primarily to align with GO - see GO:0008544." xsd:string [Term] id: UBERON:0007383 name: enveloping layer of ectoderm namespace: uberon def: "Outermost layer of cells surrounding the embryo." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim synonym: "enveloping layer" EXACT [ZFIN:ZDB-PUB-961014-576] synonym: "EVL" EXACT [ZFA:0000086] xref: EFO:0003425 xref: TAO:0000086 xref: ZFA:0000086 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: bounding_layer_of UBERON:0000922 ! embryo relationship: develops_from UBERON:0000076 ! external ectoderm property_value: UBPROP:0000001 "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000002 "relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO"} property_value: UBPROP:0000008 "Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm." xsd:string [Term] id: UBERON:0007389 name: paired limb/fin cartilage namespace: uberon def: "A cartilage tissue that is part of a paired limb or fin." [http://orcid.org/0000-0002-6601-2165] subset: homology_grouping xref: TAO:0001543 xref: ZFA:0001543 is_a: UBERON:0002418 ! cartilage tissue intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004708 ! paired limb/fin relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0004708 ! paired limb/fin property_value: UBPROP:0000001 "Cartilage which is part of one of the paired fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001543", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0007391 name: pelvic appendage cartilage tissue namespace: uberon def: "A cartilage tissue that is part of a pelvic appendage." [OBOL:automatic] synonym: "pelvic fin cartilage" RELATED [TAO:0001459] xref: TAO:0001459 xref: ZFA:0001459 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007389 ! paired limb/fin cartilage intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004709 ! pelvic appendage relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007273 ! pelvic appendage skeleton property_value: UBPROP:0000001 "Cartilage which is part of the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001459", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0007473 name: lumen of epithelial sac namespace: uberon alt_id: EHDAA2:0003079 def: "The space within an epithelial sphere." [AEO:JB] synonym: "cavity of vesicle" EXACT [AEO:0000079] xref: AEO:0000079 is_a: UBERON:0012467 ! enclosed anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0007499 ! epithelial sac relationship: luminal_space_of UBERON:0007499 ! epithelial sac relationship: part_of UBERON:0007499 ! epithelial sac [Term] id: UBERON:0007475 name: matrix-based tissue namespace: uberon alt_id: EHDAA2:0003081 def: "A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified." [AEO:JB] xref: AEO:0000081 xref: EHDAA2:0003081 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: composed_primarily_of GO:0031012 ! extracellular matrix relationship: composed_primarily_of GO:0031012 ! extracellular matrix [Term] id: UBERON:0007499 name: epithelial sac namespace: uberon def: "An epithelial tube that is open at one end only." [AEO:JB, UBERONREF:0000001] xref: AEO:0000115 xref: EHDAA2:0003115 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube is_a: UBERON:0009856 ! sac intersection_of: UBERON:0000483 ! epithelium intersection_of: has_quality PATO:0001987 ! saccular [Term] id: UBERON:0007500 name: epithelial tube open at both ends namespace: uberon def: "An epithelial tube open at both ends that allows fluid flow." [AEO:JB, UBERONREF:0000001] xref: AEO_RETIRED:0000116 xref: RETIRED_EHDAA2:0003116 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube [Term] id: UBERON:0007503 name: epithelial vesicle namespace: uberon alt_id: EHDAA2:0003119 def: "A closed epithelium with a lumen." [AEO:JB] xref: AEO:0000119 xref: EHDAA2:0003119 is_a: UBERON:0000483 {source="AEO"} ! epithelium [Term] id: UBERON:0007524 name: dense mesenchyme tissue namespace: uberon alt_id: EHDAA2:0003146 def: "Mesenchyme with little extracellular matrix." [AEO:JB] xref: AEO:0000146 xref: EHDAA2:0003146 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003104 {source="AEO"} ! mesenchyme relationship: has_part CL:0000057 {source="AEO"} ! fibroblast [Term] id: UBERON:0007530 name: migrating mesenchyme population namespace: uberon alt_id: EHDAA2:0003152 def: "Mesenchymal cells that are migrating." [AEO:JB] xref: AEO:0000152 xref: EHDAA2:0003152 is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007592 name: ciliated columnar epithelium namespace: uberon def: "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]" [FMA:64798] xref: FMA:64798 is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium is_a: UBERON:0007601 ! ciliated epithelium intersection_of: UBERON:0000485 ! simple columnar epithelium intersection_of: has_part CL:0000067 ! ciliated epithelial cell property_value: UBPROP:0000008 "In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system" xsd:string property_value: UBPROP:0000009 "Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]" xsd:string [Term] id: UBERON:0007601 name: ciliated epithelium namespace: uberon def: "Epithelium bearing vibratile cilia on the free surface." [http://medical-dictionary.thefreedictionary.com/ciliated+epithelium] is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000067 ! ciliated epithelial cell relationship: has_part CL:0000067 ! ciliated epithelial cell [Term] id: UBERON:0007616 name: layer of synovial tissue namespace: uberon def: "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." [BTO:0001338, http://www.britannica.com/EBchecked/topic/578563/synovial-tissue] synonym: "stratum synoviale" NARROW [FMA:TA] synonym: "synovial layer" NARROW [FMA:66762] synonym: "synovial membrane" NARROW [FMA:66762] synonym: "synovial tissue" RELATED [BTO:0001338] synonym: "synovium" EXACT [CALOHA:TS-0998] xref: BTO:0001338 xref: CALOHA:TS-0998 xref: FMA:66762 is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: produces UBERON:0001090 ! synovial fluid relationship: composed_primarily_of UBERON:0002384 {source="BTO"} ! connective tissue relationship: produces UBERON:0001090 ! synovial fluid [Term] id: UBERON:0007617 name: synovial cavity of joint namespace: uberon def: "An anatomical cavity that surrounded_by a synovial joint." [OBOL:automatic] synonym: "articular cavity (synovial joint)" EXACT [FMA:11356] synonym: "cavitas articularis (junctura synovialis)" EXACT [FMA:11356] synonym: "cavity of synovial joint" EXACT [FMA:11356] synonym: "joint cavity" RELATED [FMA:11356] synonym: "synovial cavity" RELATED [FMA:11356] xref: FMA:11356 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002217 ! synovial joint relationship: luminal_space_of UBERON:0002217 ! synovial joint relationship: part_of UBERON:0002217 ! synovial joint [Term] id: UBERON:0007625 name: pigment epithelium of eye namespace: uberon def: "epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules." [MP:0005200] subset: pheno_slim synonym: "eye pigment epithelium" RELATED [MESH:A09.371.670] xref: GAID:907 xref: MESH:D010857 is_a: UBERON:0019304 ! sensory organ epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0000970 ! eye [Term] id: UBERON:0007651 name: anatomical junction namespace: uberon def: "An anatomical structure that connects two structures" [http://code.google.com/p/caro2/issues/detail?id=15] subset: upper_level synonym: "anatomical junction" EXACT [] synonym: "junction" BROAD [] xref: FMA:5898 xref: SCTID:91833003 is_a: UBERON:0000061 {source="FMA"} ! anatomical structure relationship: connects UBERON:0000061 {minCardinality="2"} ! anatomical structure [Term] id: UBERON:0007688 name: anlage namespace: uberon def: "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue." [FBbt:00005426, http://flybase.org/reports/FBrf0178740.html, JB:DEF] subset: efo_slim synonym: "developmental field" EXACT [] synonym: "field" BROAD [] synonym: "future organ" RELATED [] synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 xref: FBbt:00005426 xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure [Term] id: UBERON:0007690 name: early pharyngeal endoderm namespace: uberon def: "." [http://dev.biologists.org/content/128/22/4573.full] comment: relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' subset: efo_slim synonym: "early pharyngeal arch endoderm" EXACT [EHDAA2:0001457] synonym: "pharyngeal arch endoderm" RELATED [] synonym: "pharyngeal endoderm" RELATED [ZFA:0001104] synonym: "pharyngeal region endoderm" RELATED [EHDAA2:0001456] xref: EFO:0003626 xref: EHDAA2:0001457 xref: EHDAA:962 xref: EMAPA:32754 xref: FMA:293087 xref: TAO:0001104 xref: ZFA:0001104 is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0009722 {source="cjm"} ! entire pharyngeal arch endoderm [Term] id: UBERON:0007719 name: bone of reproductive organ namespace: uberon def: "A bone that is part of a reproductive organ." [https://github.com/obophenotype/uberon/issues/1158, OBOL:automatic] synonym: "baculum" NARROW [] synonym: "os penis/os clitoris" RELATED [] is_a: UBERON:0001474 ! bone element is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003133 ! reproductive organ relationship: part_of UBERON:0003133 ! reproductive organ property_value: RO:0002161 NCBITaxon:9606 {source="Wikipedia"} [Term] id: UBERON:0007771 name: epidermis gland namespace: uberon def: "A gland that is part of a epidermis." [OBOL:automatic] subset: grouping_class synonym: "epidermal gland" EXACT [] synonym: "gland of epidermis" EXACT [FMA:59153] xref: FMA:59153 is_a: UBERON:0002419 ! skin gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001003 ! skin epidermis relationship: part_of UBERON:0001003 ! skin epidermis [Term] id: UBERON:0007779 name: transudate namespace: uberon def: "Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces" [http://medical-dictionary.thefreedictionary.com/transudate] synonym: "plasma ultrafiltrate" RELATED [] xref: FMA:12276 xref: GAID:1195 xref: MESH:D005122 xref: ncithesaurus:Transudate is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: filtered_through UBERON:0001982 ! capillary intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: transformation_of UBERON:0001969 ! blood plasma relationship: develops_from UBERON:0001969 ! blood plasma relationship: filtered_through UBERON:0001982 ! capillary relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: transformation_of UBERON:0001969 ! blood plasma property_value: UBPROP:0000007 "transudative" xsd:string property_value: UBPROP:0000010 "characteristically low in protein and cellular content (unless there has been secondary concentration)" xsd:string [Term] id: UBERON:0007794 name: secretion of serous gland namespace: uberon def: "Any fluid produced by a serous gland." [UBERON:cjm] synonym: "serosal fluid" EXACT [Wikipedia:Serous_fluid] synonym: "serous fluid" BROAD [] synonym: "serous gland fluid" EXACT [] xref: Wikipedia:Serous_fluid is_a: UBERON:0000456 ! secretion of exocrine gland is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0006314 ! bodily fluid intersection_of: produced_by UBERON:0000409 ! serous gland relationship: produced_by UBERON:0000409 ! serous gland [Term] id: UBERON:0007798 name: vascular system namespace: uberon def: "Anatomical system that consists of all blood and lymph vessels." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim xref: BTO:0001085 xref: CALOHA:TS-2053 xref: EHDAA2:0004520 xref: EMAPA:35905 xref: MA:0002718 xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system property_value: editor_note "consider merging with vasculature" xsd:string property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007808 name: adipose tissue of abdominal region namespace: uberon def: "Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots." [CALOHA:paula, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/259, MGI:csmith] subset: efo_slim synonym: "abdominal adipose tissue" RELATED [BTO:0004041] synonym: "abdominal fat" RELATED [BTO:0004041] synonym: "intra-abdominal fat" RELATED [BTO:0004041] xref: CALOHA:TS-0002 xref: EFO:0003771 is_a: UBERON:0001013 ! adipose tissue is_a: UBERON:0003567 ! abdomen connective tissue intersection_of: UBERON:0001013 ! adipose tissue intersection_of: part_of UBERON:0000916 ! abdomen property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cindyJax property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/paulacalipho [Term] id: UBERON:0007811 name: craniocervical region namespace: uberon def: "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "cephalic area" RELATED [https://github.com/obophenotype/uberon/issues/379] synonym: "cephalic part of animal" RELATED [Wikipedia:Head] synonym: "cephalic region" RELATED [https://github.com/obophenotype/uberon/issues/379] synonym: "head and neck" RELATED [FMA:280881] synonym: "head or neck" RELATED [] xref: CALOHA:TS-2356 xref: EV:0100009 xref: FMA:280881 xref: galen:HeadAndNeck xref: MA:0000006 xref: NCIT:C12418 xref: SCTID:361355005 xref: UMLS:C0460004 {source="ncithesaurus:Head_and_Neck"} xref: WikipediaCategory:Head_and_neck is_a: UBERON:0000475 {source="MA"} ! organism subdivision relationship: has_part UBERON:0000033 ! head relationship: has_part UBERON:0006562 ! pharynx relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0013702 ! body proper [Term] id: UBERON:0007823 name: appendage girdle region namespace: uberon alt_id: UBERON:0007824 def: "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] synonym: "fin girdle" RELATED SENSU [] synonym: "fin girdle region" RELATED SENSU [] synonym: "girdle" BROAD [] synonym: "girdle region" BROAD [] synonym: "limb girdle" RELATED SENSU [] synonym: "limb girdle region" RELATED SENSU [] xref: EMAPA:37854 {source="MA:th"} xref: FMA:24874 xref: VSAO:0000303 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision intersection_of: has_skeleton UBERON:0010719 ! girdle skeleton relationship: has_skeleton UBERON:0010719 ! girdle skeleton relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010707 ! appendage girdle complex property_value: IAO:0000232 "this encompasses non-skeletal tissue" xsd:string property_value: UBPROP:0000001 "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000303", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0007828 name: girdle bone/zone namespace: uberon def: "A bone that is part of a appendage girdle region." [OBOL:automatic] synonym: "girdle bone" EXACT [MA:0000291] xref: EMAPA:35379 xref: MA:0000291 is_a: UBERON:0010740 ! bone of appendage girdle complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007823 ! appendage girdle region relationship: part_of UBERON:0010719 ! girdle skeleton [Term] id: UBERON:0007830 name: pelvic girdle bone/zone namespace: uberon def: "A bone element or fused bone that is part of pelvic girdle." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: vertebrate_core synonym: "bone of pelvic girdle" EXACT [] synonym: "pelvic girdle bone" EXACT [MA:0000293] xref: EMAPA:18028 xref: MA:0000293 xref: NCIT:C33287 xref: SCTID:426214007 xref: UMLS:C0030786 {source="ncithesaurus:Pelvic_Bone"} is_a: UBERON:0003828 ! abdominal segment bone is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005179 ! pelvic region element is_a: UBERON:0005913 ! zone of bone organ is_a: UBERON:0007828 {source="MA"} ! girdle bone/zone is_a: UBERON:0010742 ! bone of pelvic complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0007832 ! pelvic girdle skeleton property_value: editor_note "check sacrum, coccyx (MA does NOT include these)" xsd:string property_value: UBPROP:0000008 "typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone" xsd:string [Term] id: UBERON:0007832 name: pelvic girdle skeleton namespace: uberon def: "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature." [VSAO:0000155, Wikipedia:Pelvis] subset: efo_slim subset: vertebrate_core synonym: "pelvic girdle" RELATED INCONSISTENT [VSAO:0000155] synonym: "pelvic girdle skeleton" EXACT [VSAO:0000155] synonym: "skeletal parts of pelvic girdle" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "skeleton of pelvic girdle" EXACT [https://orcid.org/0000-0002-6601-2165] xref: AAO:0000426 xref: AAO:0000768 xref: EFO:0000947 xref: EHDAA2:0001426 xref: EHDAA:7149 xref: EHDAA:8324 xref: EMAPA:18028 xref: FMA:87592 xref: galen:PelvicGirdle xref: http://people.eku.edu/ritchisong/pectoralgirdles.gif xref: MAT:0000182 xref: MIAA:0000182 xref: TAO:0000565 xref: VHOG:0000305 xref: VSAO:0000155 xref: Wikipedia:Pelvis xref: XAO:0003064 xref: ZFA:0000565 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010719 ! girdle skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: part_of UBERON:0001271 ! pelvic girdle region intersection_of: skeleton_of UBERON:0001271 ! pelvic girdle region relationship: develops_from UBERON:0010377 {source="PMID:21455939"} ! mesenchyme from somatopleure relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex relationship: skeleton_of UBERON:0001271 ! pelvic girdle region property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png xsd:anyURI property_value: editor_note "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string property_value: UBPROP:0000001 "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000426", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000001 "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000565", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000001 "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000155", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} property_value: UBPROP:0000003 "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000305", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" xsd:string {external_ontology="VSAO"} [Term] id: UBERON:0007842 name: membrane bone namespace: uberon def: "Bone element that arises as a result of intramembranous ossification." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/267, VSAO:0000023] synonym: "membrane bones" RELATED PLURAL [ZFA:0001636] xref: AEO:0000085 xref: EHDAA2:0003085 xref: TAO:0001645 xref: VSAO:0000023 xref: XAO:0004014 xref: ZFA:0001636 is_a: UBERON:0001474 {source="VSAO"} ! bone element relationship: output_of GO:0001957 ! intramembranous ossification property_value: UBPROP:0000001 "Bone element that arises as a result of intramembranous ossification.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000023", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} property_value: UBPROP:0000001 "Intramembranous bone that forms deep in the organism.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001645", ontology="TAO", source="TAO:wd"} [Term] id: UBERON:0007844 name: cartilage element namespace: uberon def: "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000000] subset: organ_slim subset: pheno_slim synonym: "cartilage" RELATED [VSAO:0000000] synonym: "cartilage organ" EXACT [FMA:55107] synonym: "cartilaginous element" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "chondrogenic element" EXACT [VSAO:0000000] xref: AAO:0011130 xref: CALOHA:TS-0118 xref: EMAPA:32730 xref: FMA:55107 xref: VSAO:0000000 xref: XAO:0004013 xref: ZFA:0001501 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004765 {source="VSAO"} ! skeletal element intersection_of: UBERON:0004765 ! skeletal element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:0005863 {source="VSAO"} ! cartilaginous condensation relationship: has_part UBERON:0002418 {source="VSAO"} ! cartilage tissue property_value: UBPROP:0000012 "TAO still mixes tissue and element" xsd:string {external_ontology="TAO"} [Term] id: UBERON:0007845 name: regular connective tissue namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast relationship: has_part GO:0071953 ! elastic fiber relationship: has_part UBERON:0011860 ! collection of collagen fibrils property_value: editor_note "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string [Term] id: UBERON:0007846 name: dense regular connective tissue namespace: uberon def: "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000050] synonym: "dense fibrous connective tissue" EXACT [FMA:64781] synonym: "dense regular collagenous connective tissue" EXACT [FMA:64781] synonym: "dense regular collagenous tissue" EXACT [FMA:64781] synonym: "regular dense connective tissue" EXACT [] synonym: "typus regularis (textus connectivus collagenosus compactus)" EXACT [FMA:64781] xref: FMA:64781 xref: NCIT:C33453 xref: SCTID:22560007 xref: UMLS:C0225333 {source="ncithesaurus:Regular_Dense_Connective_Tissue"} xref: VSAO:0000050 xref: Wikipedia:Dense_regular_connective_tissue xref: XAO:0004030 is_a: UBERON:0007845 {source="FMA"} ! regular connective tissue is_a: UBERON:0011823 {source="ncithesaurus"} ! dense connective tissue intersection_of: UBERON:0007845 ! regular connective tissue intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber property_value: UBPROP:0000001 "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000050", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} property_value: UBPROP:0000001 "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" xsd:string {date_retrieved="2012-08-29", external_class="FMA:64781", ontology="FMA"} [Term] id: UBERON:0007914 name: bone of craniocervical region namespace: uberon def: "A bone that is part of a craniocervical region." [OBOL:automatic] synonym: "cranial bone" RELATED [] synonym: "head or neck bone" EXACT [MA:0000569] xref: EMAPA:37245 {source="MA:th"} xref: MA:0000569 is_a: UBERON:0001474 {source="MA"} ! bone element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0007811 {source="MA"} ! craniocervical region [Term] id: UBERON:0008114 name: joint of girdle namespace: uberon def: "A skeletal joint that is part of a appendage girdle region." [OBOL:automatic] subset: grouping_class synonym: "girdle joint" EXACT [OBOL:automatic] xref: MA:0001505 is_a: UBERON:0000982 {source="MA"} ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0007823 ! appendage girdle region relationship: connects UBERON:0007828 ! girdle bone/zone relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007823 ! appendage girdle region [Term] id: UBERON:0008115 name: surface of cartilage namespace: uberon def: "A anatomical surface that is part of a cartilage element." [OBOL:automatic] synonym: "cartilage surface" EXACT [FMA:76668] xref: FMA:76668 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: bounding_layer_of UBERON:0007844 ! cartilage element relationship: bounding_layer_of UBERON:0007844 ! cartilage element relationship: part_of UBERON:0007844 ! cartilage element [Term] id: UBERON:0008203 name: pelvic cavity namespace: uberon def: "The part of the ventral body cavity that is within the pelvis." [UBERON:cjm] synonym: "cavitas pelvis" RELATED LATIN [Wikipedia:Pelvic_cavity] synonym: "space of pelvic compartment" EXACT [FMA:9738] xref: EMAPA:37235 {source="MA:th"} xref: FMA:9738 xref: MA:0003089 xref: SCTID:281903009 xref: Wikipedia:Pelvic_cavity is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002355 ! pelvic region of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen relationship: luminal_space_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0035819 ! abdominopelvic cavity property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg xsd:anyURI [Term] id: UBERON:0008229 name: craniocervical region musculature namespace: uberon def: "Musculature system of the pharyngeal and head regions." [ZFA:0000328, ZFA:curator] synonym: "head muscles" RELATED [ZFA:0000328] synonym: "head or neck muscle" EXACT [MA:0000571] synonym: "head or neck muscle" RELATED [MA:0000571] xref: EMAPA:37259 {source="MA:th"} xref: MA:0000571 xref: TAO:0000328 xref: ZFA:0000328 is_a: UBERON:0001015 {source="MA"} ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0007811 {source="MA"} ! craniocervical region property_value: UBPROP:0000012 "in MA this is restricted to skeletal muscles" xsd:string {external_ontology="MA"} [Term] id: UBERON:0008307 name: heart endothelium namespace: uberon def: "An endothelium that is part of a heart [Automatically generated definition]." [OBOL:automatic] synonym: "cardiac endothelium" RELATED [BTO:0004293] xref: BTO:0004293 is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000232 "this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class." xsd:string [Term] id: UBERON:0008814 name: pharyngeal arch system namespace: uberon def: "A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]." [GO:0060037, GOC:dph] synonym: "embryonic pharyngeal complex" EXACT [] synonym: "pharyngeal apparatus" EXACT [] synonym: "pharyngeal arch complex" RELATED [] synonym: "pharyngeal arch region" RELATED [EHDAA2:0000187] synonym: "pharyngeal arches and clefts" RELATED [] synonym: "pharyngeal complex" RELATED [] synonym: "pharyngeal system" EXACT [GO:0060037] xref: EHDAA2:0000187 xref: FMA:293041 xref: NCIT:C34248 xref: UMLS:C1519038 {source="ncithesaurus:Pharyngeal_Apparatus"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000477 ! anatomical cluster relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0009145 ! pharyngeal region of foregut property_value: editor_note "Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing" xsd:string [Term] id: UBERON:0008816 name: embryonic head namespace: uberon def: "A head that is part of a embryo." [OBOL:automatic] subset: non_informative xref: CALOHA:TS-0246 xref: FBbt:00000155 xref: FMA:293011 is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:0008823 name: neural tube derived brain namespace: uberon def: "A brain that develops_from a neural tube." [https://github.com/obophenotype/uberon/issues/338, OBOL:automatic] synonym: "vertebrate brain" NARROW [] is_a: UBERON:0000489 {source="ZFA"} ! cavitated compound organ is_a: UBERON:0000955 ! brain intersection_of: UBERON:0000955 ! brain intersection_of: develops_from UBERON:0001049 ! neural tube relationship: develops_from UBERON:0001049 ! neural tube relationship: part_of UBERON:0000033 {source="FMA"} ! head property_value: editor_note "a reasoner should automatically classify all the vertebrate ontology brain classes here" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/338 xsd:anyURI [Term] id: UBERON:0008876 name: hypodermis skeletal muscle layer namespace: uberon alt_id: UBERON:0010934 def: "Any skeletal muscle organ in the hypodermis / superficial fascia" [ISBN:0123813611, MP:0011157] subset: pheno_slim synonym: "hypodermal muscle layer" EXACT [MP:0011157] synonym: "hypodermis muscle layer" EXACT [MP:0011157] synonym: "panniculus carnosus" NARROW [MP:0011157] synonym: "superficial fascia muscular layer" EXACT [] xref: EMAPA:18188 xref: MA:0003140 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004253 ! skin muscle is_a: UBERON:0014892 ! skeletal muscle organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0002072 ! hypodermis relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: contributes_to_morphology_of UBERON:0002072 ! hypodermis relationship: has_muscle_insertion UBERON:0002097 ! skin of body relationship: located_in UBERON:0002190 {source="MP-def"} ! subcutaneous adipose tissue relationship: part_of UBERON:0002072 ! hypodermis property_value: editor_note "We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this" xsd:string [Term] id: UBERON:0008886 name: pulmonary vascular system namespace: uberon def: "The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins." [ISBN:0073040584, Wikipedia:Pulmonary_circulation] synonym: "pulmonary circulatory system" EXACT [FMA:45621] synonym: "pulmonary system" EXACT [ISBN:0073040584] xref: FMA:45621 xref: Wikipedia:Pulmonary_circulation is_a: UBERON:0007798 {source="Obol"} ! vascular system is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0002012 ! pulmonary artery relationship: has_part UBERON:0002016 ! pulmonary vein property_value: UBPROP:0000001 "Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]" xsd:string {ontology="FMA", source="FMA:45621"} [Term] id: UBERON:0008895 name: splanchnocranium namespace: uberon def: "Subdivision of endoskeleton derived from pharyngeal arches" [https://orcid.org/0000-0002-6601-2165, ISBN:0073040584, Wikipedia:Facial_skeleton] synonym: "branchial arch skeleton" RELATED [] synonym: "gill arch skeleton" RELATED [] synonym: "pharyngeal arch" RELATED INCONSISTENT [VSAO:0000149] synonym: "pharyngeal arch skeleton" RELATED [ZFA:0001216] synonym: "pharyngeal endoskeleton" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "pharyngeal skeleton" RELATED [ZFA:0001216] synonym: "visceral cranium" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "visceral skeletal system" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "visceral skeleton" RELATED [UBERONREF:0000007] synonym: "viscerocranium" EXACT INCONSISTENT [VHOG:0000315, Wikipedia:Viscerocranium, ZFA:0001216] xref: AAO:0010157 xref: TAO:0001216 xref: VHOG:0000315 xref: VSAO:0000149 xref: Wikipedia:Facial_skeleton xref: XAO:0003176 xref: ZFA:0001216 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system disjoint_from: UBERON:0011156 ! facial skeleton relationship: develops_from UBERON:0002539 {source="https://github.com/obophenotype/uberon/issues/83"} ! pharyngeal arch relationship: has_developmental_contribution_from UBERON:0003099 {notes="redundant", source="Grays", source="PMID:11237469"} ! cranial neural crest property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg xsd:anyURI property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001216", ontology="TAO", source="ZFIN:curator"} property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010157", ontology="AAO", source="AAO:EJS"} property_value: UBPROP:0000001 "The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000315", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: UBPROP:0000003 "The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000315", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235", source="http://bgee.unil.ch/"} property_value: UBPROP:0000012 "many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both" xsd:string property_value: UBPROP:0000012 "VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton." xsd:string {external_ontology="VSAO"} [Term] id: UBERON:0008907 name: dermal bone namespace: uberon def: "Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/267, VSAO:0000130] synonym: "dermal bones" RELATED PLURAL [ZFA:0001590] xref: AAO:0010769 xref: TAO:0001590 xref: VSAO:0000130 xref: Wikipedia:Dermal_bone xref: XAO:0004015 xref: ZFA:0001590 is_a: UBERON:0004756 {source="wd"} ! dermal skeletal element is_a: UBERON:0007842 {source="VSAO"} ! membrane bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010364 ! dermal skeleton relationship: part_of UBERON:0010364 {source="VSAO"} ! dermal skeleton property_value: UBPROP:0000001 "Intramembranous bone that forms superficially in the organism.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001590", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000012 "other AOs are not yet in sync with this classification" xsd:string [Term] id: UBERON:0008909 name: perichordal bone namespace: uberon def: "Bone element that is adjacent to the notochord." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000307] synonym: "perichordal bone" RELATED [ZFA:0001629] synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629] xref: AAO:0010777 xref: TAO:0001639 xref: VSAO:0000307 xref: ZFA:0001629 is_a: UBERON:0012075 {notes="not in VSAO", source="ZFA"} ! replacement bone intersection_of: UBERON:0001474 ! bone element intersection_of: adjacent_to UBERON:0002328 ! notochord relationship: adjacent_to UBERON:0002328 ! notochord property_value: editor_note "We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA" xsd:string property_value: UBPROP:0000001 "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001639", ontology="TAO", source="TAO:wd"} [Term] id: UBERON:0008947 name: respiratory primordium namespace: uberon xref: EHDAA2:0004069 xref: NCIT:C34283 xref: UMLS:C1514898 {source="ncithesaurus:Respiratory_Primordium"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001048 {source="Obol"} ! primordium relationship: has_potential_to_develop_into UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003258 ! endoderm of foregut [Term] id: UBERON:0008998 name: vasculature of brain namespace: uberon alt_id: UBERON:0005284 def: "System pertaining to blood vessels in the brain." [BTO:0003840] subset: efo_slim synonym: "brain vasculature" EXACT [] synonym: "cerebrovascular system" EXACT [BTO:0003840] synonym: "intracerebral vasculature" EXACT [FMA:61935] xref: BTO:0003840 xref: EFO:0003491 xref: EMAPA:35186 xref: FMA:242007 xref: FMA:61935 xref: SCTID:362029003 xref: TAO:0000099 xref: ZFA:0000099 is_a: UBERON:0006876 ! vasculature of organ is_a: UBERON:0036303 ! vasculature of central nervous system relationship: part_of UBERON:0000955 ! brain [Term] id: UBERON:0009030 name: left pulmonary vein namespace: uberon def: "Vein that drains left lung and returns blood to the heart." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:37165 {source="MA:th"} xref: MA:0002207 xref: NCIT:C48946 xref: SCTID:304057004 xref: UMLS:C0226670 {source="ncithesaurus:Left_Pulmonary_Vein"} is_a: UBERON:0002016 ! pulmonary vein intersection_of: UBERON:0002016 ! pulmonary vein intersection_of: drains UBERON:0002168 ! left lung relationship: drains UBERON:0002168 ! left lung property_value: UBPROP:0000001 "A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]." xsd:string {source="ncithesaurus:Left_Pulmonary_Vein"} [Term] id: UBERON:0009032 name: right pulmonary vein namespace: uberon def: "Vein that drains right lung and returns blood to the heart." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:37379 {source="MA:th"} xref: MA:0002208 xref: NCIT:C48947 xref: SCTID:304056008 xref: UMLS:C0226669 {source="ncithesaurus:Right_Pulmonary_Vein"} is_a: UBERON:0002016 ! pulmonary vein intersection_of: UBERON:0002016 ! pulmonary vein intersection_of: drains UBERON:0002167 ! right lung relationship: drains UBERON:0002167 ! right lung property_value: UBPROP:0000001 "A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]." xsd:string {source="ncithesaurus:Right_Pulmonary_Vein"} [Term] id: UBERON:0009117 name: indifferent gonad namespace: uberon def: "A gonad prior to differentiating into a definitive testis or ovary." [http://www.medterms.com/script/main/art.asp?articlekey=8981] comment: typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] subset: organ_slim synonym: "gonad rudiment" RELATED [] xref: EHDAA2:0000716 xref: NCIT:C34192 xref: UMLS:C1512703 {source="ncithesaurus:Indifferent_Gonad"} is_a: UBERON:0000991 ! gonad relationship: part_of UBERON:0009196 ! indifferent external genitalia [Term] id: UBERON:0009129 name: right atrium endocardium namespace: uberon def: "Endocardium that is part of the right atrium." [http://orcid.org/0000-0002-6601-2165] synonym: "endocardium of right atrium" EXACT [FMA:7281] synonym: "right atrial endocardium" EXACT [FMA:7281] synonym: "right atrium endocardial tissue" RELATED [VHOG:0001228] xref: EHDAA2:0000274 xref: FMA:7281 xref: NCIT:C102339 xref: SCTID:3194006 xref: VHOG:0001228 is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0002166 ! endocardium of atrium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002078 ! right cardiac atrium relationship: develops_from UBERON:0005092 {source="EHDAA2"} ! right horn of sinus venosus relationship: part_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0006218 {source="EHDAA2"} ! common atrial chamber [Term] id: UBERON:0009141 name: craniocervical region vein namespace: uberon def: "A vein that is part of a craniocervical region." [OBOL:automatic] synonym: "craniocervical vein" EXACT [] synonym: "head and neck veins" EXACT [EHDAA2:0004542] synonym: "vein of head and neck" EXACT [] xref: EHDAA2:0004542 xref: SCTID:32945007 is_a: UBERON:0013140 ! systemic vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0007811 ! craniocervical region [Term] id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: BFO:0000040 ! material entity is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000477 ! anatomical cluster relationship: composed_primarily_of UBERON:0003104 ! mesenchyme relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009145 name: pharyngeal region of foregut namespace: uberon synonym: "pharyngeal region" EXACT [EMAPA:16549] xref: EMAPA:16549 xref: RETIRED_EHDAA2:0001454 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0001041 {source="EHDAA2"} ! foregut [Term] id: UBERON:0009196 name: indifferent external genitalia namespace: uberon subset: organ_slim xref: EHDAA2:0004021 is_a: UBERON:0004176 {source="cjm"} ! external genitalia relationship: part_of UBERON:0000922 ! embryo [Term] id: UBERON:0009479 name: ectoderm of buccopharyngeal membrane namespace: uberon def: "An ectoderm that is part of a buccopharyngeal membrane." [OBOL:automatic] subset: emapa_ehdaa2 xref: EHDAA2:0000190 xref: EMAPA:16260 is_a: UBERON:0000924 ! ectoderm intersection_of: UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0006211 ! buccopharyngeal membrane relationship: part_of UBERON:0006211 ! buccopharyngeal membrane [Term] id: UBERON:0009480 name: endoderm of buccopharyngeal membrane namespace: uberon def: "An endoderm that is part of a buccopharyngeal membrane." [OBOL:automatic] subset: emapa_ehdaa2 xref: EHDAA2:0000191 xref: EMAPA:16261 is_a: UBERON:0000925 ! endoderm intersection_of: UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0006211 ! buccopharyngeal membrane relationship: part_of UBERON:0006211 ! buccopharyngeal membrane [Term] id: UBERON:0009494 name: pharyngeal arch mesenchymal region namespace: uberon def: "A portion of mesenchymal tissue associated with an individual pharyngeal arch." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "branchial arch mesenchyme" EXACT [MP:0011262] synonym: "pharyngeal arch mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] xref: EMAPA:32755 xref: FMA:295694 is_a: UBERON:0005253 ! head mesenchyme is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002539 ! pharyngeal arch relationship: has_developmental_contribution_from UBERON:0003099 {source="cjm"} ! cranial neural crest relationship: part_of UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme property_value: editor_note "this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures." xsd:string {source="MP:0011262"} [Term] id: UBERON:0009569 name: subdivision of trunk namespace: uberon subset: non_informative synonym: "region of trunk" EXACT [FMA:25054] synonym: "trunk subdivision" EXACT [FMA:25054] xref: FMA:25054 xref: SCTID:22943007 is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0002100 ! trunk [Term] id: UBERON:0009581 name: midbrain mantle layer namespace: uberon synonym: "mantle layer lateral wall mesencephalon" RELATED [VHOG:0000910] synonym: "mantle layer lateral wall midbrain" EXACT [VHOG:0000910] synonym: "midbrain lateral wall mantle layer" EXACT [] xref: EHDAA2:0001172 xref: EMAPA:16977 xref: VHOG:0000910 is_a: UBERON:0004061 ! neural tube mantle layer intersection_of: UBERON:0004061 ! neural tube mantle layer intersection_of: part_of UBERON:0009616 ! presumptive midbrain relationship: part_of UBERON:0009616 ! presumptive midbrain [Term] id: UBERON:0009583 name: spinal cord mantle layer namespace: uberon synonym: "mantle layer lateral wall spinal cord" EXACT [VHOG:0000911] synonym: "spinal cord lateral wall mantle layer" EXACT [] xref: EMAPA:17580 xref: VHOG:0000911 is_a: UBERON:0004061 ! neural tube mantle layer intersection_of: UBERON:0004061 ! neural tube mantle layer intersection_of: part_of UBERON:0006241 ! future spinal cord relationship: part_of UBERON:0006241 ! future spinal cord [Term] id: UBERON:0009584 name: 1st arch mandibular mesenchyme namespace: uberon alt_id: UBERON:0010043 def: "Mesenchyme that is part of a 1st arch mandibular component." [OBOL:automatic] synonym: "mandibular component mesenchyme" RELATED [] synonym: "mandibular mesenchyme" RELATED [] synonym: "mesenchymal region of mandibular component of first pharyngeal arch" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "mesenchyme of mandibular component" EXACT [EMAPA:16385] xref: EHDAA2:0000034 xref: EMAPA:16385 is_a: UBERON:0010042 ! 1st arch mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0007237 ! 1st arch mandibular component relationship: part_of UBERON:0007237 {source="EMAPA"} ! 1st arch mandibular component [Term] id: UBERON:0009602 name: left lung associated mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing left lung." [OBOL:automatic] synonym: "left lung mesenchyme" EXACT [EMAPA:17654] xref: EHDAA2:0000944 xref: EMAPA:16730 xref: EMAPA:17654 is_a: UBERON:0004883 ! lung mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002168 ! left lung relationship: part_of UBERON:0002168 ! left lung [Term] id: UBERON:0009603 name: right lung associated mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing right lung." [OBOL:automatic] synonym: "right lung mesenchyme" EXACT [EMAPA:17662] xref: EHDAA2:0001739 xref: EMAPA:17662 is_a: UBERON:0004883 ! lung mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002167 ! right lung relationship: part_of UBERON:0002167 ! right lung [Term] id: UBERON:0009611 name: midbrain neural plate namespace: uberon def: "A neural plate that develops_from a presumptive midbrain." [OBOL:automatic] xref: TAO:0007019 xref: ZFA:0007019 is_a: UBERON:0003075 ! neural plate intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate intersection_of: develops_from UBERON:0009616 {source="ZFA"} ! presumptive midbrain relationship: develops_from UBERON:0009616 ! presumptive midbrain relationship: part_of UBERON:0003056 {source="ZFA"} ! pre-chordal neural plate [Term] id: UBERON:0009614 name: hindbrain neural plate namespace: uberon def: "A neural plate that develops_from a presumptive hindbrain." [OBOL:automatic] xref: TAO:0007022 xref: ZFA:0007022 is_a: UBERON:0003075 ! neural plate is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate intersection_of: develops_from UBERON:0007277 {source="ZFA"} ! presumptive hindbrain relationship: develops_from UBERON:0007277 ! presumptive hindbrain relationship: part_of UBERON:0003057 {source="ZFA"} ! chordal neural plate [Term] id: UBERON:0009615 name: midbrain hindbrain boundary neural plate namespace: uberon synonym: "MHB neural plate" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 is_a: UBERON:0006598 ! presumptive structure relationship: develops_from UBERON:0007281 ! presumptive midbrain hindbrain boundary relationship: immediate_transformation_of UBERON:0007281 {notes="https://github.com/obophenotype/uberon/issues/438", source="Bgee:AN"} ! presumptive midbrain hindbrain boundary relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate property_value: editor_note "TODO - developmental relationships for lines" xsd:string [Term] id: UBERON:0009616 name: presumptive midbrain namespace: uberon def: "A presumptive structure that has the potential to develop into a midbrain." [OBOL:automatic] subset: efo_slim synonym: "early midbrain" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "future midbrain" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "mesencephalon" RELATED [EHDAA2:0000615] synonym: "presumptive mesencephalon" EXACT [ZFA:0000148] xref: BAMS:MES xref: EFO:0003432 xref: EHDAA2:0000615 xref: EMAPA:16140 xref: TAO:0000148 xref: Wikipedia:Mesencephalon xref: ZFA:0000148 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0001891 ! midbrain relationship: develops_from UBERON:0003080 ! anterior neural tube relationship: develops_from UBERON:0010286 {source="ZFA"} ! midbrain neural tube relationship: has_potential_to_develop_into UBERON:0001891 ! midbrain relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain property_value: editor_note "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0009617 name: head paraxial mesoderm namespace: uberon def: "Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles." [PMID:21610022] synonym: "cephalic paraxial mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "cephalic paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "cranial paraxial mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "cranial paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "head paraxial mesenchyme" EXACT [EHDAA2:0000736, https://github.com/obophenotype/uberon/issues/30] synonym: "somitomere" RELATED [] synonym: "somitomeric mesoderm" RELATED [] xref: EHDAA2:0000736 xref: EHDAA:364 xref: EMAPA:16171 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005253 ! head mesenchyme relationship: part_of UBERON:0003077 ! paraxial mesoderm relationship: part_of UBERON:0005253 {source="EHDAA2"} ! head mesenchyme property_value: UBPROP:0000011 "A major contributor to neurocranium [PMID:16313393]" xsd:string [Term] id: UBERON:0009618 name: trunk paraxial mesoderm namespace: uberon synonym: "trunk and cervical paraxial mesenchyme" EXACT [EHDAA2:0002094] synonym: "trunk paraxial mesenchyme" RELATED [https://github.com/obophenotype/uberon/issues/30] xref: EHDAA2:0002094 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005256 ! trunk mesenchyme relationship: part_of UBERON:0003077 ! paraxial mesoderm relationship: part_of UBERON:0005256 {source="EHDAA2"} ! trunk mesenchyme [Term] id: UBERON:0009657 name: artery of lip namespace: uberon synonym: "labial artery" EXACT [MA:0001987] xref: EMAPA:37092 {source="MA:th"} xref: MA:0001987 xref: NCIT:C52947 xref: UMLS:C1708633 {source="ncithesaurus:Labial_Artery"} is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0001833 ! lip relationship: supplies UBERON:0001833 ! lip [Term] id: UBERON:0009712 name: endocardium of right ventricle namespace: uberon def: "Any endocardium that is part of the right ventricle of the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "endocardial lining of right ventricle" RELATED [EMAPA:17341] synonym: "right ventricle endocardial tissue" RELATED [VHOG:0001235] synonym: "right ventricle endocardium" EXACT [VHOG:0001235] synonym: "right ventricular endocardium" EXACT [FMA:9536] xref: EHDAA2:0002188 xref: EMAPA:17341 xref: FMA:9536 xref: NCIT:C102343 xref: SCTID:8911002 xref: VHOG:0001235 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0001081 ! endocardium of ventricle is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001081 ! endocardium of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: attaches_to UBERON:0006567 {source="FMA"} ! right ventricle myocardium relationship: develops_from UBERON:0004706 {source="EHDAA2"} ! bulbus cordis relationship: part_of UBERON:0002080 ! heart right ventricle property_value: UBPROP:0000001 "Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk." xsd:string {source="FMA:9536"} [Term] id: UBERON:0009713 name: endocardium of left ventricle namespace: uberon def: "Any endocardium that is part of the left ventricle of the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "endocardial lining of left ventricle" RELATED [EMAPA:17338] synonym: "left ventricle endocardial tissue" RELATED [VHOG:0001233] synonym: "left ventricle endocardium" EXACT [VHOG:0001233] synonym: "left ventricular endocardium" EXACT [FMA:9559] xref: EHDAA2:0002182 xref: EMAPA:17338 xref: FMA:9559 xref: SCTID:191004004 xref: VHOG:0001233 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0001081 ! endocardium of ventricle intersection_of: UBERON:0001081 ! endocardium of ventricle intersection_of: part_of UBERON:0002084 ! heart left ventricle relationship: attaches_to UBERON:0006566 {source="FMA"} ! left ventricle myocardium relationship: part_of UBERON:0002084 ! heart left ventricle property_value: UBPROP:0000001 "Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta." xsd:string {source="FMA:9559"} [Term] id: UBERON:0009715 name: stomodeal lumen namespace: uberon def: "An anatomical cavity that surrounded_by a stomodeum." [OBOL:automatic] synonym: "lumen of stomatodaeum" EXACT [] synonym: "lumen of stomodeum" EXACT [] synonym: "stomatodeal cavity" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0000930 ! stomodeum relationship: luminal_space_of UBERON:0000930 ! stomodeum relationship: part_of UBERON:0000930 ! stomodeum [Term] id: UBERON:0009722 name: entire pharyngeal arch endoderm namespace: uberon synonym: "pharyngeal arch endoderm" RELATED [EHDAA2:0004621] xref: EHDAA2:0004621 xref: EMAPA:32754 xref: FMA:293087 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0015833 ! foregut epithelium relationship: part_of UBERON:0003929 {source="EHDAA2"} ! digestive tract epithelium relationship: part_of UBERON:0008814 ! pharyngeal arch system [Term] id: UBERON:0009751 name: cardiac mesenchyme namespace: uberon def: "The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures" [MP:0011264] subset: pheno_slim synonym: "heart mesenchyme" EXACT [EMAPA:36438] xref: EHDAA2:0004162 xref: EMAPA:36438 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart property_value: editor_note "decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts" xsd:string [Term] id: UBERON:0009842 name: glandular acinus namespace: uberon def: "The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form." [Wikipedia:Acinus] synonym: "acini" RELATED PLURAL [Wikipedia:Acinus] synonym: "acinus" BROAD [FMA:55588] xref: FMA:55588 xref: Wikipedia:Acinus is_a: UBERON:0034922 ! cell cluster intersection_of: UBERON:0034922 ! cell cluster intersection_of: has_part CL:0000151 ! secretory cell intersection_of: has_quality PATO:0002422 ! acinar intersection_of: part_of UBERON:0002530 ! gland relationship: has_part CL:0000151 ! secretory cell relationship: has_quality PATO:0002422 ! acinar relationship: part_of UBERON:0002530 ! gland property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png xsd:anyURI property_value: UBPROP:0000007 "acinar" xsd:string [Term] id: UBERON:0009854 name: digestive tract diverticulum namespace: uberon def: "Branch or outpocketing of the digestive tract." [https://orcid.org/0000-0002-6601-2165] synonym: "diverticulum of gut" RELATED [FBbt:00100316] synonym: "intestinal pouch" RELATED [] xref: FBbt:00100316 is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0009856 ! sac intersection_of: UBERON:0009856 ! sac intersection_of: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0009856 name: sac namespace: uberon synonym: "diverticulum" RELATED [] synonym: "pouch" EXACT [] xref: galen:Diverticulum is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: has_quality PATO:0001987 ! saccular relationship: has_quality PATO:0001987 ! saccular [Term] id: UBERON:0009881 name: anterior lateral plate mesoderm namespace: uberon subset: efo_slim synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm [Term] id: UBERON:0009889 name: secondary heart field namespace: uberon def: "A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract)." [GO:0003139, GOC:mtg_heart, GOC:rl] synonym: "anterior heart field" EXACT [PMID:17276708] synonym: "anterior/second heart field" EXACT [Geisha:syn, NCBITaxon:8782] synonym: "second heart field" EXACT [XAO:0004186] synonym: "SHF" RELATED [XAO:0004186] xref: XAO:0004186 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: anterior_to UBERON:0004140 {source="PMID:17276708"} ! primary heart field relationship: dorsal_to UBERON:0004140 {source="PMID:17276708"} ! primary heart field relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003081 {source="GO:0003129"} ! lateral plate mesoderm property_value: UBPROP:0000001 "extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]." xsd:string {source="PMID:17276708"} property_value: UBPROP:0000008 "In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested" xsd:string {source="PMID:17276708"} property_value: UBPROP:0000011 "in mouse has left ventricular identity[PMID:22855565]" xsd:string [Term] id: UBERON:0009891 name: facial mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing face." [OBOL:automatic] synonym: "face mesenchyme" EXACT [] synonym: "mesenchyme of face" EXACT [] xref: EMAPA:35337 xref: FMA:302884 is_a: UBERON:0005253 ! head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001456 ! face [Term] id: UBERON:0009920 name: optic neural crest namespace: uberon xref: EHDAA2:0001315 xref: EHDAA:1122 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest [Term] id: UBERON:0009953 name: post-embryonic organism namespace: uberon def: "A multicellular organism that existence_starts_with a post-embryonic stage." [OBOL:automatic] synonym: "post-hatching organism" NARROW [https://orcid.org/0000-0002-6601-2165] synonym: "post-natal organism" NARROW [https://orcid.org/0000-0002-6601-2165] synonym: "postnatal mouse" NARROW [MA:0002405] synonym: "postnatal organism" EXACT [] synonym: "TS28 mouse" NARROW [MA:0002405] xref: MA:0002405 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism intersection_of: existence_starts_with UBERON:0000092 ! post-embryonic stage relationship: existence_starts_with UBERON:0000092 ! post-embryonic stage property_value: seeAlso https://github.com/obophenotype/uberon/issues/667 xsd:anyURI [Term] id: UBERON:0010000 name: multicellular anatomical structure namespace: uberon def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: has_quality PATO:0001993 ! multicellular relationship: has_part CL:0000000 ! cell relationship: has_quality PATO:0001993 ! multicellular [Term] id: UBERON:0010031 name: 6th arch mesenchyme namespace: uberon def: "Mesenchyme that is part of a pharyngeal arch 6." [OBOL:automatic] synonym: "6th branchial arch mesenchyme" RELATED [] synonym: "6th pharyngeal arch mesenchyme" EXACT [] synonym: "pharyngeal arch 6 mesenchyme" RELATED [] xref: EHDAA2:0004076 xref: EMAPA:32765 xref: FMA:318209 is_a: UBERON:0009494 ! pharyngeal arch mesenchymal region intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003117 ! pharyngeal arch 6 relationship: part_of UBERON:0003117 ! pharyngeal arch 6 [Term] id: UBERON:0010042 name: 1st arch mesenchyme namespace: uberon def: "Mesenchyme that is part of a pharyngeal arch 1." [OBOL:automatic] synonym: "mesenchyme of 1st arch" EXACT [EMAPA:16128] xref: EMAPA:16128 is_a: UBERON:0009494 ! pharyngeal arch mesenchymal region intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0004362 ! pharyngeal arch 1 [Term] id: UBERON:0010046 name: entire pharyngeal arch associated mesenchyme namespace: uberon def: "The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells." [https://orcid.org/0000-0002-6601-2165, XAO:0004524] synonym: "associated mesenchyme of pharyngeal region" EXACT [EMAPA:16550] synonym: "entire branchial arch associated mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "pharyngeal arch associated mesenchyme" EXACT [EHDAA2:0001459] xref: EHDAA2:0001459 xref: EMAPA:16550 xref: XAO:0004524 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_developmental_contribution_from UBERON:0003099 {source="cjm"} ! cranial neural crest relationship: part_of UBERON:0008814 {source="EHDAA2"} ! pharyngeal arch system [Term] id: UBERON:0010047 name: oral gland namespace: uberon alt_id: UBERON:0003293 def: "Gland of the epithelium lining the oral cavity. The most common are the salivary glands." [ISBN:0073040584] synonym: "buccal gland" NARROW [] synonym: "gland of oral opening" RELATED [] synonym: "gland of oral region" RELATED [] synonym: "mouth gland" RELATED [] synonym: "oral cavity gland" RELATED [] synonym: "oral region gland" RELATED [] xref: EHDAA2:0001327 xref: EHDAA:2181 xref: EMAPA:16572 xref: EMAPA:16723 xref: VHOG:0000652 is_a: UBERON:0002365 ! exocrine gland is_a: UBERON:0003408 ! gland of digestive tract intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000165 ! mouth relationship: part_of UBERON:0000165 ! mouth property_value: UBPROP:0000012 "Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0010077 name: cuboidal epithelium namespace: uberon def: "An epithelium consisting of cuboidal epithelial cells." [Wikipedia:Cuboidal_epithelium] xref: NCIT:C32415 xref: UMLS:C0682577 {source="ncithesaurus:Cuboidal_Epithelium"} xref: Wikipedia:Cuboidal_epithelium is_a: UBERON:0000483 ! epithelium property_value: editor_note "TODO - coordinate with CL, add cuboidal cell" xsd:string property_value: UBPROP:0000012 "in NCIT this is glandular" xsd:string {external_ontology="NCIT"} [Term] id: UBERON:0010083 name: future dermis namespace: uberon def: "Mesenchyme that has the potential to develop into a dermis." [OBOL:automatic] xref: EHDAA2:0000598 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: has_potential_to_develop_into UBERON:0002067 ! dermis relationship: develops_from UBERON:0003089 {source="EHDAA2"} ! sclerotome relationship: develops_from UBERON:0004016 {source="XAO"} ! dermatome relationship: has_potential_to_develop_into UBERON:0002067 ! dermis relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument property_value: editor_note "check development" xsd:string [Term] id: UBERON:0010096 name: future myelencephalon namespace: uberon def: "A developing anatomical structure that has the potential to develop into a myelencephalon." [OBOL:automatic] xref: EHDAA2:0000640 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0005290 ! myelencephalon relationship: has_potential_to_develop_into UBERON:0005290 ! myelencephalon relationship: part_of UBERON:0002028 ! hindbrain [Term] id: UBERON:0010131 name: conducting tissue of heart namespace: uberon def: "Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers." [http://orcid.org/0000-0002-6601-2165] synonym: "specialized conducting tissue of heart" EXACT [FMA:83378] synonym: "specialized muscle tissue of heart" EXACT [FMA:83378] xref: EHDAA2:0004528 xref: FMA:83378 is_a: UBERON:0001133 ! cardiac muscle tissue [Term] id: UBERON:0010133 name: neuroendocrine gland namespace: uberon def: "any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli" [ISBN:0-683-40008-8, MP:0000631] subset: pheno_slim synonym: "neuroendocrine system gland" EXACT [] xref: MA:0000720 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002368 ! endocrine gland intersection_of: UBERON:0002368 ! endocrine gland intersection_of: part_of UBERON:0001016 ! nervous system relationship: has_part CL:0000165 ! neuroendocrine cell relationship: part_of UBERON:0001016 ! nervous system [Term] id: UBERON:0010161 name: lumen of blood vessel namespace: uberon def: "An anatomical cavity that surrounded_by a blood vessel." [OBOL:automatic] synonym: "blood vessel lumen" EXACT [] xref: FMA:312610 xref: SCTID:91747007 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0001981 ! blood vessel relationship: luminal_space_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel [Term] id: UBERON:0010188 name: protuberance namespace: uberon def: "A roughly circular bulge in a surface." [EHDAA2:0003250] xref: AEO:0000205 xref: EHDAA2:0003250 xref: FMA:82506 is_a: UBERON:0034944 {source="FMA"} ! zone of organ property_value: editor_note "requires review" xsd:string [Term] id: UBERON:0010190 name: pair of dorsal aortae namespace: uberon def: "the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation" [ISBN:0-914294-08-3, MP:0004787] subset: pheno_slim synonym: "paired dorsal aortae" EXACT [EHDAA2:0000410] xref: EHDAA2:0000410 xref: EMAPA:18606 xref: MA:0000476 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: has_part UBERON:0005805 ! dorsal aorta relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system [Term] id: UBERON:0010191 name: aortic system namespace: uberon xref: EHDAA2:0004512 is_a: UBERON:0011216 ! organ system subdivision relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004571 {source="Wikipedia"} ! systemic arterial system [Term] id: UBERON:0010192 name: genital artery namespace: uberon def: "One of the laterally paired arteries that supply the gonads." [ISBN:0073040584, Wikipedia:Gonadal_artery] synonym: "gonadal artery" EXACT [] xref: Wikipedia:Gonadal_artery is_a: UBERON:0012254 ! abdominal aorta artery intersection_of: UBERON:0004573 ! systemic artery intersection_of: supplies UBERON:0000991 ! gonad relationship: supplies UBERON:0000991 ! gonad [Term] id: UBERON:0010199 name: bona-fide anatomical boundary namespace: uberon def: "An anatomical boundary that corresponds to some physical discontinuity." [CARO:0001004] comment: One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) subset: upper_level xref: CARO:0001004 is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity [Term] id: UBERON:0010227 name: future cardiac atrium namespace: uberon def: "Multi-tissue structure that is part of the heart tube and will become the cardiac atrium." [ZFA:0001718] synonym: "presumptive atrium heart tube" EXACT [ZFA:0001718] synonym: "primordial atrium" EXACT [FMA:71005] synonym: "primordial cardiac atrium" EXACT [FMA:71005] xref: FMA:71005 xref: TAO:0002228 xref: ZFA:0001718 is_a: UBERON:0006598 ! presumptive structure relationship: has_potential_to_develop_into UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube [Term] id: UBERON:0010230 name: eyeball of camera-type eye namespace: uberon def: "The core globe-shaped component of the camera-type eye." [UBERON:cjm] subset: pheno_slim synonym: "bulbus oculi" EXACT [] synonym: "eye" RELATED INCONSISTENT [] synonym: "eye globe" EXACT [VHOG:0001616] synonym: "eyeball" EXACT [FMA:12513] synonym: "globe" RELATED [HP:0100886, MIAA:0000283] xref: FMA:12513 xref: MIAA:0000283 xref: SCTID:244486005 xref: VHOG:0001616 xref: Wikipedia:Globe_(human_eye) is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye property_value: IAO:0000232 "See notes for camera-type eye" xsd:string property_value: UBPROP:0000202 FMA:264089 [Term] id: UBERON:0010252 name: 1st arch mandibular mesenchyme from neural crest namespace: uberon def: "Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme." [OBOL:automatic] xref: EHDAA2:0000037 is_a: UBERON:0009584 ! 1st arch mandibular mesenchyme is_a: UBERON:0010259 {source="inferred"} ! 1st arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0009584 ! 1st arch mandibular mesenchyme relationship: develops_from UBERON:0007098 ! mandibular neural crest relationship: part_of UBERON:0009584 {source="EHDAA2"} ! 1st arch mandibular mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest [Term] id: UBERON:0010257 name: 6th arch mesenchyme from neural crest namespace: uberon def: "Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme." [OBOL:automatic] synonym: "branchial arch 6 mesenchyme from neural crest" RELATED [] synonym: "neural crest derived arch 6 mesenchyme" EXACT [] synonym: "pharyngeal arch 6 mesenchyme from neural crest" EXACT [] xref: EHDAA2:0004077 is_a: UBERON:0010031 ! 6th arch mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010031 ! 6th arch mesenchyme relationship: part_of UBERON:0010031 {source="EHDAA2"} ! 6th arch mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest [Term] id: UBERON:0010258 name: mesenchyme from rhombencephalic neural crest namespace: uberon def: "Mesenchyme that develops_from a rhombencephalon neural crest." [OBOL:automatic] xref: EHDAA2:0004423 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0003852 ! rhombencephalon neural crest relationship: develops_from UBERON:0003852 ! rhombencephalon neural crest relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest [Term] id: UBERON:0010259 name: 1st arch mesenchyme from neural crest namespace: uberon def: "Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme." [OBOL:automatic] synonym: "branchial arch 1 mesenchyme from neural crest" RELATED [] synonym: "mesenchyme derived from neural crest of mesenchyme of 1st arch" EXACT [EMAPA:16129] synonym: "neural crest derived arch 1 mesenchyme" EXACT [] synonym: "pharyngeal arch 1 mesenchyme from neural crest" EXACT [] xref: EMAPA:16129 is_a: UBERON:0010042 ! 1st arch mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010042 ! 1st arch mesenchyme relationship: part_of UBERON:0010042 ! 1st arch mesenchyme [Term] id: UBERON:0010285 name: midbrain basal plate namespace: uberon def: "Portion of tissue that is dorsolateral to the floor plate and part of the midbrain." [ZFA:0000761] subset: efo_slim synonym: "basal plate midbrain" EXACT [TAO:0000761] synonym: "basal plate midbrain region" EXACT [ZFA:0000761] xref: DHBA:12322 xref: EFO:0003567 xref: EHDAA2:0004375 xref: TAO:0000761 xref: ZFA:0000761 is_a: UBERON:0002020 {source="EHDAA2"} ! gray matter relationship: part_of UBERON:0009581 {source="EHDAA2"} ! midbrain mantle layer relationship: part_of UBERON:0010286 {source="ZFA"} ! midbrain neural tube [Term] id: UBERON:0010286 name: midbrain neural tube namespace: uberon def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] xref: TAO:0007039 xref: ZFA:0007039 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003080 {source="ZFA"} ! anterior neural tube property_value: editor_note "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string [Term] id: UBERON:0010291 name: layer of sclera namespace: uberon def: "." [Wikipedia:Sclera#Histology] xref: Wikipedia:Sclera#Histology is_a: UBERON:0004923 ! organ component layer is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001773 {source="cjm"} ! sclera [Term] id: UBERON:0010294 name: scleral endothelium namespace: uberon def: "An endothelium that is part of a sclera." [OBOL:automatic] is_a: UBERON:0001986 ! endothelium is_a: UBERON:0010291 {source="Wikipedia"} ! layer of sclera is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001773 ! sclera [Term] id: UBERON:0010295 name: substantia propria of sclera namespace: uberon def: "A stroma that is part of a sclera." [OBOL:automatic] synonym: "scleral stroma" EXACT [FMA:58365] synonym: "stroma of sclera" EXACT [FMA:58365] synonym: "subsantia propria" BROAD [] synonym: "subsantia propria sclerae" EXACT [FMA:58365] synonym: "substantia propria sclerae" EXACT LATIN [FMA:58365, FMA:TA] xref: FMA:58365 xref: NCIT:C33652 xref: SCTID:368851004 xref: UMLS:C1704397 {source="ncithesaurus:Substantia_Propria"} is_a: UBERON:0003891 ! stroma is_a: UBERON:0010291 {source="Wikipedia"} ! layer of sclera intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001773 ! sclera [Term] id: UBERON:0010299 name: scleral mesenchyme namespace: uberon def: "Mesenchyme surrounding the developing optic cup which develops into the sclera." [https://orcid.org/0000-0002-6601-2165, PMID:16496288] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: has_potential_to_develop_into UBERON:0001773 ! sclera relationship: has_potential_to_develop_into UBERON:0001773 ! sclera relationship: surrounds UBERON:0003072 ! optic cup property_value: UBPROP:0000011 "The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288" xsd:string [Term] id: UBERON:0010303 name: extraembryonic epithelium namespace: uberon def: "An epithelium that is part of a extraembryonic structure." [OBOL:automatic] synonym: "extra-embryonic epithelium" EXACT [] is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005292 ! extraembryonic tissue intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0000478 ! extraembryonic structure [Term] id: UBERON:0010312 name: immature eye namespace: uberon def: "Developing anatomical structure that develops into the eyeball and associated structures." [ZFA:0001678] synonym: "future eye" EXACT [] xref: TAO:0002201 xref: ZFA:0001678 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: has_developmental_contribution_from UBERON:0003071 ! eye primordium relationship: develops_from UBERON:0003071 {evidence="definitional"} ! eye primordium relationship: has_developmental_contribution_from UBERON:0003071 ! eye primordium property_value: UBPROP:0000001 "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002201", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0010313 name: neural crest-derived structure namespace: uberon def: "An anatomical structure that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000061 ! anatomical structure intersection_of: develops_from UBERON:0002342 ! neural crest relationship: develops_from UBERON:0002342 ! neural crest property_value: IAO:0000232 "Grouping term for query purposes" xsd:string [Term] id: UBERON:0010314 name: structure with developmental contribution from neural crest namespace: uberon def: "An anatomical structure that has some part that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest property_value: IAO:0000232 "Grouping term for query purposes" xsd:string [Term] id: UBERON:0010316 name: germ layer / neural crest namespace: uberon is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0002532 ! epiblast (generic) [Term] id: UBERON:0010321 name: skeletal element of eye region namespace: uberon def: "A skeletal element that is part of a orbital region." [OBOL:automatic] synonym: "eye skeleton" RELATED [] synonym: "ocular skeleton" RELATED [] synonym: "skeletal element of orbital region" RELATED [] is_a: UBERON:0004765 ! skeletal element is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0004765 ! skeletal element intersection_of: part_of UBERON:0004088 ! orbital region relationship: part_of UBERON:0004088 ! orbital region relationship: part_of UBERON:0011156 ! facial skeleton [Term] id: UBERON:0010323 name: cranial skeletal system namespace: uberon def: "Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000049] synonym: "cranial skeleton" NARROW [] synonym: "cranium" RELATED INCONSISTENT [ZFA:0000737] synonym: "osteocranium" NARROW [] xref: AAO:0000109 xref: AAO:0000971 xref: AAO:0010185 xref: TAO:0000737 xref: VSAO:0000049 xref: XAO:0003075 xref: ZFA:0000737 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0011137 ! axial skeletal system property_value: editor_note "we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)" xsd:string property_value: IAO:0000232 "that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium" xsd:string property_value: UBPROP:0000001 "Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000109", ontology="AAO", source="AAO:LAP"} property_value: UBPROP:0000001 "Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000737", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0010329 name: paired limb/fin bud mesenchyme namespace: uberon def: "Mesenchyme that is part of a limb/fin bud." [OBOL:automatic] is_a: UBERON:0010377 ! mesenchyme from somatopleure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0004357 ! paired limb/fin bud relationship: develops_from UBERON:0010377 {source="EHDAA2-abduced"} ! mesenchyme from somatopleure relationship: part_of UBERON:0004357 ! paired limb/fin bud [Term] id: UBERON:0010336 name: mandibular process mesenchyme from neural crest namespace: uberon def: "Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme." [OBOL:automatic] xref: EHDAA2:0004603 is_a: UBERON:0006905 ! mandibular process mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0006905 ! mandibular process mesenchyme relationship: develops_from UBERON:0010252 {source="EHDAA2"} ! 1st arch mandibular mesenchyme from neural crest relationship: part_of UBERON:0006905 {source="EHDAA2"} ! mandibular process mesenchyme [Term] id: UBERON:0010337 name: mandibular process mesenchyme from head mesenchyme namespace: uberon def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme." [OBOL:automatic] xref: EHDAA2:0004604 is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0006905 ! mandibular process mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0006905 ! mandibular process mesenchyme relationship: develops_from UBERON:0010339 {source="EHDAA2"} ! 1st arch mandibular mesenchyme from head mesenchyme relationship: part_of UBERON:0006905 {source="EHDAA2"} ! mandibular process mesenchyme [Term] id: UBERON:0010339 name: 1st arch mandibular mesenchyme from head mesenchyme namespace: uberon def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme." [OBOL:automatic] xref: EHDAA2:0000036 is_a: UBERON:0009584 ! 1st arch mandibular mesenchyme is_a: UBERON:0010341 ! 1st arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0009584 ! 1st arch mandibular mesenchyme relationship: part_of UBERON:0009584 {source="EHDAA2"} ! 1st arch mandibular mesenchyme [Term] id: UBERON:0010341 name: 1st arch mesenchyme from head mesenchyme namespace: uberon def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme." [OBOL:automatic] synonym: "mesenchyme derived from head mesoderm of mesenchyme of 1st arch" EXACT [EMAPA:16130] xref: EMAPA:16130 is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010042 ! 1st arch mesenchyme is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010042 ! 1st arch mesenchyme relationship: part_of UBERON:0010042 {source="EMAPA"} ! 1st arch mesenchyme [Term] id: UBERON:0010347 name: 6th arch mesenchyme from head mesenchyme namespace: uberon def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme." [OBOL:automatic] synonym: "branchial arch 6 mesenchyme from head mesenchyme" RELATED [] synonym: "head mesenchyme derived arch 6 mesenchyme" EXACT [] synonym: "pharyngeal arch 6 mesenchyme from head mesenchyme" EXACT [] xref: EHDAA2:0004078 is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010031 ! 6th arch mesenchyme is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010031 ! 6th arch mesenchyme relationship: part_of UBERON:0010031 {source="EHDAA2"} ! 6th arch mesenchyme [Term] id: UBERON:0010359 name: pharyngeal arch mesenchyme from neural crest namespace: uberon def: "Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme." [OBOL:automatic] comment: Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme synonym: "arch mesenchyme from neural crest" EXACT [] synonym: "branchial arch mesenchyme from neural crest" EXACT [] synonym: "neural crest derived arch mesenchyme" EXACT [] is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme [Term] id: UBERON:0010360 name: pharyngeal arch mesenchyme from head mesenchyme namespace: uberon def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme." [OBOL:automatic] comment: Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme synonym: "arch mesenchyme from head mesenchyme" EXACT [] synonym: "branchial arch mesenchyme from head mesenchyme" EXACT [] synonym: "head mesenchyme derived arch mesenchyme" EXACT [] is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme relationship: develops_from UBERON:0006904 ! head mesenchyme from mesoderm relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme [Term] id: UBERON:0010362 name: endoskeleton namespace: uberon def: "Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000037] synonym: "replacement skeleton" EXACT [VSAO:curator] xref: VSAO:0000037 xref: Wikipedia:Endoskeleton xref: XAO:0004026 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton relationship: composed_primarily_of UBERON:0010522 ! replacement element relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: UBPROP:0000001 "An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t" xsd:string {source="Wikipedia:Endoskeleton"} [Term] id: UBERON:0010363 name: endochondral element namespace: uberon def: "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000139] synonym: "endochondral replacement element" EXACT [VSAO:0000139] xref: VSAO:0000139 xref: XAO:0004017 xref: ZFA:0005620 is_a: UBERON:0004765 {source="VSAO"} ! skeletal element property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern xsd:anyURI [Term] id: UBERON:0010364 name: dermal skeleton namespace: uberon def: "Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000035] comment: This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO synonym: "dermal skeletal system" RELATED [VSAO:curator] synonym: "dermoskeleton" RELATED [VSAO:curator] synonym: "desmoskeleton" RELATED [VSAO:curator] synonym: "exoskeleton" BROAD INCONSISTENT [VSAO:curator] xref: VSAO:0000035 xref: XAO:0004025 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0010371 name: ecto-epithelium namespace: uberon def: "Epithelium composed of cells that develops from the ectoderm[FMA,modified]." [FMA:69064] synonym: "ectoderm-derived epithelium" EXACT [] xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium intersection_of: develops_from UBERON:0000924 ! ectoderm relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell [Term] id: UBERON:0010377 name: mesenchyme from somatopleure namespace: uberon def: "Mesenchyme that develops_from a somatopleure." [OBOL:automatic] xref: EHDAA2:0001120 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0004874 ! somatopleure intersection_of: part_of UBERON:0000922 ! embryo relationship: develops_from UBERON:0004874 ! somatopleure relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme property_value: editor_note "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string [Term] id: UBERON:0010378 name: mesenchyme from splanchnopleure namespace: uberon def: "Mesenchyme that develops_from a splanchnopleure." [OBOL:automatic] xref: EHDAA2:0001122 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0004873 ! splanchnopleure intersection_of: part_of UBERON:0000922 ! embryo relationship: develops_from UBERON:0004873 ! splanchnopleure relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme [Term] id: UBERON:0010409 name: ocular surface region namespace: uberon def: "The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms." [MP:0013754] subset: pheno_slim synonym: "eye surface" EXACT [MA:0002486] synonym: "eye surface region" EXACT [] synonym: "ocular surface" EXACT [] xref: EMAPA:35336 xref: MA:0002486 is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye relationship: superficial_to UBERON:0022288 ! surface of eyeball [Term] id: UBERON:0010427 name: ciliary processes namespace: uberon def: "The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens." [Wikipedia:Ciliary_processes] synonym: "ciliary process" RELATED [Wikipedia:Ciliary_processes] synonym: "ciliary processes" EXACT [FMA:76551] synonym: "ciliary processes set" EXACT [FMA:76551] synonym: "processus ciliares" EXACT LATIN [FMA:TA] synonym: "processus ciliares" RELATED LATIN [Wikipedia:Ciliary_processes] synonym: "set of ciliary processes" EXACT [FMA:76551] xref: FMA:76551 xref: SCTID:280860001 xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png xsd:anyURI [Term] id: UBERON:0010428 name: flat bone namespace: uberon def: "A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow." [Wikipedia:Flat_bone] comment: Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs synonym: "os planum" RELATED LATIN [Wikipedia:Flat_bone] xref: FMA:7476 xref: galen:FlatBone xref: NCIT:C32616 xref: SCTID:332907008 xref: UMLS:C0222649 {source="ncithesaurus:Flat_Bone"} xref: Wikipedia:Flat_bone is_a: UBERON:0001474 {source="FMA"} ! bone element relationship: has_quality PATO:0000407 ! flat property_value: UBPROP:0000008 "In an adult mammal, most red blood cells are formed in flat bones" xsd:string property_value: UBPROP:0000009 "Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment" xsd:string [Term] id: UBERON:0010498 name: pseudostratified columnar epithelium namespace: uberon def: "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels." [http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium, Wikipedia:Pseudostratified_columnar_epithelium] xref: FMA:45572 xref: NCIT:C33419 xref: NCIT:C49316 xref: UMLS:C0836138 {source="ncithesaurus:Pseudostratified_Columnar_Epithelium"} xref: UMLS:C1514590 {source="ncithesaurus:Pseudostratified_Epithelium"} xref: Wikipedia:Pseudostratified_columnar_epithelium is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium property_value: UBPROP:0000009 "Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia." xsd:string property_value: UBPROP:0000012 "glandular in NCIT; we consider the two NCIT terms synonymous" xsd:string {external_ontology="NCIT"} [Term] id: UBERON:0010499 name: pseudostratified ciliated columnar epithelium namespace: uberon def: "Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile." [NCIT:NCIT] synonym: "epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)" EXACT [FMA:13146] xref: FMA:13146 xref: NCIT:C13181 xref: UMLS:C0506992 {source="ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium"} is_a: UBERON:0007592 ! ciliated columnar epithelium is_a: UBERON:0010498 ! pseudostratified columnar epithelium intersection_of: UBERON:0010498 ! pseudostratified columnar epithelium intersection_of: has_part CL:0000067 ! ciliated epithelial cell [Term] id: UBERON:0010522 name: replacement element namespace: uberon def: "Skeletal element that forms as a replacement or substitution of another element or tissue." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000135] xref: VSAO:0000135 xref: XAO:0004016 xref: ZFA:0005624 is_a: UBERON:0004765 {source="VSAO"} ! skeletal element relationship: part_of UBERON:0010362 {source="cjm"} ! endoskeleton [Term] id: UBERON:0010523 name: microcirculatory vessel namespace: uberon def: "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses." [http://orcid.org/0000-0002-6601-2165, MESH:A07.231.432, ZFA:0005251] synonym: "microcirculatory vessels" RELATED PLURAL [TAO:0005251] xref: MESH:A07.231.432 xref: TAO:0005251 xref: ZFA:0005251 is_a: UBERON:0000055 ! vessel relationship: part_of UBERON:0002049 {source="ZFA"} ! vasculature [Term] id: UBERON:0010707 name: appendage girdle complex namespace: uberon def: "An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton, https://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "appendage complex" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "appendage-girdle complex" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "appendage/girdle complex" EXACT [VSAO:0000214] synonym: "girdle plus limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "limb" RELATED INCONSISTENT [FMA:7182] xref: EMAPA:37858 {source="MA:th"} xref: FMA:7182 xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure relationship: functionally_related_to GO:0040011 ! locomotion relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata property_value: editor_note "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string property_value: UBPROP:0000001 "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000214", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} property_value: UBPROP:0000005 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000214", ontology="VSAO", source="Curator"} property_value: UBPROP:0000012 "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" xsd:string {external_ontology="FMA"} created_by: haendel creation_date: 2012-04-23T10:46:51Z [Term] id: UBERON:0010709 name: pelvic complex namespace: uberon def: "Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle." [VSAO:0000215] subset: pheno_slim synonym: "lower limb" RELATED INCONSISTENT [FMA:7184] synonym: "lower limb and pelvic girdle" RELATED HUMAN_PREFERRED [https://orcid.org/0000-0002-6601-2165] synonym: "lower limb and pelvis" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "pelvic appendage/girdle complex" EXACT [VSAO:0000215] synonym: "pelvic girdle plus pelvic limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "pelvic girdle plus posterior limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] xref: EMAPA:37863 {source="MA:th"} xref: FMA:7184 xref: SCTID:416631005 xref: VSAO:0000215 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001271 ! pelvic girdle region relationship: has_part UBERON:0001271 ! pelvic girdle region relationship: has_skeleton UBERON:0012476 ! skeleton of pelvic complex property_value: UBPROP:0000001 "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000215", ontology="VSAO", source="VSAO:MAH"} property_value: UBPROP:0000012 "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0010719 name: girdle skeleton namespace: uberon def: "The subdivision of the skeleton of either the pectoral or pelvic girdle." [https://orcid.org/0000-0002-6601-2165] synonym: "skeleton of girdle" EXACT [] xref: AAO:0010686 xref: VSAO:0000302 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0007823 ! appendage girdle region relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0007823 ! appendage girdle region relationship: proximally_connected_to UBERON:0002090 ! postcranial axial skeleton relationship: skeleton_of UBERON:0007823 ! appendage girdle region property_value: UBPROP:0000001 "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} [Term] id: UBERON:0010740 name: bone of appendage girdle complex namespace: uberon def: "A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: pheno_slim synonym: "bone of extended limb/fin region" RELATED [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] synonym: "limb bone" RELATED [MA:0000688, UBERONREF:0000003] xref: EMAPA:35494 xref: MA:0000688 is_a: UBERON:0001474 ! bone element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010707 ! appendage girdle complex relationship: contributes_to_morphology_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0002091 {notes="UBERONREF:0000003"} ! appendicular skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex [Term] id: UBERON:0010742 name: bone of pelvic complex namespace: uberon def: "A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: pheno_slim synonym: "hindlimb bone" RELATED [MA:0000660, UBERONREF:0000003] xref: EMAPA:32633 xref: EMAPA:35934 xref: MA:0000660 is_a: UBERON:0010740 {source="MA"} ! bone of appendage girdle complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0010709 ! pelvic complex property_value: UBPROP:0000012 "the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle" xsd:string {external_ontology="MA"} [Term] id: UBERON:0010890 name: pelvic complex muscle namespace: uberon def: "Muscles of the pelvic girdle, hindlimb or pelvic fin." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "lower limb muscle" RELATED INCONSISTENT [FMA:9622] synonym: "muscle of lower limb" RELATED INCONSISTENT [FMA:9622] synonym: "muscle of pelvic girdle and leg" RELATED [] synonym: "pelvic girdle and hind limb muscles" EXACT [AAO:0000218] synonym: "pelvic girdle or hind limb muscle" NARROW [https://orcid.org/0000-0002-6601-2165] synonym: "pelvic girdle or posterior limb muscle" NARROW [https://orcid.org/0000-0002-6601-2165] xref: AAO:0000218 xref: EMAPA:32634 xref: FMA:9622 xref: MA:0000663 is_a: UBERON:0014892 ! skeletal muscle organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0014792 {source="prolog"} ! musculature of pelvic complex property_value: UBPROP:0000001 "Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000218", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0010912 name: subdivision of skeleton namespace: uberon def: "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal subdivision" EXACT [VSAO:0000042] synonym: "subdivision of skeleton (in vivo)" RELATED [FMA:23879] xref: FMA:23879 xref: SCTID:129140006 xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0010959 name: craniocervical muscle namespace: uberon def: "Any muscle organ that is part of either the head or the neck." [http://orcid.org/0000-0002-6601-2165] synonym: "muscle of head and neck" RELATED [] synonym: "muscle of head or neck" EXACT [] xref: NCIT:C32716 xref: UMLS:C0448281 {source="ncithesaurus:Head_and_Neck_Muscle"} is_a: UBERON:0014892 ! skeletal muscle organ intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0008229 {source="prolog"} ! craniocervical region musculature [Term] id: UBERON:0011004 name: pharyngeal arch cartilage namespace: uberon def: "A cartilage element that is part of a splanchnocranium." [OBOL:automatic] subset: efo_slim synonym: "pharyngeal arch cartilages" EXACT PLURAL [ZFA:0001460] synonym: "splanchnocranium cartilage" EXACT [ZFA:0001460] xref: EFO:0003689 xref: TAO:0001460 xref: ZFA:0001460 is_a: UBERON:0003933 {source="ZFA"} ! cranial cartilage is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0008895 ! splanchnocranium relationship: develops_from UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0008895 {source="ZFA"} ! splanchnocranium [Term] id: UBERON:0011090 name: skeleton of right pelvic girdle namespace: uberon def: "A skeleton of pelvic girdle that is part of a right pelvic girdle region." [OBOL:automatic] xref: FMA:87593 is_a: UBERON:0007832 ! pelvic girdle skeleton intersection_of: UBERON:0007832 ! pelvic girdle skeleton intersection_of: part_of UBERON:0011092 ! right pelvic girdle region relationship: part_of UBERON:0011092 ! right pelvic girdle region [Term] id: UBERON:0011091 name: skeleton of left pelvic girdle namespace: uberon def: "A skeleton of pelvic girdle that is part of a left pelvic girdle region." [OBOL:automatic] xref: FMA:87594 is_a: UBERON:0007832 ! pelvic girdle skeleton intersection_of: UBERON:0007832 ! pelvic girdle skeleton intersection_of: part_of UBERON:0011093 ! left pelvic girdle region relationship: part_of UBERON:0011093 ! left pelvic girdle region [Term] id: UBERON:0011092 name: right pelvic girdle region namespace: uberon def: "A pelvic girdle region that is in the right side of a multicellular organism." [OBOL:automatic] synonym: "right pelvic girdle" EXACT INCONSISTENT [FMA:16582] xref: FMA:16582 is_a: UBERON:0001271 ! pelvic girdle region intersection_of: UBERON:0001271 ! pelvic girdle region intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: has_skeleton UBERON:0011090 ! skeleton of right pelvic girdle relationship: in_right_side_of UBERON:0000468 ! multicellular organism property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0011093 name: left pelvic girdle region namespace: uberon def: "A pelvic girdle region that is in the left side of a multicellular organism." [OBOL:automatic] synonym: "left pelvic girdle" EXACT INCONSISTENT [FMA:16583] xref: FMA:16583 is_a: UBERON:0001271 ! pelvic girdle region intersection_of: UBERON:0001271 ! pelvic girdle region intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: has_skeleton UBERON:0011091 ! skeleton of left pelvic girdle relationship: in_left_side_of UBERON:0000468 ! multicellular organism property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI [Term] id: UBERON:0011107 name: synovial joint of pelvic girdle namespace: uberon def: "A synovial joint that is part of a pelvic girdle region." [OBOL:automatic] synonym: "joint of pelvic girdle" EXACT [] synonym: "pelvic girdle joint" EXACT [FMA:35173] xref: FMA:35173 xref: NCIT:C32890 xref: UMLS:C0827002 {source="ncithesaurus:Joint_of_the_Pelvic_Girdle"} is_a: UBERON:0002217 ! synovial joint is_a: UBERON:0008114 ! joint of girdle intersection_of: UBERON:0002217 ! synovial joint intersection_of: part_of UBERON:0001271 ! pelvic girdle region relationship: connects UBERON:0007830 ! pelvic girdle bone/zone relationship: part_of UBERON:0001271 ! pelvic girdle region [Term] id: UBERON:0011134 name: nonsynovial joint namespace: uberon def: "Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis." [FMA:7491] synonym: "solid joint" EXACT [FMA:7491] xref: FMA:7491 is_a: UBERON:0000982 {source="FMA"} ! skeletal joint [Term] id: UBERON:0011137 name: axial skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] xref: FMA:7483 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: has_part UBERON:0000982 ! skeletal joint relationship: has_part UBERON:0005944 ! axial skeleton plus cranial skeleton property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI [Term] id: UBERON:0011138 name: postcranial axial skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints." [https://github.com/obophenotype/uberon/issues/44, https://orcid.org/0000-0002-6601-2165] synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/wiki/The-axial-skeleton] synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI [Term] id: UBERON:0011156 name: facial skeleton namespace: uberon def: "Subdivision of skull that consists of the facial bones." [http://www.bartleby.com/107/37.html, https://orcid.org/0000-0002-6601-2165, MP:0005274, Wikipedia:Facial_skeleton] subset: pheno_slim synonym: "facial bone" RELATED [MA:0000318] synonym: "facial skeleton" EXACT [FMA:53673] synonym: "ossa facialia" RELATED LATIN [Wikipedia:Facial_skeleton] synonym: "ossa faciei" RELATED LATIN [Wikipedia:Facial_skeleton] synonym: "viscerocranium" RELATED INCONSISTENT [MA:0000318] xref: EHDAA2:0002206 xref: EHDAA:8361 xref: EMAPA:18022 xref: FMA:53673 xref: MA:0000318 xref: Wikipedia:Facial_skeleton is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull relationship: part_of UBERON:0001456 {source="FMA"} ! face property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg xsd:anyURI [Term] id: UBERON:0011158 name: primary subdivision of skull namespace: uberon def: "The skull can be divided into two: the neurocranium and the facial skeleton" [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "skull subdivision" EXACT [FMA:54964] synonym: "subdivision of skull" EXACT [FMA:54964] xref: FMA:54964 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: part_of UBERON:0003129 ! skull [Term] id: UBERON:0011159 name: primary subdivision of cranial skeletal system namespace: uberon subset: non_informative is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: part_of UBERON:0010323 ! cranial skeletal system [Term] id: UBERON:0011164 name: neurocranium bone namespace: uberon def: "A bone that is part of a neurocranium [Automatically generated definition]." [OBOL:automatic] synonym: "chondrocranium bone" EXACT [MA:0001478] xref: EMAPA:35238 xref: MA:0001478 xref: SCTID:120229002 is_a: UBERON:0004766 ! cranial bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0001703 ! neurocranium [Term] id: UBERON:0011215 name: central nervous system cell part cluster namespace: uberon def: "A multi cell part structure that is part of a central nervous system." [OBOL:automatic] subset: upper_level synonym: "cell part cluster of neuraxis" EXACT [FMA:83143] synonym: "neuraxis layer" EXACT [FMA:83143] xref: FMA:83143 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system [Term] id: UBERON:0011216 name: organ system subdivision namespace: uberon def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2165] subset: upper_level xref: FBbt:00007330 xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system [Term] id: UBERON:0011222 name: intra-ocular muscle namespace: uberon synonym: "intrinsic muscle of eyeball" EXACT [] synonym: "intrinsic ocular muscle" EXACT [EMAPA:18808] xref: AAO:0010038 xref: EMAPA:18808 xref: FMA:49150 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004277 ! eye muscle relationship: part_of UBERON:0003386 {source="EMAPA"} ! smooth muscle of eye property_value: UBPROP:0000001 "Muscles within the eye (bulbus oculi).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010038", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0011233 name: synovial membrane of synovial tendon sheath namespace: uberon def: "Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa." [FMA:45087, Wikipedia:Synovial_sheath] comment: Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath] synonym: "synovium" BROAD [BTO:0001823] xref: BTO:0001823 xref: FMA:40878 xref: Wikipedia:Synovial_sheath is_a: UBERON:0007616 ! layer of synovial tissue intersection_of: UBERON:0007616 ! layer of synovial tissue intersection_of: bounding_layer_of UBERON:0000304 ! tendon sheath relationship: bounding_layer_of UBERON:0000304 ! tendon sheath relationship: part_of UBERON:0000304 ! tendon sheath [Term] id: UBERON:0011234 name: fibrous membrane of synovial tendon sheath namespace: uberon xref: FMA:40877 is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000304 ! tendon sheath intersection_of: composed_primarily_of UBERON:0011824 ! fibrous connective tissue relationship: bounding_layer_of UBERON:0000304 ! tendon sheath relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue relationship: part_of UBERON:0000304 ! tendon sheath [Term] id: UBERON:0011249 name: appendicular skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] xref: FMA:7484 xref: VHOG:0001666 xref: VSAO:0000306 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: has_part UBERON:0000982 ! skeletal joint relationship: has_part UBERON:0002091 ! appendicular skeleton property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton xsd:anyURI property_value: UBPROP:0000001 "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000306", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0011270 name: dorsal trunk namespace: uberon def: "The part of the trunk that is in the dorsum[cjm]." [UBERONREF:0000006, Wikipedia:Human_back] synonym: "back of trunk" EXACT [FMA:25056] synonym: "dorsal part of trunk" EXACT [] synonym: "dorsum of trunk" EXACT [FMA:25056] synonym: "trunk back" EXACT [FMA:25056] xref: EMAPA:35162 xref: FMA:25056 xref: MA:0000020 xref: Wikipedia:Human_back is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk relationship: part_of UBERON:0001137 {source="FMA"} ! dorsum property_value: UBPROP:0000008 "In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]" xsd:string [Term] id: UBERON:0011272 name: embryonic skin basal layer namespace: uberon synonym: "basal cell layer of skin" RELATED [] synonym: "outer epithelium of body" RELATED [Wikipathways:WP2062] xref: EHDAA2:0001845 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument property_value: editor_note "compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'" xsd:string [Term] id: UBERON:0011362 name: cranial blood vasculature namespace: uberon def: "A blood vasculature that is part of a head." [OBOL:automatic] synonym: "cranial blood vessel" EXACT [ZFA:0005297] synonym: "cranial blood vessels" RELATED PLURAL [TAO:0005297] synonym: "set of blood vessels of head" EXACT [] xref: TAO:0005297 xref: ZFA:0005297 is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0004537 ! blood vasculature intersection_of: UBERON:0004537 ! blood vasculature intersection_of: part_of UBERON:0000033 ! head property_value: UBPROP:0000001 "Blood vessel part of cranial vasculature.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005297", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0011565 name: lumen of gastrointestinal system namespace: uberon synonym: "cavity of digestive tract" EXACT [] synonym: "cavity of gastrointestinal tract" EXACT [] synonym: "gastrointestinal tract lumen" EXACT [FMA:54364] synonym: "lumen of gastrointestinal tract" EXACT [FMA:54364] xref: FMA:54364 xref: SCTID:432899004 is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001007 ! digestive system [Term] id: UBERON:0011566 name: lumen of esophagus namespace: uberon def: "An anatomical cavity that is part of a esophagus." [OBOL:automatic] subset: pheno_slim synonym: "cavity of eosophagus" EXACT [] synonym: "cavity of esophagus" EXACT [FMA:9398] synonym: "eosophageal cavity" EXACT [] synonym: "eosophageal lumen" EXACT [] synonym: "eosophagus lumen" EXACT [] synonym: "esophageal cavity" EXACT [FMA:9398] synonym: "esophageal lumen" EXACT [FMA:9398] synonym: "esophagus lumen" EXACT [FMA:9398] xref: EMAPA:18380 xref: FMA:9398 xref: SCTID:322648002 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0001043 ! esophagus relationship: luminal_space_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0011565 {source="FMA"} ! lumen of gastrointestinal system [Term] id: UBERON:0011582 name: paired limb/fin skeleton namespace: uberon def: "The collection of all skeletal elements in an individual limb or fin." [https://orcid.org/0000-0002-6601-2165] subset: homology_grouping synonym: "limb/fin skeleton" EXACT [VSAO:0000301] synonym: "skeletal parts of limb/fin" EXACT [] synonym: "skeleton of limb/fin" EXACT [] xref: VSAO:0000301 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0004708 ! paired limb/fin relationship: develops_from UBERON:0003081 {source="ISBN:9780878932504"} ! lateral plate mesoderm relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0004708 ! paired limb/fin relationship: skeleton_of UBERON:0004708 ! paired limb/fin property_value: UBPROP:0000001 "Skeletal subdivision that is part of the paired limb/fin.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000301", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} [Term] id: UBERON:0011585 name: cell condensation namespace: uberon def: "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000006] xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011595 name: jaw region namespace: uberon def: "A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:32905 xref: NCIT:C114916 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000475 ! organism subdivision intersection_of: has_skeleton UBERON:0001708 ! jaw skeleton relationship: has_skeleton UBERON:0001708 ! jaw skeleton relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000165 {source="EMAPA", source="FMA-abduced", source="ZFA-abduced"} ! mouth property_value: seeAlso http://eol.org/collections/11578 xsd:anyURI [Term] id: UBERON:0011596 name: future lower lip namespace: uberon synonym: "lower jaw future lip" EXACT [EHDAA2:0001020] xref: EHDAA2:0001020 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0003236 ! epithelium of lower jaw relationship: develops_from UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! mandibular prominence [Term] id: UBERON:0011642 name: oral epithelium from ectoderm namespace: uberon def: "An epithelium that develops_from a ectoderm and is part of a oral epithelium." [OBOL:automatic] xref: EHDAA2:0004137 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002424 ! oral epithelium is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0002424 ! oral epithelium relationship: develops_from UBERON:0009479 {source="EHDAA2"} ! ectoderm of buccopharyngeal membrane relationship: part_of UBERON:0002424 ! oral epithelium [Term] id: UBERON:0011676 name: subdivision of organism along main body axis namespace: uberon def: "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column." [https://orcid.org/0000-0002-6601-2165] subset: upper_level synonym: "axial subdivision of organism" EXACT [] synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 name: embryonic cardiovascular system namespace: uberon def: "A cardiovascular system that is part of a conceptus." [OBOL:automatic] synonym: "conceptus cardiovascular system" EXACT [] synonym: "embryonic circulatory system" RELATED [] synonym: "fetal circulatory system" RELATED [] xref: EHDAA2:0000216 xref: FMA:305965 xref: NCIT:C34148 is_a: UBERON:0004535 ! cardiovascular system intersection_of: UBERON:0004535 ! cardiovascular system intersection_of: part_of UBERON:0004716 ! conceptus relationship: part_of UBERON:0004716 ! conceptus [Term] id: UBERON:0011772 name: lower jaw opening namespace: uberon def: "An anatomical space that is part of a bone of lower jaw." [OBOL:automatic] xref: AAO:0000273 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0004768 ! bone of lower jaw relationship: luminal_space_of UBERON:0004768 ! bone of lower jaw relationship: part_of UBERON:0004768 ! bone of lower jaw [Term] id: UBERON:0011779 name: nerve of head region namespace: uberon def: "A nerve that is part of a head." [OBOL:automatic] subset: grouping_class synonym: "cephalic nerve" RELATED [] synonym: "head nerve" RELATED [] is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head [Term] id: UBERON:0011814 name: non-neurogenic ectodermal placode namespace: uberon def: "Ectodermal placode that does not develop into a component of the nervous system." [http://orcid.org/0000-0002-6601-2165, PMID:11523831] is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode [Term] id: UBERON:0011820 name: atrioventricular region namespace: uberon def: "An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "atrial ventricular junction" RELATED [GO:0003294] synonym: "atrioventricular junction" RELATED [FMA:85125, GO:0003294] synonym: "atrioventricular segment" RELATED [PMID:21234997] synonym: "AV region" RELATED [PMID:21234997] synonym: "AV segment" RELATED [PMID:21234997] xref: EHDAA2:0004149 xref: FMA:85125 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0002081 ! cardiac atrium intersection_of: connects UBERON:0002082 ! cardiac ventricle intersection_of: part_of UBERON:0000948 ! heart relationship: connects UBERON:0002081 ! cardiac atrium relationship: connects UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0000948 ! heart [Term] id: UBERON:0011821 name: irregular connective tissue namespace: uberon def: "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20107] xref: FMA:20107 is_a: UBERON:0002384 {source="FMA"} ! connective tissue [Term] id: UBERON:0011822 name: dense irregular connective tissue namespace: uberon def: "Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20109, Wikipedia:Dense_irregular_connective_tissue] synonym: "irregular dense connective tissue" EXACT [] synonym: "typus irregularis (textus connectivus collagenosus compactus)" EXACT [FMA:20109] xref: FMA:20109 xref: NCIT:C32882 xref: UMLS:C0738366 {source="ncithesaurus:Irregular_Dense_Connective_Tissue"} xref: Wikipedia:Dense_irregular_connective_tissue is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue is_a: UBERON:0011823 ! dense connective tissue intersection_of: UBERON:0011821 ! irregular connective tissue intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber relationship: has_part GO:0071953 ! elastic fiber property_value: UBPROP:0000001 "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Irregular_Dense_Connective_Tissue", ontology="NCIT"} [Term] id: UBERON:0011823 name: dense connective tissue namespace: uberon def: "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets" [Wikipedia:Dense_connective_tissue] xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils disjoint_from: UBERON:0011825 ! loose connective tissue relationship: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils property_value: editor_note "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string property_value: UBPROP:0000001 "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Dense_Connective_Tissue", ontology="NCIT"} [Term] id: UBERON:0011824 name: fibrous connective tissue namespace: uberon xref: FMA:75634 xref: SCTID:363130003 is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue [Term] id: UBERON:0011825 name: loose connective tissue namespace: uberon def: "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue." [FMA:19783] synonym: "textus connectivus collagenosus laxus" EXACT LATIN [FMA:19783, FMA:TA] synonym: "textus connectivus laxus" EXACT LATIN [FMA:19783, FMA:TA] xref: FMA:19783 xref: NCIT:C33007 xref: UMLS:C1253917 {source="ncithesaurus:Loose_Connective_Tissue"} xref: Wikipedia:Loose_connective_tissue is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue [Term] id: UBERON:0011858 name: acinus of exocrine gland namespace: uberon def: "An acinus that is part of a exocrine gland." [OBOL:automatic] synonym: "exocrine gland acinus" EXACT [] is_a: UBERON:0009842 ! glandular acinus intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0002365 ! exocrine gland relationship: part_of UBERON:0002365 ! exocrine gland [Term] id: UBERON:0011860 name: collection of collagen fibrils namespace: uberon xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: composed_primarily_of GO:0005581 ! collagen trimer relationship: composed_primarily_of GO:0098643 ! banded collagen fibril property_value: seeAlso UBERON:0007377 property_value: UBPROP:0000012 "the FMA class specifically refers to ureter" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0011861 name: aorta collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity" [MP:0011640] subset: pheno_slim is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia relationship: contributes_to_morphology_of UBERON:0004664 ! aorta tunica adventitia relationship: part_of UBERON:0004664 ! aorta tunica adventitia [Term] id: UBERON:0011862 name: pulmonary collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity" [MP:0011641] subset: pheno_slim is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0002048 ! lung relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung [Term] id: UBERON:0011863 name: bone collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity" [MP:0011642] subset: pheno_slim is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element [Term] id: UBERON:0011864 name: tendon collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity" [MP:0011643] subset: pheno_slim is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0000043 ! tendon relationship: contributes_to_morphology_of UBERON:0000043 ! tendon relationship: part_of UBERON:0000043 ! tendon [Term] id: UBERON:0011865 name: corneal stroma collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity" [MP:0011650] subset: pheno_slim is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0001777 ! substantia propria of cornea relationship: contributes_to_morphology_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea [Term] id: UBERON:0011892 name: anterior uvea namespace: uberon def: "Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris." [MP:0005194] subset: pheno_slim synonym: "anterior part of uveal tract" EXACT [] synonym: "anterior uveal tract" EXACT [] synonym: "anterior vascular layer of the eyeball" EXACT [] synonym: "anterior vascular tunic of the eye" EXACT [] synonym: "ciliary body and iris" RELATED [] synonym: "Haller tunica vascula" EXACT [MP:0005194] synonym: "tunica vasculosa bulbosa" EXACT [MP:0005194] synonym: "vasculosa oculi" RELATED [MP:0005194] synonym: "ventral uveal tract" EXACT [] xref: EMAPA:37417 {source="MA:th"} xref: SCTID:280656002 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: contributes_to_morphology_of UBERON:0001768 ! uvea relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001768 {source="MP"} ! uvea [Term] id: UBERON:0011899 name: epimysium namespace: uberon def: "Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous." [Wikipedia:Epimysium] synonym: "epimysia" RELATED PLURAL [Wikipedia:Epimysium] synonym: "fascia of muscle organ" EXACT [FMA:9726] xref: FMA:9726 xref: NCIT:C32527 xref: UMLS:C0504096 {source="ncithesaurus:Epimysium"} xref: Wikipedia:Epimysium is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: bounding_layer_of UBERON:0014892 ! skeletal muscle organ relationship: continuous_with UBERON:0000043 ! tendon relationship: part_of UBERON:0001134 {source="FMA"} ! skeletal muscle tissue property_value: UBPROP:0000009 "The Epimysium also protects muscles from friction against other muscles and bones" xsd:string [Term] id: UBERON:0011997 name: coelom namespace: uberon def: "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen." [UBERON:cjm, Wikipedia:Body_cavity, Wikipedia:Coelom] synonym: "coelem" RELATED [] synonym: "coelomic cavity" RELATED [EHDAA2:0004731] synonym: "enterocoelom" NARROW [NCBITaxon:33511] synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: only_in_taxon NCBITaxon:33213 ! Bilateria property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: UBPROP:0000007 "coelomic" xsd:string [Term] id: UBERON:0012054 name: myocoele namespace: uberon def: "The cavity within a myotome" [http://medical-dictionary.thefreedictionary.com/myocoele] xref: EMAPA:31134 xref: VHOG:0001283 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0003082 ! myotome relationship: luminal_space_of UBERON:0003082 ! myotome relationship: part_of UBERON:0003082 ! myotome property_value: UBPROP:0000003 "The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001283", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6", source="http://bgee.unil.ch/"} [Term] id: UBERON:0012075 name: replacement bone namespace: uberon def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628] synonym: "replacement bones" EXACT PLURAL [ZFA:0001628] xref: AAO:0010768 xref: TAO:0001637 xref: ZFA:0001628 is_a: UBERON:0001474 {source="ZFA"} ! bone element is_a: UBERON:0010522 {source="ZFA"} ! replacement element property_value: UBPROP:0000001 "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"} property_value: UBPROP:0000012 "This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element." xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0012125 name: dermatological-muscosal system namespace: uberon def: "Anatomical system that consists of the integumental system plus all mucosae and submucosae." [https://github.com/obophenotype/uberon/issues/53] synonym: "dermatological system" RELATED [OBI:MC] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000467 ! anatomical system relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000009 ! submucosa relationship: has_part UBERON:0000344 ! mucosa relationship: has_part UBERON:0002072 ! hypodermis relationship: has_part UBERON:0002097 ! skin of body property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/mcourtot [Term] id: UBERON:0012180 name: head or neck skin namespace: uberon def: "A zone of skin that is part of a craniocervical region." [OBOL:automatic] xref: EMAPA:37276 {source="MA:th"} xref: MA:0000574 xref: NCIT:C12294 xref: UMLS:C1522650 {source="ncithesaurus:Skin_of_the_Scalp_and_Neck"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0007811 ! craniocervical region [Term] id: UBERON:0012254 name: abdominal aorta artery namespace: uberon def: "An artery that originates from the abdominal aorta" [https://orcid.org/0000-0002-6601-2165, Wikipedia:Abdominal_aorta#Branches] subset: pheno_slim synonym: "abdominal artery" EXACT [] synonym: "artery of abdomen" EXACT [] xref: SCTID:281470000 is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery intersection_of: branching_part_of UBERON:0001516 ! abdominal aorta relationship: branching_part_of UBERON:0001516 ! abdominal aorta relationship: part_of UBERON:0001516 ! abdominal aorta [Term] id: UBERON:0012274 name: columnar epithelium namespace: uberon def: "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]" [Wikipedia:Columnar_epithelium] xref: Wikipedia:Columnar_epithelium is_a: UBERON:0000483 ! epithelium relationship: has_part CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: UBERON:0012275 name: meso-epithelium namespace: uberon def: "Epithelium that derives from the mesoderm. [Automatically generated definition]." [OBOL:automatic] synonym: "mesoderm-derived epithelium" EXACT [] synonym: "mesoepithelium" EXACT [] xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium intersection_of: develops_from UBERON:0000926 ! mesoderm [Term] id: UBERON:0012314 name: embryonic facial prominence namespace: uberon def: "One of five swellings formed during the development of the face" [http://www.indiana.edu/~anat550/hnanim/face/face.html] synonym: "embryonic facial process" RELATED [] synonym: "facial primordium" RELATED [] synonym: "primordium of face" RELATED [] xref: FMA:293103 xref: SCTID:89066004 is_a: UBERON:0002050 ! embryonic structure relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000033 ! head [Term] id: UBERON:0012320 name: cervical artery namespace: uberon def: "An artery of the neck" [https://orcid.org/0000-0002-6601-2165] xref: EMAPA:37075 {source="MA:th"} xref: NCIT:C52850 xref: UMLS:C1707349 {source="ncithesaurus:Cervical_Artery"} is_a: UBERON:0001637 ! artery is_a: UBERON:0003502 ! neck blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0000974 ! neck [Term] id: UBERON:0012321 name: deep cervical artery namespace: uberon def: "The deep cervical artery (Profunda cervicalis) is an artery of the neck." [Wikipedia:Deep_cervical_artery] synonym: "profunda cervicalis" RELATED [Wikipedia:Deep_cervical_artery] xref: FMA:10659 xref: SCTID:244223002 xref: Wikipedia:Deep_cervical_artery is_a: UBERON:0012320 ! cervical artery intersection_of: UBERON:0012320 ! cervical artery intersection_of: part_of UBERON:0035551 ! deep vasculature relationship: branching_part_of UBERON:0004688 {source="FMA"} ! costo-cervical trunk relationship: part_of UBERON:0004688 ! costo-cervical trunk relationship: part_of UBERON:0035551 ! deep vasculature [Term] id: UBERON:0012360 name: bone of jaw namespace: uberon def: "A bone element that is part of a jaw region." [OBOL:automatic] synonym: "jaw bone" EXACT [] xref: EMAPA:35453 xref: MA:0003130 xref: SCTID:369003004 is_a: UBERON:0003462 ! facial bone is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0011595 ! jaw region relationship: part_of UBERON:0001708 ! jaw skeleton property_value: editor_note "Do not manually classify under here - bones are automatically classified" xsd:string [Term] id: UBERON:0012375 name: subserosa namespace: uberon def: "A layer of tissue between the muscularis and serosa." [Wikipedia:Subserosa] comment: Contains nerves, blood vessels, lymphatics and lymph nodes xref: FMA:45636 xref: NCIT:C94494 xref: SCTID:2255006 xref: UMLS:C0225334 {source="ncithesaurus:Subserosa"} xref: Wikipedia:Subserosa is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0000042 ! serous membrane intersection_of: composed_primarily_of UBERON:0006815 ! areolar connective tissue relationship: adjacent_to UBERON:0000042 ! serous membrane relationship: composed_primarily_of UBERON:0006815 ! areolar connective tissue relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0012416 name: respiratory system arterial smooth muscle namespace: uberon xref: EMAPA:37567 {source="MA:th"} xref: MA:0001802 is_a: UBERON:0004297 ! respiratory system blood vessel smooth muscle is_a: UBERON:0004695 ! arterial system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003643 ! respiratory system arterial blood vessel relationship: part_of UBERON:0003643 ! respiratory system arterial blood vessel [Term] id: UBERON:0012418 name: respiratory system venous smooth muscle namespace: uberon def: "A smooth muscle tissue that is part of a respiratory system venous blood vessel." [OBOL:automatic] xref: EMAPA:37586 {source="MA:th"} xref: MA:0001812 is_a: UBERON:0004696 ! venous system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003476 ! respiratory system venous blood vessel relationship: part_of UBERON:0003476 ! respiratory system venous blood vessel [Term] id: UBERON:0012429 name: hematopoietic tissue namespace: uberon def: "Blood-forming tissue, consisting of reticular fibers and cells." [http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue] synonym: "bone marrow tissue" NARROW [NCBITaxon:9606] synonym: "haemopoietic tissue" EXACT [FMA:14073] synonym: "hematopoietic tissue" EXACT [FMA:14073] synonym: "hemopoietic tissue" EXACT [FMA:14073] synonym: "textus haemopoieticus" EXACT [FMA:14073] xref: CALOHA:TS-2142 xref: FMA:14073 xref: NCIT:C13051 xref: UMLS:C0229619 {source="ncithesaurus:Hematopoietic_Tissue"} is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis property_value: UBPROP:0000008 "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" xsd:string [Term] id: UBERON:0012430 name: tunica fibrosa of eyeball namespace: uberon def: "The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth." [Wikipedia:Fibrous_tunic_of_eyeball] synonym: "corneosclera" RELATED [Wikipedia:Fibrous_tunic_of_eyeball] synonym: "fibrous layer of eyeball" EXACT [FMA:58102] synonym: "fibrous tunic" RELATED [Wikipedia:Fibrous_tunic_of_eyeball] synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000964 ! cornea relationship: has_part UBERON:0001773 ! sclera relationship: part_of UBERON:0010230 ! eyeball of camera-type eye property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0012466 name: extraembryonic cavity namespace: uberon synonym: "extraembryonic cavities" RELATED PLURAL [EHDAA2:0000472] xref: EHDAA2:0000472 xref: EMAPA:16054 xref: VHOG:0000767 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0016887 ! entire extraembryonic component relationship: part_of UBERON:0016887 ! entire extraembryonic component [Term] id: UBERON:0012467 name: enclosed anatomical space namespace: uberon def: "An anatomical space with no opening to another space or to the exterior." [AEO:0000222] synonym: "closed anatomical space" EXACT [] xref: AEO:0000222 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: has_quality PATO:0000608 ! closed relationship: has_quality PATO:0000608 ! closed [Term] id: UBERON:0012476 name: skeleton of pelvic complex namespace: uberon def: "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "bones of lower limb" RELATED [FMA:24140] synonym: "lower limb skeleton" RELATED [FMA:24140] synonym: "ossa membri inferioris" RELATED [FMA:TA] synonym: "pelvic complex skeleton" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "set of bones of lower limb" RELATED [FMA:24140] synonym: "skeleton of posterior limb/fin and girdle" RELATED [https://orcid.org/0000-0002-6601-2165] xref: FMA:24140 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0010709 {source="FMA"} ! pelvic complex relationship: skeleton_of UBERON:0010709 ! pelvic complex [Term] id: UBERON:0012504 name: adventitia of esophagus namespace: uberon def: "A adventitia that is part of a esophagus." [OBOL:automatic] synonym: "adventitia of oesophagus" EXACT [FMA:63006] synonym: "adventitious layer of esophagus" EXACT [FMA:63006] synonym: "esophageal adventitia" EXACT [FMA:63006] synonym: "esophagus adventitia" EXACT [FMA:63006] synonym: "tunica adventitia (esophagus)" EXACT [FMA:63006] synonym: "tunica adventitia oesophageae" EXACT [FMA:TA] xref: FMA:63006 xref: SCTID:85950006 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005742 ! adventitia intersection_of: UBERON:0005742 ! adventitia intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus [Term] id: UBERON:0013126 name: vein of abdomen namespace: uberon def: "A vein that is part of a abdomen." [OBOL:automatic] subset: grouping_class synonym: "abdominal vein" EXACT [] xref: SCTID:281473003 is_a: UBERON:0001638 ! vein is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000916 ! abdomen property_value: editor_note "TODO mirror representation of abdominal aorta" xsd:string property_value: IAO:0000232 "this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein" xsd:string [Term] id: UBERON:0013136 name: vein of lip namespace: uberon def: "A vein that drains a lip." [OBOL:automatic] synonym: "labial vein" RELATED [] synonym: "labial vein of face" EXACT [] synonym: "lip vein" EXACT [OBOL:automatic] synonym: "vena labialis" EXACT LATIN [] xref: SCTID:367664002 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001833 ! lip relationship: drains UBERON:0001833 ! lip relationship: part_of UBERON:0001653 ! facial vein relationship: tributary_of UBERON:0001653 {source="FMA"} ! facial vein [Term] id: UBERON:0013140 name: systemic vein namespace: uberon def: "Any vein within the general circulation that transports blood back to the right atrium of the heart." [ncithesaurus:Systemic_Vein] synonym: "systemic venous tree organ part" EXACT [FMA:66644] xref: FMA:66644 xref: NCIT:C33719 xref: SCTID:244389004 xref: UMLS:C0447117 {source="ncithesaurus:Systemic_Vein"} is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0004581 ! systemic venous system relationship: part_of UBERON:0004581 ! systemic venous system [Term] id: UBERON:0013232 name: serous acinus namespace: uberon def: "The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] synonym: "acinus of serous gland" EXACT [] xref: FMA:86279 is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0000409 ! serous gland relationship: composed_primarily_of CL:0000313 ! serous secreting cell relationship: part_of UBERON:0000409 ! serous gland [Term] id: UBERON:0013411 name: cranial cavity namespace: uberon def: "Anatomical cavity that is the lumen of the skull and contains the brain." [UBERON:cjm] synonym: "cavitas cranii" EXACT LATIN [FMA:9644, FMA:TA] synonym: "intracranial cavity" RELATED [Wikipedia:Cranial_cavity] synonym: "intracranial space" RELATED [Wikipedia:Cranial_cavity] xref: EMAPA:37497 {source="MA:th"} xref: FMA:9644 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2806 xref: MA:0003061 xref: NCIT:C77638 xref: SCTID:264452006 xref: UMLS:C0230041 {source="ncithesaurus:Cranial_Cavity"} xref: Wikipedia:Cranial_cavity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0003129 ! skull relationship: luminal_space_of UBERON:0003129 ! skull relationship: part_of UBERON:0003129 {source="Wikipedia"} ! skull property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg xsd:anyURI [Term] id: UBERON:0013479 name: lung endothelium namespace: uberon def: "A blood vessel endothelium that is part of a lung [Automatically generated definition]." [OBOL:automatic] synonym: "respiratory endothelium" RELATED [BTO:0004128] xref: BTO:0004128 xref: CALOHA:TS-0573 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000115 ! lung epithelium is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0004638 ! blood vessel endothelium intersection_of: part_of UBERON:0002048 ! lung [Term] id: UBERON:0013514 name: space surrounding organism namespace: uberon def: "The space that surrounds an organism." [https://orcid.org/0000-0002-6601-2165] synonym: "external to organism" EXACT [] synonym: "outside of body" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: surrounds UBERON:0000468 ! multicellular organism relationship: surrounds UBERON:0000468 ! multicellular organism [Term] id: UBERON:0013522 name: subdivision of tube namespace: uberon is_a: UBERON:0000064 ! organ part relationship: has_part UBERON:0000060 ! anatomical wall relationship: has_part UBERON:0000464 ! anatomical space relationship: part_of UBERON:0000025 ! tube relationship: subdivision_of UBERON:0000025 ! tube [Term] id: UBERON:0013685 name: foramen of skull namespace: uberon def: "Anatomical space that is an opening in a bone of the skull." [http://orcid.org/0000-0002-6601-2165, TAO:curator] synonym: "cranial conduit" NARROW [FMA:53165] synonym: "cranial foramen" NARROW [] synonym: "foramen of skull" EXACT [Wikipedia:Foramina_of_the_skull] synonym: "foramina of the skull" RELATED PLURAL [Wikipedia:Foramina_of_the_skull] xref: FMA:53165 xref: SCTID:276742007 xref: Wikipedia:Foramina_of_the_skull is_a: UBERON:0005744 ! bone foramen intersection_of: UBERON:0005744 ! bone foramen intersection_of: part_of UBERON:0003129 ! skull relationship: part_of UBERON:0003129 ! skull [Term] id: UBERON:0013686 name: anatomical conduit space namespace: uberon def: "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]." [FMA:9338, http://orcid.org/0000-0002-6601-2165] synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space relationship: connects UBERON:0000464 {minCardinality="2", maxCardinality="2"} ! anatomical space relationship: luminal_space_of UBERON:0004111 ! anatomical conduit relationship: part_of UBERON:0004111 ! anatomical conduit [Term] id: UBERON:0013694 name: brain endothelium namespace: uberon def: "Vascular endothelium found in blood vessels of the blood-brain-barrier." [CALOHA:TS-0092] synonym: "cerebromicrovascular endothelium" RELATED [CALOHA:TS-0092] xref: BTO:0001852 xref: BTO:0003248 xref: CALOHA:TS-0092 is_a: UBERON:0001986 ! endothelium is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain [Term] id: UBERON:0013700 name: axial musculature namespace: uberon def: "Musculature of the head and neck, spine, and ribs." [HP:0003327] xref: EHDAA2:0000159 xref: EMAPA:18166 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: attaches_to UBERON:0005944 ! axial skeleton plus cranial skeleton intersection_of: part_of UBERON:0013701 ! main body axis relationship: attaches_to UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0013701 ! main body axis [Term] id: UBERON:0013701 name: main body axis namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa [Term] id: UBERON:0013702 name: body proper namespace: uberon def: "The region of the organism associated with the visceral organs." [AEO:0000103] subset: non_informative synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0013704 name: notochordal canal namespace: uberon def: "A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily." [http://medical-dictionary.thefreedictionary.com/notochordal+canal] synonym: "chordal canal" RELATED [] xref: FMA:293127 xref: NCIT:C34230 xref: UMLS:C1518428 {source="ncithesaurus:Notochordal_Canal"} is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0006268 ! notochordal process relationship: part_of UBERON:0006268 ! notochordal process [Term] id: UBERON:0013727 name: notochordal fluid namespace: uberon def: "Fluid contained within the notochordal canal" [http://animaldiversity.org/accounts/Latimeria_chalumnae/, http://orcid.org/0000-0002-6601-2165] comment: Distinct feature of coelocanths synonym: "notochord fluid" EXACT [] synonym: "portion of notochordal fluid" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0006314 ! bodily fluid intersection_of: located_in UBERON:0013704 ! notochordal canal intersection_of: part_of UBERON:0036242 ! post-embryonic notochord relationship: located_in UBERON:0013704 ! notochordal canal relationship: part_of UBERON:0036242 ! post-embryonic notochord [Term] id: UBERON:0013754 name: integumentary system layer namespace: uberon def: "A organ component layer that is part of a integumental system." [OBOL:automatic] subset: non_informative synonym: "layer of skin" NARROW [] synonym: "skin layer" NARROW [] xref: SCTID:314820002 is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0002416 ! integumental system relationship: part_of UBERON:0002416 ! integumental system [Term] id: UBERON:0013755 name: arterial blood namespace: uberon def: "A blood that is part of a artery." [OBOL:automatic] subset: pheno_slim synonym: "arterial blood" EXACT [FMA:83066] synonym: "blood in artery" EXACT [FMA:83066] synonym: "portion of arterial blood" EXACT [FMA:83066] xref: FMA:83066 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery [Term] id: UBERON:0013756 name: venous blood namespace: uberon def: "A blood that is part of a vein." [OBOL:automatic] synonym: "blood in vein" EXACT [FMA:83067] synonym: "portion of venous blood" EXACT [FMA:83067] synonym: "venous blood" EXACT [FMA:83067] xref: FMA:83067 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein [Term] id: UBERON:0013757 name: capillary blood namespace: uberon def: "A blood that is part of a capillary." [OBOL:automatic] synonym: "blood in capillary" EXACT [] synonym: "portion of blood in capillary" EXACT [FMA:263901] synonym: "portion of capillary blood" EXACT [] xref: FMA:263901 xref: NCIT:C32212 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood intersection_of: part_of UBERON:0001982 ! capillary relationship: part_of UBERON:0001982 ! capillary [Term] id: UBERON:0013765 name: digestive system element namespace: uberon def: "Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class subset: pheno_slim synonym: "digestive organ" EXACT [] synonym: "digestive system organ" EXACT [] xref: EMAPA:37843 {source="MA:th"} xref: SCTID:272627002 is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0001007 ! digestive system relationship: part_of UBERON:0001007 ! digestive system [Term] id: UBERON:0013768 name: great vessel of heart namespace: uberon def: "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart." [Wikipedia:Great_vessels] comment: Groupings may vary - typically pulmonary vessels and aorta and vena cavae subset: grouping_class synonym: "great vessel" BROAD [] synonym: "great vessel of thorax" EXACT [] xref: EMAPA:36460 xref: SCTID:304066000 xref: Wikipedia:Great_vessels is_a: UBERON:0001981 ! blood vessel [Term] id: UBERON:0014387 name: mesenchyme derived from neural crest namespace: uberon def: "Mesenchyme that develops_from the neural crest[Automatically generated definition]." [https://github.com/obophenotype/uberon/issues/248, OBOL:automatic] synonym: "mesenchyme from neural crest" EXACT [] synonym: "neural crest derived mesenchyme" EXACT [] synonym: "neural crest mesenchyme" EXACT [] xref: EMAPA:32735 xref: FMA:293883 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0002342 ! neural crest [Term] id: UBERON:0014398 name: respiratory muscle namespace: uberon def: "Muscle that is part of the respiratory system." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim is_a: UBERON:0003831 ! respiratory system muscle intersection_of: UBERON:0001630 ! muscle organ intersection_of: capable_of_part_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: capable_of_part_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue property_value: IAO:0000232 "this class may be merged with 'respiratory system muscle'; check intercostals" xsd:string [Term] id: UBERON:0014399 name: sinusoidal space namespace: uberon def: "A anatomical space that is enclosed by a sinusoid." [OBOL:automatic] synonym: "lumen of sinusoid" EXACT [FMA:63133] synonym: "sinusoid lumen" EXACT [FMA:63133] xref: FMA:63133 is_a: UBERON:0010161 ! lumen of blood vessel intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0003909 ! sinusoid relationship: luminal_space_of UBERON:0003909 ! sinusoid relationship: part_of UBERON:0003909 ! sinusoid [Term] id: UBERON:0014455 name: subcutaneous abdominal adipose tissue namespace: uberon def: "Subcutaneous adipose tissue that is located in the abdominal region." [CALOHA:paula, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/259, MGI:csmith] synonym: "abdominal subcutaneous adipose tissue" EXACT [] synonym: "subcutaneous abdominal fat" EXACT [] synonym: "subcutaneous fat of abdominal region" EXACT [] xref: CALOHA:TS-2406 is_a: UBERON:0002190 ! subcutaneous adipose tissue is_a: UBERON:0007808 ! adipose tissue of abdominal region intersection_of: UBERON:0001013 ! adipose tissue intersection_of: part_of UBERON:0000916 ! abdomen intersection_of: part_of UBERON:0002072 ! hypodermis property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cindyJax property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/paulacalipho [Term] id: UBERON:0014477 name: thoracic skeleton namespace: uberon def: "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Rib_cage] subset: pheno_slim synonym: "skeleton of thorax" EXACT [] synonym: "thoracic part of axial skeleton" EXACT [] synonym: "thoracic skeleton" EXACT [EHDAA2:0002013] xref: EHDAA2:0002013 xref: FMA:77169 xref: Wikipedia:Thoracic_skeleton is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton [Term] id: UBERON:0014776 name: midbrain neuromere namespace: uberon def: "A neuromere that is part of the presumptive midbrain" [http://orcid.org/0000-0002-6601-2165] synonym: "future mesencephalon" RELATED [] synonym: "mesomere" BROAD [] synonym: "mesomere group" RELATED [EHDAA2:0004352] synonym: "mesomere of nervous system" EXACT [] synonym: "midbrain segment" BROAD [] synonym: "neuromere of mesomere group" EXACT [] synonym: "segment of midbrain" BROAD [] xref: EHDAA2:0004352 xref: FMA:61997 is_a: UBERON:0004731 ! neuromere intersection_of: UBERON:0004731 ! neuromere intersection_of: part_of UBERON:0009616 ! presumptive midbrain relationship: part_of UBERON:0009616 ! presumptive midbrain [Term] id: UBERON:0014777 name: spinal neuromere namespace: uberon def: "A neuromere that is part of the presumptive spinal cord" [http://orcid.org/0000-0002-6601-2165] synonym: "spinal cord metameric segment" EXACT [] synonym: "spinal cord segment" RELATED [TAO:0001332] synonym: "spinal neuromeres" EXACT PLURAL [TAO:0001332] xref: TAO:0001332 xref: ZFA:0001332 is_a: UBERON:0004731 ! neuromere intersection_of: UBERON:0004731 ! neuromere intersection_of: part_of UBERON:0006241 ! future spinal cord relationship: part_of UBERON:0006241 ! future spinal cord [Term] id: UBERON:0014792 name: musculature of pelvic complex namespace: uberon def: "Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin." [OBOL:automatic] synonym: "muscles of lower limb" NARROW [FMA:71297] synonym: "musculature of lower limb" NARROW [FMA:71297] synonym: "musculi membri inferioris" NARROW [FMA:TA] xref: EMAPA:37864 {source="MA:th"} xref: FMA:71297 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0010709 ! pelvic complex property_value: editor_note "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0014795 name: pelvic appendage muscle namespace: uberon def: "Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin)." [OBOL:automatic] is_a: UBERON:0010890 ! pelvic complex muscle intersection_of: UBERON:0014892 ! skeletal muscle organ intersection_of: part_of UBERON:0004709 ! pelvic appendage relationship: part_of UBERON:0007270 {source="prolog"} ! pelvic appendage musculature [Term] id: UBERON:0014892 name: skeletal muscle organ namespace: uberon def: "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles)." [GOC:dos] synonym: "skeletal muscle" BROAD [] xref: AAO:0011099 xref: BTO:0001103 xref: CALOHA:TS-0933 xref: EFO:0000888 xref: EHDAA:5035 xref: EHDAA:5043 xref: EHDAA:5978 xref: EHDAA:5984 xref: EMAPA:35988 xref: EV:0100377 xref: GAID:141 xref: MA:0003148 xref: MAT:0000302 xref: MESH:D018482 xref: MIAA:0000302 xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA xref: TAO:0005277 xref: VHOG:0000319 xref: XAO:0000174 xref: ZFA:0005277 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue intersection_of: develops_from UBERON:0003082 ! myotome intersection_of: surrounded_by UBERON:0011899 ! epimysium intersection_of: synapsed_by CL:0000100 ! motor neuron relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: develops_from UBERON:0003082 ! myotome relationship: part_of UBERON:0018254 ! skeletal musculature relationship: surrounded_by UBERON:0011899 ! epimysium relationship: synapsed_by CL:0000100 ! motor neuron [Term] id: UBERON:0014903 name: primordial vasculature namespace: uberon def: "A portion of tissue that will develop into vasculature." [ZFA:0005076, ZFA:curator] xref: EFO:0003708 xref: TAO:0005076 xref: ZFA:0005076 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system [Term] id: UBERON:0015128 name: subepicardial layer of epicardium namespace: uberon synonym: "perimysial connective tissue of subepicardium" EXACT [FMA:83105] synonym: "subepicardial connective tissue" EXACT [FMA:83105] xref: FMA:83105 is_a: UBERON:0007188 ! mesothelium of serous pericardium relationship: part_of UBERON:0002348 {source="FMA"} ! epicardium property_value: editor_note "consider merging into myocardial compact layer" xsd:string [Term] id: UBERON:0015129 name: epicardial fat namespace: uberon def: "Visceral intrapericardial fat contiguous with the myocardial surface." [DOI:10.5935/abc.20130138] synonym: "epicardial adipose tissue" EXACT [] synonym: "pericardial adipose tissue" EXACT [] xref: FMA:9871 xref: SCTID:42267001 is_a: UBERON:0003837 ! thoracic segment connective tissue is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0035814 ! pericardial fat intersection_of: UBERON:0001013 ! adipose tissue intersection_of: adjacent_to UBERON:0002348 ! epicardium intersection_of: adjacent_to UBERON:0002425 ! visceral serous pericardium intersection_of: surrounds UBERON:0000948 ! heart relationship: adjacent_to UBERON:0002348 ! epicardium relationship: adjacent_to UBERON:0002425 ! visceral serous pericardium relationship: composed_primarily_of CL:1000309 ! epicardial adipocyte relationship: part_of UBERON:0015128 ! subepicardial layer of epicardium [Term] id: UBERON:0015152 name: gland of ocular region namespace: uberon def: "A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/614] synonym: "ocular gland" EXACT [] synonym: "orbital gland" RELATED [] is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0004088 ! orbital region relationship: part_of UBERON:0035639 {source="inferred"} ! ocular adnexa property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: UBPROP:0000008 "the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]" xsd:string property_value: UBPROP:0000008 "the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]" xsd:string [Term] id: UBERON:0015165 name: multi-unit eye namespace: uberon def: "An eye consisting of multiple light-sensing organs" [http://orcid.org/0000-0002-6601-2165, PMID:21062451] is_a: UBERON:0000970 ! eye intersection_of: UBERON:0000970 ! eye intersection_of: composed_primarily_of UBERON:0000020 ! sense organ relationship: composed_primarily_of UBERON:0000020 ! sense organ property_value: RO:0002161 NCBITaxon:7742 property_value: RO:0002175 NCBITaxon:6340 {notes="present on tentacular crown", source="PMID:21062451"} property_value: RO:0002175 NCBITaxon:6544 {notes="present on mantle edge in arcacean Bivalvia", source="PMID:21062451"} property_value: RO:0002175 NCBITaxon:7588 {notes="The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species", source="PMID:21062451"} [Term] id: UBERON:0015178 name: somite border namespace: uberon def: "A region of somite adjacent to presomitic mesoderm." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "inter-somited border" RELATED [] synonym: "intersomitic boundary" RELATED [] synonym: "intersomitic fissure" RELATED [] synonym: "intersomitic junction" RELATED [XAO:0004074] synonym: "segmental border" RELATED [] synonym: "somite boundary" RELATED [ZFA:0001462] xref: TAO:0001462 xref: XAO:0004074 xref: ZFA:0001462 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: adjacent_to UBERON:0003059 ! presomitic mesoderm intersection_of: part_of UBERON:0002329 ! somite relationship: adjacent_to UBERON:0003059 ! presomitic mesoderm relationship: part_of UBERON:0002329 ! somite [Term] id: UBERON:0015179 name: somite boundary epithelium namespace: uberon def: "Epithelium located in the intersomitic region." [XAO:0004077, XAO:EJS] synonym: "intersomitic epithelium" EXACT [XAO:0004077] synonym: "intersomitic membrane" EXACT [XAO:0004077] xref: XAO:0004077 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0015178 ! somite border relationship: part_of UBERON:0015178 ! somite border [Term] id: UBERON:0015212 name: lateral structure namespace: uberon def: "Any structure that is placed on one side of the left-right axis of a bilaterian." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000465 ! material anatomical entity property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string [Term] id: UBERON:0015228 name: circulatory organ namespace: uberon def: "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "cardiac pump" EXACT [] synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system [Term] id: UBERON:0015329 name: respiratory system basement membrane namespace: uberon def: "A basement membrane of epithelium that is part of a respiratory system." [OBOL:automatic] xref: EMAPA:37570 {source="MA:th"} xref: MA:0001815 is_a: UBERON:0005769 ! basement membrane of epithelium intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003570 {source="MA"} ! respiratory system connective tissue [Term] id: UBERON:0015410 name: heart plus pericardium namespace: uberon synonym: "heart/pericardium" EXACT [MA:0002449] xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system [Term] id: UBERON:0015757 name: heterogeneous tissue namespace: uberon synonym: "portion of heterogeneous tissue" EXACT [FMA:62798] xref: FMA:62798 is_a: UBERON:0000479 {source="FMA"} ! tissue [Term] id: UBERON:0015783 name: smooth muscle layer in fatty layer of subcutaneous tissue namespace: uberon def: "A smooth muscle tissue that is part of a hypodermis." [OBOL:automatic] synonym: "muscle layer in fatty layer of subcutaneous tissue" EXACT [FMA:77862] synonym: "stratum musculosum panniculi adiposi telae subcutaneae" EXACT LATIN [FMA:77862, FMA:TA] xref: FMA:77862 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002072 ! hypodermis relationship: part_of UBERON:0002072 ! hypodermis [Term] id: UBERON:0015808 name: eye epithelium namespace: uberon def: "A epithelium that is part of a camera-type eye." [OBOL:automatic] xref: EMAPA:35957 xref: MA:0003162 is_a: UBERON:0007625 ! pigment epithelium of eye is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye [Term] id: UBERON:0015833 name: foregut epithelium namespace: uberon def: "A epithelium that is part of a foregut." [OBOL:automatic] xref: EMAPA:32922 xref: MA:0003204 is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001041 ! foregut relationship: part_of UBERON:0001041 ! foregut [Term] id: UBERON:0016405 name: pulmonary capillary namespace: uberon def: "A capillary that is part of a lung." [OBOL:automatic] subset: pheno_slim synonym: "capillary of lung" EXACT [FMA:14121] xref: FMA:14121 is_a: UBERON:0003512 ! lung blood vessel is_a: UBERON:0003526 ! respiratory system capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002048 ! lung [Term] id: UBERON:0016509 name: cavity of right ventricle namespace: uberon def: "Luminal space of the right ventricle of the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "right ventricle lumen" EXACT [EMAPA:26047] synonym: "right ventricular cavity" EXACT [FMA:FMA] xref: EMAPA:26047 xref: FMA:9291 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002080 ! heart right ventricle relationship: luminal_space_of UBERON:0002080 ! heart right ventricle relationship: part_of UBERON:0002080 ! heart right ventricle [Term] id: UBERON:0016513 name: cavity of left atrium namespace: uberon def: "luminal space of the left atrium of the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "left atrial cavity" EXACT [FMA:FMA] synonym: "left atrium lumen" EXACT [EMAPA:26011] xref: EMAPA:26011 xref: FMA:9465 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002079 ! left cardiac atrium relationship: luminal_space_of UBERON:0002079 ! left cardiac atrium relationship: part_of UBERON:0002079 ! left cardiac atrium [Term] id: UBERON:0016514 name: cavity of left ventricle namespace: uberon def: "luminal space of the left ventricle of the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "left ventricular cavity" EXACT [FMA:FMA] xref: EMAPA:26038 xref: FMA:9466 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002084 ! heart left ventricle relationship: luminal_space_of UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0002084 ! heart left ventricle [Term] id: UBERON:0016522 name: cavity of right atrium namespace: uberon def: "luminal space of the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165] synonym: "right atrial cavity" EXACT [FMA:FMA] xref: EMAPA:26020 xref: FMA:11359 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0002078 ! right cardiac atrium relationship: luminal_space_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0002078 ! right cardiac atrium [Term] id: UBERON:0016545 name: pharyngeal ectoderm namespace: uberon alt_id: UBERON:2001379 def: "The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches." [http://orcid.org/0000-0002-6601-2165, PMID:23020903] xref: TAO:0001379 xref: ZFA:0001379 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0003351 ! pharyngeal epithelium is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: part_of UBERON:0000076 ! external ectoderm intersection_of: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0000076 ! external ectoderm [Term] id: UBERON:0016548 name: central nervous system gray matter layer namespace: uberon def: "A layer of of the central nervous system that is part of gray matter." [http://orcid.org/0000-0002-6601-2165] synonym: "CNS gray matter layer" EXACT [] synonym: "CNS grey matter layer" EXACT [] synonym: "gray matter layer of neuraxis" EXACT [FMA:83142] synonym: "grey matter layer" BROAD [] synonym: "grey matter layer of neuraxis" EXACT [] xref: FMA:83142 is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer intersection_of: composed_primarily_of UBERON:0002020 ! gray matter relationship: composed_primarily_of UBERON:0002020 ! gray matter [Term] id: UBERON:0016570 name: lamina of gray matter of spinal cord namespace: uberon synonym: "rexed lamina" EXACT [FMA:68861] xref: FMA:68861 xref: http://neurolex.org/wiki/Category\:Rexed_spinal_cord_parcellation_scheme_region xref: Wikipedia:Rexed_laminae is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer intersection_of: part_of UBERON:0002315 ! gray matter of spinal cord relationship: part_of UBERON:0002315 ! gray matter of spinal cord [Term] id: UBERON:0016879 name: future central nervous system namespace: uberon alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system" [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system relationship: develops_from UBERON:0000924 ! ectoderm relationship: develops_from UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! neurectoderm relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system relationship: part_of UBERON:0016880 ! future nervous system [Term] id: UBERON:0016880 name: future nervous system namespace: uberon alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system" [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system [Term] id: UBERON:0016887 name: entire extraembryonic component namespace: uberon def: "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism." [AEO:0000195, AEO:JB] synonym: "extra-embryonic component" EXACT [] synonym: "extraembryonic component" EXACT [AEO:0000195] xref: AEO:0000195 xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus [Term] id: UBERON:0016888 name: transitional anatomical structure namespace: uberon def: "An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development." [AEO:0000132, AEO:JB] xref: AEO:0000132 is_a: UBERON:0005423 {source="AEO"} ! developing anatomical structure [Term] id: UBERON:0017650 name: developing mesenchymal structure namespace: uberon def: "A mesenchyme-derived anatomical entity undergoing a transtion to become another structure." [AEO:0001016, AEO:JB] xref: AEO:0001016 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: composed_primarily_of UBERON:0003104 ! mesenchyme relationship: composed_primarily_of UBERON:0003104 ! mesenchyme [Term] id: UBERON:0017672 name: abdominal viscera namespace: uberon def: "A viscus that is part of a abdomen." [OBOL:automatic] subset: pheno_slim synonym: "abdominal viscera" EXACT [FMA:32413] synonym: "abdominal viscera set" EXACT [FMA:32413] synonym: "set of abdominal viscera" EXACT [FMA:32413] xref: FMA:32413 xref: FMA:67355 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005172 ! abdomen element intersection_of: UBERON:0002075 ! viscus intersection_of: part_of UBERON:0000916 ! abdomen [Term] id: UBERON:0018135 name: fibrocollagenous connective tissue namespace: uberon xref: FMA:83521 is_a: UBERON:0011824 ! fibrous connective tissue intersection_of: UBERON:0011824 ! fibrous connective tissue intersection_of: has_quality PATO:0002462 ! collagenous relationship: has_quality PATO:0002462 ! collagenous [Term] id: UBERON:0018150 name: skin of lower lip namespace: uberon def: "A zone of skin that is part of a lower lip." [OBOL:automatic] synonym: "lower lip skin" EXACT [FMA:24767] xref: FMA:24767 xref: SCTID:281630002 is_a: UBERON:0001458 ! skin of lip is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001835 ! lower lip relationship: part_of UBERON:0001835 ! lower lip [Term] id: UBERON:0018239 name: rhombomere boundary namespace: uberon def: "A boundary delimiting a rhombomere." [GO:0021654] synonym: "rhombomere junction" EXACT [] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0001892 ! rhombomere relationship: connects UBERON:0001892 ! rhombomere relationship: part_of UBERON:0007277 ! presumptive hindbrain [Term] id: UBERON:0018254 name: skeletal musculature namespace: uberon subset: grouping_class xref: EHDAA2:0001842 xref: EMAPA:35578 xref: MA:0000165 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure relationship: composed_primarily_of UBERON:0014892 ! skeletal muscle organ relationship: part_of UBERON:0000383 {source="MA"} ! musculature of body property_value: editor_note "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string [Term] id: UBERON:0018257 name: submucosa of digestive tract namespace: uberon def: "Any portion of submucosa that lines the digestive tract." [http://orcid.org/0000-0002-6601-2165] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000009 ! submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract [Term] id: UBERON:0018260 name: layer of muscle tissue namespace: uberon def: "Any organ component layer that consists of muscle tissue." [http://orcid.org/0000-0002-6601-2165] xref: FMA:45634 xref: NCIT:C75444 xref: UMLS:C0225358 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue relationship: composed_primarily_of UBERON:0002385 ! muscle tissue property_value: UBPROP:0000012 "NCITA class may refer to smooth muscle only" xsd:string {external_ontology="NCIT"} [Term] id: UBERON:0018649 name: cardiac muscle tissue of ventricle namespace: uberon synonym: "ventricular cardiac muscle tissue" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "ventricular heart muscle" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "ventricular muscle" RELATED [http://orcid.org/0000-0002-6601-2165] xref: FMA:83450 is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0001083 ! myocardium of ventricle [Term] id: UBERON:0018674 name: heart vasculature namespace: uberon def: "An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart." [ZFA:0005811, ZFA:CVS] synonym: "cardiac vasculature" EXACT [FMA:73747] xref: FMA:73747 xref: ZFA:0005811 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002201 ! vasculature of trunk is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart [Term] id: UBERON:0019042 name: reproductive system mucosa namespace: uberon synonym: "genital mucosa" EXACT [BTO:0002439] xref: BTO:0002439 is_a: UBERON:0000344 ! mucosa is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000990 ! reproductive system [Term] id: UBERON:0019143 name: intramuscular adipose tissue namespace: uberon def: "Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes." [BTO:0004043] synonym: "intramuscular fat" RELATED [BTO:0004043] xref: BTO:0004043 is_a: UBERON:0001013 ! adipose tissue intersection_of: UBERON:0001013 ! adipose tissue intersection_of: part_of UBERON:0014892 ! skeletal muscle organ relationship: part_of UBERON:0014892 ! skeletal muscle organ [Term] id: UBERON:0019189 name: carotid artery endothelium namespace: uberon synonym: "carotid endothelium" RELATED [BTO:0004626] synonym: "carotid epithelium" RELATED [] xref: BTO:0004626 is_a: UBERON:0001917 ! endothelium of artery intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0005396 ! carotid artery segment relationship: part_of UBERON:0005396 ! carotid artery segment [Term] id: UBERON:0019204 name: skin epithelium namespace: uberon def: "Any region of epithelium that is part of a skin region." [http://orcid.org/0000-0002-6601-2165] xref: BTO:0004382 is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000014 ! zone of skin relationship: part_of UBERON:0000014 ! zone of skin [Term] id: UBERON:0019207 name: chorioretinal region namespace: uberon def: "The part of the eye that consists of both the retina and the optic choroid" [http://orcid.org/0000-0002-6601-2165, UBERON:drseb] subset: pheno_slim synonym: "chorioretina" EXACT [] synonym: "choroid and retina" EXACT [] synonym: "retinachoroid" EXACT [] synonym: "retinachoroidal region" EXACT [] xref: SCTID:110701000 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000966 ! retina relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0010230 ! eyeball of camera-type eye [Term] id: UBERON:0019263 name: gray matter of hindbrain namespace: uberon synonym: "gray matter of the hindbrain" EXACT [DHBA:HGM] xref: DHBA:10654 xref: FMA:268630 is_a: UBERON:0003528 ! brain gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain [Term] id: UBERON:0019267 name: gray matter of midbrain namespace: uberon xref: DHBA:10649 xref: FMA:83913 is_a: UBERON:0003528 ! brain gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001891 ! midbrain [Term] id: UBERON:0019304 name: sensory organ epithelium namespace: uberon xref: EMAPA:35952 xref: MA:0003174 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000020 ! sense organ relationship: part_of UBERON:0000020 ! sense organ [Term] id: UBERON:0019319 name: exocrine gland of integumental system namespace: uberon def: "An exocrine gland that is part of a integumental system." [GOC:dos, http://orcid.org/0000-0002-6601-2165] synonym: "integumental exocrine gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "integumental system exocrine gland" EXACT [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0002365 ! exocrine gland is_a: UBERON:0003297 ! gland of integumental system intersection_of: UBERON:0002365 ! exocrine gland intersection_of: part_of UBERON:0002416 ! integumental system [Term] id: UBERON:0022288 name: surface of eyeball namespace: uberon synonym: "surface of region of wall of eyeball" RELATED [FMA:58315] xref: FMA:58315 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: bounding_layer_of UBERON:0010230 ! eyeball of camera-type eye relationship: bounding_layer_of UBERON:0010230 ! eyeball of camera-type eye relationship: part_of UBERON:0010230 ! eyeball of camera-type eye [Term] id: UBERON:0022293 name: reproductive gland secretion namespace: uberon def: "A portion of organism substance that is secreted by a reproductive gland." [UBERON:cjm] synonym: "genital fluid" RELATED [] synonym: "genital secretion" RELATED [] synonym: "reproductive system fluid" RELATED [] synonym: "reproductive system fluid/secretion" RELATED [] synonym: "reproductive system secretion" RELATED [] is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0003937 ! reproductive gland relationship: produced_by UBERON:0003937 ! reproductive gland [Term] id: UBERON:0022303 name: nervous system cell part layer namespace: uberon def: "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]." [NLX:149357] subset: cumbo synonym: "lamina" BROAD [CUMBO:CUMBO] synonym: "layer" BROAD [CUMBO:CUMBO] xref: NLX:149357 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure intersection_of: has_quality PATO:0002124 ! laminar intersection_of: part_of UBERON:0001016 ! nervous system relationship: has_quality PATO:0002124 ! laminar relationship: part_of UBERON:0001016 ! nervous system property_value: editor_note "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string [Term] id: UBERON:0022350 name: visceral serous membrane namespace: uberon def: "Serous membrane layer that is adjacent to and lines an organ." [http://orcid.org/0000-0002-6601-2165] synonym: "visceral wall of serous membrane" EXACT [FMA:15860] xref: FMA:15860 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0000062 ! organ intersection_of: part_of UBERON:0000042 ! serous membrane relationship: adjacent_to UBERON:0000062 ! organ relationship: part_of UBERON:0000042 ! serous membrane [Term] id: UBERON:0022351 name: parietal serous membrane namespace: uberon def: "Serous membrane layer that lines to a body cavity." [http://orcid.org/0000-0002-6601-2165] synonym: "cavity lining" BROAD [MA:0002448] synonym: "parietal wall of serous membrane" EXACT [FMA:15859] xref: FMA:15859 xref: MA:0002448 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0002553 ! anatomical cavity intersection_of: part_of UBERON:0000042 ! serous membrane relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0000042 ! serous membrane [Term] id: UBERON:0022361 name: lung field namespace: uberon def: "A specific region of the foregut into the area in which the lung will develop." [GOC:dph, GOC:mtg_lung] synonym: "lung field" EXACT [] xref: SCTID:34922002 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage intersection_of: has_potential_to_develop_into UBERON:0002048 ! lung relationship: has_potential_to_develop_into UBERON:0002048 ! lung relationship: part_of UBERON:0003258 ! endoderm of foregut [Term] id: UBERON:0034705 name: developing neuroepithelium namespace: uberon def: "An embryonic or larval epithelium that is committed to form part of the nervous system." [AEO:0001008, AEO:JB] synonym: "embryonic neuroepithelium" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "neurepithelium" BROAD [BTO:0000314] synonym: "neuroepithelium" EXACT [AEO:0001008] xref: AEO:0001008 xref: BTO:0000314 xref: EHDAA2_RETIRED:0004654 xref: FMA:64807 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000483 ! epithelium relationship: part_of UBERON:0001016 ! nervous system [Term] id: UBERON:0034706 name: proliferating neuroepithelium namespace: uberon def: "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells." [AEO:0001009] xref: AEO:0001009 is_a: UBERON:0034705 {source="AEO"} ! developing neuroepithelium [Term] id: UBERON:0034707 name: differentiating neuroepithelium namespace: uberon def: "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells." [AEO:0001010] xref: AEO:0001010 is_a: UBERON:0034705 {source="AEO"} ! developing neuroepithelium relationship: has_part CL:0000031 ! neuroblast (sensu Vertebrata) [Term] id: UBERON:0034709 name: hindbrain marginal layer namespace: uberon synonym: "marginal zone of hindbrain" EXACT [DHBA:12694] synonym: "MZH" RELATED ABBREVIATION [DHBA:12694] xref: DHBA:12694 xref: EMAPA:32916 is_a: UBERON:0004062 ! neural tube marginal layer is_a: UBERON:0011215 ! central nervous system cell part cluster intersection_of: UBERON:0004062 ! neural tube marginal layer intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain [Term] id: UBERON:0034710 name: spinal cord ventricular layer namespace: uberon synonym: "spinal cord lateral wall ventricular layer" EXACT [EHDAA2:0001267] xref: EHDAA2:0001267 xref: EMAPA:17585 is_a: UBERON:0004060 ! neural tube ventricular layer intersection_of: UBERON:0004060 ! neural tube ventricular layer intersection_of: part_of UBERON:0006241 ! future spinal cord relationship: part_of UBERON:0005496 {source="EHDAA2"} ! neural tube lateral wall relationship: part_of UBERON:0006241 ! future spinal cord [Term] id: UBERON:0034769 name: lymphomyeloid tissue namespace: uberon xref: FMA:79770 xref: NCIT:C41168 is_a: UBERON:0015757 {source="FMA"} ! heterogeneous tissue [Term] id: UBERON:0034873 name: bodily gas namespace: uberon def: "Any substance in the body or expelled from the body that is in a gaseous state." [http://orcid.org/0000-0002-6601-2165] synonym: "gas in anatomical space" EXACT [] synonym: "portion of gas in anatomical space" EXACT [FMA:84580] xref: FMA:84580 is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: has_quality PATO:0001547 ! quality of a gas relationship: has_quality PATO:0001547 ! quality of a gas [Term] id: UBERON:0034874 name: air in respiratory system namespace: uberon def: "Any portion of gas located in a part of the respiratory system that is composed primarily of air." [http://orcid.org/0000-0002-6601-2165] synonym: "respiratory air" EXACT [FMA:84581] synonym: "respiratory system air" EXACT [] xref: FMA:84581 is_a: UBERON:0034947 ! gas in respiratory system intersection_of: UBERON:0034873 ! bodily gas intersection_of: composed_primarily_of CHEBI:25805 ! oxygen atom intersection_of: located_in UBERON:0001004 ! respiratory system relationship: composed_primarily_of CHEBI:25805 ! oxygen atom [Term] id: UBERON:0034878 name: prechordal mesoderm namespace: uberon def: "the area of axial mesoderm that develops into the prechordal plate" [MGI:anna] synonym: "prechordal mesenchyme" EXACT [] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: has_potential_to_develop_into UBERON:0003063 ! prechordal plate intersection_of: part_of UBERON:0003068 ! axial mesoderm relationship: has_potential_to_develop_into UBERON:0003063 ! prechordal plate relationship: part_of UBERON:0003068 ! axial mesoderm [Term] id: UBERON:0034903 name: left atrium endocardium namespace: uberon def: "Endocardium that is part of the left atrium." [http://orcid.org/0000-0002-6601-2165] synonym: "endocardium of left atrium" EXACT [FMA:7286] synonym: "left atrial endocardium" EXACT [] synonym: "left atrium endocardial tissue" RELATED [VHOG:0001226] xref: FMA:7286 xref: SCTID:190064008 xref: VHOG:0001226 is_a: UBERON:0002166 ! endocardium of atrium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002079 ! left cardiac atrium relationship: part_of UBERON:0002079 ! left cardiac atrium property_value: UBPROP:0000001 "Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein." xsd:string {source="FMA:7286"} [Term] id: UBERON:0034905 name: gland lumen namespace: uberon synonym: "lumen of gland" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0002530 ! gland relationship: luminal_space_of UBERON:0002530 ! gland relationship: part_of UBERON:0002530 ! gland [Term] id: UBERON:0034921 name: multi organ part structure namespace: uberon def: "An multicellular anatomical structure that has subparts of multiple organs as a part." [CARO:0020001] synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: composed_primarily_of UBERON:0000064 ! organ part [Term] id: UBERON:0034922 name: cell cluster namespace: uberon def: "A cluster of cells, largely surrounded by a morphological boundary." [CARO:0020002] xref: CARO:0020002 xref: FMA:62807 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: surrounded_by UBERON:0000015 ! non-material anatomical boundary [Term] id: UBERON:0034925 name: anatomical collection namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0000465 ! material anatomical entity relationship: has_member UBERON:0000061 ! anatomical structure property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string [Term] id: UBERON:0034929 name: external soft tissue zone namespace: uberon def: "A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures." [http://orcid.org/0000-0002-6601-2165] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010000 ! multicellular anatomical structure relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature relationship: has_part UBERON:0001021 ! nerve relationship: has_part UBERON:0002049 ! vasculature relationship: part_of UBERON:0000475 ! organism subdivision [Term] id: UBERON:0034933 name: layer of smooth muscle tissue namespace: uberon def: "Any organ component layer that consists of smooth muscle tissue." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0018260 ! layer of muscle tissue intersection_of: UBERON:0004923 ! organ component layer intersection_of: composed_primarily_of UBERON:0001135 ! smooth muscle tissue relationship: composed_primarily_of UBERON:0001135 ! smooth muscle tissue [Term] id: UBERON:0034944 name: zone of organ namespace: uberon synonym: "organ region with floating fiat boundary" RELATED [FMA:55268] synonym: "organ sector" EXACT [FMA:55268] synonym: "organ zonal region" EXACT [] synonym: "organ zone" EXACT [FMA:55268] xref: FMA:55268 is_a: UBERON:0000064 ! organ part [Term] id: UBERON:0034947 name: gas in respiratory system namespace: uberon def: "Any portion of gas located in a part of the respiratory system." [http://orcid.org/0000-0002-6601-2165] synonym: "respiratory gas" EXACT [] synonym: "respiratory system gas" EXACT [] is_a: UBERON:0034873 ! bodily gas intersection_of: UBERON:0034873 ! bodily gas intersection_of: located_in UBERON:0001004 ! respiratory system relationship: located_in UBERON:0001004 ! respiratory system [Term] id: UBERON:0034969 name: epithelial layer of duct namespace: uberon synonym: "duct epithelium" RELATED [] synonym: "ductal epithelium" RELATED [] xref: NCIT:C25787 xref: UMLS:C1512086 is_a: UBERON:0003914 ! epithelial tube intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000058 ! duct relationship: part_of UBERON:0000058 ! duct [Term] id: UBERON:0034995 name: jaw mesenchyme namespace: uberon def: "Mesenchyme that is part of a developing jaw [Automatically generated definition]." [OBOL:automatic] xref: EMAPA:32907 xref: EMAPA:35454 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005253 ! head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0011595 ! jaw region relationship: part_of UBERON:0011595 ! jaw region [Term] id: UBERON:0035037 name: jaw epithelium namespace: uberon xref: EMAPA:32904 xref: MA:0003220 is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0011595 ! jaw region relationship: part_of UBERON:0011595 ! jaw region [Term] id: UBERON:0035118 name: material entity in digestive tract namespace: uberon def: "Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included." [https://github.com/EnvironmentOntology/envo/issues/110] synonym: "digestive tract contents" EXACT PLURAL [] synonym: "ingested material entity" RELATED [] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: located_in UBERON:0006909 ! lumen of digestive tract relationship: located_in UBERON:0006909 ! lumen of digestive tract property_value: editor_note "Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat" xsd:string [Term] id: UBERON:0035159 name: entire surface of organism namespace: uberon def: "Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface." [FMA:61695] synonym: "surface of body" EXACT [FMA:61695] xref: FMA:61695 xref: NCIT:C29667 xref: SCTID:261060002 xref: UMLS:C0489451 is_a: UBERON:0006984 ! anatomical surface intersection_of: UBERON:0006984 ! anatomical surface intersection_of: surrounds UBERON:0000468 ! multicellular organism relationship: surrounds UBERON:0000468 ! multicellular organism [Term] id: UBERON:0035398 name: branch of external carotid artery namespace: uberon synonym: "external carotid arterial subdivision" EXACT [FMA:70505] synonym: "subdivision of external carotid artery" EXACT [FMA:70505] xref: FMA:70505 xref: NCIT:C32552 xref: SCTID:244216003 xref: UMLS:C0447038 is_a: UBERON:0004573 ! systemic artery is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001637 ! artery intersection_of: branching_part_of UBERON:0001070 ! external carotid artery relationship: branching_part_of UBERON:0001070 ! external carotid artery relationship: part_of UBERON:0001070 ! external carotid artery [Term] id: UBERON:0035539 name: esophageal artery namespace: uberon def: "Any of several arteries that arise from the aorta and supply blood to the esophagus." [ncithesaurus:Esophageal_Artery] synonym: "aortic esophageal artery" EXACT [FMA:4149] synonym: "oesophageal artery" EXACT [FMA:4149] xref: FMA:4149 xref: NCIT:C32535 xref: SCTID:56548006 xref: UMLS:C0226294 is_a: UBERON:0003834 ! thoracic segment blood vessel is_a: UBERON:0004573 {source="FMA"} ! systemic artery intersection_of: UBERON:0001637 ! artery intersection_of: supplies UBERON:0001043 ! esophagus relationship: branching_part_of UBERON:0001515 {source="FMA"} ! thoracic aorta relationship: part_of UBERON:0001515 ! thoracic aorta relationship: supplies UBERON:0001043 ! esophagus [Term] id: UBERON:0035546 name: uveal vein namespace: uberon synonym: "ciliary vein" EXACT [FMA:51797] xref: FMA:51797 xref: SCTID:149683007 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001768 ! uvea relationship: drains UBERON:0001768 ! uvea [Term] id: UBERON:0035549 name: vasculature of integument namespace: uberon def: "The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin." [http://orcid.org/0000-0002-6601-2165] synonym: "dermis vasculature" NARROW [] synonym: "hypodermis vasculature" NARROW [] synonym: "skin vasculature" RELATED [] synonym: "subcutaneous vasculature" RELATED [] synonym: "superficial part of circulatory system" EXACT [] synonym: "superficial vasculature" EXACT [] synonym: "vasculature of skin" RELATED [FMA:225275] xref: FMA:225275 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: located_in UBERON:0002199 ! integument relationship: capable_of_part_of GO:0001659 ! temperature homeostasis relationship: located_in UBERON:0002199 ! integument [Term] id: UBERON:0035550 name: superficial vein namespace: uberon def: "Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers." [ncithesaurus:Superficial_Vein] synonym: "superfical vein" RELATED [Wikipedia:Superficial_vein] synonym: "superficial veins" RELATED [Wikipedia:Superficial_vein] synonym: "superficial vessels" RELATED [Wikipedia:Superficial_vein] xref: FMA:76719 xref: NCIT:C33666 xref: SCTID:341382008 xref: UMLS:C0226513 xref: Wikipedia:Superficial_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0035549 ! vasculature of integument relationship: part_of UBERON:0035549 ! vasculature of integument [Term] id: UBERON:0035551 name: deep vasculature namespace: uberon def: "The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin." [http://orcid.org/0000-0002-6601-2165] synonym: "deep part of circulatory system" EXACT [] is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: deep_to UBERON:0002199 ! integument relationship: deep_to UBERON:0002199 ! integument [Term] id: UBERON:0035552 name: deep vein namespace: uberon def: "A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery." [ncithesaurus:Deep_Vein] synonym: "deep veins" RELATED [Wikipedia:Deep_vein] synonym: "deep vessels" RELATED [Wikipedia:Deep_vein] xref: FMA:76718 xref: NCIT:C32444 xref: SCTID:341484008 xref: UMLS:C0226514 xref: Wikipedia:Deep_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0035551 ! deep vasculature relationship: part_of UBERON:0035551 ! deep vasculature [Term] id: UBERON:0035553 name: left cardiac chamber namespace: uberon def: "Any chamber of the left side of the heart" [http://orcid.org/0000-0002-6601-2165] xref: FMA:7166 xref: SCTID:362008007 is_a: UBERON:0004151 ! cardiac chamber is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0004151 ! cardiac chamber intersection_of: in_left_side_of UBERON:0000948 ! heart relationship: in_left_side_of UBERON:0000948 ! heart [Term] id: UBERON:0035554 name: right cardiac chamber namespace: uberon def: "Any chamber of the right side of the heart" [http://orcid.org/0000-0002-6601-2165] xref: FMA:7165 xref: SCTID:362007002 is_a: UBERON:0004151 ! cardiac chamber is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0004151 ! cardiac chamber intersection_of: in_right_side_of UBERON:0000948 ! heart relationship: in_right_side_of UBERON:0000948 ! heart [Term] id: UBERON:0035639 name: ocular adnexa namespace: uberon def: "The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva" [HPO:pr, http://medical-dictionary.thefreedictionary.com/ocular+adnexa, https://github.com/obophenotype/uberon/issues/1132, UBERON:cjm] synonym: "accessory parts of orbital region" RELATED [] synonym: "accessory visual structures" RELATED [Wikipedia:Accessory_visual_structures] synonym: "accessory visual structures" RELATED [FMA:76554] synonym: "accessory visual structures set" RELATED [FMA:76554] synonym: "adnexa oculi" EXACT LATIN [http://medical-dictionary.thefreedictionary.com/ocular+adnexa] synonym: "adnexal parts of orbital region" RELATED [] synonym: "appendage of eye" RELATED [http://medical-dictionary.thefreedictionary.com/ocular+adnexa] synonym: "appendages of the eye" RELATED PLURAL [http://medical-dictionary.thefreedictionary.com/ocular+adnexa] synonym: "eye adnexa" RELATED [] synonym: "set of accessory visual structures" RELATED [FMA:76554] synonym: "structurae oculi accessoriae" RELATED LATIN [Wikipedia:Accessory_visual_structures] xref: FMA:76554 xref: NCIT:C32574 xref: SCTID:120612006 xref: UMLS:C0229243 xref: Wikipedia:Accessory_visual_structures is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0004088 ! orbital region [Term] id: UBERON:0035763 name: cavity of cardiac chamber namespace: uberon synonym: "cardiac chamber cavity" EXACT [FMA:9464] synonym: "heart cavity" EXACT [FMA:9464] synonym: "heart lumen" EXACT [EHDAA2:0004181] xref: EHDAA2:0004181 xref: FMA:9464 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0004151 ! cardiac chamber relationship: luminal_space_of UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0004151 ! cardiac chamber relationship: surrounded_by UBERON:0002165 {source="FMA"} ! endocardium [Term] id: UBERON:0035804 name: future mouth namespace: uberon def: "The primordial mouth region of the developing head." [MP:0003119] synonym: "primitive mouth" EXACT [FMA:293105] synonym: "primordial mouth" EXACT [] xref: FMA:293105 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0013522 ! subdivision of tube relationship: has_part UBERON:0000925 ! endoderm relationship: has_part UBERON:0000930 ! stomodeum relationship: part_of UBERON:0007026 ! presumptive gut [Term] id: UBERON:0035809 name: serous cavity namespace: uberon xref: FMA:12241 xref: SCTID:304404008 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: luminal_space_of UBERON:0005906 ! serous sac relationship: luminal_space_of UBERON:0005906 ! serous sac relationship: part_of UBERON:0005906 ! serous sac [Term] id: UBERON:0035814 name: pericardial fat namespace: uberon def: "The sum of epicardial and paracardial fat deposits." [DOI:10.5935/abc.20130138] xref: SCTID:42267001 xref: ZFA:0005765 is_a: UBERON:0035818 ! visceral fat intersection_of: UBERON:0001013 ! adipose tissue intersection_of: surrounds UBERON:0000948 ! heart relationship: surrounds UBERON:0000948 ! heart [Term] id: UBERON:0035815 name: paracardial fat namespace: uberon def: "Fat deposits in the mediastinum outside the parietal pericardium ." [DOI:10.5935/abc.20130138] synonym: "intrathoracic fat" EXACT [DOI:10.5935/abc.20130138] is_a: UBERON:0035814 ! pericardial fat intersection_of: UBERON:0001013 ! adipose tissue intersection_of: adjacent_to UBERON:0002408 ! parietal serous pericardium intersection_of: surrounds UBERON:0000948 ! heart relationship: adjacent_to UBERON:0002408 ! parietal serous pericardium [Term] id: UBERON:0035818 name: visceral fat namespace: uberon def: "Any fat deposit surrounding a visceral organ." [UBERON:cjm] is_a: UBERON:0001013 ! adipose tissue intersection_of: UBERON:0001013 ! adipose tissue intersection_of: surrounds UBERON:0000062 ! organ relationship: surrounds UBERON:0000062 ! organ [Term] id: UBERON:0035819 name: abdominopelvic cavity namespace: uberon def: "The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity." [UBERON:cjm] synonym: "cavitas abdominis et pelvis" EXACT LATIN [FMA:TA] xref: FMA:12267 xref: Wikipedia:Abdominopelvic_cavity is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: luminal_space_of UBERON:0002417 ! abdominal segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen relationship: luminal_space_of UBERON:0002417 ! abdominal segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: part_of UBERON:0002417 ! abdominal segment of trunk [Term] id: UBERON:0035965 name: wall of blood vessel namespace: uberon synonym: "blood vessel wall" EXACT [FMA:67473] synonym: "vascular wall" RELATED [BTO:0004378] xref: BTO:0004378 xref: EMAPA:37987 {source="MA:th"} xref: FMA:67473 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001981 ! blood vessel relationship: composed_primarily_of UBERON:0004797 ! blood vessel layer relationship: part_of UBERON:0001981 ! blood vessel [Term] id: UBERON:0036072 name: respiratory primordium epithelium namespace: uberon xref: EHDAA2:0004070 is_a: UBERON:0004185 ! endodermal part of digestive tract is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007499 ! epithelial sac is_a: UBERON:0009854 ! digestive tract diverticulum is_a: UBERON:0015833 ! foregut epithelium intersection_of: UBERON:0007499 ! epithelial sac intersection_of: part_of UBERON:0008947 ! respiratory primordium relationship: develops_from UBERON:0007690 {source="EHDAA2"} ! early pharyngeal endoderm relationship: part_of UBERON:0008947 ! respiratory primordium [Term] id: UBERON:0036073 name: respiratory primordium mesenchyme namespace: uberon synonym: "respiratory primordium associated mesenchyme" EXACT [EHDAA2:0004071] xref: EHDAA2:0004071 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0008947 ! respiratory primordium relationship: develops_from UBERON:0004873 {source="EHDAA2"} ! splanchnopleure relationship: part_of UBERON:0008947 ! respiratory primordium [Term] id: UBERON:0036146 name: cardiopharyngeal field namespace: uberon def: "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles." [BGEE:ann, http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1] is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage [Term] id: UBERON:0036186 name: fibroelastic connective tissue namespace: uberon xref: FMA:83520 is_a: UBERON:0002521 ! elastic tissue is_a: UBERON:0011824 ! fibrous connective tissue intersection_of: UBERON:0011824 ! fibrous connective tissue intersection_of: composed_primarily_of GO:0071953 ! elastic fiber [Term] id: UBERON:0036215 name: anatomical surface region namespace: uberon def: "Material anatomical entity that forms the outermost boundary of an anatomical structure." [https://github.com/obophenotype/uberon/issues/1324] xref: AAO:0010270 xref: AEO:0000154 xref: ZFA:0005594 is_a: UBERON:0000465 ! material anatomical entity relationship: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0000061 ! anatomical structure [Term] id: UBERON:0036217 name: coelomic fluid namespace: uberon def: "A bodily fluid that is located in the coelom." [https://github.com/obophenotype/uberon/issues/1326, PMID:10874572] xref: BTO:0001708 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0006314 ! bodily fluid intersection_of: located_in UBERON:0011997 ! coelom relationship: located_in UBERON:0011997 ! coelom property_value: UBPROP:0000009 "he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]" xsd:string [Term] id: UBERON:0036225 name: respiratory system gland namespace: uberon def: "Any gland that is part os the respiratory system." [UBERON:cjm] is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system [Term] id: UBERON:0036242 name: post-embryonic notochord namespace: uberon def: "A notochord that has persisted beyond the embryonic stage." [UBERON:cjm] is_a: UBERON:0002328 ! notochord intersection_of: UBERON:0002328 ! notochord intersection_of: part_of UBERON:0009953 ! post-embryonic organism relationship: part_of UBERON:0009953 ! post-embryonic organism property_value: RO:0002161 NCBITaxon:32524 property_value: RO:0002175 NCBITaxon:118072 property_value: RO:0002175 NCBITaxon:7737 property_value: RO:0002175 NCBITaxon:7746 property_value: RO:0002175 NCBITaxon:7878 property_value: RO:0002175 NCBITaxon:8292 [Term] id: UBERON:0036244 name: secretion of serous membrane namespace: uberon def: "A transudate found in the serous sac." [FMA:20932] synonym: "serous fluid" BROAD [FMA:20932] synonym: "serous sac fluid" EXACT [] xref: FMA:20932 is_a: UBERON:0007779 ! transudate intersection_of: UBERON:0007779 ! transudate intersection_of: filtered_through UBERON:0000042 ! serous membrane relationship: filtered_through UBERON:0000042 ! serous membrane relationship: located_in UBERON:0005906 ! serous sac [Term] id: UBERON:0036253 name: orifice of skull namespace: uberon synonym: "cranial orifice" EXACT [FMA:53133] synonym: "skull orifice" EXACT [FMA:53133] xref: FMA:53133 is_a: UBERON:0000161 ! orifice intersection_of: UBERON:0000161 ! orifice intersection_of: part_of UBERON:0003129 ! skull relationship: part_of UBERON:0003129 ! skull [Term] id: UBERON:0036268 name: pelvic vein namespace: uberon xref: SCTID:13152008 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0002355 ! pelvic region of trunk relationship: drains UBERON:0002355 ! pelvic region of trunk [Term] id: UBERON:0036285 name: wall of left ventricle namespace: uberon def: "Wall of ventricle which is continuous with the wall of aorta." [FMA:9556] synonym: "left ventricular wall" EXACT [FMA:9556] xref: FMA:9556 is_a: UBERON:0004784 {source="FMA"} ! heart ventricle wall intersection_of: UBERON:0004784 ! heart ventricle wall intersection_of: part_of UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0002084 {source="FMA"} ! heart left ventricle [Term] id: UBERON:0036286 name: wall of right ventricle namespace: uberon def: "Wall of ventricle which is continuous with the wall of pulmonary trunk." [FMA:9533] synonym: "right ventricular wall" EXACT [FMA:9533] xref: FMA:9533 is_a: UBERON:0004784 {source="FMA"} ! heart ventricle wall intersection_of: UBERON:0004784 ! heart ventricle wall intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: part_of UBERON:0002080 {source="FMA"} ! heart right ventricle [Term] id: UBERON:0036288 name: anterior wall of left ventricle namespace: uberon xref: FMA:9560 is_a: UBERON:0036285 ! wall of left ventricle intersection_of: UBERON:0004784 ! heart ventricle wall intersection_of: in_anterior_side_of UBERON:0002084 ! heart left ventricle relationship: in_anterior_side_of UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0036285 {source="FMA"} ! wall of left ventricle [Term] id: UBERON:0036289 name: anterior wall of right ventricle namespace: uberon def: "Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle." [FMA:9553] xref: FMA:9553 is_a: UBERON:0036286 ! wall of right ventricle intersection_of: UBERON:0004784 ! heart ventricle wall intersection_of: in_anterior_side_of UBERON:0002080 ! heart right ventricle relationship: in_anterior_side_of UBERON:0002080 ! heart right ventricle [Term] id: UBERON:0036290 name: myocardium of anterior wall of left ventricle namespace: uberon xref: FMA:87177 is_a: UBERON:0006566 ! left ventricle myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0036288 ! anterior wall of left ventricle relationship: part_of UBERON:0036288 ! anterior wall of left ventricle [Term] id: UBERON:0036291 name: myocardium of anterior wall of right ventricle namespace: uberon xref: FMA:260877 is_a: UBERON:0006567 ! right ventricle myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0036289 ! anterior wall of right ventricle relationship: part_of UBERON:0036289 ! anterior wall of right ventricle [Term] id: UBERON:0036294 name: mucosa of lip namespace: uberon def: "A mucosa that is part of a lip region [Automatically generated definition]." [OBOL:automatic] synonym: "labial mucosa" EXACT [UBERON:cjm] xref: NCIT:C12226 is_a: UBERON:0003729 ! mouth mucosa is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip [Term] id: UBERON:0036302 name: vasculature of central nervous system plus retina namespace: uberon is_a: UBERON:0002049 ! vasculature union_of: UBERON:0004864 ! vasculature of retina union_of: UBERON:0036303 ! vasculature of central nervous system [Term] id: UBERON:0036303 name: vasculature of central nervous system namespace: uberon xref: FMA:259905 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0036302 ! vasculature of central nervous system plus retina intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system [Term] id: UBERON:0036422 name: wall of pulmonary artery namespace: uberon synonym: "pulmonary arterial wall" EXACT [FMA:18211] xref: FMA:18211 is_a: UBERON:0000415 {source="FMA"} ! artery wall is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 {source="FMA"} ! pulmonary artery [Term] id: UBERON:0036553 name: wall of synovial tendon sheath namespace: uberon xref: FMA:231590 is_a: UBERON:0000042 {source="FMA"} ! serous membrane is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000304 ! tendon sheath relationship: part_of UBERON:0000304 {source="FMA"} ! tendon sheath [Term] id: UBERON:0036925 name: wall of eyeball namespace: uberon synonym: "eyeball wall" EXACT [FMA:58098] xref: FMA:58098 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0010230 ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye [Term] id: UBERON:0037094 name: wall of common carotid artery namespace: uberon synonym: "common carotid arterial wall" EXACT [FMA:66284] xref: FMA:66284 is_a: UBERON:0000415 {source="FMA"} ! artery wall is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001530 ! common carotid artery plus branches relationship: part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches [Term] id: UBERON:0037144 name: wall of heart namespace: uberon def: "wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees." [FMA:7274] synonym: "cardiac wall" EXACT [FMA:7274] xref: FMA:7274 is_a: CARO:0000003 ! connected anatomical structure is_a: UBERON:0000060 {source="FMA"} ! anatomical wall is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000948 ! heart relationship: attaches_to UBERON:0002406 {source="FMA"} ! pericardial sac relationship: attaches_to UBERON:0004292 {source="FMA"} ! cardiac skeleton relationship: part_of UBERON:0000948 {source="FMA"} ! heart [Term] id: UBERON:1000021 name: skin of face namespace: uberon def: "A zone of skin that is part of the face." [https://github.com/obophenotype/uberon/issues/34, UBERON:EJS] subset: pheno_slim subset: phenotype_rcn synonym: "face skin" EXACT [EMAPA:36657, FMA:24758] synonym: "facial skin" RELATED [] xref: EMAPA:36657 xref: FMA:24758 xref: NCIT:C33561 xref: SCTID:361703006 xref: UMLS:C0222084 {source="ncithesaurus:Skin_of_the_Face"} is_a: UBERON:0001084 ! skin of head intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001456 ! face property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/seger created_by: eriks creation_date: 2012-02-05T05:23:01Z [Term] id: UBERON:1100000 name: digestive tract junction namespace: uberon def: "An anatomical junction between two parts of the digestive tract." [ORCID:0000-0002-7073-9172] is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0004921 ! subdivision of digestive tract relationship: connects UBERON:0004921 ! subdivision of digestive tract relationship: dc-creator http://orcid.org/0000-0002-7073-9172 creation_date: 2021-02-05T11:19:31Z [Term] id: UBERON:2001457 name: postcranial axial cartilage namespace: uberon def: "Cartilage which is part of the axial skeleton." [ZFIN:curator] xref: ZFA:0001457 is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002090 ! postcranial axial skeleton relationship: part_of UBERON:0002090 ! postcranial axial skeleton property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string created_by: teleost_anatomy_curators [Term] id: UBERON:2001544 name: sublingual cartilage namespace: uberon def: "Pharyngeal arch cartilage that is the median cartilage of the ventral hyoid arch, generally lying between the paired ventral hypohyals." [TAO:wd] is_a: UBERON:0011004 ! pharyngeal arch cartilage property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string created_by: teleost_anatomy_curators [Term] id: UBERON:2005260 name: fenestrated capillary namespace: uberon def: "Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse" [Wikipedia:Capillary#Types, Wikipedia:Fenestra_(histology)] synonym: "fenestrated blood vessel endothelium" BROAD [ZFA:0005260] synonym: "fenestrated capillary vessel" EXACT [FMA:63196] xref: FMA:63196 xref: NCIT:C32595 xref: TAO:0005260 xref: UMLS:C1179615 {source="ncithesaurus:Fenestrated_Capillary"} xref: Wikipedia:Capillary#Types xref: ZFA:0005260 is_a: UBERON:0001982 {source="FMA"} ! capillary is_a: UBERON:0004638 {source="ZFA"} ! blood vessel endothelium property_value: editor_note "the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences" xsd:string property_value: UBPROP:0000001 "Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]." xsd:string [Term] id: UBERON:3000961 name: external integument structure namespace: uberon def: "Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument." [AAO:EJS] comment: Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 is_a: UBERON:0003102 ! surface structure intersection_of: UBERON:0003102 ! surface structure intersection_of: part_of UBERON:0002199 ! integument relationship: part_of UBERON:0002199 ! integument property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string created_by: amphibian_anatomy_curators [Term] id: UBERON:3000972 name: head external integument structure namespace: uberon def: "Dermal, epidermal, glandular and pigment structures of the external head integument." [AAO:EJS] is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string created_by: amphibian_anatomy_curators [Term] id: UBERON:3000977 name: body external integument structure namespace: uberon def: "Dermal, epidermal, glandular and pigment structures of the body integument." [AAO:EJS] is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string created_by: amphibian_anatomy_curators [Term] id: UBERON:3010200 name: vasculature of respiratory integument namespace: uberon def: "Blood vessels in respiratory skin." [AAO:EJS] is_a: UBERON:0003504 ! respiratory system blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001004 ! respiratory system intersection_of: part_of UBERON:0002199 ! integument relationship: part_of UBERON:0002199 ! integument property_value: editor_note "Modified from the original AAO source" xsd:string created_by: amphibian_anatomy_curators [Term] id: UBERON:4200230 name: surface of bone namespace: uberon def: "An anatomical surface that is part of a bone." [PHENOSCAPE] synonym: "bone surface" EXACT [] is_a: UBERON:0006984 ! anatomical surface intersection_of: UBERON:0006984 ! anatomical surface intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element [Term] id: UBERON:8000006 name: left side of back namespace: uberon def: "Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." [https://microbiomedb.org/] is_a: UBERON:0001137 ! dorsum is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001137 ! dorsum intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: in_left_side_of UBERON:0000468 ! multicellular organism created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8000007 name: right side of back namespace: uberon def: "Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." [https://microbiomedb.org/] is_a: UBERON:0001137 ! dorsum is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001137 ! dorsum intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: in_right_side_of UBERON:0000468 ! multicellular organism created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: UO:0000000 name: unit comment: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] [Term] id: UO:0000001 name: length unit def: "A unit which is a standard measure of the distance between two points." [] comment: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "length unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000002 name: mass unit def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [] comment: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "mass unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000003 name: time unit def: "A unit which is a standard measure of the dimension in which events occur in sequence." [] comment: "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "time derived unit" xsd:string [Term] id: UO:0000004 name: electric current unit comment: "A unit which is a standard measure of the flow of electric charge." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000005 name: temperature unit comment: "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "temperature unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "temperature derived unit" xsd:string [Term] id: UO:0000006 name: substance unit comment: "A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "substance unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000007 name: luminous intensity unit comment: "A unit which is a standard measure of the wavelength-weighted power emitted by a light source in a particular direction." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000008 name: meter def: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [] comment: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000008 ! meter based unit property_value: IAO:0000111 "meter" xsd:string property_value: IAO:0000118 "m" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "m" xsd:string property_value: oboInOwl:hasExactSynonym "metre" xsd:string [Term] id: UO:0000009 name: kilogram def: "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [] comment: "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000021 ! gram based unit intersection_of: UO:1000021 ! gram based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: IAO:0000111 "kilogram" xsd:string property_value: IAO:0000118 "kg" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "kg" xsd:string [Term] id: UO:0000010 name: second def: "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [] comment: "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000010 ! second based unit property_value: IAO:0000111 "second" xsd:string property_value: IAO:0000118 "s" xsd:string property_value: IAO:0000118 "sec" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "s" xsd:string [Term] id: UO:0000011 name: ampere comment: "An electric current unit which is equal to the constant current which, if maintained in two straight parallel conductors of infinite length, of negligible circular cross-section, and placed 1 m apart in vacuum, would produce between these conductors a force equal to 2 x 10^[-7] newton per meter of length." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000011 ! ampere based unit property_value: oboInOwl:hasExactSynonym "A" xsd:string [Term] id: UO:0000012 name: kelvin comment: "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000012 ! kelvin based unit property_value: oboInOwl:hasExactSynonym "K" xsd:string [Term] id: UO:0000013 name: mole comment: "A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000013 ! mole based unit property_value: oboInOwl:hasExactSynonym "mol" xsd:string [Term] id: UO:0000014 name: candela comment: "A luminous intensity unit which equal to the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian." [BIPM:BIPM, NIST:NIST] is_a: UO:0000045 ! base unit is_a: UO:1000014 ! candela based unit property_value: oboInOwl:hasExactSynonym "cd" xsd:string [Term] id: UO:0000015 name: centimeter def: "A length unit which is equal to one hundredth of a meter or 10^[-2] m." [] comment: "A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST] is_a: UO:1000008 ! meter based unit intersection_of: UO:1000008 ! meter based unit intersection_of: has:prefix UO:0000298 ! centi relationship: has:prefix UO:0000298 ! centi property_value: IAO:0000111 "centimeter" xsd:string property_value: IAO:0000118 "cm" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "centimetre" xsd:string property_value: oboInOwl:hasExactSynonym "cm" xsd:string [Term] id: UO:0000016 name: millimeter def: "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [] comment: "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST] is_a: UO:1000008 ! meter based unit intersection_of: UO:1000008 ! meter based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: IAO:0000111 "millimeter" xsd:string property_value: IAO:0000118 "mm" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "micrometre" xsd:string property_value: oboInOwl:hasExactSynonym "mm" xsd:string [Term] id: UO:0000017 name: micrometer def: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [] comment: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] is_a: UO:1000008 ! meter based unit intersection_of: UO:1000008 ! meter based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: IAO:0000111 "micrometer" xsd:string property_value: IAO:0000118 "um" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "micrometre" xsd:string property_value: oboInOwl:hasExactSynonym "micron" xsd:string property_value: oboInOwl:hasExactSynonym "um" xsd:string [Term] id: UO:0000018 name: nanometer def: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [] comment: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] is_a: UO:1000008 ! meter based unit intersection_of: UO:1000008 ! meter based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: IAO:0000111 "nanometer" xsd:string property_value: IAO:0000118 "nm" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "nanometre" xsd:string property_value: oboInOwl:hasExactSynonym "nm" xsd:string [Term] id: UO:0000019 name: angstrom def: "A length unit which is equal to 10 [-10] m." [] comment: "A length unit which is equal to 10 [-10] m." [NIST:NIST] is_a: UO:1000019 ! angstrom based unit property_value: IAO:0000111 "angstrom" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "Å" xsd:string [Term] id: UO:0000020 name: picometer comment: "A length unit which is equal to 10^[-12] m." [NIST:NIST] is_a: UO:1000008 ! meter based unit intersection_of: UO:1000008 ! meter based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: oboInOwl:hasExactSynonym "picometre" xsd:string property_value: oboInOwl:hasExactSynonym "pm" xsd:string [Term] id: UO:0000021 name: gram def: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [] comment: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST] is_a: UO:1000021 ! gram based unit property_value: IAO:0000111 "gram" xsd:string property_value: IAO:0000118 "g" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "g" xsd:string [Term] id: UO:0000022 name: milligram def: "A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [] comment: "A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG] is_a: UO:1000021 ! gram based unit intersection_of: UO:1000021 ! gram based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: IAO:0000111 "milligram" xsd:string property_value: IAO:0000118 "mg" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "mg" xsd:string [Term] id: UO:0000023 name: microgram def: "A mass unit which is equal to one millionth of a gram or 10^[-6] g." [] comment: "A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG] is_a: UO:1000021 ! gram based unit intersection_of: UO:1000021 ! gram based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: IAO:0000111 "microgram" xsd:string property_value: IAO:0000118 "ug" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "ug" xsd:string [Term] id: UO:0000024 name: nanogram def: "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [] comment: "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG] is_a: UO:1000021 ! gram based unit intersection_of: UO:1000021 ! gram based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: IAO:0000111 "nanogram" xsd:string property_value: IAO:0000118 "ng" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "ng" xsd:string [Term] id: UO:0000025 name: picogram def: "A mass unit which is equal to 10^[-12] g." [] comment: "A mass unit which is equal to 10^[-12] g." [UOC:GVG] is_a: UO:1000021 ! gram based unit intersection_of: UO:1000021 ! gram based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: IAO:0000111 "picogram" xsd:string property_value: IAO:0000118 "pg" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "pg" xsd:string [Term] id: UO:0000026 name: femtogram comment: "A mass unit which is equal to 10^[-15] g." [NIST:NIST] is_a: UO:1000021 ! gram based unit intersection_of: UO:1000021 ! gram based unit intersection_of: has:prefix UO:0000303 ! femto relationship: has:prefix UO:0000303 ! femto property_value: oboInOwl:hasExactSynonym "fg" xsd:string [Term] id: UO:0000027 name: degree Celsius def: "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [] comment: "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] is_a: UO:1000027 ! degree Celsius based unit property_value: IAO:0000111 "degree Celsius" xsd:string property_value: IAO:0000118 "C" xsd:string property_value: IAO:0000118 "degree C" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "C" xsd:string [Term] id: UO:0000028 name: millisecond comment: "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] is_a: UO:1000010 ! second based unit intersection_of: UO:1000010 ! second based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "ms" xsd:string [Term] id: UO:0000029 name: microsecond comment: "A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST] is_a: UO:1000010 ! second based unit intersection_of: UO:1000010 ! second based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "us" xsd:string [Term] id: UO:0000030 name: picosecond comment: "A time unit which is equal to 10^[-12] s." [NIST:NIST] is_a: UO:1000010 ! second based unit intersection_of: UO:1000010 ! second based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: oboInOwl:hasExactSynonym "ps" xsd:string [Term] id: UO:0000031 name: minute def: "A time unit which is equal to 60 seconds." [] comment: "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] is_a: UO:1000031 ! minute based unit property_value: IAO:0000111 "minute" xsd:string property_value: IAO:0000118 "min" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "min" xsd:string [Term] id: UO:0000032 name: hour def: "A time unit which is equal to 3600 seconds or 60 minutes." [] comment: "A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia] is_a: UO:1000032 ! hour based unit property_value: IAO:0000111 "hour" xsd:string property_value: IAO:0000118 "h" xsd:string property_value: IAO:0000118 "hr" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "h" xsd:string [Term] id: UO:0000033 name: day def: "A time unit which is equal to 24 hours." [] comment: "A time unit which is equal to 24 hours." [Wikipedia:Wikipedia] is_a: UO:1000033 ! day based unit property_value: IAO:0000111 "day" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000034 name: week def: "A time unit which is equal to 7 days." [] comment: "A time unit which is equal to 7 days." [Wikipedia:Wikipedia] is_a: UO:1000034 ! week based unit property_value: IAO:0000111 "week" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000035 name: month def: "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [] comment: "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia] is_a: UO:1000035 ! month based unit property_value: IAO:0000111 "month" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000036 name: year def: "A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days." [] comment: "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia] is_a: UO:1000036 ! year based unit property_value: IAO:0000111 "year" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000037 name: milliampere comment: "An electric current unit current which is equal to one thousandth of an ampere or 10^[-3] A." [UOC:GVG] is_a: UO:1000011 ! ampere based unit intersection_of: UO:1000011 ! ampere based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mA" xsd:string [Term] id: UO:0000038 name: microampere comment: "An electric current unit current which is equal to one millionth of an ampere or 10^[-6] A." [UOC:GVG] is_a: UO:1000011 ! ampere based unit intersection_of: UO:1000011 ! ampere based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "uA" xsd:string [Term] id: UO:0000039 name: micromole def: "A substance unit equal to a millionth of a mol or 10^[-6] mol." [] comment: "A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: IAO:0000111 "micromole" xsd:string property_value: IAO:0000118 "umol" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "umol" xsd:string [Term] id: UO:0000040 name: millimole comment: "A substance unit equal to a thousandth of a mol or 10^[-3] mol." [NIST:NIST] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mmol" xsd:string [Term] id: UO:0000041 name: nanomole def: "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." [] comment: "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." [NIST:NIST] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: IAO:0000111 "nanomole" xsd:string property_value: IAO:0000118 "nmol" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "nmol" xsd:string [Term] id: UO:0000042 name: picomole def: "A substance unit equal to 10^[-12] mol." [] comment: "A substance unit equal to 10^[-12] mol." [NIST:NIST] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: IAO:0000111 "picomole" xsd:string property_value: IAO:0000118 "pmol" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "pmol" xsd:string [Term] id: UO:0000043 name: femtomole comment: "A substance unit equal to 10^[-15] mol." [NIST:NIST] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000303 ! femto relationship: has:prefix UO:0000303 ! femto property_value: oboInOwl:hasExactSynonym "fmol" xsd:string [Term] id: UO:0000044 name: attomole comment: "A substance unit equal to 10^[-18] mol." [NIST:NIST] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000304 ! atto relationship: has:prefix UO:0000304 ! atto property_value: oboInOwl:hasExactSynonym "amol" xsd:string [Term] id: UO:0000045 name: base unit comment: "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000046 name: prefix [Term] id: UO:0000047 name: area unit comment: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] is_a: UO:0000000 ! unit [Term] id: UO:0000048 name: acceleration unit comment: "A unit which is a standard measure of the rate of change of velocity in either speed or direction." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000049 name: angular velocity unit comment: "A unit which is a standard measure of the rate of angular movement about an axis; the angle rotated in a given time." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000050 name: angular acceleration unit comment: "A unit which is a standard measure of the rate of change of angular velocity." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000051 name: concentration unit comment: "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "concentration unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000052 name: mass density unit comment: "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] is_a: UO:0000182 ! density unit property_value: oboInOwl:hasExactSynonym "mass per unit volume" xsd:string [Term] id: UO:0000053 name: luminance unit comment: "A unit which is a standard measure of the luminous intensity impinging on a given area." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000054 name: area density unit comment: "A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia] is_a: UO:0000182 ! density unit property_value: oboInOwl:hasExactSynonym "mass per unit area unit" xsd:string [Term] id: UO:0000055 name: molar mass unit comment: "A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] is_a: UO:0000002 ! mass unit [Term] id: UO:0000056 name: molar volume unit comment: "A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] is_a: UO:0000095 ! volume unit [Term] id: UO:0000057 name: momentum unit comment: "A unit which is a standard measure of the quantity of motion measured by the product of mass and velocity." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000058 name: rotational frequency unit comment: "A unit which is a standard measure of the number of rotations in a given time." [NIST:NIST] is_a: UO:0000105 ! frequency unit [Term] id: UO:0000059 name: specific volume unit comment: "A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia] is_a: UO:0000095 ! volume unit [Term] id: UO:0000060 name: speed/velocity unit comment: "A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000061 name: unit of molarity comment: "A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000062 name: molar def: "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [] comment: "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG] is_a: UO:1000062 ! molar based unit property_value: IAO:0000111 "molar" xsd:string property_value: IAO:0000118 "M" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "M" xsd:string [Term] id: UO:0000063 name: millimolar def: "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [] comment: "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG] is_a: UO:1000062 ! molar based unit intersection_of: UO:1000062 ! molar based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: IAO:0000111 "millimolar" xsd:string property_value: IAO:0000118 "mM" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "mM" xsd:string [Term] id: UO:0000064 name: micromolar def: "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [] comment: "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG] is_a: UO:1000062 ! molar based unit intersection_of: UO:1000062 ! molar based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: IAO:0000111 "micromolar" xsd:string property_value: IAO:0000118 "uM" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "uM" xsd:string [Term] id: UO:0000065 name: nanomolar def: "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [] comment: "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG] is_a: UO:1000062 ! molar based unit intersection_of: UO:1000062 ! molar based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: IAO:0000111 "nanomolar" xsd:string property_value: IAO:0000118 "nM" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "nM" xsd:string [Term] id: UO:0000066 name: picomolar def: "A unit of molarity which is equal to 10^[-12] M." [] comment: "A unit of molarity which is equal to 10^[-12] M." [UOC:GVG] is_a: UO:1000062 ! molar based unit intersection_of: UO:1000062 ! molar based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: IAO:0000111 "picomolar" xsd:string property_value: IAO:0000118 "pM" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "pM" xsd:string [Term] id: UO:0000067 name: unit of molality comment: "A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000068 name: molal comment: "A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG] is_a: UO:1000068 ! molal based unit property_value: oboInOwl:hasExactSynonym "m" xsd:string [Term] id: UO:0000069 name: millimolal comment: "A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG] is_a: UO:1000068 ! molal based unit intersection_of: UO:1000068 ! molal based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mm" xsd:string [Term] id: UO:0000070 name: micromolal comment: "A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG] is_a: UO:1000068 ! molal based unit intersection_of: UO:1000068 ! molal based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "um" xsd:string [Term] id: UO:0000071 name: nanomolal comment: "A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG] is_a: UO:1000068 ! molal based unit intersection_of: UO:1000068 ! molal based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: oboInOwl:hasExactSynonym "nm" xsd:string [Term] id: UO:0000072 name: picomolal comment: "A molality unit which is equal to 10^[-12] m." [UOC:GVG] is_a: UO:1000068 ! molal based unit intersection_of: UO:1000068 ! molal based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: oboInOwl:hasExactSynonym "pm" xsd:string [Term] id: UO:0000073 name: femtomolar comment: "A unit of molarity which is equal to 10^[-15] M." [UOC:GVG] is_a: UO:1000062 ! molar based unit intersection_of: UO:1000062 ! molar based unit intersection_of: has:prefix UO:0000303 ! femto relationship: has:prefix UO:0000303 ! femto property_value: oboInOwl:hasExactSynonym "fM" xsd:string [Term] id: UO:0000074 name: unit of normality comment: "A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000075 name: normal comment: "A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia] is_a: UO:1000075 ! normal based unit property_value: oboInOwl:hasExactSynonym "N" xsd:string [Term] id: UO:0000076 name: mole fraction comment: "A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia] is_a: UO:1000076 ! mole fraction based unit property_value: oboInOwl:hasExactSynonym "(x)" xsd:string property_value: oboInOwl:hasExactSynonym "chi" xsd:string [Term] id: UO:0000077 name: meter per second per second comment: "An acceleration unit which is equal to the acceleration an object changing its velocity by 1meter/s over a time period that equals one second." [NIST:NIST] is_a: UO:1000077 ! meter per second per second based unit property_value: oboInOwl:hasExactSynonym "m/s^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "metre per second per second" xsd:string [Term] id: UO:0000078 name: radian per second per second comment: "An angular unit acceleration which is equal to the angular acceleration of an object changing its angular velocity by 1rad/s over a time period that equals one second." [NIST:NIST] is_a: UO:1000078 ! radian per second per second based unit property_value: oboInOwl:hasExactSynonym "alpha" xsd:string property_value: oboInOwl:hasExactSynonym "rad/s^[2]" xsd:string [Term] id: UO:0000079 name: radian per second comment: "An angular unit velocity which is equal to about 9.54930 rpm (revolutions per minute)." [NIST:NIST] is_a: UO:1000079 ! radian per second based unit property_value: oboInOwl:hasExactSynonym "rad/s" xsd:string [Term] id: UO:0000080 name: square meter comment: "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST] is_a: UO:1000080 ! square meter based unit property_value: oboInOwl:hasExactSynonym "m^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "square metre" xsd:string [Term] id: UO:0000081 name: square centimeter comment: "An area unit which is equal to one ten thousandth of a square meter or 10^[-4] m^[2]." [NIST:NIST] is_a: UO:1000081 ! square centimeter based unit property_value: oboInOwl:hasExactSynonym "cm^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "square centimetre" xsd:string [Term] id: UO:0000082 name: square millimeter comment: "An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2]." [NIST:NIST] is_a: UO:1000082 ! square millimeter based unit property_value: oboInOwl:hasExactSynonym "mm^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "square millimetre" xsd:string [Term] id: UO:0000083 name: kilogram per cubic meter comment: "A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG] is_a: UO:0000052 ! mass density unit property_value: oboInOwl:hasExactSynonym "kg/m^[3]" xsd:string property_value: oboInOwl:hasExactSynonym "kilogram per cubic metre" xsd:string [Term] id: UO:0000084 name: gram per cubic centimeter comment: "A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG] is_a: UO:1000084 ! gram per cubic centimeter based unit property_value: oboInOwl:hasExactSynonym "g/cm^[3]" xsd:string property_value: oboInOwl:hasExactSynonym "gram per cubic centimetre" xsd:string [Term] id: UO:0000085 name: candela per square meter comment: "A luminance unit which is equal to a luminous intensity of one candela radiating from a surface whose area is one square meter." [NIST:NIST] is_a: UO:1000085 ! candela per square meter based unit property_value: oboInOwl:hasExactSynonym "candela per square metre" xsd:string property_value: oboInOwl:hasExactSynonym "cd/m^[2]" xsd:string [Term] id: UO:0000086 name: kilogram per square meter comment: "An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared." [NIST:NIST] is_a: UO:1010049 ! gram per square meter based unit intersection_of: UO:1010049 ! gram per square meter based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "Body Mass Index (BMI)" xsd:string property_value: oboInOwl:hasExactSynonym "kg/m^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "kilogram per square metre" xsd:string [Term] id: UO:0000087 name: kilogram per mole comment: "A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST] is_a: UO:1000088 ! gram per mole based unit intersection_of: UO:1000088 ! gram per mole based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "kg/mol" xsd:string [Term] id: UO:0000088 name: gram per mole comment: "A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST] is_a: UO:1000088 ! gram per mole based unit property_value: oboInOwl:hasExactSynonym "g/mol" xsd:string [Term] id: UO:0000089 name: cubic meter per mole comment: "A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] is_a: UO:1000089 ! cubic meter per mole based unit property_value: oboInOwl:hasExactSynonym "cubic metre per mole" xsd:string property_value: oboInOwl:hasExactSynonym "m^[3]/mol" xsd:string [Term] id: UO:0000090 name: cubic centimeter per mole comment: "A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] is_a: UO:1000090 ! cubic centimeter per mole based unit property_value: oboInOwl:hasExactSynonym "cm^[3]/mol" xsd:string property_value: oboInOwl:hasExactSynonym "cubic centimetre per mole" xsd:string [Term] id: UO:0000091 name: kilogram meter per second comment: "A momentum unit which is equal to the momentum of a one kilogram mass object with a speed of one meter per second." [NIST:NIST] is_a: UO:0000057 ! momentum unit property_value: oboInOwl:hasExactSynonym "kg.m/s" xsd:string property_value: oboInOwl:hasExactSynonym "kilogram metre per second" xsd:string [Term] id: UO:0000092 name: turns per second comment: "A rotational frequency unit which is equal to the number complete turn in a period of time that equals to 1 second." [NIST:NIST] is_a: UO:1000092 ! turns per second based unit property_value: oboInOwl:hasExactSynonym "1/s" xsd:string property_value: oboInOwl:hasExactSynonym "one turn per second" xsd:string [Term] id: UO:0000093 name: cubic meter per kilogram comment: "A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST] is_a: UO:1000093 ! cubic meter per kilogram based unit property_value: oboInOwl:hasExactSynonym "cubic metre per kilogram" xsd:string property_value: oboInOwl:hasExactSynonym "m^[3]/kg" xsd:string [Term] id: UO:0000094 name: meter per second comment: "A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST] is_a: UO:1000094 ! meter per second based unit property_value: oboInOwl:hasExactSynonym "m/s" xsd:string property_value: oboInOwl:hasExactSynonym "metre per second" xsd:string [Term] id: UO:0000095 name: volume unit comment: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "volume unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000096 name: cubic meter comment: "A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST] is_a: UO:1000096 ! cubic meter based unit property_value: oboInOwl:hasExactSynonym "cubic metre" xsd:string property_value: oboInOwl:hasExactSynonym "m^[3]" xsd:string [Term] id: UO:0000097 name: cubic centimeter def: "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [] comment: "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST] is_a: UO:1000097 ! cubic centimeter based unit property_value: IAO:0000111 "cubic centimeter" xsd:string property_value: IAO:0000118 "cc" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "cc" xsd:string property_value: oboInOwl:hasExactSynonym "cm^3" xsd:string property_value: oboInOwl:hasExactSynonym "cubic centimetre" xsd:string [Term] id: UO:0000098 name: milliliter def: "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [] comment: "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] is_a: UO:1000099 ! liter based unit intersection_of: UO:1000099 ! liter based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: IAO:0000111 "milliliter" xsd:string property_value: IAO:0000118 "ml" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "millilitre" xsd:string property_value: oboInOwl:hasExactSynonym "ml" xsd:string [Term] id: UO:0000099 name: liter def: "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [] comment: "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST] is_a: UO:1000099 ! liter based unit property_value: IAO:0000111 "liter" xsd:string property_value: IAO:0000118 "L" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "L" xsd:string property_value: oboInOwl:hasExactSynonym "l" xsd:string property_value: oboInOwl:hasExactSynonym "litre" xsd:string [Term] id: UO:0000100 name: cubic decimeter def: "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [] comment: "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST] is_a: UO:1000100 ! cubic decimeter based unit property_value: IAO:0000111 "cubic decimeter" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "cubic decimetre" xsd:string property_value: oboInOwl:hasExactSynonym "dm^[3]" xsd:string [Term] id: UO:0000101 name: microliter def: "A volume unit which is equal to one millionth of a liter or 10^[-6] L." [] comment: "A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST] is_a: UO:1000099 ! liter based unit intersection_of: UO:1000099 ! liter based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: IAO:0000111 "microliter" xsd:string property_value: IAO:0000118 "ul" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "microlitre" xsd:string property_value: oboInOwl:hasExactSynonym "ul" xsd:string [Term] id: UO:0000102 name: nanoliter def: "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [] comment: "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST] is_a: UO:1000099 ! liter based unit intersection_of: UO:1000099 ! liter based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: IAO:0000111 "nanoliter" xsd:string property_value: IAO:0000118 "nl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "nanolitre" xsd:string property_value: oboInOwl:hasExactSynonym "nl" xsd:string [Term] id: UO:0000103 name: picoliter def: "A volume unit which is equal to 10^[-12] L." [] comment: "A volume unit which is equal to 10^[-12] L." [NIST:NIST] is_a: UO:1000099 ! liter based unit intersection_of: UO:1000099 ! liter based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: IAO:0000111 "picoliter" xsd:string property_value: IAO:0000118 "pl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "picolitre" xsd:string property_value: oboInOwl:hasExactSynonym "pl" xsd:string [Term] id: UO:0000104 name: femtoliter comment: "A volume unit which is equal to 10^[-15] L." [NIST:NIST] is_a: UO:1000099 ! liter based unit intersection_of: UO:1000099 ! liter based unit intersection_of: has:prefix UO:0000303 ! femto relationship: has:prefix UO:0000303 ! femto property_value: oboInOwl:hasExactSynonym "femtolitre" xsd:string property_value: oboInOwl:hasExactSynonym "fl" xsd:string [Term] id: UO:0000105 name: frequency unit comment: "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "frequency unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000106 name: hertz def: "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [] comment: "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST] is_a: UO:1000106 ! hertz based unit property_value: IAO:0000111 "hertz" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "Hz" xsd:string property_value: oboInOwl:hasExactSynonym "s^1" xsd:string [Term] id: UO:0000107 name: force unit comment: "A unit which is a standard measure of the force is applied when a mass is accelerated." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000108 name: newton comment: "A force unit which is equal to the force required to cause an acceleration of 1m/s2 of a mass of 1 Kg in the direction of the force." [NIST:NIST] is_a: UO:1000108 ! newton based unit property_value: oboInOwl:hasExactSynonym "N" xsd:string [Term] id: UO:0000109 name: pressure unit comment: "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000110 name: pascal comment: "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST] is_a: UO:1000110 ! pascal based unit property_value: oboInOwl:hasExactSynonym "Pa" xsd:string [Term] id: UO:0000111 name: energy unit comment: "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000112 name: joule comment: "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST] is_a: UO:1000112 ! joule based unit property_value: oboInOwl:hasExactSynonym "J" xsd:string [Term] id: UO:0000113 name: power unit comment: "A unit which is a standard measure power or the rate of doing work." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000114 name: watt comment: "A power unit which is equal to the power used when work is done at the rate of 1 joule per second." [NIST:NIST] is_a: UO:1000114 ! watt based unit property_value: oboInOwl:hasExactSynonym "W" xsd:string [Term] id: UO:0000115 name: illuminance unit comment: "A unit which is a standard measure of the luminous flux incident on a unit area." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000116 name: lux comment: "An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 m^[2]." [NIST:NIST] is_a: UO:1000116 ! lux based unit property_value: oboInOwl:hasExactSynonym "lx" xsd:string [Term] id: UO:0000117 name: luminous flux unit comment: "A unit which is a standard measure of the flow of radiant energy." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000118 name: lumen comment: "A luminous flux unit which is equal to the luminous flux emitted into 1 steradian by a point source of 1 candela." [NIST:NIST] is_a: UO:1000118 ! lumen based unit property_value: oboInOwl:hasExactSynonym "lm" xsd:string [Term] id: UO:0000119 name: catalytic activity unit comment: "A unit which is a standard measure of the amount of the action of a catalyst." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000120 name: katal comment: "A catalytic unit activity which is equal to the activity of a catalyst in moles per second, such as the amount of an enzyme needed to transform one mole of substrate per second." [NIST:NIST] is_a: UO:1000120 ! katal based unit property_value: oboInOwl:hasExactSynonym "kat" xsd:string [Term] id: UO:0000121 name: angle unit comment: "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000122 name: plane angle unit comment: "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] is_a: UO:0000121 ! angle unit [Term] id: UO:0000123 name: radian comment: "A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST] is_a: UO:1000123 ! radian based unit property_value: oboInOwl:hasExactSynonym "rad" xsd:string [Term] id: UO:0000124 name: solid angle unit comment: "A unit which is a standard measure of the angle formed by three or more planes intersecting at a common point." [Wikipedia:Wikipedia] is_a: UO:0000121 ! angle unit [Term] id: UO:0000125 name: steradian comment: "A solid angle unit which is equal to the solid angle subtended at the center of a sphere by an area on the surface of the sphere that is equal to the radius squared." [NIST:NIST] is_a: UO:1000125 ! steradian based unit property_value: oboInOwl:hasExactSynonym "sr" xsd:string [Term] id: UO:0000127 name: radiation unit comment: "A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source." [OCRBS:OCRBS] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit [Term] id: UO:0000128 name: activity (of a radionuclide) unit comment: "A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance." [DEFRA:DEFRA] is_a: UO:0000127 ! radiation unit [Term] id: UO:0000129 name: absorbed dose unit comment: "A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue." [DEFRA:DEFRA] is_a: UO:0000127 ! radiation unit [Term] id: UO:0000130 name: dose equivalent unit comment: "A unit which is a standard measure of the expression of dose in terms of its biological effect." [ORCBS:ORCBS] is_a: UO:0000127 ! radiation unit [Term] id: UO:0000131 name: exposure unit comment: "A unit which is a standard measure of the quantity that expresses the ability of radiation to ionize air and thereby create electric charges which can be collected and measured." [ORCBS:ORCBS] is_a: UO:0000127 ! radiation unit [Term] id: UO:0000132 name: becquerel comment: "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second (dps)." [NIST:NIST] is_a: UO:1000132 ! becquerel based unit property_value: oboInOwl:hasExactSynonym "Bq" xsd:string [Term] id: UO:0000133 name: curie comment: "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps)." [ORCBS:ORCBS] is_a: UO:1000133 ! curie based unit property_value: oboInOwl:hasExactSynonym "Ci" xsd:string [Term] id: UO:0000134 name: gray comment: "An absorbed dose unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST] is_a: UO:1000134 ! gray based unit property_value: oboInOwl:hasExactSynonym "Gy" xsd:string [Term] id: UO:0000135 name: rad comment: "An absorbed dose unit which is equal to 0.01 gray (Gy)." [Wikipedia:Wikipedia] is_a: UO:1000135 ! rad based unit [Term] id: UO:0000136 name: roentgen comment: "An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs." [Wikipedia:Wikipedia] is_a: UO:1000136 ! roentgen based unit property_value: oboInOwl:hasExactSynonym "R" xsd:string [Term] id: UO:0000137 name: sievert comment: "A dose equivalent unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST] is_a: UO:1000137 ! sievert based unit property_value: oboInOwl:hasExactSynonym "Sv" xsd:string [Term] id: UO:0000138 name: millisievert comment: "A dose equivalent unit which is equal to one thousandth of a sievert or 10^[-3] Sv." [NIST:NIST] is_a: UO:1000137 ! sievert based unit intersection_of: UO:1000137 ! sievert based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mSv" xsd:string [Term] id: UO:0000139 name: microsievert comment: "A dose equivalent unit which is equal to one millionth of a sievert or 10^[-6] Sv." [NIST:NIST] is_a: UO:1000137 ! sievert based unit intersection_of: UO:1000137 ! sievert based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "uSv" xsd:string [Term] id: UO:0000140 name: Roentgen equivalent man comment: "A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem." [Wikipedia:Wikipedia] is_a: UO:1000140 ! Roentgen equivalent man based unit property_value: oboInOwl:hasExactSynonym "rem" xsd:string [Term] id: UO:0000141 name: microgray comment: "An absorbed dose unit which is equal to one millionth of a gray or 10^[-6] Gy." [NIST:NIST] is_a: UO:1000134 ! gray based unit intersection_of: UO:1000134 ! gray based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "uGy" xsd:string [Term] id: UO:0000142 name: milligray comment: "An absorbed dose unit which is equal to one thousandth of a gray or 10^[-3] Gy." [NIST:NIST] is_a: UO:1000134 ! gray based unit intersection_of: UO:1000134 ! gray based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mGy" xsd:string [Term] id: UO:0000143 name: nanogray comment: "An absorbed dose unit which is equal to one thousandth of a millionth of a gray or 10^[-9] Gy." [NIST:NIST] is_a: UO:1000134 ! gray based unit intersection_of: UO:1000134 ! gray based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: oboInOwl:hasExactSynonym "nGy" xsd:string [Term] id: UO:0000144 name: nanosievert comment: "A dose equivalent unit which is equal to one thousandth of a millionth of a sievert or 10^[-9] Sv." [NIST:NIST] is_a: UO:1000137 ! sievert based unit intersection_of: UO:1000137 ! sievert based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: oboInOwl:hasExactSynonym "nSv" xsd:string [Term] id: UO:0000145 name: millicurie comment: "An activity (of a radionuclide) unit which is equal to one thousandth of a curie or 10^[-3] Ci." [ORCBS:ORCBS] is_a: UO:1000133 ! curie based unit intersection_of: UO:1000133 ! curie based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mCi" xsd:string [Term] id: UO:0000146 name: microcurie comment: "An activity (of a radionuclide) unit which is equal to one millionth of a curie or 10^[-6] Ci." [ORCBS:ORCBS] is_a: UO:1000133 ! curie based unit intersection_of: UO:1000133 ! curie based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "uCi" xsd:string [Term] id: UO:0000147 name: disintegrations per minute comment: "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute." [ORCBS:ORCBS] is_a: UO:1000147 ! disintegrations per minute based unit property_value: oboInOwl:hasExactSynonym "dpm" xsd:string [Term] id: UO:0000148 name: counts per minute comment: "An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute." [ORCBS:ORCBS] is_a: UO:1000148 ! counts per minute based unit property_value: oboInOwl:hasExactSynonym "cpm" xsd:string [Term] id: UO:0000150 name: nanosecond comment: "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] is_a: UO:1000010 ! second based unit intersection_of: UO:1000010 ! second based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: oboInOwl:hasExactSynonym "ns" xsd:string [Term] id: UO:0000151 name: century comment: "A time unit which is equal to 100 years." [Wikipedia:Wikipedia] is_a: UO:1000151 ! century based unit [Term] id: UO:0000152 name: half life comment: "A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED] is_a: UO:1000152 ! half life based unit [Term] id: UO:0000153 name: foot candle comment: "An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 foot^[2]. One footcandle is equal to 10.76 lux." [Wikipedia:Wikipedia] is_a: UO:1000153 ! foot candle based unit property_value: oboInOwl:hasExactSynonym "ft-c" xsd:string [Term] id: UO:0000154 name: irradiance unit comment: "A unit which is a standard measure of the power of electromagnetic radiation at a surface, per unit area." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000155 name: watt per square meter comment: "An irradiance unit which is equal to 1 watt of radiant power incident per one square meter surface area." [NIST:NIST] is_a: UO:1000155 ! watt per square meter based unit property_value: oboInOwl:hasExactSynonym "W/m^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "watt per square metre" xsd:string [Term] id: UO:0000156 name: einstein per square meter per second comment: "An irradiance unit which is equal to one einstein per square meter per second. One einstein is one mole of photons, regardless of their frequency. Therefore, the number of photons in an einstein is Avogadro's number." [Wikipedia:Wikipedia] is_a: UO:1000156 ! einstein per square meter per second based unit property_value: oboInOwl:hasExactSynonym "einstein per square metre per second" xsd:string property_value: oboInOwl:hasExactSynonym "einstein/sm^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "mole per second and square meter mol/sm^2" xsd:string [Term] id: UO:0000157 name: light unit comment: "A unit which is a standard measure of the intensity of light." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000158 name: watt per steradian per square meter comment: "A radiance unit which is equal to one watt of radiant power incident per steradian solid angle per one square meter projected area of the source, as viewed from the given direction." [NIST:NIST] is_a: UO:1000158 ! watt per steradian per square meter based unit property_value: oboInOwl:hasExactSynonym "W/sr m^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "watt per steradian per square metre" xsd:string [Term] id: UO:0000159 name: radiant intensity unit comment: "A unit which is a standard measure of the intensity of electromagnetic radiation." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000160 name: microeinstein per square meter per second comment: "An irradiance unit which is equal to one microeinstein per square meter per second or 10^[-6] microeinstein/sm^[2]." [Wikipedia:Wikipedia] is_a: UO:1000156 ! einstein per square meter per second based unit intersection_of: UO:1000156 ! einstein per square meter per second based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "microeinstein per square metre per second" xsd:string property_value: oboInOwl:hasExactSynonym "micromole per second and square meter mmol/sm^2" xsd:string property_value: oboInOwl:hasExactSynonym "umicroeinstein/sm^[2]" xsd:string [Term] id: UO:0000161 name: radiance unit comment: "A unit which is a standard measure of the power of electromagnetic radiation through space or through a material medium in the form of electromagnetic waves." [Wikipedia:Wikipedia] is_a: UO:0000157 ! light unit [Term] id: UO:0000162 name: watt per steradian comment: "A radiant intensity unit which is equal to one kilogram meter squared per second cubed per steradian." [NIST:NIST] is_a: UO:1000162 ! watt per steradian based unit property_value: oboInOwl:hasExactSynonym "W/sr" xsd:string [Term] id: UO:0000163 name: mass percentage def: "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [] comment: "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia] is_a: UO:1000163 ! mass percentage based unit property_value: IAO:0000111 "mass percentage" xsd:string property_value: IAO:0000118 "% w/w" xsd:string property_value: IAO:0000118 "percent weight pr weight" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "w/w" xsd:string property_value: oboInOwl:hasExactSynonym "weight-weight percentage" xsd:string [Term] id: UO:0000164 name: mass volume percentage def: "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [] comment: "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG] is_a: UO:1000164 ! mass volume percentage based unit property_value: IAO:0000111 "mass volume percentage" xsd:string property_value: IAO:0000118 "% w/v" xsd:string property_value: IAO:0000118 "percent vol per vol" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "(w/v)" xsd:string property_value: oboInOwl:hasExactSynonym "weight-volume percentage" xsd:string [Term] id: UO:0000165 name: volume percentage def: "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [] comment: "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG] is_a: UO:1000165 ! volume percentage based unit property_value: IAO:0000111 "volume percentage" xsd:string property_value: IAO:0000118 "% v/v" xsd:string property_value: IAO:0000118 "percent vol per vol" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "% (v/v)" xsd:string [Term] id: UO:0000166 name: parts per notation unit comment: "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia] is_a: UO:0000186 ! dimensionless unit [Term] id: UO:0000167 name: parts per hundred comment: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 100 regardless of the units of measure as long as they are the same." [UOC:GVG] is_a: UO:1000167 ! parts per hundred based unit property_value: oboInOwl:hasExactSynonym "10^[-2]" xsd:string property_value: oboInOwl:hasExactSynonym "pph" xsd:string [Term] id: UO:0000168 name: parts per thousand comment: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same." [UOC:GVG] is_a: UO:1000168 ! parts per thousand based unit property_value: oboInOwl:hasExactSynonym "10^[-3]" xsd:string property_value: oboInOwl:hasExactSynonym "ppth" xsd:string [Term] id: UO:0000169 name: parts per million comment: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG] is_a: UO:1000169 ! parts per million based unit property_value: oboInOwl:hasExactSynonym "10^[-6]" xsd:string property_value: oboInOwl:hasExactSynonym "ppm" xsd:string [Term] id: UO:0000170 name: parts per billion comment: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9]." [UOC:GVG] is_a: UO:1000170 ! parts per billion based unit property_value: oboInOwl:hasExactSynonym "10^[-9]" xsd:string property_value: oboInOwl:hasExactSynonym "ppb" xsd:string [Term] id: UO:0000171 name: parts per trillion comment: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[12]." [UOC:GVG] is_a: UO:1000171 ! parts per trillion based unit property_value: oboInOwl:hasExactSynonym "10^[-12]" xsd:string property_value: oboInOwl:hasExactSynonym "ppt" xsd:string [Term] id: UO:0000172 name: parts per quadrillion comment: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[15]." [UOC:GVG] is_a: UO:1000172 ! parts per quadrillion based unit property_value: oboInOwl:hasExactSynonym "10^[-15]" xsd:string property_value: oboInOwl:hasExactSynonym "ppq" xsd:string [Term] id: UO:0000173 name: gram per milliliter comment: "A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG] is_a: UO:1000173 ! gram per milliliter based unit property_value: oboInOwl:hasExactSynonym "g/ml" xsd:string property_value: oboInOwl:hasExactSynonym "gram per millilitre" xsd:string [Term] id: UO:0000174 name: kilogram per liter comment: "A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG] is_a: UO:1000175 ! gram per liter based unit intersection_of: UO:1000175 ! gram per liter based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "kg/L" xsd:string property_value: oboInOwl:hasExactSynonym "kilogram per litre" xsd:string [Term] id: UO:0000175 name: gram per liter def: "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [] comment: "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] is_a: UO:1000175 ! gram per liter based unit property_value: IAO:0000111 "gram per liter" xsd:string property_value: IAO:0000118 "g per L" xsd:string property_value: IAO:0000118 "g/L" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "g/L" xsd:string property_value: oboInOwl:hasExactSynonym "gram per litre" xsd:string [Term] id: UO:0000176 name: milligram per milliliter def: "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [] comment: "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [UOC:GVG] is_a: UO:1000175 ! gram per liter based unit intersection_of: UO:1000175 ! gram per liter based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: IAO:0000111 "milligram per milliliter" xsd:string property_value: IAO:0000118 "mg per ml" xsd:string property_value: IAO:0000118 "mg/ml" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "mg/ml" xsd:string property_value: oboInOwl:hasExactSynonym "milligram per millilitre" xsd:string [Term] id: UO:0000177 name: unit per volume unit comment: "A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000178 name: unit per milliliter comment: "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd] is_a: UO:1000178 ! unit per milliliter based unit property_value: oboInOwl:hasExactSynonym "U/ml" xsd:string property_value: oboInOwl:hasExactSynonym "unit per millilitre" xsd:string [Term] id: UO:0000179 name: unit per liter comment: "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG] is_a: UO:1000179 ! unit per liter based unit property_value: oboInOwl:hasExactSynonym "U/l" xsd:string property_value: oboInOwl:hasExactSynonym "unit per litre" xsd:string [Term] id: UO:0000180 name: mass per unit volume comment: "A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia] is_a: UO:1000180 ! mass per unit volume based unit [Term] id: UO:0000181 name: enzyme unit comment: "A catalytic unit activity which is equal to the amount of the enzyme that catalyzes the conversion of 1 micro mole of substrate per minute." [Wikipedia:Wikipedia] is_a: UO:1000181 ! enzyme unit based unit property_value: oboInOwl:hasExactSynonym "U" xsd:string [Term] id: UO:0000182 name: density unit comment: "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000183 name: linear density unit comment: "A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object." [Wikipedia:Wikipedia] is_a: UO:0000182 ! density unit [Term] id: UO:0000184 name: kilogram per meter comment: "An area density unit which is equal to the mass of an object in kilograms divided by one meter." [NIST:NIST] is_a: UO:0000183 ! linear density unit property_value: oboInOwl:hasExactSynonym "kg/m" xsd:string property_value: oboInOwl:hasExactSynonym "kilogram per metre" xsd:string [Term] id: UO:0000185 name: degree comment: "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] is_a: UO:1000185 ! degree based unit [Term] id: UO:0000186 name: dimensionless unit comment: "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000187 name: percent comment: "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] is_a: UO:0000190 ! ratio property_value: oboInOwl:hasExactSynonym "%" xsd:string [Term] id: UO:0000188 name: pi comment: "A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry." [Wikipedia:Wikipedia] is_a: UO:1000188 ! pi based unit [Term] id: UO:0000189 name: count unit comment: "A dimensionless unit which denotes a simple count of things." [MGED:MGED] is_a: UO:0000186 ! dimensionless unit property_value: oboInOwl:hasExactSynonym "count" xsd:string [Term] id: UO:0000190 name: ratio comment: "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] is_a: UO:0000186 ! dimensionless unit [Term] id: UO:0000191 name: fraction comment: "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] is_a: UO:0000190 ! ratio [Term] id: UO:0000192 name: molecule count comment: "A dimensionless count unit which denotes the number of molecules." [MGED:MGED] is_a: UO:1000192 ! molecule count based unit [Term] id: UO:0000193 name: purity percentage comment: "A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED] is_a: UO:1000193 ! purity percentage based unit [Term] id: UO:0000194 name: confluence percentage comment: "A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED] is_a: UO:1000194 ! confluence percentage based unit [Term] id: UO:0000195 name: degree Fahrenheit def: "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [] comment: "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia] is_a: UO:1000195 ! degree Fahrenheit based unit property_value: IAO:0000111 "degree Fahrenheit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "F" xsd:string [Term] id: UO:0000196 name: pH def: "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [] comment: "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia] is_a: UO:1000196 ! pH based unit property_value: IAO:0000111 "pH" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000197 name: liter per kilogram comment: "A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST] is_a: UO:1000197 ! liter per kilogram based unit property_value: oboInOwl:hasExactSynonym "l/kg" xsd:string property_value: oboInOwl:hasExactSynonym "litre per kilogram" xsd:string [Term] id: UO:0000198 name: milliliter per kilogram comment: "A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST] is_a: UO:1000197 ! liter per kilogram based unit intersection_of: UO:1000197 ! liter per kilogram based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "millilitre per kilogram" xsd:string property_value: oboInOwl:hasExactSynonym "ml/kg" xsd:string [Term] id: UO:0000199 name: microliter per kilogram comment: "A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST] is_a: UO:1000197 ! liter per kilogram based unit intersection_of: UO:1000197 ! liter per kilogram based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "microlitre per kilogram" xsd:string property_value: oboInOwl:hasExactSynonym "ul/kg" xsd:string [Term] id: UO:0000200 name: cell concentration unit comment: "A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000201 name: cells per milliliter comment: "A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline] is_a: UO:1000201 ! cells per milliliter based unit property_value: oboInOwl:hasExactSynonym "cells per millilitre" xsd:string property_value: oboInOwl:hasExactSynonym "cells per ml" xsd:string [Term] id: UO:0000202 name: catalytic (activity) concentration unit comment: "A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000203 name: katal per cubic meter comment: "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST] is_a: UO:1000203 ! katal per cubic meter based unit property_value: oboInOwl:hasExactSynonym "kat/m^[3]" xsd:string property_value: oboInOwl:hasExactSynonym "katal per cubic metre" xsd:string [Term] id: UO:0000204 name: katal per liter comment: "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST] is_a: UO:1000204 ! katal per liter based unit property_value: oboInOwl:hasExactSynonym "kat/l" xsd:string property_value: oboInOwl:hasExactSynonym "katal per litre" xsd:string [Term] id: UO:0000205 name: volume per unit volume comment: "A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000206 name: milliliter per cubic meter comment: "A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST] is_a: UO:0000205 ! volume per unit volume property_value: oboInOwl:hasExactSynonym "millilitre per cubic metre" xsd:string property_value: oboInOwl:hasExactSynonym "ml/m^[3]" xsd:string [Term] id: UO:0000207 name: milliliter per liter def: "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [] comment: "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST] is_a: UO:0000205 ! volume per unit volume property_value: IAO:0000111 "milliliter per liter" xsd:string property_value: IAO:0000118 "ml per L" xsd:string property_value: IAO:0000118 "ml/l" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "millilitre per litre" xsd:string property_value: oboInOwl:hasExactSynonym "ml/l" xsd:string [Term] id: UO:0000208 name: gram per deciliter def: "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [] comment: "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG] is_a: UO:1000208 ! gram per deciliter based unit property_value: IAO:0000111 "gram per deciliter" xsd:string property_value: IAO:0000118 "g/dl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "g/dl" xsd:string property_value: oboInOwl:hasExactSynonym "gram per decilitre" xsd:string [Term] id: UO:0000209 name: deciliter comment: "A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST] is_a: UO:1000099 ! liter based unit intersection_of: UO:1000099 ! liter based unit intersection_of: has:prefix UO:0000296 ! deci relationship: has:prefix UO:0000296 ! deci property_value: oboInOwl:hasExactSynonym "decilitre" xsd:string property_value: oboInOwl:hasExactSynonym "dl" xsd:string [Term] id: UO:0000210 name: colony forming unit comment: "A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia] is_a: UO:1000210 ! colony forming unit based unit property_value: oboInOwl:hasExactSynonym "cfu" xsd:string [Term] id: UO:0000211 name: plaque forming unit comment: "A dimensionless count unit which a measure of plague forming units in a given volume." [Wikipedia:Wikipedia] is_a: UO:1000211 ! plaque forming unit based unit property_value: oboInOwl:hasExactSynonym "pfu" xsd:string [Term] id: UO:0000212 name: colony forming unit per volume def: "A concentration unit which a measure of viable bacterial numbers in a given volume." [] comment: "A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia] is_a: UO:0000051 ! concentration unit property_value: IAO:0000111 "colony forming unit per volume" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000213 name: colony forming unit per milliliter comment: "A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia] is_a: UO:1000213 ! colony forming unit per milliliter based unit property_value: oboInOwl:hasExactSynonym "cfu/ml" xsd:string property_value: oboInOwl:hasExactSynonym "colony forming unit per millilitre" xsd:string [Term] id: UO:0000214 name: plaque forming unit per volume comment: "A concentration unit which a measure of plague forming units in a given volume." [UOC:GVG] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000215 name: plaque forming unit per milliliter comment: "A concentration unit which a measure of plague forming units in one milliliter." [UOC:GVG] is_a: UO:1000215 ! plaque forming unit per milliliter based unit property_value: oboInOwl:hasExactSynonym "pfu/ml" xsd:string property_value: oboInOwl:hasExactSynonym "plaque forming unit per millilitre" xsd:string [Term] id: UO:0000216 name: disintegrations per second comment: "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second." [ORCBS:ORCBS] is_a: UO:1000216 ! disintegrations per second based unit property_value: oboInOwl:hasExactSynonym "dps" xsd:string [Term] id: UO:0000217 name: electric potential difference unit comment: "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000218 name: volt comment: "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia] is_a: UO:1000218 ! volt based unit property_value: oboInOwl:hasExactSynonym "V" xsd:string [Term] id: UO:0000219 name: electric charge comment: "A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons." [WordNet:WordNet] is_a: UO:0000000 ! unit [Term] id: UO:0000220 name: coulomb comment: "An electrical charge unit which is equal to the amount of charge transferred by a current of 1 ampere in 1 second." [WordNet:WordNet] is_a: UO:1000220 ! coulomb based unit property_value: oboInOwl:hasExactSynonym "C" xsd:string [Term] id: UO:0000221 name: dalton comment: "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia] is_a: UO:1000221 ! dalton based unit property_value: oboInOwl:hasExactSynonym "amu" xsd:string property_value: oboInOwl:hasExactSynonym "Da" xsd:string property_value: oboInOwl:hasExactSynonym "u" xsd:string property_value: oboInOwl:hasExactSynonym "unified atomic mass unit" xsd:string [Term] id: UO:0000222 name: kilodalton comment: "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia] is_a: UO:1000221 ! dalton based unit intersection_of: UO:1000221 ! dalton based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "kDa" xsd:string [Term] id: UO:0000223 name: watt-hour comment: "An energy unit which is equal to the amount of electrical energy equivalent to a one-watt load drawing power for one hour." [Wikipedia:Wikipedia] is_a: UO:1000223 ! watt-hour based unit property_value: oboInOwl:hasExactSynonym "Wh" xsd:string [Term] id: UO:0000224 name: kilowatt-hour comment: "An energy unit which is equal to 1,000 watt-hours." [Wikipedia:Wikipedia] is_a: UO:1000223 ! watt-hour based unit intersection_of: UO:1000223 ! watt-hour based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo [Term] id: UO:0000225 name: magnetic flux unit comment: "A unit which is a standard measure of quantity of magnetism, taking account of the strength and the extent of a magnetic field." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000226 name: weber comment: "A magnetic flux unit which is equal to the amount of flux that when linked with a single turn of wire for an interval of one second will induce an electromotive force of one volt." [ScienceLobby:ScienceLobby] is_a: UO:1000226 ! weber based unit property_value: oboInOwl:hasExactSynonym "V s" xsd:string property_value: oboInOwl:hasExactSynonym "Wb" xsd:string property_value: oboInOwl:hasRelatedSynonym "volt-second" xsd:string [Term] id: UO:0000227 name: magnetic flux density unit comment: "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet] is_a: UO:0000000 ! unit property_value: oboInOwl:hasExactSynonym "B" xsd:string [Term] id: UO:0000228 name: tesla comment: "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet] is_a: UO:1000228 ! tesla based unit property_value: oboInOwl:hasExactSynonym "T" xsd:string property_value: oboInOwl:hasExactSynonym "Wb/m2" xsd:string [Term] id: UO:0000229 name: volt-hour comment: "A magnetic flux unit which is equal to 3600 Wb." [UOC:GVG] is_a: UO:1000229 ! volt-hour based unit property_value: oboInOwl:hasExactSynonym "Vh" xsd:string [Term] id: UO:0000230 name: kilovolt-hour comment: "A magnetic flux unit which is equal to one thousand volt-hours." [UOC:GVG] is_a: UO:1000229 ! volt-hour based unit intersection_of: UO:1000229 ! volt-hour based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "kVh" xsd:string [Term] id: UO:0000231 name: information unit comment: "A unit which is a standard measure of the amount of information." [Wikipedia:Wikipedia] is_a: UO:0000000 ! unit [Term] id: UO:0000232 name: bit comment: "An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1)." [Wikipedia:Wikipedia] is_a: UO:1000232 ! bit based unit [Term] id: UO:0000233 name: byte comment: "An information unit which is equal to 8 bits." [Wikipedia:Wikipedia] is_a: UO:1000233 ! byte based unit property_value: oboInOwl:hasExactSynonym "B" xsd:string [Term] id: UO:0000234 name: kilobyte comment: "An information unit which is equal to 1000 bytes." [Wikipedia:Wikipedia] is_a: UO:1000233 ! byte based unit intersection_of: UO:1000233 ! byte based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "kB" xsd:string [Term] id: UO:0000235 name: megabyte comment: "An information unit which is equal to 1000 kB." [Wikipedia:Wikipedia] is_a: UO:1000233 ! byte based unit intersection_of: UO:1000233 ! byte based unit intersection_of: has:prefix UO:0000293 ! mega relationship: has:prefix UO:0000293 ! mega property_value: oboInOwl:hasExactSynonym "MB" xsd:string [Term] id: UO:0000236 name: image resolution unit comment: "An information unit which is a standard measure of the detail an image holds." [Wikipedia:Wikipedia] is_a: UO:0000231 ! information unit [Term] id: UO:0000237 name: chroma sampling unit comment: "An image resolution unit which is a standard measure of the amount of spatial detail in an image." [Wikipedia:Wikipedia] is_a: UO:1000237 ! chroma sampling unit based unit [Term] id: UO:0000238 name: dynamic range unit comment: "An image resolution unit which is a standard measure of the amount of contrast available in a pixel." [Wikipedia:Wikipedia] is_a: UO:1000238 ! dynamic range unit based unit [Term] id: UO:0000239 name: spatial resolution unit comment: "An image resolution unit which is a standard measure of the way luminance and chrominance may be sampled at different levels." [Wikipedia:Wikipedia] is_a: UO:0000236 ! image resolution unit [Term] id: UO:0000240 name: dots per inch comment: "A spatial resolution unit which is a standard measure of the printing resolution, in particular the number of individual dots of ink a printer or toner can produce within a linear one-inch space." [Wikipedia:Wikipedia] is_a: UO:1000240 ! dots per inch based unit property_value: oboInOwl:hasExactSynonym "dpi" xsd:string [Term] id: UO:0000241 name: micron pixel comment: "A spatial resolution unit which is equal to a pixel size of one micrometer." [Wikipedia:Wikipedia] is_a: UO:0000239 ! spatial resolution unit property_value: oboInOwl:hasExactSynonym "micrometer pixel" xsd:string [Term] id: UO:0000242 name: pixels per inch comment: "A spatial resolution unit which is a standard measure of the resolution of a computer display, related to the size of the display in inches and the total number of pixels in the horizontal and vertical directions." [Wikipedia:Wikipedia] is_a: UO:1000242 ! pixels per inch based unit property_value: oboInOwl:hasExactSynonym "pixel density" xsd:string property_value: oboInOwl:hasExactSynonym "ppi" xsd:string [Term] id: UO:0000243 name: pixels per millimeter comment: "A spatial resolution unit which is a standard measure of the number of pixels in one millimeter length or width of a digital image divided by the physical length or width of a printed image." [Wikipedia:Wikipedia] is_a: UO:1000243 ! pixels per millimeter based unit property_value: oboInOwl:hasExactSynonym "pixels per millimetre" xsd:string [Term] id: UO:0000244 name: base pair comment: "A count unit which contains one nucleotide." [UO:GVG] is_a: UO:1000244 ! base pair based unit property_value: oboInOwl:hasExactSynonym "basepair" xsd:string property_value: oboInOwl:hasExactSynonym "bp" xsd:string [Term] id: UO:0000245 name: kibibyte comment: "An information unit which is equal to 1024 B." [NIST:NIST] is_a: UO:1000245 ! kibibyte based unit property_value: oboInOwl:hasExactSynonym "KiB" xsd:string [Term] id: UO:0000246 name: mebibyte comment: "An information unit which is equal to 1024 KiB." [NIST:NIST] is_a: UO:1000246 ! mebibyte based unit property_value: oboInOwl:hasExactSynonym "MiB" xsd:string [Term] id: UO:0000247 name: millivolt comment: "An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG] is_a: UO:1000218 ! volt based unit intersection_of: UO:1000218 ! volt based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mV" xsd:string [Term] id: UO:0000248 name: kilovolt comment: "An electric potential difference unit which is equal to one thousand volts or 10^[3] V." [UOC:GVG] is_a: UO:1000218 ! volt based unit intersection_of: UO:1000218 ! volt based unit intersection_of: has:prefix UO:0000294 ! kilo relationship: has:prefix UO:0000294 ! kilo property_value: oboInOwl:hasExactSynonym "kV" xsd:string [Term] id: UO:0000249 name: microvolt comment: "An electric potential difference unit which is equal to one millionth of a volt or 10^[-6] V." [UOC:GVG] is_a: UO:1000218 ! volt based unit intersection_of: UO:1000218 ! volt based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "uV" xsd:string [Term] id: UO:0000250 name: nanovolt comment: "An electric potential difference unit which is equal to one billionth of a volt or 10^[-12] V." [UOC:GVG] is_a: UO:1000218 ! volt based unit intersection_of: UO:1000218 ! volt based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: oboInOwl:hasExactSynonym "nV" xsd:string [Term] id: UO:0000251 name: picovolt comment: "An electric potential difference unit which is equal to one trillionth of a volt or 10^[-12] V." [UOC:GVG] is_a: UO:1000218 ! volt based unit intersection_of: UO:1000218 ! volt based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: oboInOwl:hasExactSynonym "pV" xsd:string [Term] id: UO:0000252 name: megavolt comment: "An electric potential difference unit which is equal to one million volts or 10^[6] V." [UOC:GVG] is_a: UO:1000218 ! volt based unit intersection_of: UO:1000218 ! volt based unit intersection_of: has:prefix UO:0000293 ! mega relationship: has:prefix UO:0000293 ! mega property_value: oboInOwl:hasExactSynonym "MV" xsd:string [Term] id: UO:0000253 name: surface tension unit comment: "A unit which is a standard measure of the ability of a liguid to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces." [NIST:NIST] is_a: UO:0000000 ! unit [Term] id: UO:0000254 name: newton per meter comment: "A surface tension unit which is equal to one newton per meter." [NIST:NIST] is_a: UO:1000254 ! newton per meter based unit property_value: oboInOwl:hasExactSynonym "N/m" xsd:string property_value: oboInOwl:hasExactSynonym "newton per metre" xsd:string [Term] id: UO:0000255 name: dyne per cm comment: "A surface tension unit which is equal to one dyne per centimeter." [Wikipedia:Wikipedia] is_a: UO:1000255 ! dyne per cm based unit property_value: oboInOwl:hasExactSynonym "dyn/cm" xsd:string [Term] id: UO:0000256 name: viscosity unit comment: "A unit which is a standard measure of the internal resistance of fluids to flow." [UOC:GVG] is_a: UO:0000000 ! unit [Term] id: UO:0000257 name: pascal second comment: "A viscosity unit which is equal to one pascale per second." [NIST:NIST] is_a: UO:1000257 ! pascal second based unit property_value: oboInOwl:hasExactSynonym "Pa s" xsd:string [Term] id: UO:0000258 name: poise comment: "A viscosity unit which is equal to one dyne second per square centimeter." [Wikipedia:Wikipedia] is_a: UO:1000258 ! poise based unit property_value: oboInOwl:hasExactSynonym "dyne s/cm^2" xsd:string property_value: oboInOwl:hasExactSynonym "P" xsd:string [Term] id: UO:0000259 name: decibel comment: "A ratio unit which is an indicator of sound power per unit area." [techtarget:techtarget] is_a: UO:0000190 ! ratio property_value: oboInOwl:hasExactSynonym "dB" xsd:string [Term] id: UO:0000260 name: effective dose unit comment: "A unit which is a standard measure of the estimate of the stochastic effect that a non-uniform radiation dose has on a human." [Wikipedia:Wikipedia] is_a: UO:1000260 ! effective dose unit based unit [Term] id: UO:0000261 name: conduction unit comment: "A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG] is_a: UO:0000000 ! unit [Term] id: UO:0000262 name: electrical conduction unit comment: "A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG] is_a: UO:0000261 ! conduction unit [Term] id: UO:0000263 name: heat conduction unit comment: "A unit which represents a standard measurement of the spontaneous transfer of thermal energy through matter, from a region of higher temperature to a region of lower temperature." [Wikipedia:Wikipedia] is_a: UO:0000261 ! conduction unit [Term] id: UO:0000264 name: siemens comment: "An electrical conduction unit which is equal to A/V." [NIST:NIST] is_a: UO:1000264 ! siemens based unit property_value: oboInOwl:hasExactSynonym "A V^-1" xsd:string property_value: oboInOwl:hasExactSynonym "mho " xsd:string property_value: oboInOwl:hasRelatedSynonym "S" xsd:string [Term] id: UO:0000265 name: watt per meter kelvin comment: "An heat conduction unit which is equal to one watt divided by meter kelvin." [NIST:NIST] is_a: UO:1000265 ! watt per meter kelvin based unit property_value: oboInOwl:hasExactSynonym "W/m K" xsd:string property_value: oboInOwl:hasExactSynonym "watt per metre kelvin" xsd:string [Term] id: UO:0000266 name: electronvolt comment: "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia] is_a: UO:1000266 ! electronvolt based unit property_value: oboInOwl:hasExactSynonym "electron volt" xsd:string property_value: oboInOwl:hasExactSynonym "eV" xsd:string [Term] id: UO:0000267 name: electric field strength unit comment: "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\\://en.wikipedia.org/wiki/Electric_field] is_a: UO:0000000 ! unit property_value: oboInOwl:hasExactSynonym "E-field strength " xsd:string [Term] id: UO:0000268 name: volt per meter comment: "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\\://en.wikipedia.org/wiki/Electric_field] is_a: UO:1000268 ! volt per meter based unit property_value: oboInOwl:hasExactSynonym "V/m" xsd:string property_value: oboInOwl:hasExactSynonym "volt per metre" xsd:string [Term] id: UO:0000269 name: absorbance unit comment: "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\\://en.wikipedia.org/wiki/Absorbance] is_a: UO:1000269 ! absorbance unit based unit property_value: oboInOwl:hasExactSynonym "AU" xsd:string [Term] id: UO:0000270 name: volumetric flow rate unit comment: "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "volumetric flow rate unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000271 name: microliters per minute def: "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [] comment: "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG] is_a: UO:0000270 ! volumetric flow rate unit property_value: IAO:0000111 "microliters per minute" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "microlitres per minute" xsd:string property_value: oboInOwl:hasExactSynonym "uL/min" xsd:string [Term] id: UO:0000272 name: millimetres of mercury comment: "A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth." [url:en.wiktionary.org/wiki/mmHg] is_a: UO:0000109 ! pressure unit property_value: oboInOwl:hasExactSynonym "millimeters of mercury" xsd:string property_value: oboInOwl:hasExactSynonym "mmHg" xsd:string [Term] id: UO:0000273 name: milligram per liter comment: "A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG] is_a: UO:1000175 ! gram per liter based unit intersection_of: UO:1000175 ! gram per liter based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mg/L" xsd:string property_value: oboInOwl:hasExactSynonym "milligram per litre" xsd:string [Term] id: UO:0000274 name: microgram per milliliter comment: "A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG] is_a: UO:1000173 ! gram per milliliter based unit intersection_of: UO:1000173 ! gram per milliliter based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "microgram per millilitre" xsd:string property_value: oboInOwl:hasExactSynonym "ug/ml" xsd:string [Term] id: UO:0000275 name: nanogram per milliliter comment: "A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG] is_a: UO:1000173 ! gram per milliliter based unit intersection_of: UO:1000173 ! gram per milliliter based unit intersection_of: has:prefix UO:0000300 ! nano relationship: has:prefix UO:0000300 ! nano property_value: oboInOwl:hasExactSynonym "nanogram per millilitre" xsd:string property_value: oboInOwl:hasExactSynonym "ng/ml" xsd:string [Term] id: UO:0000279 name: milliunits per milliliter comment: "A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG] is_a: UO:0000177 ! unit per volume unit property_value: oboInOwl:hasExactSynonym "milliunits per millilitre" xsd:string property_value: oboInOwl:hasExactSynonym "mU/ml" xsd:string [Term] id: UO:0000280 name: rate unit comment: "A unit which represents a standard measurement occurrence of a process per unit time." [UOC:GVG] is_a: IAO:0000003 ! measurement unit label is_a: UO:0000000 ! unit property_value: IAO:0000111 "rate unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000281 name: count per nanomolar second def: "A rate unit which is equal to one over one nanomolar second." [] comment: "A rate unit which is equal to one over one nanomolar second." [UOC:GVG] is_a: UO:1000281 ! count per nanomolar second based unit property_value: IAO:0000111 "count per nanomolar second" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "nM^-1 s^-1" xsd:string [Term] id: UO:0000282 name: count per molar second def: "A rate unit which is equal to one over one molar second." [] comment: "A rate unit which is equal to one over one molar second." [UOC:GVG] is_a: UO:1000282 ! count per molar second based unit property_value: IAO:0000111 "count per molar second" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "M^-1 s^-1" xsd:string [Term] id: UO:0000283 name: kilogram per hectare comment: "An area density unit which is equal to the mass of an object in kilograms divided by the surface area in hectares." [UO:GVG] is_a: UO:0000054 ! area density unit [Term] id: UO:0000284 name: count per nanomolar def: "A rate unit which is equal to one over one nanomolar." [] comment: "A rate unit which is equal to one over one nanomolar." [UO:GVG] is_a: UO:1000284 ! count per nanomolar based unit property_value: IAO:0000111 "count per nanomolar" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "1/nM" xsd:string property_value: oboInOwl:hasExactSynonym "nM^-1" xsd:string [Term] id: UO:0000285 name: count per molar def: "A rate unit which is equal to one over one molar." [] comment: "A rate unit which is equal to one over one molar." [UO:GVG] is_a: UO:1000285 ! count per molar based unit property_value: IAO:0000111 "count per molar" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "1/M" xsd:string property_value: oboInOwl:hasExactSynonym "M^-1" xsd:string [Term] id: UO:0000292 name: giga comment: "A prefix in the metric system denoting a factor of ten to the power of 9." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[9]" xsd:string property_value: oboInOwl:hasExactSynonym "G" xsd:string [Term] id: UO:0000293 name: mega comment: "A prefix in the metric system denoting a factor of million." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[6]" xsd:string property_value: oboInOwl:hasExactSynonym "M" xsd:string [Term] id: UO:0000294 name: kilo comment: "A prefix in the metric system denoting a factor of one thousand." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[3]" xsd:string property_value: oboInOwl:hasExactSynonym "k" xsd:string [Term] id: UO:0000296 name: deci comment: "A prefix in the metric system denoting a factor of one tenth." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-1]" xsd:string property_value: oboInOwl:hasExactSynonym "d" xsd:string [Term] id: UO:0000297 name: milli comment: "A prefix in the metric system denoting a factor of one thousand." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-3]" xsd:string property_value: oboInOwl:hasExactSynonym "m" xsd:string [Term] id: UO:0000298 name: centi comment: "A prefix in the metric system denoting a factor of one hundred." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-2]" xsd:string property_value: oboInOwl:hasExactSynonym "c" xsd:string [Term] id: UO:0000299 name: micro comment: "A prefix in the metric system denoting a factor of 10 to the power of -6." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-6]" xsd:string [Term] id: UO:0000300 name: nano comment: "A prefix in the metric system denoting a factor of 10 to the power of -9." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-9]" xsd:string property_value: oboInOwl:hasExactSynonym "n" xsd:string [Term] id: UO:0000301 name: microgram per liter def: "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [] comment: "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG] is_a: UO:1000175 ! gram per liter based unit intersection_of: UO:1000175 ! gram per liter based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: IAO:0000111 "microgram per liter" xsd:string property_value: IAO:0000118 "ng/ml" xsd:string property_value: IAO:0000118 "ug/L" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: oboInOwl:hasExactSynonym "microgram per litre" xsd:string property_value: oboInOwl:hasExactSynonym "ug/L" xsd:string [Term] id: UO:0000302 name: pico comment: "A prefix in the metric system denoting a factor of 10 to the power of -12." [GVG:UO] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-12]" xsd:string property_value: oboInOwl:hasExactSynonym "n" xsd:string [Term] id: UO:0000303 name: femto comment: "A prefix in the metric system denoting a factor of 10 to the power of -15." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "10^[-15]" xsd:string property_value: oboInOwl:hasExactSynonym "f" xsd:string [Term] id: UO:0000304 name: atto comment: "A prefix in the metric system denoting a factor of 10 to the power of -18." [UO:GVG] is_a: UO:0000046 ! prefix property_value: oboInOwl:hasExactSynonym "a" xsd:string property_value: oboInOwl:hasRelatedSynonym "10^[-18]" xsd:string [Term] id: UO:0000307 name: dose unit comment: "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC] is_a: UO:0000051 ! concentration unit [Term] id: UO:0000308 name: milligram per kilogram comment: "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC] is_a: UO:0000307 ! dose unit [Term] id: UO:0000309 name: milligram per square meter comment: "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC] is_a: UO:0000307 ! dose unit is_a: UO:1010049 ! gram per square meter based unit intersection_of: UO:1010049 ! gram per square meter based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli [Term] id: UO:0000310 name: dosage unit comment: "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC] is_a: UO:1000310 ! dosage unit based unit [Term] id: UO:0000312 name: relative light unit comment: "A derived unit which is a measure of relative light intensity, as typically measured by a luminometer, spectrophotometer, or fluorimeter in biological research applications." [UO:PC] is_a: UO:1000312 ! relative light unit based unit [Term] id: UO:0000313 name: relative luminescence unit comment: "A relative light unit which is a measure of relative luminescence intensity." [UO:PC] is_a: UO:1000313 ! relative luminescence unit based unit [Term] id: UO:0000314 name: relative fluorescence unit comment: "A relative light unit which is a measure of relative fluorescence intensity." [UO:PC] is_a: UO:1000314 ! relative fluorescence unit based unit [Term] id: UO:0000325 name: megaHertz comment: "A frequency unit which is equal to one million hertz or 10^[6] V." [UOC:GVG] is_a: UO:0000105 ! frequency unit property_value: oboInOwl:hasRelatedSynonym "mH" xsd:string [Term] id: UO:0000326 name: centiMorgan comment: "A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] is_a: UO:0000001 ! length unit property_value: oboInOwl:hasExactSynonym "cM" xsd:string [Term] id: UO:0000327 name: centiRay comment: "A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] is_a: UO:0000001 ! length unit property_value: oboInOwl:hasExactSynonym "cR" xsd:string [Term] id: UO:0000329 name: mega base pair comment: "A unit equal to one million base pairs" [UOC:GVG] is_a: UO:1000244 ! base pair based unit intersection_of: UO:1000244 ! base pair based unit intersection_of: has:prefix UO:0000293 ! mega relationship: has:prefix UO:0000293 ! mega property_value: oboInOwl:hasExactSynonym "Mb" xsd:string property_value: oboInOwl:hasExactSynonym "megabasepair" xsd:string [Term] id: UO:0000330 name: giga base pair comment: "A unit equal to one billion base pairs." [UOC:GVG] is_a: UO:1000244 ! base pair based unit intersection_of: UO:1000244 ! base pair based unit intersection_of: has:prefix UO:0000292 ! giga relationship: has:prefix UO:0000292 ! giga property_value: oboInOwl:hasExactSynonym "Gb" xsd:string property_value: oboInOwl:hasExactSynonym "gigabasepair" xsd:string [Term] id: UO:0010001 name: square micrometer comment: "An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long." [NIST:NIST] is_a: UO:1010001 ! square micrometer based unit property_value: oboInOwl:hasExactSynonym "square micrometre" xsd:string [Term] id: UO:0010002 name: millisiemens comment: "An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST] is_a: UO:1000264 ! siemens based unit intersection_of: UO:1000264 ! siemens based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasRelatedSynonym "mS" xsd:string [Term] id: UO:0010003 name: micromole per litre comment: "A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST] is_a: UO:0000067 ! unit of molality [Term] id: UO:0010004 name: micromole per kilogram comment: "A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR] is_a: UO:0000067 ! unit of molality [Term] id: UO:0010005 name: millimeters per day comment: "A speed/velocity unit which is equal to the speed of an object traveling 1 millimeter distance in one day." [UOB:LKSR] is_a: UO:0000060 ! speed/velocity unit property_value: oboInOwl:hasExactSynonym "mm/day" xsd:string [Term] id: UO:0010008 name: kilometer per hour comment: "A speed/velocity unit which is equal to the speed of an object traveling 1 kilometer distance in one hour." [NIST:NIST] is_a: UO:0000060 ! speed/velocity unit property_value: oboInOwl:hasExactSynonym "kilometre per hour" xsd:string property_value: oboInOwl:hasExactSynonym "km/h" xsd:string [Term] id: UO:0010009 name: milli comment: "A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia] is_a: UO:0000002 ! mass unit property_value: oboInOwl:hasExactSynonym "mDa" xsd:string property_value: oboInOwl:hasExactSynonym "milli unified atomic mass unit" xsd:string property_value: oboInOwl:hasExactSynonym "millidalton" xsd:string property_value: oboInOwl:hasExactSynonym "mmu" xsd:string [Term] id: UO:0010010 name: hectare comment: "An area unit which is equal to an area of 10,000 square meters. Equivalent to 2.471 acres." [Wikipedia:Wikipedia] is_a: UO:1010010 ! hectare based unit property_value: oboInOwl:hasExactSynonym "HA" xsd:string [Term] id: UO:0010011 name: inch comment: "A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010011 ! inch based unit property_value: oboInOwl:hasExactSynonym "in" xsd:string [Term] id: UO:0010012 name: thou comment: "A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010012 ! thou based unit property_value: oboInOwl:hasExactSynonym "mil" xsd:string property_value: oboInOwl:hasExactSynonym "th" xsd:string [Term] id: UO:0010013 name: foot comment: "A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010013 ! foot based unit property_value: oboInOwl:hasExactSynonym "ft" xsd:string [Term] id: UO:0010014 name: yard comment: "A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010014 ! yard based unit property_value: oboInOwl:hasExactSynonym "yd" xsd:string [Term] id: UO:0010015 name: chain comment: "A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010015 ! chain based unit property_value: oboInOwl:hasExactSynonym "ch" xsd:string [Term] id: UO:0010016 name: furlong comment: "A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010016 ! furlong based unit property_value: oboInOwl:hasExactSynonym "fur" xsd:string [Term] id: UO:0010017 name: mile comment: "A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010017 ! mile based unit property_value: oboInOwl:hasExactSynonym "mi" xsd:string [Term] id: UO:0010018 name: league comment: "A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia] is_a: UO:0000045 ! base unit is_a: UO:1010018 ! league based unit property_value: oboInOwl:hasExactSynonym "lea" xsd:string [Term] id: UO:0010019 name: maritime length unit comment: "A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia] is_a: UO:1010019 ! maritime length unit based unit [Term] id: UO:0010020 name: fathom comment: "A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia] is_a: UO:1010020 ! fathom based unit property_value: oboInOwl:hasExactSynonym "ftm" xsd:string [Term] id: UO:0010021 name: cable comment: "A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia] is_a: UO:1010021 ! cable based unit [Term] id: UO:0010022 name: nautical mile comment: "A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia] is_a: UO:1010022 ! nautical mile based unit [Term] id: UO:0010023 name: perch comment: "An area unit which is equal to an area of 25.292,852,64 square meters, or 1 square rod." [Wikipedia:Wikipedia] is_a: UO:1010023 ! perch based unit [Term] id: UO:0010024 name: rood comment: "An area unit which is equivalent to 1 furlong x 1 rod. This is equal to an area of 1,011.714,1056 square meters, or 40 square rods." [Wikipedia:Wikipedia] is_a: UO:1010024 ! rood based unit [Term] id: UO:0010025 name: acre comment: "An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia] is_a: UO:1010025 ! acre based unit [Term] id: UO:0010026 name: fluid ounce comment: "An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia] is_a: UO:1010026 ! fluid ounce based unit property_value: oboInOwl:hasExactSynonym "fl oz" xsd:string [Term] id: UO:0010027 name: gill comment: "An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia] is_a: UO:1010027 ! gill based unit property_value: oboInOwl:hasExactSynonym "gi" xsd:string [Term] id: UO:0010028 name: pint comment: "An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia] is_a: UO:1010028 ! pint based unit property_value: oboInOwl:hasExactSynonym "pt" xsd:string [Term] id: UO:0010029 name: quart comment: "An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia] is_a: UO:1010029 ! quart based unit property_value: oboInOwl:hasExactSynonym "qt" xsd:string [Term] id: UO:0010030 name: gallon comment: "An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia] is_a: UO:1010030 ! gallon based unit property_value: oboInOwl:hasExactSynonym "gal" xsd:string [Term] id: UO:0010031 name: grain comment: "An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia] is_a: UO:1010031 ! grain based unit property_value: oboInOwl:hasExactSynonym "gr" xsd:string [Term] id: UO:0010032 name: drachm comment: "An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia] is_a: UO:1010032 ! drachm based unit property_value: oboInOwl:hasExactSynonym "dr" xsd:string [Term] id: UO:0010033 name: ounce comment: "An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia] is_a: UO:1010033 ! ounce based unit property_value: oboInOwl:hasExactSynonym "oz" xsd:string [Term] id: UO:0010034 name: pound comment: "An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia] is_a: UO:1010034 ! pound based unit property_value: oboInOwl:hasExactSynonym "lb" xsd:string [Term] id: UO:0010035 name: stone comment: "An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia] is_a: UO:1010035 ! stone based unit property_value: oboInOwl:hasExactSynonym "st" xsd:string [Term] id: UO:0010036 name: quarter comment: "An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia] is_a: UO:1010036 ! quarter based unit property_value: oboInOwl:hasExactSynonym "qr" xsd:string property_value: oboInOwl:hasExactSynonym "qtr" xsd:string [Term] id: UO:0010037 name: hundredweight comment: "An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia] is_a: UO:1010037 ! hundredweight based unit property_value: oboInOwl:hasExactSynonym "cwt" xsd:string [Term] id: UO:0010038 name: ton comment: "An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia] is_a: UO:1010038 ! ton based unit property_value: oboInOwl:hasExactSynonym "t" xsd:string [Term] id: UO:0010039 name: slug comment: "An imperial gravitational unit which is equivalent to a mass that accelerates by 1ft/s² when a force of one pound (lbf) is exerted on it." [Wikipedia:Wikipedia] is_a: UO:1010039 ! slug based unit [Term] id: UO:0010040 name: teaspoon comment: "A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon] is_a: UO:1010040 ! teaspoon based unit property_value: oboInOwl:hasExactSynonym "metric teaspoon" xsd:string property_value: oboInOwl:hasExactSynonym "tsp" xsd:string [Term] id: UO:0010048 name: micromole comment: "A substance unit which is equal to one millionth of a mole." [UOB:LTS] is_a: UO:1000013 ! mole based unit intersection_of: UO:1000013 ! mole based unit intersection_of: has:prefix UO:0000299 ! micro relationship: has:prefix UO:0000299 ! micro property_value: oboInOwl:hasExactSynonym "mmol" xsd:string [Term] id: UO:0010049 name: gram per square meter comment: "An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST] is_a: UO:1010049 ! gram per square meter based unit property_value: oboInOwl:hasExactSynonym "g/m^[2]" xsd:string property_value: oboInOwl:hasExactSynonym "gram per square metre" xsd:string [Term] id: UO:0010050 name: nanogram per microliter comment: "A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS] is_a: UO:0000052 ! mass density unit property_value: oboInOwl:hasExactSynonym "nanogram per microlitre" xsd:string property_value: oboInOwl:hasExactSynonym "ng/ul" xsd:string [Term] id: UO:0010051 name: large calorie comment: "A unit of energy widely used in nutrition, equivalent to the amount of heat needed to cause one kilogram of water to rise in temperature by one degree Celsius." [Wikipedia:Wikipedia] is_a: UO:1010051 ! large calorie based unit property_value: oboInOwl:hasExactSynonym "big calorie" xsd:string property_value: oboInOwl:hasExactSynonym "cal" xsd:string property_value: oboInOwl:hasExactSynonym "calorie" xsd:string property_value: oboInOwl:hasExactSynonym "food calorie" xsd:string property_value: oboInOwl:hasExactSynonym "kcal" xsd:string property_value: oboInOwl:hasExactSynonym "kilocalorie" xsd:string [Term] id: UO:0010053 name: micrograms per wheaton bottle comment: "A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS] is_a: UO:0000052 ! mass density unit property_value: oboInOwl:hasExactSynonym "micrograms per bottle" xsd:string [Term] id: UO:0010054 name: picoampere comment: "An electric current unit current which is equal to one trillionth of an ampere or 10^[-12] A." [UOB:LTS] is_a: UO:1000011 ! ampere based unit intersection_of: UO:1000011 ! ampere based unit intersection_of: has:prefix UO:0000302 ! pico relationship: has:prefix UO:0000302 ! pico property_value: oboInOwl:hasExactSynonym "pA" xsd:string [Term] id: UO:0010055 name: centigray comment: "An absorbed dose unit which is equal to 0.01 gray (Gy)" is_a: UO:1000134 ! gray based unit intersection_of: UO:1000134 ! gray based unit intersection_of: has:prefix UO:0000298 ! centi relationship: has:prefix UO:0000298 ! centi property_value: oboInOwl:hasExactSynonym "cGy" xsd:string [Term] id: UO:0010056 name: gigaelectronvolt comment: "A unit of energy that is equal to one thousand million electronvolts." is_a: UO:1000266 ! electronvolt based unit intersection_of: UO:1000266 ! electronvolt based unit intersection_of: has:prefix UO:0000292 ! giga relationship: has:prefix UO:0000292 ! giga property_value: oboInOwl:hasExactSynonym "GeV" xsd:string [Term] id: UO:0010057 name: gigaelectronvolt per nucleon comment: "Derived unit which is equal to the total kinetic energy of an atomic nucleus in GeV divided by the number of nucleons in the nucleus" is_a: UO:0000111 ! energy unit property_value: oboInOwl:hasExactSynonym "GeV/nucleon" xsd:string [Term] id: UO:0010058 name: megaelectronvolt per nucleon comment: "Derived unit which is equal to the total kinetic energy of an atomic nucleus in MeV divided by the number of nucleons in the nucleus" is_a: UO:0000111 ! energy unit property_value: oboInOwl:hasExactSynonym "MeV/nucleon" xsd:string [Term] id: UO:0010059 name: kiloelectronvolt per micron comment: "A derived unit equal to the energy deposited by ionizing radiation per micron of path length in matter" is_a: UO:0000111 ! energy unit property_value: oboInOwl:hasExactSynonym "keV/micron" xsd:string [Term] id: UO:0010060 name: gray per minute comment: "A derived absorbed dose unit which is equal to one gray absorbed per minute." is_a: UO:1010060 ! gray per minute based unit property_value: oboInOwl:hasExactSynonym "Gy/min" xsd:string [Term] id: UO:0010061 name: centigray per minute comment: "A derived absorbed dose unit which is equal to one centigray absorbed per minute." is_a: UO:1010060 ! gray per minute based unit intersection_of: UO:1010060 ! gray per minute based unit intersection_of: has:prefix UO:0000298 ! centi relationship: has:prefix UO:0000298 ! centi property_value: oboInOwl:hasExactSynonym "cGy/min" xsd:string [Term] id: UO:0010062 name: milligray per minute comment: "A derived absorbed dose unit which is equal to one milligray absorbed per minute." is_a: UO:1010060 ! gray per minute based unit intersection_of: UO:1010060 ! gray per minute based unit intersection_of: has:prefix UO:0000297 ! milli relationship: has:prefix UO:0000297 ! milli property_value: oboInOwl:hasExactSynonym "mGy/min" xsd:string [Term] id: UO:0010063 name: milligray per day comment: "A derived absorbed dose unit which is equal to one milligray absorbed per day." is_a: UO:0000129 ! absorbed dose unit property_value: oboInOwl:hasExactSynonym "mGy/min" xsd:string [Term] id: UO:1000008 name: meter based unit is_a: UO:0000001 ! length unit [Term] id: UO:1000010 name: second based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000011 name: ampere based unit is_a: UO:0000004 ! electric current unit [Term] id: UO:1000012 name: kelvin based unit is_a: UO:0000005 ! temperature unit [Term] id: UO:1000013 name: mole based unit is_a: UO:0000006 ! substance unit [Term] id: UO:1000014 name: candela based unit is_a: UO:0000007 ! luminous intensity unit [Term] id: UO:1000019 name: angstrom based unit is_a: UO:0000001 ! length unit [Term] id: UO:1000021 name: gram based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1000027 name: degree Celsius based unit is_a: UO:0000005 ! temperature unit [Term] id: UO:1000031 name: minute based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000032 name: hour based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000033 name: day based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000034 name: week based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000035 name: month based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000036 name: year based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000062 name: molar based unit is_a: UO:0000061 ! unit of molarity [Term] id: UO:1000068 name: molal based unit is_a: UO:0000067 ! unit of molality [Term] id: UO:1000075 name: normal based unit is_a: UO:0000074 ! unit of normality [Term] id: UO:1000076 name: mole fraction based unit is_a: UO:0000051 ! concentration unit is_a: UO:0000191 ! fraction [Term] id: UO:1000077 name: meter per second per second based unit is_a: UO:0000048 ! acceleration unit [Term] id: UO:1000078 name: radian per second per second based unit is_a: UO:0000050 ! angular acceleration unit [Term] id: UO:1000079 name: radian per second based unit is_a: UO:0000049 ! angular velocity unit [Term] id: UO:1000080 name: square meter based unit is_a: UO:0000047 ! area unit [Term] id: UO:1000081 name: square centimeter based unit is_a: UO:0000047 ! area unit [Term] id: UO:1000082 name: square millimeter based unit is_a: UO:0000047 ! area unit [Term] id: UO:1000084 name: gram per cubic centimeter based unit is_a: UO:0000052 ! mass density unit [Term] id: UO:1000085 name: candela per square meter based unit is_a: UO:0000053 ! luminance unit [Term] id: UO:1000088 name: gram per mole based unit is_a: UO:0000055 ! molar mass unit [Term] id: UO:1000089 name: cubic meter per mole based unit is_a: UO:0000056 ! molar volume unit [Term] id: UO:1000090 name: cubic centimeter per mole based unit is_a: UO:0000056 ! molar volume unit [Term] id: UO:1000092 name: turns per second based unit is_a: UO:0000058 ! rotational frequency unit [Term] id: UO:1000093 name: cubic meter per kilogram based unit is_a: UO:0000059 ! specific volume unit [Term] id: UO:1000094 name: meter per second based unit is_a: UO:0000060 ! speed/velocity unit [Term] id: UO:1000096 name: cubic meter based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1000097 name: cubic centimeter based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1000099 name: liter based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1000100 name: cubic decimeter based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1000106 name: hertz based unit is_a: UO:0000105 ! frequency unit [Term] id: UO:1000108 name: newton based unit is_a: UO:0000107 ! force unit [Term] id: UO:1000110 name: pascal based unit is_a: UO:0000109 ! pressure unit [Term] id: UO:1000112 name: joule based unit is_a: UO:0000111 ! energy unit [Term] id: UO:1000114 name: watt based unit is_a: UO:0000113 ! power unit [Term] id: UO:1000116 name: lux based unit is_a: UO:0000115 ! illuminance unit [Term] id: UO:1000118 name: lumen based unit is_a: UO:0000117 ! luminous flux unit [Term] id: UO:1000120 name: katal based unit is_a: UO:0000119 ! catalytic activity unit [Term] id: UO:1000123 name: radian based unit is_a: UO:0000122 ! plane angle unit [Term] id: UO:1000125 name: steradian based unit is_a: UO:0000124 ! solid angle unit [Term] id: UO:1000132 name: becquerel based unit is_a: UO:0000128 ! activity (of a radionuclide) unit [Term] id: UO:1000133 name: curie based unit is_a: UO:0000128 ! activity (of a radionuclide) unit [Term] id: UO:1000134 name: gray based unit is_a: UO:0000129 ! absorbed dose unit [Term] id: UO:1000135 name: rad based unit is_a: UO:0000129 ! absorbed dose unit [Term] id: UO:1000136 name: roentgen based unit is_a: UO:0000131 ! exposure unit [Term] id: UO:1000137 name: sievert based unit is_a: UO:0000130 ! dose equivalent unit [Term] id: UO:1000140 name: Roentgen equivalent man based unit is_a: UO:0000130 ! dose equivalent unit [Term] id: UO:1000147 name: disintegrations per minute based unit is_a: UO:0000128 ! activity (of a radionuclide) unit [Term] id: UO:1000148 name: counts per minute based unit is_a: UO:0000128 ! activity (of a radionuclide) unit [Term] id: UO:1000151 name: century based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000152 name: half life based unit is_a: UO:0000003 ! time unit [Term] id: UO:1000153 name: foot candle based unit is_a: UO:0000115 ! illuminance unit [Term] id: UO:1000155 name: watt per square meter based unit is_a: UO:0000154 ! irradiance unit [Term] id: UO:1000156 name: einstein per square meter per second based unit is_a: UO:0000154 ! irradiance unit [Term] id: UO:1000158 name: watt per steradian per square meter based unit is_a: UO:0000161 ! radiance unit [Term] id: UO:1000162 name: watt per steradian based unit is_a: UO:0000159 ! radiant intensity unit [Term] id: UO:1000163 name: mass percentage based unit is_a: UO:0000051 ! concentration unit is_a: UO:0000187 ! percent [Term] id: UO:1000164 name: mass volume percentage based unit is_a: UO:0000051 ! concentration unit is_a: UO:0000187 ! percent [Term] id: UO:1000165 name: volume percentage based unit is_a: UO:0000187 ! percent is_a: UO:0000205 ! volume per unit volume [Term] id: UO:1000167 name: parts per hundred based unit is_a: UO:0000166 ! parts per notation unit [Term] id: UO:1000168 name: parts per thousand based unit is_a: UO:0000166 ! parts per notation unit [Term] id: UO:1000169 name: parts per million based unit is_a: UO:0000166 ! parts per notation unit [Term] id: UO:1000170 name: parts per billion based unit is_a: UO:0000166 ! parts per notation unit [Term] id: UO:1000171 name: parts per trillion based unit is_a: UO:0000166 ! parts per notation unit [Term] id: UO:1000172 name: parts per quadrillion based unit is_a: UO:0000166 ! parts per notation unit [Term] id: UO:1000173 name: gram per milliliter based unit is_a: UO:0000052 ! mass density unit [Term] id: UO:1000175 name: gram per liter based unit is_a: UO:0000052 ! mass density unit [Term] id: UO:1000178 name: unit per milliliter based unit is_a: UO:0000177 ! unit per volume unit [Term] id: UO:1000179 name: unit per liter based unit is_a: UO:0000177 ! unit per volume unit [Term] id: UO:1000180 name: mass per unit volume based unit is_a: UO:0000051 ! concentration unit [Term] id: UO:1000181 name: enzyme unit based unit is_a: UO:0000119 ! catalytic activity unit [Term] id: UO:1000185 name: degree based unit is_a: UO:0000122 ! plane angle unit [Term] id: UO:1000188 name: pi based unit is_a: UO:0000186 ! dimensionless unit [Term] id: UO:1000192 name: molecule count based unit is_a: UO:0000189 ! count unit [Term] id: UO:1000193 name: purity percentage based unit is_a: UO:0000187 ! percent [Term] id: UO:1000194 name: confluence percentage based unit is_a: UO:0000187 ! percent [Term] id: UO:1000195 name: degree Fahrenheit based unit is_a: UO:0000005 ! temperature unit [Term] id: UO:1000196 name: pH based unit is_a: UO:0000051 ! concentration unit is_a: UO:0000186 ! dimensionless unit [Term] id: UO:1000197 name: liter per kilogram based unit is_a: UO:0000059 ! specific volume unit [Term] id: UO:1000201 name: cells per milliliter based unit is_a: UO:0000200 ! cell concentration unit [Term] id: UO:1000203 name: katal per cubic meter based unit is_a: UO:0000202 ! catalytic (activity) concentration unit [Term] id: UO:1000204 name: katal per liter based unit is_a: UO:0000202 ! catalytic (activity) concentration unit [Term] id: UO:1000208 name: gram per deciliter based unit is_a: UO:0000052 ! mass density unit [Term] id: UO:1000210 name: colony forming unit based unit is_a: UO:0000189 ! count unit [Term] id: UO:1000211 name: plaque forming unit based unit is_a: UO:0000189 ! count unit [Term] id: UO:1000213 name: colony forming unit per milliliter based unit is_a: UO:0000212 ! colony forming unit per volume [Term] id: UO:1000215 name: plaque forming unit per milliliter based unit is_a: UO:0000214 ! plaque forming unit per volume [Term] id: UO:1000216 name: disintegrations per second based unit is_a: UO:0000128 ! activity (of a radionuclide) unit [Term] id: UO:1000218 name: volt based unit is_a: UO:0000217 ! electric potential difference unit [Term] id: UO:1000220 name: coulomb based unit is_a: UO:0000219 ! electric charge [Term] id: UO:1000221 name: dalton based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1000223 name: watt-hour based unit is_a: UO:0000111 ! energy unit [Term] id: UO:1000226 name: weber based unit is_a: UO:0000225 ! magnetic flux unit [Term] id: UO:1000228 name: tesla based unit is_a: UO:0000227 ! magnetic flux density unit [Term] id: UO:1000229 name: volt-hour based unit is_a: UO:0000225 ! magnetic flux unit [Term] id: UO:1000232 name: bit based unit is_a: UO:0000231 ! information unit [Term] id: UO:1000233 name: byte based unit is_a: UO:0000231 ! information unit [Term] id: UO:1000237 name: chroma sampling unit based unit is_a: UO:0000236 ! image resolution unit [Term] id: UO:1000238 name: dynamic range unit based unit is_a: UO:0000236 ! image resolution unit [Term] id: UO:1000240 name: dots per inch based unit is_a: UO:0000239 ! spatial resolution unit [Term] id: UO:1000242 name: pixels per inch based unit is_a: UO:0000239 ! spatial resolution unit [Term] id: UO:1000243 name: pixels per millimeter based unit is_a: UO:0000239 ! spatial resolution unit [Term] id: UO:1000244 name: base pair based unit is_a: UO:0000189 ! count unit [Term] id: UO:1000245 name: kibibyte based unit is_a: UO:0000231 ! information unit [Term] id: UO:1000246 name: mebibyte based unit is_a: UO:0000231 ! information unit [Term] id: UO:1000254 name: newton per meter based unit is_a: UO:0000253 ! surface tension unit [Term] id: UO:1000255 name: dyne per cm based unit is_a: UO:0000253 ! surface tension unit [Term] id: UO:1000257 name: pascal second based unit is_a: UO:0000256 ! viscosity unit [Term] id: UO:1000258 name: poise based unit is_a: UO:0000256 ! viscosity unit [Term] id: UO:1000260 name: effective dose unit based unit is_a: UO:0000127 ! radiation unit [Term] id: UO:1000264 name: siemens based unit is_a: UO:0000262 ! electrical conduction unit [Term] id: UO:1000265 name: watt per meter kelvin based unit is_a: UO:0000263 ! heat conduction unit [Term] id: UO:1000266 name: electronvolt based unit is_a: UO:0000111 ! energy unit [Term] id: UO:1000268 name: volt per meter based unit is_a: UO:0000267 ! electric field strength unit [Term] id: UO:1000269 name: absorbance unit based unit is_a: UO:0000186 ! dimensionless unit [Term] id: UO:1000281 name: count per nanomolar second based unit is_a: UO:0000280 ! rate unit [Term] id: UO:1000282 name: count per molar second based unit is_a: UO:0000280 ! rate unit [Term] id: UO:1000284 name: count per nanomolar based unit is_a: UO:0000280 ! rate unit [Term] id: UO:1000285 name: count per molar based unit is_a: UO:0000280 ! rate unit [Term] id: UO:1000310 name: dosage unit based unit is_a: UO:0000051 ! concentration unit [Term] id: UO:1000312 name: relative light unit based unit is_a: UO:0000157 ! light unit [Term] id: UO:1000313 name: relative luminescence unit based unit is_a: UO:0000312 ! relative light unit [Term] id: UO:1000314 name: relative fluorescence unit based unit is_a: UO:0000312 ! relative light unit [Term] id: UO:1010001 name: square micrometer based unit is_a: UO:0000047 ! area unit [Term] id: UO:1010010 name: hectare based unit is_a: UO:0000047 ! area unit [Term] id: UO:1010011 name: inch based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010012 name: thou based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010013 name: foot based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010014 name: yard based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010015 name: chain based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010016 name: furlong based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010017 name: mile based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010018 name: league based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010019 name: maritime length unit based unit is_a: UO:0000001 ! length unit [Term] id: UO:1010020 name: fathom based unit is_a: UO:0010019 ! maritime length unit [Term] id: UO:1010021 name: cable based unit is_a: UO:0010019 ! maritime length unit [Term] id: UO:1010022 name: nautical mile based unit is_a: UO:0010019 ! maritime length unit [Term] id: UO:1010023 name: perch based unit is_a: UO:0000047 ! area unit [Term] id: UO:1010024 name: rood based unit is_a: UO:0000047 ! area unit [Term] id: UO:1010025 name: acre based unit is_a: UO:0000047 ! area unit [Term] id: UO:1010026 name: fluid ounce based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1010027 name: gill based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1010028 name: pint based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1010029 name: quart based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1010030 name: gallon based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1010031 name: grain based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010032 name: drachm based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010033 name: ounce based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010034 name: pound based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010035 name: stone based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010036 name: quarter based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010037 name: hundredweight based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010038 name: ton based unit is_a: UO:0000002 ! mass unit [Term] id: UO:1010039 name: slug based unit is_a: UO:0000111 ! energy unit [Term] id: UO:1010040 name: teaspoon based unit is_a: UO:0000095 ! volume unit [Term] id: UO:1010049 name: gram per square meter based unit is_a: UO:0000054 ! area density unit [Term] id: UO:1010051 name: large calorie based unit is_a: UO:0000111 ! energy unit [Term] id: UO:1010060 name: gray per minute based unit is_a: UO:0000129 ! absorbed dose unit [Typedef] id: BFO:0000054 name: realized in comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process property_value: example_of_usage "this disease is realized in this disease course" xsd:string property_value: example_of_usage "this fragility is realized in this shattering" xsd:string property_value: example_of_usage "this investigator role is realized in this investigation" xsd:string property_value: IAO:0000111 "realized in" xsd:string property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process inverse_of: BFO:0000055 ! realizes [Typedef] id: BFO:0000055 name: realizes comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process property_value: example_of_usage "this disease course realizes this disease" xsd:string property_value: example_of_usage "this investigation realizes this investigator role" xsd:string property_value: example_of_usage "this shattering realizes this fragility" xsd:string property_value: IAO:0000111 "realizes" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity [Typedef] id: BFO:0000057 name: has participant [Typedef] id: COB:0000023 name: characteristic of inverse_of: COB:0000512 ! has characteristic [Typedef] id: COB:0000030 name: quality of inverse_of: COB:0000041 ! has quality [Typedef] id: COB:0000041 name: has quality comment: Note: this will end up being a subproperty of has-characteristic when we add it, TBD depends on discussion of whether has-characteristic is functional range: COB:0000001 ! quality [Typedef] id: COB:0000047 name: has part inverse_of: COB:0000072 ! part of [Typedef] id: COB:0000072 name: part of is_transitive: true [Typedef] id: COB:0000512 name: has characteristic property_value: seeAlso https://github.com/oborel/obo-relations/pull/284 xsd:string range: COB:0000502 ! characteristic is_inverse_functional: true [Typedef] id: ENVO:01001307 name: partially_surrounded_by def: "x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x" [] comment: Definition modified from 'surrounded by'. property_value: example_of_usage "A duck swimming in a pond is partially surrounded by air and partially surrounded by water." xsd:string [Typedef] id: IAO:0000039 name: has measurement unit label range: IAO:0000003 ! measurement unit label is_functional: true is_a: has_part ! has_part [Typedef] id: IAO:0000136 name: is about def: "A (currently) primitive relation that relates an information artifact to an entity." [] property_value: editor_note "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \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: example_of_usage "This document is about information artifacts and their representations" xsd:string property_value: IAO:0000114 IAO:0000125 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:0000221 name: is quality measurement of def: "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q" [] property_value: editor_note "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later" xsd:string property_value: editor_note "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]\n\nThis one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details.\n--\nFrom the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]\n\nunit of measure is a quality, e.g. the length of a ruler.\n\n[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]\n\n[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]\n\na represents b means either a denotes b or a describes\n\ndescribe:\na describes b means a is about b and a allows an inference of at least one quality of b\n\nWe have had a long discussion about denotes versus describes." xsd:string property_value: editor_note "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.\n\na is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality." xsd:string property_value: editor_note "From the second meeting on IAO:\n\nAn attempt at defining assay using Barry's \"reliability\" wording\n\nassay:\nprocess and has_input some material entity\nand has_output some information content entity \nand which is such that instances of this process type reliably generate \noutputs that describes the input." xsd:string property_value: editor_note "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string domain: IAO:0000109 ! measurement datum range: BFO:0000019 ! quality is_a: IAO:0000136 ! is about inverse_of: IAO:0000417 ! is quality measured as [Typedef] id: IAO:0000417 name: is quality measured as def: "inverse of the relation of is quality measurement of" [] property_value: editor_note "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Typedef] id: OBI:0000124 name: is_supported_by_data def: "The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process" [] property_value: example_of_usage "The relation between the conclusion \"Gene tpbA is involved in EPS production\" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. " xsd:string property_value: IAO:0000111 "is_supported_by_data" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "OBI" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000119 "Philly 2011 workshop" xsd:string domain: OBI:0001909 ! conclusion based on data range: IAO:0000027 ! data item [Typedef] id: OBI:0000293 name: has_specified_input def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] property_value: editor_note "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string property_value: example_of_usage "see is_input_of example_of_usage" xsd:string property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000111 "has_specified_input" 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 Coutot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000295 ! is_specified_input_of [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] property_value: example_of_usage "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string property_value: IAO:0000111 "is_specified_input_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 range: OBI:0000011 ! planned process is_a: participates_in ! participates in [Typedef] id: OBI:0000299 name: has_specified_output 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 "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 inverse_of: OBI:0000312 ! is_specified_output_of [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: participates_in ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] property_value: example_of_usage "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string property_value: IAO:0000111 "achieves_planned_objective" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "BP, AR, PPPB branch" xsd:string property_value: IAO:0000119 "PPPB branch derived" xsd:string property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string domain: OBI:0000011 ! planned process range: IAO:0000005 ! objective specification inverse_of: OBI:0000833 ! objective_achieved_by [Typedef] id: OBI:0000833 name: objective_achieved_by def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] property_value: IAO:0000111 "objective_achieved_by" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "OBI" xsd:string property_value: IAO:0000119 "OBI" xsd:string domain: IAO:0000005 ! objective specification range: OBI:0000011 ! planned process [Typedef] id: OBI:0001938 name: has value specification def: "A relation between an information content entity and a value specification that specifies its value." [] property_value: IAO:0000111 "has value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string property_value: IAO:0000119 "OBI" xsd:string domain: IAO:0000030 ! information content entity range: OBI:0001933 ! value specification is_a: has_part ! has_part [Typedef] id: RO:0000052 name: characteristic of name: inheres in 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." [] def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] 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: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string property_value: example_of_usage "this fragility inheres in this vase" xsd:string property_value: example_of_usage "this fragility is a characteristic of this vase" xsd:string property_value: example_of_usage "this red color inheres in this apple" xsd:string property_value: example_of_usage "this red color is a characteristic of this apple" xsd:string property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! inheres in part of inverse_of: bearer_of ! bearer of [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: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: example_of_usage "this blood coagulation has participant this blood clot" xsd:string property_value: example_of_usage "this investigation has participant this investigator" xsd:string property_value: example_of_usage "this process has participant this input material (or this output material)" xsd:string 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:0000118 "has_participant" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: has_part RO:0000057 [Typedef] id: RO:0000058 name: is concretized as def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] property_value: example_of_usage "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: example_of_usage "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant range: BFO:0000020 ! specifically dependent continuant inverse_of: RO:0000059 ! concretizes [Typedef] id: RO:0000059 name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: example_of_usage "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: example_of_usage "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000020 ! specifically dependent continuant range: BFO:0000031 ! generically dependent continuant [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: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: example_of_usage "this catalysis function is a function of this enzyme" 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 ! inheres in 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: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: example_of_usage "this red color is a quality of this apple" xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! inheres in inverse_of: has_quality ! 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: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: example_of_usage "this investigator role is a role of this person" xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! inheres in 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: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: example_of_usage "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: bearer_of ! bearer of [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: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: example_of_usage "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: bearer_of ! bearer of [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: bearer_of ! bearer of 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 ! inheres in [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: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string property_value: example_of_usage "this cell derives from this parent cell (cell division)" xsd:string property_value: example_of_usage "this nucleus derives from this parent nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 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 [Typedef] id: RO:0001018 name: contained in domain: BFO:0000040 ! material entity range: BFO:0000004 ! independent continuant holds_over_chain: located_in part_of inverse_of: contains ! contains [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: has_component ! 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"} property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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:0002084 name: during which ends comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: RO:0002222 ! temporally related to [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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_transitive: true is_a: RO:0002222 ! temporally related to [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:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! 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: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] is_a: develops_into ! develops_into [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: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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent [Typedef] id: RO:0002231 name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in is_a: RO:0002479 ! has part that occurs in [Typedef] id: RO:0002232 name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in is_a: RO:0002479 ! has part that occurs in [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:0000118 "consumes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000015 ! process holds_over_chain: starts_with RO:0002233 is_a: RO:0000057 ! has participant inverse_of: input_of ! input of [Typedef] id: RO:0002234 name: has output def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] 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:0000118 "produces" xsd:string holds_over_chain: ends_with RO:0002234 is_a: RO:0000057 ! has participant inverse_of: output_of ! output of [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce [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: example_of_usage "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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: example_of_usage "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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 "Chris Mungall" xsd:string is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by [Typedef] id: RO:0002303 name: has habitat def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. subset: ro-eco property_value: example_of_usage "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 name: inheres in 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." [] def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string 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 "defining-property-chains-involving-reflexivity" 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:0002321 name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: editor_note "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [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: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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 "Chris Mungall" xsd:string 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 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: example_of_usage "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: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 property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: capable_of ! capable_of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has_part transitive_over: RO:0002017 ! has component activity [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: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: participates_in ! 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: functionally_related_to ! functionally related to is_a: RO:0000057 ! has participant [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:0000589 "regulated by (processual)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002354 name: formed as result of property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: output_of ! output of [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: part_of ! part_of [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] is_a: overlaps ! overlaps [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 "Chris Mungall" xsd:string domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] is_a: RO:0002384 ! has developmental potential involving [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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: preceded_by ! 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: immediately_preceded_by ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002410 name: causally related to def: "This relation groups causal relations between material entities and causal relations between processes" [] property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\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:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl [Typedef] id: RO:0002411 name: causally upstream of def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_transitive: true is_a: precedes ! 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 both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] synonym: "affects" RELATED [] property_value: editor_note "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:0000118 "influences (processual)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates 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: editor_note "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: functionally_related_to ! functionally related to is_a: RO:0002264 ! acts upstream of or within 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] holds_over_chain: RO:0002327 occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps [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: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI 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:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso ECO:0000353 property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI is_symmetric: true is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates property_value: editor_note "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 "Vasundra Touré" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 "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 "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: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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl [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." [] domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: has_part occurs_in {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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage domain: BFO:0000004 ! independent continuant [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))" [] is_a: RO:0002487 ! relation between physical entity and a process or stage [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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco property_value: editor_note "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string property_value: example_of_usage "A coral reef environment is determined by a particular coral reef" xsd:string property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string is_a: part_of ! part_of is_a: RO:0002509 ! determined by part of is_a: RO:0002559 ! causally influenced by [Typedef] id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: overlaps ! overlaps is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002559 name: causally influenced by property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 "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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure is_a: functionally_related_to ! functionally related to [Typedef] id: RO:0002578 name: directly regulates def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] 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:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0002575 RO:0002211 is_a: regulates ! 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: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: has_part capable_of is_a: functionally_related_to ! 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: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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: example_of_usage "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl holds_over_chain: capable_of regulates 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl holds_over_chain: capable_of negatively_regulates 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: example_of_usage "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl holds_over_chain: capable_of positively_regulates 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002629 name: directly positively regulates def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] 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: positively_regulates ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] 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: negatively_regulates ! negatively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0004028 name: realized in response to stimulus def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] domain: BFO:0000017 ! realizable entity range: BFO:0000040 ! material entity holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to created_by: cjm creation_date: 2017-12-26T19:45:49Z [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: functionally_related_to ! functionally related to created_by: cjm 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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 creation_date: 2018-01-26T23:53:22Z [Typedef] id: RO:0004046 name: causally upstream of or within, negative effect property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002418 is_a: RO:0002418 ! causally upstream of or within created_by: cjm creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002418 is_a: RO:0002418 ! causally upstream of or within created_by: cjm creation_date: 2018-03-13T23:55:19Z [Typedef] id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [RO:cjm] property_value: example_of_usage "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: example_of_usage "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: example_of_usage "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to [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 "Vasundra Touré" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences [Typedef] id: adjacent_to name: adjacent to name: adjacent_to namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] def: "x adjacent_to y iff: 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: editor_note "This relation acts as a join point with BSPO" xsd:string property_value: example_of_usage "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: example_of_usage "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: example_of_usage "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: example_of_usage "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:0000117 "Chris Mungall" xsd:string 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 name: anterior_to namespace: uberon 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] 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 bisects an organism from head end to opposite end of body or tail: bearer" [http://orcid.org/0000-0002-6601-2165] xref: BSPO:0000096 is_transitive: true inverse_of: posterior_to ! posterior to created_by: cjm creation_date: 2009-07-31T02:15:46Z [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: connected_to ! connected to is_a: posterior_to ! posterior to [Typedef] id: attaches_to name: attached to name: attaches_to namespace: uberon def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] xref: RO:0002371 property_value: seeAlso FMA:85990 is_symmetric: true is_a: attaches_to_part_of ! attached to part of is_a: connected_to ! connected to is_a: connects ! connects [Typedef] id: attaches_to_part_of name: attached to part of name: attaches_to_part_of namespace: uberon def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure holds_over_chain: attaches_to part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002567 ! biomechanically related to equivalent_to_chain: attaches_to part_of ! part_of [Typedef] id: bearer_of name: bearer of name: has characteristic namespace: uberon def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] def: "Inverse of characteristic_of" [] xref: RO:0000053 property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string property_value: example_of_usage "this apple is bearer of this red color" xsd:string property_value: example_of_usage "this vase is bearer of this fragility" xsd:string property_value: IAO:0000111 "bearer of" 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: boundary_of name: 2D boundary of namespace: uberon def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 inverse_of: has_boundary ! has 2D boundary [Typedef] id: bounding_layer_of name: bounding layer of namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string range: BFO:0000040 ! material entity is_a: part_of ! part_of [Typedef] id: branching_part_of name: branching part of name: branching_part_of namespace: uberon def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] xref: RO:0002380 property_value: editor_note "we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve" xsd:string property_value: seeAlso FMA:85994 is_a: part_of ! part_of is_a: RO:0002375 ! in branching relationship with inverse_of: has_branching_part ! has branching part [Typedef] id: capable_of name: capable of name: capable_of namespace: protein namespace: uberon 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 xref: RO:0002215 property_value: example_of_usage "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: example_of_usage "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_transitive: false is_a: capable_of_part_of ! capable of part of is_a: functionally_related_to ! functionally related to [Typedef] id: capable_of_part_of name: capable of part of namespace: uberon 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." [] xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso "defining-property-chains-involving-reflexivity" property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: functionally_related_to ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] domain: UBERON:0004111 ! anatomical conduit range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon is_transitive: true [Typedef] id: composed_primarily_of name: composed primarily of namespace: uberon def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] def: "x composed_primarily_of y iff: more than half of the mass of x is made from parts of y" [] subset: ro-eco xref: RO:0002473 property_value: example_of_usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: has_part ! has_part [Typedef] id: conduit_for name: conduit for namespace: uberon def: "x is a conduit for y iff y passes through the lumen of x." [] [Typedef] id: connected_to name: connected to namespace: uberon def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] def: "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] comment: Connection does not imply overlaps. xref: RO:0002170 property_value: seeAlso SIO:000652 [Typedef] id: connects name: connects namespace: uberon def: "Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] xref: RO:0002176 property_value: editor_note "this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)" xsd:string domain: BFO:0000004 ! independent continuant [Typedef] id: contains name: contains namespace: uberon xref: RO:0001019 [Typedef] id: contains_process name: contains process namespace: uberon 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 xref: BFO:0000067 property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Typedef] id: continuous_with name: continuous with name: continuous_with namespace: uberon def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] xref: RO:0002150 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_symmetric: true [Typedef] id: contributes_to_morphology_of name: contributes to morphology of namespace: uberon def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] xref: RO:0002433 is_a: overlaps ! overlaps [Typedef] id: dc-creator name: Creator name: creator namespace: uberon comment: An entity primarily responsible for making the content \n of the resource. xref: http://purl.org/dc/elements/1.1/creator property_value: dc-description "Examples of a Creator include a person, an organisation,\n or a service. Typically, the name of a Creator should \n be used to indicate the entity." xsd:string property_value: isDefinedBy http://purl.org/dc/elements/1.1/ is_metadata_tag: true [Typedef] id: dc-description name: Description name: description namespace: uberon comment: An account of the content of the resource. xref: http://purl.org/dc/elements/1.1/description property_value: dc-description "Description may include but is not limited to: an abstract,\n table of contents, reference to a graphical representation\n of content or a free-text account of the content." xsd:string property_value: isDefinedBy http://purl.org/dc/elements/1.1/ is_metadata_tag: true [Typedef] id: dc-title name: Title name: title namespace: uberon comment: A name given to the resource. xref: http://purl.org/dc/elements/1.1/title property_value: dc-description "\n Typically, a Title will be a name by which the resource is\n formally known.\n " xsd:string property_value: isDefinedBy http://purl.org/dc/elements/1.1/ is_metadata_tag: true [Typedef] id: dcterms-license name: license namespace: uberon xref: http://purl.org/dc/terms/license property_value: http://purl.org/dc/elements/1.1/date 2018-05-11T13:47:29Z xsd:dateTime property_value: IAO:0000117 "Mark Miller" xsd:string is_metadata_tag: true [Typedef] id: deep_to name: deep to name: deep_to namespace: uberon 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: developmentally_contributes_to name: developmentally contributes to namespace: uberon def: "inverse of has developmental contribution from" [] subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: develops_into part_of is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to is_a: RO:0002286 ! developmentally succeeded by [Typedef] id: developmentally_induced_by name: developmentally induced by name: developmentally_induced_by namespace: uberon def: "t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T." [GO:0001759] def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T" [] comment: sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) xref: RO:0002256 domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces [Typedef] id: developmentally_preceded_by name: developmentally preceded by namespace: uberon 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 xref: RO:0002258 property_value: editor_note "false" xsd:boolean property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string 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: developmentally_replaces name: developmentally replaces name: developmentally_replaces namespace: uberon def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] xref: RO:0002285 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_from name: develops from name: develops_from namespace: uberon 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 xref: RO:0002202 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 "Melissa Haendel" xsd:string property_value: IAO:0000117 "Terry Meehan" xsd:string property_value: IAO:0000117 "Terry Meehan" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant holds_over_chain: part_of develops_from is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops_into transitive_over: part_of ! part_of [Typedef] id: develops_from_part_of name: develops from part of namespace: uberon def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] xref: RO:0002225 holds_over_chain: directly_develops_from part_of is_a: develops_from ! develops from [Typedef] id: develops_in name: develops in namespace: uberon def: "x develops_in y if x is located in y whilst x is developing" [] comment: This relation take from EHDAA2 - precise semantics yet to be defined xref: RO:0002226 domain: CARO:0000000 ! anatomical entity holds_over_chain: directly_develops_from located_in is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into name: develops_into namespace: uberon def: "inverse of develops from" [] subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 "Terry Meehan" xsd:string is_transitive: true is_a: has_potential_to_develop_into ! has potential to develop into is_a: has_potential_to_directly_develop_into ! has potential to directly develop into is_a: RO:0002286 ! developmentally succeeded by [Typedef] id: directly_develops_from name: directly develops from namespace: uberon def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] xref: RO:0002207 is_a: develops_from ! develops from inverse_of: RO:0002210 ! directly develops into [Typedef] id: distally_connected_to name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: connected_to ! connected to inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: dorsal_to name: dorsal to name: dorsal_to namespace: uberon 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] 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly)." [http://orcid.org/0000-0002-6601-2165] xref: BSPO:0000098 is_transitive: true inverse_of: ventral_to ! ventral_to [Typedef] id: drains name: drains namespace: uberon def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] comment: source: Wikipedia synonym: "drains blood from" EXACT [] synonym: "drains from" EXACT [] xref: RO:0002179 domain: UBERON:0001638 ! vein is_a: connected_to ! connected to [Typedef] id: editor_note name: editor note namespace: uberon xref: IAO:0000116 property_value: IAO:0000114 IAO:0000122 is_metadata_tag: true [Typedef] id: ends name: ends namespace: uberon def: "inverse of ends with" [] def: "Relation between occurrents, shares an end boundary with." [Allen:starts, https://orcid.org/0000-0002-6601-2165, ZFS:finishes] subset: ro-eco synonym: "finishes" EXACT [] xref: RO:0002229 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: part_of ! part_of is_a: RO:0002222 ! temporally related to inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] xref: RO:0002230 is_transitive: true is_a: has_part ! has_part [Typedef] id: example_of_usage name: example of usage namespace: uberon def: "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." [] xref: IAO:0000112 property_value: IAO:0000111 "example" xsd:string property_value: IAO:0000111 "example of usage" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl is_metadata_tag: true [Typedef] id: existence_ends_during name: existence ends during namespace: uberon def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] synonym: "ceases_to_exist_during" EXACT [] xref: RO:0002492 is_a: existence_ends_during_or_before ! existence ends during or before is_a: RO:0002490 ! existence overlaps transitive_over: part_of ! part_of [Typedef] id: existence_ends_during_or_before name: existence ends during or before namespace: uberon 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." [] xref: RO:0002497 holds_over_chain: part_of existence_ends_during_or_before holds_over_chain: RO:0002286 existence_ends_during_or_before is_a: RO:0002487 ! relation between physical entity and a process or stage transitive_over: part_of ! part_of transitive_over: precedes ! precedes transitive_over: simultaneous_with ! simultaneous with [Typedef] id: existence_ends_with name: existence ends with namespace: uberon def: "Relation between continuant and occurrent, such that c ceases to exist at the end of p." [https://orcid.org/0000-0002-6601-2165] def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] xref: RO:0002493 is_a: existence_ends_during ! existence ends during [Typedef] id: existence_starts_and_ends_during name: existence starts and ends during namespace: uberon def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] xref: RO:0002491 is_a: existence_ends_during ! existence ends during is_a: existence_starts_during ! existence starts during [Typedef] id: existence_starts_during name: existence starts during namespace: uberon def: "Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s." [https://orcid.org/0000-0002-6601-2165] def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] synonym: "begins_to_exist_during" EXACT [] xref: RO:0002488 is_a: existence_starts_during_or_after ! existence starts during or after is_a: RO:0002490 ! existence overlaps transitive_over: part_of ! part_of [Typedef] id: existence_starts_during_or_after name: existence starts during or after namespace: uberon 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)." [] xref: RO:0002496 holds_over_chain: developmentally_preceded_by existence_starts_during_or_after holds_over_chain: part_of existence_starts_during_or_after is_a: RO:0002487 ! relation between physical entity and a process or stage transitive_over: part_of ! part_of transitive_over: preceded_by ! preceded_by transitive_over: simultaneous_with ! simultaneous with [Typedef] id: existence_starts_with name: existence starts with namespace: uberon def: "Relation between continuant and occurrent, such that c comes into existence at the start of p." [https://orcid.org/0000-0002-6601-2165] def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] xref: RO:0002489 is_a: existence_starts_during ! existence starts during [Typedef] id: filtered_through name: filtered through namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed [Typedef] id: functionally_related_to name: functionally related to namespace: uberon def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl [Typedef] id: has_boundary name: has 2D boundary name: has boundary namespace: uberon def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity [Typedef] id: has_branching_part name: has branching part namespace: uberon def: "inverse of branching part of" [] xref: RO:0002569 is_transitive: true is_a: RO:0002375 ! in branching relationship with [Typedef] id: has_component name: has component name: has_component namespace: uberon 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 xref: RO:0002180 property_value: editor_note "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:0000114 IAO:0000125 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: has_developmental_contribution_from name: has developmental contribution from namespace: uberon def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] xref: RO:0002254 property_value: example_of_usage "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 "Chris Mungall" xsd:string domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity holds_over_chain: has_part develops_from is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to [Typedef] id: has_member name: has member namespace: uberon def: "has member is a mereological relation between a collection and an item." [] xref: RO:0002351 property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: has_part ! has_part [Typedef] id: has_muscle_insertion name: has muscle insertion namespace: uberon def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [Wikipedia:Insertion_(anatomy)] comment: The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles xref: RO:0002373 property_value: seeAlso dbpprop:insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure is_a: attaches_to ! attaches_to is_a: RO:0002567 ! biomechanically related to [Typedef] id: has_part name: has part name: has_part namespace: chebi_ontology namespace: external namespace: protein namespace: quality namespace: uberon def: "a core relation that holds between a whole and its part" [] def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [] comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. 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: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\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: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\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: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_cyclic: false is_transitive: true is_a: overlaps ! overlaps [Typedef] id: has_potential_to_develop_into name: has potential to develop into namespace: uberon def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] xref: RO:0002387 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002384 ! has developmental potential involving [Typedef] id: has_potential_to_developmentally_contribute_to name: has potential to developmentally contribute to namespace: uberon def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] xref: RO:0002385 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002384 ! has developmental potential involving [Typedef] id: has_potential_to_directly_develop_into name: has potential to directly develop into namespace: uberon def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] xref: RO:0002388 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: has_potential_to_develop_into ! has potential to develop into [Typedef] id: has_quality name: has quality namespace: uberon def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] xref: RO:0000086 property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: example_of_usage "this apple has quality this red color" xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: bearer_of ! bearer of [Typedef] id: has_skeleton name: has skeleton namespace: uberon def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] def: "A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision." [http://orcid.org/0000-0002-6601-2165] synonym: "has sekeletal support" RELATED [] synonym: "has supporting framework" RELATED [] xref: RO:0002551 domain: CARO:0000003 ! connected anatomical structure domain: UBERON:0000475 ! organism subdivision range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity range: UBERON:0010912 ! subdivision of skeleton is_a: has_part ! has_part inverse_of: skeleton_of ! skeleton of is_asymmetric: true [Typedef] id: immediate_transformation_of name: immediate transformation of namespace: uberon def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] synonym: "direct_transformation_of" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "immediately transforms from" EXACT [SIO:000658] xref: RO:0002495 property_value: seeAlso SIO:000658 is_a: directly_develops_from ! directly develops from is_a: transformation_of ! transformation of [Typedef] id: immediately_deep_to name: immediately deep to name: immediately_deep_to namespace: uberon def: "This relation holds when both the deep_to and ajdacent_to relationship similarly hold." [http://orcid.org/0000-0002-6601-2165] def: "x immediately deep to y iff x deep_to y and x is contiguous with y." [BSPO:curators] xref: BSPO:0001107 is_a: adjacent_to ! adjacent_to is_a: deep_to ! deep to inverse_of: immediately_superficial_to ! immediately superficial to [Typedef] id: immediately_preceded_by name: immediately preceded by name: immediately_preceded_by namespace: uberon def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" [] comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) synonym: "directly preceded by" EXACT [] synonym: "is directly preceded by" EXACT [] synonym: "is immediately preceded by" EXACT [SIO:000251] synonym: "starts_at_end_of" EXACT [] xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso SIO:000251 property_value: UBPROP:0000001 "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string {source="SIO:000251"} holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded_by inverse_of: RO:0002090 ! immediately precedes [Typedef] id: immediately_superficial_to name: immediately superficial to name: immediately_superficial_to namespace: uberon def: "x immediately superficial to y iff x superficial to y and x is contiguous with y." [BSPO:curators] xref: BSPO:0015014 is_a: adjacent_to ! adjacent_to is_a: superficial_to ! superficial_to [Typedef] id: in_anterior_side_of name: in anterior side of name: in_anterior_side_of namespace: uberon def: "X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion." [BSPO:PATO_mtg_2009] def: "X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion." [BSPO:PATO_mtg_2009] xref: BSPO:0000123 is_a: part_of ! part_of [Typedef] id: in_distal_side_of name: in distal side of name: in_distal_side_of namespace: uberon def: "X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion." [BSPO:PATO_mtg_2009] def: "x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion." [BSPO:PATO_mtg_2009] xref: BSPO:0000125 is_a: part_of ! part_of [Typedef] id: in_lateral_side_of name: in lateral side of name: in_lateral_side_of namespace: uberon 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] 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" [https://orcid.org/0000-0002-6601-2165] xref: BSPO:0000126 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 name: in_left_side_of namespace: uberon 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] def: "X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion." [BSPO:PATO_mtg_2009] 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 inverse_of: in_right_side_of ! in_right_side_of [Typedef] id: in_posterior_side_of name: in posterior side of name: in_posterior_side_of namespace: uberon def: "X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion." [BSPO:PATO_mtg_2009] def: "X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion." [BSPO:PATO_mtg_2009] xref: BSPO:0000122 is_a: part_of ! part_of [Typedef] id: in_proximal_side_of name: in proximal side of name: in_proximal_side_of namespace: uberon def: "x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion." [BSPO:PATO_mtg_2009] def: "X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion." [BSPO:PATO_mtg_2009] xref: BSPO:0000124 is_a: part_of ! part_of inverse_of: in_distal_side_of ! in distal side of [Typedef] id: in_right_side_of name: in right side of name: in_right_side_of namespace: uberon 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] def: "X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion." [BSPO:PATO_mtg_2009] 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: in_taxon name: in taxon namespace: uberon def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] xref: RO:0002162 holds_over_chain: attaches_to in_taxon holds_over_chain: capable_of in_taxon holds_over_chain: connected_to in_taxon holds_over_chain: connects in_taxon holds_over_chain: continuous_with in_taxon holds_over_chain: developmentally_induced_by in_taxon holds_over_chain: develops_from in_taxon holds_over_chain: develops_from_part_of in_taxon holds_over_chain: existence_ends_during in_taxon holds_over_chain: existence_starts_during in_taxon holds_over_chain: has_developmental_contribution_from in_taxon holds_over_chain: has_part in_taxon holds_over_chain: has_potential_to_develop_into in_taxon holds_over_chain: overlaps in_taxon holds_over_chain: part_of in_taxon holds_over_chain: produced_by in_taxon holds_over_chain: produces in_taxon holds_over_chain: supplies in_taxon [Typedef] id: input_of name: input of namespace: uberon def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in [Typedef] id: located_in name: located in name: located_in namespace: uberon def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0001025 property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: example_of_usage "my brain is located in my head" xsd:string property_value: example_of_usage "this rat is located in this cage" xsd:string property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: part_of ! part_of [Typedef] id: location_of name: location of name: location_of namespace: uberon def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] xref: RO:0001015 is_transitive: true inverse_of: located_in ! located in [Typedef] id: lumen_of name: lumen of namespace: uberon 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." [] xref: RO:0002571 range: BFO:0000040 ! material entity is_a: part_of ! part_of [Typedef] id: luminal_space_of name: luminal space of namespace: uberon def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] xref: RO:0002572 domain: BFO:0000141 ! immaterial entity is_a: lumen_of ! lumen of is_a: part_of ! part_of [Typedef] id: member_of name: member of namespace: uberon def: "is member of is a mereological relation between a item and a collection." [] xref: RO:0002350 property_value: example_of_usage "An organism that is a member of a population of organisms" xsd:string property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: part_of ! part_of inverse_of: has_member ! has member [Typedef] id: negatively_regulates name: negatively regulates namespace: external def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] 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:0002212 property_value: IAO:0000117 "Chris Mungall" xsd:string 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: regulates ! regulates is_a: RO:0002305 ! causally upstream of, negative effect inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: occurs_in 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 xref: BFO:0000066 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 occurs_in inverse_of: contains_process ! contains process transitive_over: part_of ! part_of [Typedef] id: only_in_taxon name: only in taxon namespace: uberon def: "S only_in_taxon T iff: S SubClassOf in_taxon only T" [PMID:20973947] def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] xref: RO:0002160 is_a: in_taxon ! in taxon [Typedef] id: output_of name: output of namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in [Typedef] id: overlaps name: overlaps namespace: uberon def: "A overlaps B if they share some part in common." [] 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] 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl 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_a: RO:0002323 ! mereotopologically related to transitive_over: part_of ! part_of expand_expression_to: "BFO_0000051 some (BFO_0000050 some ?Y)" [] 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: protein namespace: quality 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: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\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: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\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: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000118 "part_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: part_of_structure_that_is_capable_of name: part of structure that is capable of namespace: uberon def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] xref: RO:0002329 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: functionally_related_to ! functionally related to [Typedef] id: participates_in name: participates in name: participates_in namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 property_value: example_of_usage "this blood clot participates in this blood coagulation" xsd:string property_value: example_of_usage "this input material (or this output material) participates in this process" xsd:string property_value: example_of_usage "this investigator participates in this investigation" xsd:string property_value: IAO:0000111 "participates in" xsd:string property_value: IAO:0000118 "participates_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant [Typedef] id: positively_regulates name: positively regulates namespace: external def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] 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:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string 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: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true is_a: regulates ! regulates is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by [Typedef] id: posterior_to name: posterior to name: posterior_to namespace: uberon 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] 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 bisects an organism from head end to opposite end of body or tail." [http://orcid.org/0000-0002-6601-2165] synonym: "caudal_to" NARROW [] xref: BSPO:0000099 is_transitive: true [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: anterior_to ! anterior_to is_a: connected_to ! connected to [Typedef] id: preceded_by name: preceded by name: preceded_by namespace: uberon 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." [] def: "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)" [] subset: ro-eco synonym: "is preceded by" EXACT [SIO:000249] synonym: "takes place after" EXACT [Allen:precedes] xref: BFO:0000062 property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string 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:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by is_transitive: true is_a: RO:0002086 ! ends after inverse_of: precedes ! precedes [Typedef] id: precedes name: precedes namespace: uberon 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 xref: BFO:0000063 property_value: IAO:0000111 "precedes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to [Typedef] id: produced_by name: produced by name: produced_by namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] xref: RO:0003001 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: produces name: produces namespace: uberon 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." [] xref: RO:0003000 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced_by [Typedef] id: protects name: protects namespace: uberon [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: connected_to ! connected to [Typedef] id: proximalmost_part_of name: proximalmost part of name: proximalmost_part_of namespace: uberon def: "X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y" [https://orcid.org/0000-0002-6601-2165] def: "X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y" [https://orcid.org/0000-0002-6601-2165] xref: BSPO:0001106 is_a: in_proximal_side_of ! in_proximal_side_of [Typedef] id: regulates name: regulates namespace: external def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] 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:0002211 property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string 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 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: ends_with regulates 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: results_in_developmental_progression_of name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso Ontology:extensions is_a: RO:0002324 ! developmentally related to [Typedef] id: results_in_formation_of name: results in formation of 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: example_of_usage "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: example_of_usage "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of is_a: RO:0002234 ! has output [Typedef] id: simultaneous_with name: simultaneous with namespace: uberon def: "Relation between occurrents, shares start and end boundaries." [Allen:is_equal_to, https://orcid.org/0000-0002-6601-2165] synonym: "coincides_with" EXACT [] synonym: "is_equal_to" EXACT [] xref: RO:0002082 is_transitive: true is_a: ends ! ends is_a: starts ! starts [Typedef] id: site_of name: site_of namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part" [] synonym: "capable_of_has_part" RELATED [] [Typedef] id: skeleton_of name: skeleton of namespace: uberon def: "inverse of has skeleton" [] xref: RO:0002576 domain: CARO:0000003 ! connected anatomical structure range: CARO:0000003 ! connected anatomical structure is_a: part_of ! part_of [Typedef] id: starts name: starts namespace: uberon def: "inverse of starts with" [] def: "Relation between occurrents, shares a start boundary with." [Allen:starts, https://orcid.org/0000-0002-6601-2165] xref: RO:0002223 is_a: part_of ! part_of inverse_of: starts_with ! starts with [Typedef] id: starts_with name: starts with namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] xref: RO:0002224 is_transitive: true is_a: has_part ! has_part [Typedef] id: subdivision_of name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B [Typedef] id: superficial_to name: superficial to name: superficial_to namespace: uberon 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: supplies name: supplies namespace: uberon def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] def: "relation between an artery and the structure is supplies with blood." [] comment: source: FMA synonym: "arterial supply of" EXACT [FMA:86003] xref: RO:0002178 property_value: seeAlso FMA:86003 domain: UBERON:0001637 ! artery is_a: connected_to ! connected to [Typedef] id: surrounded_by name: surrounded by name: surrounded_by namespace: uberon def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] def: "x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y" [https://orcid.org/0000-0002-6601-2165] xref: RO:0002219 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0001900 RO:0001901 is_a: adjacent_to ! adjacent_to inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds namespace: uberon def: "inverse of surrounded by" [] def: "inverse of surrounded_by" [https://orcid.org/0000-0002-6601-2165] xref: RO:0002221 is_a: adjacent_to ! adjacent_to [Typedef] id: synapsed_by name: synapsed by namespace: uberon def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it." [] [Typedef] id: transformation_of name: transformation of namespace: uberon def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] synonym: "transforms from" EXACT [SIO:000657] xref: RO:0002494 property_value: seeAlso SIO:000657 is_transitive: true is_a: develops_from ! develops from [Typedef] id: tributary_of name: tributary of name: tributary_of namespace: uberon def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] synonym: "drains into" RELATED [dbpowl:drainsTo] xref: RO:0002376 is_a: RO:0002375 ! in branching relationship with [Typedef] id: ventral_to name: ventral to name: ventral_to namespace: uberon 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] 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly)." [http://orcid.org/0000-0002-6601-2165] xref: BSPO:0000102 is_transitive: true