format-version: 1.2 data-version: releases/2024-04-19 subsetdef: abnormal_slim "" subsetdef: absent_slim "" subsetdef: Angiosperm "" subsetdef: Arabidopsis "" subsetdef: attribute_slim "" subsetdef: cell_quality "" subsetdef: Citrus "" subsetdef: CL "" subsetdef: disposition_slim "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" subsetdef: goslim_drosophila "" subsetdef: goslim_flybase_ribbon "" subsetdef: goslim_generic "" subsetdef: goslim_metagenomics "" subsetdef: goslim_mouse "" subsetdef: goslim_pir "" subsetdef: goslim_plant "" subsetdef: goslim_pombe "" subsetdef: goslim_prokaryote "" subsetdef: goslim_yeast "" subsetdef: Gymnosperms "" 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: Maize "" subsetdef: mpath_slim "" subsetdef: Musa "" subsetdef: Poaceae "" subsetdef: Potato "" subsetdef: Pteridophytes "" subsetdef: reference "" subsetdef: relational_slim "" subsetdef: Rice "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: Tomato "" subsetdef: TraitNet "" subsetdef: value_slim "" synonymtypedef: blast_name "" synonymtypedef: common_name "" synonymtypedef: equivalent_name "" synonymtypedef: genbank_common_name "" synonymtypedef: German "" synonymtypedef: in_part "" synonymtypedef: Japanese "" synonymtypedef: OMO:0003003 "" synonymtypedef: OMO:0003004 "" synonymtypedef: Spanish "" synonymtypedef: synonym "" ontology: gallont property_value: http://purl.org/dc/terms/description "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "Plant Gall Ontology" xsd:string property_value: owl:versionInfo "2024-04-19" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {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." [] disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 {all_only="true"} ! continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity relationship: part_of BFO:0000003 {all_only="true"} ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {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 {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 {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 {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 {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 {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: "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])" [] comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! characteristic relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant [Term] id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "t-region" xsd:string property_value: BFO:0000180 "TemporalRegion" xsd:string property_value: IAO:0000116 "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} property_value: IAO:0000600 "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process 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])" [] comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent relationship: part_of BFO:0000015 {all_only="true"} ! process [Term] id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role [Term] id: BFO:0000017 name: realizable 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 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! characteristic relationship: part_of BFO:0000019 {all_only="true"} ! quality [Term] id: BFO:0000020 name: characteristic name: specifically dependent continuant 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])" [] comment: 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. is_a: BFO:0000002 ! continuant relationship: has_part BFO:0000020 {all_only="true"} ! characteristic relationship: part_of BFO:0000020 {all_only="true"} ! 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: 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 [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition [Term] id: BFO:0000038 name: one-dimensional temporal region is_a: BFO:0000008 ! temporal region property_value: BFO:0000179 "1d-t-region" xsd:string property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string property_value: IAO:0000116 "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." xsd:string property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} 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 [Term] id: CARO:0000005 name: anatomical space 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." [] [Term] id: CARO:0000030 name: asexual organism is_a: OBI:0100026 ! organism [Term] id: CARO:0000048 name: gonochoristic organism is_a: OBI:0100026 ! organism [Term] id: ENVO:03000096 name: season is_a: BFO:0000038 ! one-dimensional temporal region [Term] id: FLOPO:0900042 name: succulent def: "A gall trait in which the gall parenchyma is juicy, as in the tissue of some fruits (for example grapes, starfruit)." [] is_a: GALLONT:0000007 ! internal quality property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/2011488555 property_value: seeAlso https://www.inaturalist.org/observations/81385187 [Term] id: GALLONT:0000001 name: DEPRECATED plant gall comment: Updated the class definition to reflect that this structure is a response to biotic stress property_value: seeAlso GALLONT:0000025 is_obsolete: true [Term] id: GALLONT:0000002 name: emergence hole def: "An anatomical space that is an opening through which a gall-inhabiting organism has emerged." [] is_a: PO:0025117 ! plant anatomical space property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-19T19:43:46Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33275700 [Term] id: GALLONT:0000003 name: plant gall cavity def: "A plant anatomical space that is located inside a gall." [] is_a: PO:0025117 ! plant anatomical space property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-19T19:44:42Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/117192961 [Term] id: GALLONT:0000004 name: kapéllo def: "A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall" [] is_a: PO:0025496 ! multi-tissue plant structure relationship: part_of GALLONT:0000025 ! plant gall property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-22T01:51:19Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/61878883 [Term] id: GALLONT:0000005 name: larval chamber def: "A gall structure wherein the gall inducer and/or its associates resides and which includes a portion of nutritive tissue." [] is_a: PO:0025498 ! cardinal part of multi-tissue plant structure relationship: has_part GALLONT:0000040 ! nutritive tissue relationship: has_part GALLONT:0000041 ! larval cavity property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-22T01:54:05Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/139401882 [Term] id: GALLONT:0000006 name: detached chamber def: "A larval chamber that is detached from the plant but enclosed in a cavity." [] is_a: GALLONT:0000005 ! larval chamber property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-22T02:01:48Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/117192961 [Term] id: GALLONT:0000007 name: internal quality def: "A quality that inheres in the portion of a gall that is internal." [] is_a: PATO:0000051 ! morphology property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-23T21:16:13Z" xsd:string [Term] id: GALLONT:0000008 name: filamentous def: "A gall trait in which a larval chamber is suspended medially in the parenchyma by radiating plant fibers inside a largely hollow chamber." [] is_a: GALLONT:0000007 ! internal quality property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-24T01:32:39Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/168120575 [Term] id: GALLONT:0000009 name: monothalamous def: "An internal gall trait in which a gall has a single larval chamber for the gall-inducing insect." [] is_a: GALLONT:0000007 ! internal quality disjoint_from: GALLONT:0000011 ! polythalamous property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-24T01:37:35Z" xsd:string property_value: IAO:0000118 "single chambered" xsd:string property_value: IAO:0000118 "unilocular" xsd:string [Term] id: GALLONT:0000010 name: pithy def: "An internal gall trait in which the tissue is reminiscent of pith, the relatively soft tissue at the center of a shoot axis." [] is_a: GALLONT:0000007 ! internal quality property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-24T01:41:48Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/138512674 [Term] id: GALLONT:0000011 name: polythalamous def: "An internal gall trait in which more than one larval chamber is present for the inducer species." [] is_a: GALLONT:0000007 ! internal quality property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-24T01:44:34Z" xsd:string property_value: IAO:0000118 "multi-celled" xsd:string property_value: IAO:0000118 "multichambered" xsd:string property_value: IAO:0000118 "multilocular" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33275700 [Term] id: GALLONT:0000012 name: solid def: "An internal gall trait in which the gall lacks macroscopic anatomical space(s) that is/are not the larval chamber." [] is_a: GALLONT:0000007 ! internal quality disjoint_from: PATO:0002078 ! hollow property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-24T01:58:04Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/138512674 [Term] id: GALLONT:0000013 name: nectarous def: "A gall quality in which a gall has nectaries present." [] is_a: PATO:0000051 ! morphology property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-24T02:13:52Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/47182384 [Term] id: GALLONT:0000014 name: caneliform def: "A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling a canelé, a French pastry." [] is_a: PATO:0002266 ! 3-D shape property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T00:21:14Z" xsd:string property_value: http://purl.org/dc/terms/source https://en.wikipedia.org/w/index.php?title=Canel%C3%A9&oldid=1160295465 [Term] id: GALLONT:0000015 name: cupuliform def: "A shape inhering in a bearer by virtue of the bearer resembling a cup, with a depression and rim-like edge apically." [] is_a: PATO:0002266 ! 3-D shape property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T00:30:40Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/2011488555 property_value: IAO:0000118 "cup-like" xsd:string [Term] id: GALLONT:0000016 name: echinoform def: "A shape trait in which a gall has radiating, spine-like processes that resemble the spines of a sea urchin (cf. Cidaridae)." [] is_a: PATO:0002266 ! 3-D shape property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T00:38:13Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/8139 [Term] id: GALLONT:0000017 name: infundibuliform def: "A shape quality inhering in a bearer by virtue of the bearer being shaped like a funnel, abruptly widening from a narrow cylindrical part, to a wider distal part." [] is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T00:47:37Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/2011488555 property_value: seeAlso https://www.inaturalist.org/observations/105016514 [Term] id: GALLONT:0000018 name: lenticular def: "A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lentil, with convex upper and lower surfaces." [] is_a: PATO:0001865 ! spheroid property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T00:52:58Z" xsd:string property_value: http://purl.org/dc/terms/source lenticular property_value: seeAlso https://www.inaturalist.org/observations/30408125 property_value: seeAlso PATO:0000409 [Term] id: GALLONT:0000019 name: semiterete def: "A shape quality inhering in a bearer by virtue of the bearer's appearing semicircular in cross-section, flat on one side, rounded on the other." [] is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T02:03:26Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/2011488555 [Term] id: GALLONT:0000020 name: confluent def: "A spatial pattern (or gall arrangement) in which adjacent objects (galls) are positioned in such a way that each gall cannot readily be distinguished as an individual." [] is_a: PATO:0000060 ! spatial pattern property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T19:44:11Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/48455940 [Term] id: GALLONT:0000021 name: linear color gradient def: "A color pattern inhering in a bearer by virtue of bearer's being marked with one hue or degree of saturation near one pole and a different hue or degree of saturation at the opposite pole and a color gradient between the two poles." [] is_a: PATO:0001533 ! multi-colored property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-25T20:11:58Z" xsd:string [Term] id: GALLONT:0000022 name: corrugated def: "A texture quality in which the surface is marked by alternating parallel ridges and grooves." [] is_a: PATO:0000150 ! texture disjoint_from: PATO:0002442 ! unornamented property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T21:21:38Z" xsd:string property_value: http://purl.org/dc/terms/source PORO:0000234 property_value: IAO:0000118 "ribbed" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/46514828 [Term] id: GALLONT:0000023 name: crackled def: "A texture quality in which the surface is marked by a network of cracks, as in craquelure." [] is_a: PATO:0000700 ! rough property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T21:25:58Z" xsd:string property_value: http://purl.org/dc/terms/source https://en.wikipedia.org/w/index.php?title=Craquelure&oldid=1117468584 property_value: seeAlso https://www.inaturalist.org/observations/61507036 [Term] id: GALLONT:0000024 name: dimpled def: "A surface feature shape in which a surface has a dimple, a depression or indentation on a surface." [] is_a: PATO:0001925 ! surface feature shape disjoint_from: PATO:0002442 ! unornamented property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T21:30:22Z" xsd:string property_value: http://purl.org/dc/terms/source https://dictionary.cambridge.org/us/dictionary/english/dimpled property_value: seeAlso https://www.inaturalist.org/observations/47442195 [Term] id: GALLONT:0000025 name: plant gall def: "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." [] is_a: PO:0025496 ! multi-tissue plant structure property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-24T21:38:29Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/62135900 [Term] id: GALLONT:0000026 name: faceted def: "A texture quality in which a surface is covered or partially by with facets." [] is_a: PATO:0000150 ! texture property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T21:35:23Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33275277 [Term] id: GALLONT:0000027 name: moss-like def: "A texture quality in which a surface has the appearance and/or consistency of moss, especially those species in Polytrichaceae (Bryophyta)." [] is_a: PATO:0000150 ! texture disjoint_from: PATO:0000701 ! smooth disjoint_from: PATO:0002442 ! unornamented property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T21:41:40Z" xsd:string property_value: IAO:0000118 "mossy" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/134718736 [Term] id: GALLONT:0000028 name: papery def: "A texture quality in which a surface has the consistency and thickness of a paper bag (thin and dry)." [] is_a: PATO:0000150 ! texture property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T21:48:32Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/62933356 [Term] id: GALLONT:0000029 name: felt-like def: "A quality inhering in a bearer by virtue of the bearer's being covered in short, dense, fine hairs, which give the appearance of felt." [] is_a: PATO:0000454 ! hairy property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-26T22:01:09Z" xsd:string property_value: IAO:0000118 "felted" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/54851258 [Term] id: GALLONT:0000030 name: pruinose def: "A coating quality in which a surface is covered in a whitish, powdery film or dust." [] is_a: PATO:0002012 ! coating disjoint_from: PATO:0002442 ! unornamented property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-27T00:31:53Z" xsd:string property_value: http://purl.org/dc/terms/source https://en.wikipedia.org/w/index.php?title=Pruinescence&oldid=1068715610 property_value: seeAlso https://www.inaturalist.org/observations/64626028 [Term] id: GALLONT:0000031 name: semideciduous def: "A shedability quality in which a part can readily be detached from its location but it normally (in nature) stays attached; detachable." [] is_a: PATO:0001729 ! shedability property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-27T01:16:14Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/167537899 [Term] id: GALLONT:0000032 name: brittle def: "A structural quality inhering in an object by virtue of the object's susceptibility to breaks, without significant deformation (strain) when subjected to stress." [] is_a: PATO:0001543 ! flexibility property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-06-27T01:41:01Z" xsd:string [Term] id: GALLONT:0000033 name: DEPRECATED erineum comment: logic needed to be fixed property_value: seeAlso GALLONT:0000048 is_obsolete: true [Term] id: GALLONT:0000034 name: blister gall def: "A plant gall that is part of a leaf and which appears as a portion of swollen tissue, similar to a blister." [] is_a: GALLONT:0000025 ! plant gall relationship: part_of PO:0025034 ! leaf property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T22:15:28Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 [Term] id: GALLONT:0000035 name: bud gall def: "A plant gall that is located on a bud." [] is_a: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000025 ! plant gall intersection_of: part_of PO:0000055 ! bud relationship: part_of PO:0000055 ! bud property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T22:23:57Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: seeAlso https://www.inaturalist.org/observations/48455720 [Term] id: GALLONT:0000036 name: bullet gall def: "A plant gall that is monothalamous and solid, with a shape reminiscent of a bullet. Gall is usually subspherical or subelliptical in shape." [] is_a: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000025 ! plant gall intersection_of: RO:0000086 GALLONT:0000009 ! has quality monothalamous intersection_of: RO:0000086 GALLONT:0000012 ! has quality solid intersection_of: RO:0000086 GALLONT:0000031 ! has quality semideciduous intersection_of: RO:0000086 PATO:0001865 ! has quality spheroid relationship: RO:0000086 GALLONT:0000009 ! has quality monothalamous relationship: RO:0000086 GALLONT:0000012 ! has quality solid relationship: RO:0000086 GALLONT:0000031 ! has quality semideciduous relationship: RO:0000086 PATO:0001865 ! has quality spheroid property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T22:28:40Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: seeAlso https://www.inaturalist.org/observations/58434690 [Term] id: GALLONT:0000037 name: roly-poly gall def: "A plant gall that has a detached larval chamber capable of rolling around a hollow chamber located inside the gall." [] is_a: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000025 ! plant gall intersection_of: has_part GALLONT:0000006 ! detached chamber intersection_of: RO:0000086 PATO:0002078 ! has quality hollow relationship: has_part GALLONT:0000006 ! detached chamber relationship: RO:0000086 PATO:0002078 ! has quality hollow property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-02T01:35:34Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: seeAlso https://www.inaturalist.org/observations/117192961 [Term] id: GALLONT:0000038 name: rosette gall def: "A plant gall that is located on a bud and which consists of layers of scale leaves or similar phyllomes that surround the inducer's chamber." [] is_a: GALLONT:0000035 ! bud gall is_a: UBERON:0001062 ! anatomical entity relationship: has_part PO:0006001 ! phyllome property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-02T01:43:13Z" xsd:string property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: IAO:0000118 "bunch gall" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33495996 [Term] id: GALLONT:0000039 name: Acraspis erinacei (agamic) is_a: CARO:0000030 ! asexual organism is_a: NCBITaxon:2714064 ! Acraspis erinacei property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:00Z" xsd:dateTime [Term] id: GALLONT:0000040 name: nutritive tissue comment: A portion of plant tissue that is fed upon by a gall inhabitant. is_a: PO:0009007 ! portion of plant tissue relationship: part_of GALLONT:0000005 ! larval chamber property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-19T02:22:00Z" xsd:string property_value: seeAlso https://doi.org/10.3390%2Finsects12100850 [Term] id: GALLONT:0000041 name: larval cavity def: "A cavity that is occupied by one or more gall inhabitants." [] is_a: GALLONT:0000003 ! plant gall cavity property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-19T02:27:40Z" xsd:string [Term] id: GALLONT:0000042 name: Quercus sect. Quercus is_a: NCBITaxon:3511 ! Quercus property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T01:26:41Z" xsd:string [Term] id: GALLONT:0000043 name: Disholcaspis quercusglobulus (sexgen) is_a: CARO:0000048 ! gonochoristic organism is_a: NCBITaxon:1540852 ! Disholcaspis quercusglobulus property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:09Z" xsd:string [Term] id: GALLONT:0000044 name: Disholcaspis quercusglobulus (agamic) is_a: CARO:0000030 ! asexual organism is_a: NCBITaxon:1540852 ! Disholcaspis quercusglobulus property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:48Z" xsd:string [Term] id: GALLONT:0000045 name: Acraspis erinacei (sexgen) is_a: CARO:0000048 ! gonochoristic organism is_a: NCBITaxon:2714064 ! Acraspis erinacei property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:17Z" xsd:dateTime [Term] id: GALLONT:0000046 name: Aceria triplacis is_a: NCBITaxon:109362 ! Aceria property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTime [Term] id: GALLONT:0000047 name: Acraspis gemula is_a: NCBITaxon:1934078 ! Acraspis property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTime [Term] id: GALLONT:0000048 name: erineum def: "A plant gall that is induced by mites (Acariformes) on leaves and which consists of an area of leaf epidermis that has increased hairiness." [] is_a: GALLONT:0000050 ! zoocecidium is_a: UBERON:0001062 ! anatomical entity intersection_of: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000059 NCBITaxon:6946 ! induced by Acariformes intersection_of: has_part PO:0006504 ! leaf trichome relationship: GALLONT:0000059 NCBITaxon:6946 ! induced by Acariformes relationship: has_part PO:0006504 ! leaf trichome property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T21:56:59Z" xsd:string [Term] id: GALLONT:0000049 name: plant gall aggregate name: plant gall cluster def: "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." [] is_a: PO:0025496 ! multi-tissue plant structure relationship: has_part GALLONT:0000025 ! plant gall property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-04-11T14:32:57Z" xsd:dateTime [Term] id: GALLONT:0000050 name: zoocecidium def: "A plant gall that is induced by an animal" [] is_a: GALLONT:0000025 ! plant gall is_a: OBI:0100026 ! organism intersection_of: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000059 NCBITaxon:33208 ! induced by Metazoa relationship: GALLONT:0000059 NCBITaxon:33208 ! induced by Metazoa property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-04-15T13:33:50Z" xsd:dateTime property_value: http://purl.org/dc/terms/source 978-94-017-6230-4:9 [Term] id: GALLONT:0000051 name: plant gall abscission zone def: "An abscission zone (PO:0000146) that is part of a plant gall." [] is_a: PO:0000146 ! abscission zone property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-04-18T13:34:27Z" xsd:dateTime property_value: seeAlso https://www.inaturalist.org/observations/129032167 [Term] id: GALLONT:0000053 name: plant gall dehiscence zone def: "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." [] is_a: PO:0025092 ! dehiscence zone property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-04-18T14:16:58Z" xsd:dateTime property_value: seeAlso https://www.inaturalist.org/observations/179039203 [Term] id: GO:0003674 name: gene product or complex activity name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. comment: This is the same as GO molecular function subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "molecular function" EXACT [] is_a: BFO:0000015 ! process disjoint_from: GO:0008150 ! biological process [Term] id: GO:0003824 name: catalytic activity namespace: molecular_function def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] subset: goslim_agr subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] xref: Wikipedia:Enzyme is_a: GO:0003674 ! molecular_function [Term] id: GO:0008150 name: biological process name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended 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. comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process relationship: has_part GO:0003674 ! molecular_function property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0016301 name: kinase activity namespace: molecular_function def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. subset: goslim_chembl subset: goslim_drosophila subset: goslim_metagenomics subset: goslim_plant subset: goslim_yeast synonym: "phosphokinase activity" EXACT [] xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups [Term] id: GO:0016740 name: transferase activity namespace: molecular_function def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast xref: EC:2.-.-.- xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK" xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248" is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016772 name: transferase activity, transferring phosphorus-containing groups namespace: molecular_function def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. subset: goslim_chembl xref: EC:2.7.-.- is_a: GO:0016740 ! transferase activity [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." [] property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 "GROUP:OBI:" xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: NCBITaxon:1 name: root namespace: ncbi_taxonomy synonym: "all" RELATED synonym [] xref: GC_ID:1 xref: PMID:30365038 xref: PMID:32761142 is_a: OBI:0100026 ! organism [Term] id: NCBITaxon:109362 name: Aceria is_a: NCBITaxon:70320 ! Eriophyidae [Term] id: NCBITaxon:1206794 name: Ecdysozoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33317 ! Protostomia property_value: has_rank NCBITaxon:clade [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:1389465 name: Disholcaspis is_a: NCBITaxon:75144 ! Cynipini [Term] id: NCBITaxon:1540852 name: Disholcaspis quercusglobulus is_a: NCBITaxon:1389465 ! Disholcaspis [Term] id: NCBITaxon:1934078 name: Acraspis is_a: NCBITaxon:75144 ! Cynipini [Term] id: NCBITaxon:197562 name: Pancrustacea namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:10874751 xref: PMID:11557979 is_a: NCBITaxon:197563 ! Mandibulata property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:197563 name: Mandibulata namespace: ncbi_taxonomy synonym: "mandibulates" EXACT OMO:0003003 [] xref: GC_ID:1 xref: PMID:11557979 xref: PMID:9727836 is_a: NCBITaxon:6656 ! Arthropoda property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:2714064 name: Acraspis erinacei is_a: NCBITaxon:1934078 ! Acraspis [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 OMO:0003003 [] 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 property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" EXACT OMO:0003003 [] synonym: "green plants" RELATED blast_name [] xref: GC_ID:1 xref: PMID:16248873 xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom [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 property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 name: Metazoa namespace: ncbi_taxonomy synonym: "Animalia" RELATED synonym [] synonym: "animals" RELATED blast_name [] synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33317 name: Protostomia namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33406 name: Cecidomyiidae is_a: NCBITaxon:7147 ! Diptera [Term] id: NCBITaxon:3503 name: Fagaceae is_a: NCBITaxon:33090 ! Viridiplantae [Term] id: NCBITaxon:3511 name: Quercus is_a: NCBITaxon:3503 ! Fagaceae [Term] id: NCBITaxon:3513 name: Quercus alba is_a: GALLONT:0000042 ! Quercus sect. Quercus [Term] id: NCBITaxon:50557 name: Insecta namespace: ncbi_taxonomy synonym: "insects" RELATED blast_name [] synonym: "true insects" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:6960 ! Hexapoda property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:6656 name: Arthropoda namespace: ncbi_taxonomy synonym: "arthropods" EXACT genbank_common_name [] synonym: "arthropods" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:88770 ! Panarthropoda property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6946 name: Acariformes is_a: NCBITaxon:6656 ! Arthropoda [Term] id: NCBITaxon:6960 name: Hexapoda namespace: ncbi_taxonomy synonym: "Atelocerata" RELATED in_part [] synonym: "hexapods" RELATED blast_name [] synonym: "insects" EXACT genbank_common_name [] synonym: "Tracheata" RELATED in_part [] synonym: "Uniramia" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:197562 ! Pancrustacea property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:70320 name: Eriophyidae is_a: NCBITaxon:6946 ! Acariformes [Term] id: NCBITaxon:7147 name: Diptera is_a: NCBITaxon:50557 ! Insecta [Term] id: NCBITaxon:73401 name: Cynipidae is_a: NCBITaxon:7399 ! Hymenoptera [Term] id: NCBITaxon:7399 name: Hymenoptera is_a: NCBITaxon:50557 ! Insecta [Term] id: NCBITaxon:75144 name: Cynipini is_a: NCBITaxon:73401 ! Cynipidae [Term] id: NCBITaxon:88770 name: Panarthropoda namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:1206794 ! Ecdysozoa property_value: has_rank NCBITaxon:clade [Term] id: NCIT:C48440 name: solitary def: "Not accompanied by another or others; exclusive of anyone or anything else." [] is_a: PATO:0000060 ! spatial pattern property_value: seeAlso https://www.inaturalist.org/observations/53326034 [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 property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000112 "animal" xsd:string property_value: IAO:0000112 "fungus" xsd:string property_value: IAO:0000112 "plant" xsd:string property_value: IAO:0000112 "virus" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "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: IAO:0000116 "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: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" 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 ! characteristic [Term] id: PATO:0000011 name: age namespace: quality def: "A time quality inhering in a bearer by virtue of how long the bearer has existed." [WordNet:WordNet] subset: attribute_slim subset: scalar_slim is_a: PATO:0000165 ! time [Term] id: PATO:0000014 name: color namespace: quality alt_id: PATO:0000020 def: "A composite chromatic quality composed of hue, saturation and intensity parts." [PATOC:GVG] subset: attribute_slim synonym: "colour" EXACT [] synonym: "relative color" EXACT [] is_a: PATO:0000051 ! morphology is_a: PATO:0001300 ! optical quality [Term] id: PATO:0000019 name: color pattern namespace: quality def: "A chromatic property that is the relative position of different hues or degrees of saturation." [PATOC:GVG] subset: attribute_slim is_a: PATO:0000060 ! spatial pattern [Term] id: PATO:0000051 name: morphology namespace: quality def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0000052 name: shape namespace: quality alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim synonym: "relational shape quality" EXACT [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000060 name: spatial pattern namespace: quality alt_id: PATO:0000132 alt_id: PATO:0001565 def: "A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts." [PATOC:GVG] subset: attribute_slim subset: hpo_slim synonym: "distribution" EXACT [] synonym: "pattern" RELATED [] is_a: PATO:0000051 ! morphology property_value: IAO:0000118 "distribution" xsd:string [Term] id: PATO:0000066 name: pilosity namespace: quality def: "A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles." [PATOC:GVG] subset: attribute_slim subset: scalar_slim is_a: PATO:0000150 ! texture [Term] id: PATO:0000068 name: qualitative namespace: quality comment: TODO: define this or obsolete it and move children somewhere else. is_a: PATO:0000001 ! quality [Term] id: PATO:0000069 name: deviation (from_normal) namespace: quality def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] subset: attribute_slim is_a: PATO:0000068 ! qualitative [Term] id: PATO:0000070 name: amount namespace: quality alt_id: PATO:0000053 alt_id: PATO:0000071 alt_id: PATO:0001169 alt_id: PATO:0001226 def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG] def: "The number of entities of this type that are part of the whole organism. For galls, the number of entities of some type that are part of or located in a whole gall." [] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-2119-4663"} comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. subset: attribute_slim synonym: "count in organism" RELATED [] synonym: "number" RELATED [] synonym: "presence" RELATED [] synonym: "presence or absence in organism" EXACT [] synonym: "quantitative" EXACT [] is_a: PATO:0000068 ! qualitative relationship: RO:0015012 PATO:0001555 ! reciprocal of has number of [Term] id: PATO:0000117 name: size namespace: quality def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [WordNet:WordNet] def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] subset: attribute_slim subset: scalar_slim is_a: PATO:0000051 ! morphology [Term] id: PATO:0000119 name: height namespace: quality def: "A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension." [PATOC:GVG] subset: attribute_slim subset: scalar_slim is_a: PATO:0001708 ! 1-D extent [Term] id: PATO:0000122 name: length namespace: quality def: "A 1-D extent quality which is equal to the distance between two points." [PATOC:GVG] comment: Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion. subset: attribute_slim subset: mpath_slim subset: scalar_slim is_a: PATO:0001708 ! 1-D extent property_value: seeAlso "https://github.com/pato-ontology/pato/issues/337" xsd:string [Term] id: PATO:0000140 name: position namespace: quality alt_id: PATO:0001032 alt_id: PATO:0001631 def: "A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity." [PATOC:GVG] subset: attribute_slim synonym: "location" EXACT [] synonym: "placement" EXACT [] synonym: "relational spatial quality" EXACT [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000141 name: structure namespace: quality alt_id: PATO:0001452 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." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] synonym: "relational structural quality" EXACT [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000150 name: texture namespace: quality def: "A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics." [PATOC:GVG] subset: attribute_slim is_a: PATO:0000051 ! morphology [Term] id: PATO:0000165 name: time namespace: quality def: "A quality in which events occur in sequence." [PATOC:GVG] subset: attribute_slim subset: scalar_slim is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000309 name: young namespace: quality def: "An age which is relatively low." [PATOC:GVG] subset: value_slim is_a: PATO:0000011 ! age property_value: RO:0002604 PATO:0000308 property_value: seeAlso https://www.inaturalist.org/observations/127002034 [Term] id: PATO:0000317 name: black namespace: quality def: "A color that lacks any hues as parts." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000014 ! color [Term] id: PATO:0000320 name: green namespace: quality def: "A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers." [Dictionary:http\://dictionary.reference.com/] subset: mpath_slim subset: value_slim is_a: PATO:0000014 ! color [Term] id: PATO:0000322 name: red namespace: quality def: "A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers." [Dictionary:http\://dictionary.reference.com/] subset: mpath_slim subset: value_slim is_a: PATO:0000014 ! color [Term] id: PATO:0000324 name: yellow namespace: quality def: "A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers." [Dictionary:http\://dictionary.reference.com/] subset: mpath_slim subset: value_slim is_a: PATO:0000014 ! color [Term] id: PATO:0000329 name: blotchy namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's being marked with irregularly shaped spots or blots of a different hue or degree of saturation." [Dictionary.com:Dictionary.com] subset: value_slim synonym: "blotched" EXACT [] is_a: PATO:0001533 ! multi-colored property_value: seeAlso https://www.inaturalist.org/observations/93589998 [Term] id: PATO:0000330 name: irregular spatial pattern namespace: quality def: "A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency." [PATOC:GVG] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0000060 ! spatial pattern property_value: RO:0002604 PATO:0000440 [Term] id: PATO:0000333 name: spotted namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's being marked with a round area of different hue or degree of saturation." [PATOC:GVG] subset: value_slim is_a: PATO:0001533 ! multi-colored property_value: seeAlso https://www.inaturalist.org/observations/62655170 [Term] id: PATO:0000406 name: curved namespace: quality def: "A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend." [WordNet:WordNet] subset: cell_quality subset: value_slim synonym: "bowing" NARROW [] synonym: "curled" RELATED [] is_a: PATO:0001591 ! curvature property_value: seeAlso https://www.inaturalist.org/observations/73691614 [Term] id: PATO:0000409 name: oblate namespace: quality def: "A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting an equatorial diameter greater than its polar diameter." [WordNet:WordNet] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "oblate spheroid" EXACT [] is_a: PATO:0001865 ! spheroid property_value: seeAlso "lenticular" xsd:string [Term] id: PATO:0000411 name: circular namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center." [thefreedictionary.com:thefreedictionary.com] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "round" RELATED [] synonym: "rounded" RELATED [] is_a: PATO:0000947 ! elliptic [Term] id: PATO:0000453 name: glabrous namespace: quality def: "A pilosity quality inhering in a bearer by virtue of the bearer's lack of hairs or bristles." [PATOC:CJM, PATOC:GVG] subset: mpath_slim subset: value_slim synonym: "hairless" RELATED [] is_a: PATO:0000066 ! pilosity disjoint_from: PATO:0000454 ! hairy property_value: seeAlso https://www.inaturalist.org/observations/129032167 [Term] id: PATO:0000454 name: hairy namespace: quality def: "A pilosity quality inhering in a bearer by virtue of the bearer's being covered with hair or hairlike projections." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000066 ! pilosity disjoint_from: PATO:0002442 ! unornamented [Term] id: PATO:0000461 name: normal namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] subset: abnormal_slim subset: mpath_slim subset: value_slim synonym: "average" RELATED [] is_a: PATO:0000068 ! qualitative property_value: RO:0002604 PATO:0000460 [Term] id: PATO:0000463 name: conspicuous namespace: quality def: "A quality inhering in a bearer by virtue of being clearly visible." [thefreedictionary:thefreedictionary] def: "A quality inhering in a bearer by virtue of being clearly visible. For a gall, a quality in which the gall is clearly visible externally." [] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-2119-4663"} subset: mpath_slim subset: value_slim synonym: "distinct" RELATED [] is_a: PATO:0001998 ! conspicuousness property_value: RO:0002604 PATO:0000464 property_value: seeAlso https://www.inaturalist.org/observations/118068854 [Term] id: PATO:0000464 name: inconspicuous namespace: quality def: "A quality inhering in a bearer by virtue of not being clearly visible." [thefreedictionary:thefreedictionary] def: "A quality inhering in a bearer by virtue of not being clearly visible. For a gall, a quality in which the gall is not clearly visible externally." [] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-2119-4663"} subset: mpath_slim subset: value_slim synonym: "faint" RELATED [] is_a: PATO:0001998 ! conspicuousness property_value: IAO:0000118 "cryptic" xsd:string property_value: RO:0002604 PATO:0000463 property_value: seeAlso https://www.inaturalist.org/observations/64672866 [Term] id: PATO:0000467 name: present namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG] subset: absent_slim subset: value_slim synonym: "present in organism" RELATED [] is_a: PATO:0000070 ! amount property_value: RO:0002604 PATO:0000462 [Term] id: PATO:0000470 name: increased amount namespace: quality alt_id: PATO:0000420 alt_id: PATO:0000650 def: "An amount which is relatively high." [PATOC:GVG] subset: value_slim synonym: "accessory" RELATED [] synonym: "increased" RELATED [] synonym: "increased number" EXACT [] synonym: "present in greater numbers in organism" EXACT [] synonym: "supernumerary" EXACT [] is_a: PATO:0000467 ! present is_a: PATO:0002300 ! increased quality intersection_of: PATO:0000070 ! amount intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001997 [Term] id: PATO:0000570 name: increased height namespace: quality def: "A height which is relatively high." [PATOC:GVG] subset: value_slim synonym: "tall" RELATED [] is_a: PATO:0000119 ! height is_a: PATO:0000586 ! increased size intersection_of: PATO:0000119 ! height intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0000569 [Term] id: PATO:0000573 name: increased length namespace: quality def: "A length quality which is relatively large." [PATOC:GVG] subset: value_slim synonym: "long" EXACT [] is_a: PATO:0000122 ! length is_a: PATO:0000586 ! increased size intersection_of: PATO:0000122 ! length intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0000574 [Term] id: PATO:0000586 name: increased size namespace: quality alt_id: PATO:0001202 def: "A size quality which is relatively high." [PATOC:GVG] subset: value_slim synonym: "big" RELATED [] synonym: "enlarged" RELATED [] synonym: "expanded" RELATED [] synonym: "great" RELATED [] synonym: "large" RELATED [] is_a: PATO:0000117 ! size is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000117 ! size intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0000587 [Term] id: PATO:0000600 name: increased width namespace: quality def: "A width which is relatively large." [PATOC:GVG] subset: value_slim synonym: "broad" RELATED [] synonym: "wide" RELATED [] synonym: "wide/broad" RELATED [] is_a: PATO:0000586 ! increased size is_a: PATO:0000921 ! width intersection_of: PATO:0000921 ! width intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0000599 [Term] id: PATO:0000623 name: exserted namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's protruding or projecting from the body." [sdvc:sdvc] subset: value_slim synonym: "prolapse" RELATED [] synonym: "prolapsed" RELATED [] is_a: PATO:0001598 ! protruding [Term] id: PATO:0000700 name: rough namespace: quality alt_id: PATO:0001616 def: "A texture quality inhering in a bearer by virtue of the bearer's irregular surface." [PATOC:GVG] subset: mpath_slim subset: value_slim synonym: "coarse" EXACT [] is_a: PATO:0000150 ! texture disjoint_from: PATO:0000701 ! smooth property_value: RO:0002604 PATO:0000701 property_value: seeAlso https://www.inaturalist.org/observations/32852385 [Term] id: PATO:0000701 name: smooth namespace: quality def: "A texture quality inhering in a bearer by virtue of the bearer's processing a surface free of roughness or irregularities." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000150 ! texture disjoint_from: PATO:0001365 ! spiny property_value: RO:0002604 PATO:0000700 [Term] id: PATO:0000921 name: width namespace: quality def: "A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite." [PATOC:GVG] comment: Width often refers to the dimension that is greater than the extent in only one of the other two orthogonal dimensions, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion. subset: attribute_slim subset: scalar_slim synonym: "breadth" RELATED [] is_a: PATO:0001708 ! 1-D extent property_value: seeAlso "https://github.com/pato-ontology/pato/issues/337" xsd:string [Term] id: PATO:0000944 name: sharpness namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point." [PATOC:GVG] subset: attribute_slim subset: cell_quality synonym: "apiculate" EXACT [] is_a: PATO:0000052 ! shape [Term] id: PATO:0000947 name: elliptic namespace: quality def: "A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section." [PATOC:GVG] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "ellipse-shaped" EXACT [] synonym: "ellipsoid" EXACT [] synonym: "elliptical" EXACT [] synonym: "oval" RELATED [] synonym: "ovoid" RELATED [] is_a: PATO:0002318 ! superelliptic [Term] id: PATO:0000952 name: brown namespace: quality def: "A color consisting of dark orange, red, of very low intensity." [Wikipedia:http\://en.wikipedia.org/wiki/Brown] subset: mpath_slim subset: value_slim is_a: PATO:0000014 ! color [Term] id: PATO:0000954 name: pink namespace: quality def: "Red color having medium to high brightness and low to moderate saturation." [PATOC:MAH] subset: mpath_slim subset: value_slim is_a: PATO:0000322 ! red [Term] id: PATO:0000957 name: opacity namespace: quality def: "An optical quality which obtains by virtue of the ability of the bearer to absorb visible light." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001300 ! optical quality [Term] id: PATO:0000963 name: opaque namespace: quality 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." [PATOC:GVG] subset: mpath_slim subset: value_slim synonym: "clouding" RELATED [] synonym: "cloudy" RELATED [] synonym: "non-transparent" EXACT [] is_a: PATO:0000957 ! opacity property_value: RO:0002604 PATO:0000964 property_value: seeAlso https://www.inaturalist.org/observations/130540535 [Term] id: PATO:0000970 name: permeability namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion)." [Biology-online:Biology-online] subset: attribute_slim subset: disposition_slim subset: scalar_slim is_a: PATO:0000141 ! structure [Term] id: PATO:0000982 name: permeable namespace: quality def: "A permeability quality inhering in a bearer by virtue of the bearer's being capable to be permeated or pervaded by a gas or liquid (as by osmosis or diffusion)." [Biology-online:Biology-online] subset: disposition_slim subset: value_slim synonym: "porous" RELATED [] is_a: PATO:0000970 ! permeability property_value: RO:0002604 PATO:0000983 [Term] id: PATO:0001018 name: physical quality namespace: quality alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] xref: Wikipedia:Physical_property is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001241 name: physical object quality namespace: quality alt_id: PATO:0001237 alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] synonym: "monadic quality of an object" NARROW [] synonym: "monadic quality of continuant" NARROW [] synonym: "multiply inhering quality of a physical entity" EXACT [] synonym: "quality of a continuant" EXACT [] synonym: "quality of a single physical entity" EXACT [] synonym: "quality of an object" EXACT [] synonym: "quality of continuant" EXACT [] xref: snap:Quality is_a: PATO:0000001 ! quality [Term] id: PATO:0001246 name: light brown namespace: quality def: "A color consisting of brown hue and high brightness." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000952 ! brown [Term] id: PATO:0001250 name: light green namespace: quality def: "A color consisting of green hue and high brightness." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000320 ! green [Term] id: PATO:0001264 name: light yellow namespace: quality def: "A color consisting of yellow hue and high brightness." [PATOC:GVG] subset: mpath_slim subset: value_slim synonym: "blond" RELATED [] is_a: PATO:0000324 ! yellow [Term] id: PATO:0001287 name: red brown namespace: quality def: "A color consisting of red and brown hue." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000952 ! brown [Term] id: PATO:0001300 name: optical quality namespace: quality def: "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." [] def: "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." [PATOC:GVG] subset: attribute_slim is_a: PATO:0070060 ! quality of interaction of a substance with electromagnetic radiation [Term] id: PATO:0001332 name: amorphous namespace: quality def: "A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology." [PATOC:GVG] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0000051 ! morphology property_value: seeAlso https://www.inaturalist.org/observations/62126917 [Term] id: PATO:0001334 name: diameter namespace: quality def: "A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary." [Wikipedia:http\://en.wikipedia.org/wiki/Diameter] subset: attribute_slim subset: mpath_slim subset: scalar_slim is_a: PATO:0001708 ! 1-D extent [Term] id: PATO:0001354 name: translucent namespace: quality def: "A optical quality inhering in a bearer by virtue of the bearer's exhibiting low opacity." [PATOC:GVG] subset: value_slim is_a: PATO:0000957 ! opacity property_value: seeAlso https://www.inaturalist.org/observations/82728541 [Term] id: PATO:0001359 name: rugose namespace: quality def: "A surface feature shape quality inhering in a bearer by virtue of the bearer's having many wrinkles or creases on the surface." [PATOC:GVG] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0000700 ! rough is_a: PATO:0001925 ! surface feature shape property_value: seeAlso https://www.inaturalist.org/observations/61705956 [Term] id: PATO:0001361 name: warty namespace: quality def: "A texture quality inhering in a bearer by virtue of the bearer's being covered with warts or projections that resemble warts resulting in a hard rough surface." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000700 ! rough property_value: seeAlso https://www.inaturalist.org/observations/55941836 [Term] id: PATO:0001362 name: fragile namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's disposition to being easily damaged or destroyed." [WordNet:WordNet] subset: disposition_slim subset: value_slim is_a: PATO:0001662 ! fragility disjoint_from: PATO:0001716 ! non-fragile property_value: RO:0002604 PATO:0001716 [Term] id: PATO:0001365 name: spiny namespace: quality def: "A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface." [PATOC:GVG] subset: cell_quality subset: value_slim is_a: PATO:0000150 ! texture is_a: PATO:0001925 ! surface feature shape disjoint_from: PATO:0002442 ! unornamented property_value: seeAlso https://www.inaturalist.org/observations/83838615 [Term] id: PATO:0001370 name: viscid namespace: quality def: "A coating quality which is sticky or clammy." [PATOC:GVG] subset: value_slim is_a: PATO:0002012 ! coating property_value: seeAlso https://www.inaturalist.org/observations/46296688 [Term] id: PATO:0001409 name: spindle-shaped namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's resembling a long tapered rod." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0002007 ! convex 3-D shape property_value: seeAlso https://www.inaturalist.org/observations/93643117 [Term] id: PATO:0001419 name: sharp namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge." [PATOC:GVG] subset: cell_quality subset: value_slim is_a: PATO:0000944 ! sharpness [Term] id: PATO:0001435 name: attachment quality namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's having connection or association with another entity." [PATOC:GVG] subset: attribute_slim subset: relational_slim is_a: PATO:0000141 ! structure [Term] id: PATO:0001436 name: sessile (sensu botany) namespace: quality def: "An attachment quality inhering in a flower by virtue of the bearer's lacking a stalk, as in flowers or leaves that grow directly from the stem." [Wikipedia:http\://en.wikipedia.org/wiki/Sessility_(botany)] subset: relational_slim subset: value_slim is_a: PATO:0001435 ! attachment quality property_value: seeAlso https://www.inaturalist.org/observations/96365780 [Term] id: PATO:0001438 name: pedicellate namespace: quality def: "A attachment quality inhering in a bearer by virtue of the bearer's having or being supported by a pedicel or pedicle." [MedTerms:MedTerms] subset: relational_slim subset: value_slim is_a: PATO:0001435 ! attachment quality property_value: seeAlso https://www.inaturalist.org/observations/53325638 [Term] id: PATO:0001475 name: increased position namespace: quality def: "A position which is relatively high." [PATOC:GVG] subset: value_slim synonym: "high position" RELATED [] is_a: PATO:0000140 ! position is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000140 ! position intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001476 [Term] id: PATO:0001480 name: spongy namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's resembling a sponge in elasticity, absorbency, or porousness." [Answers.com:Answers.com] subset: mpath_slim subset: value_slim is_a: GALLONT:0000007 ! internal quality is_a: PATO:0000141 ! structure relationship: has_part PATO:0000982 ! permeable property_value: IAO:0000118 "sponge-like" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/138124736 [Term] id: PATO:0001487 name: senescent namespace: quality def: "A time quality inhering in a bearer by virtue of the bearer's growing old; aging." [answers.com:answers.com] subset: mpath_slim subset: value_slim is_a: PATO:0000011 ! age property_value: seeAlso https://www.inaturalist.org/observations/138291646 [Term] id: PATO:0001499 name: spherical namespace: quality alt_id: PATO:0000408 def: "A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter)." [WordNet:WordNet] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "globular" EXACT [] synonym: "rotund" RELATED [] is_a: PATO:0001865 ! spheroid relationship: RO:0015011 PATO:0000411 ! has cross section circular property_value: seeAlso https://www.inaturalist.org/observations/134523229 [Term] id: PATO:0001500 name: tapered namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end." [WordNet:WordNet] subset: cell_quality subset: value_slim synonym: "taper" EXACT [] is_a: PATO:0001419 ! sharp property_value: IAO:0000118 "taper" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/165344292 [Term] id: PATO:0001532 name: mono-colored namespace: quality def: "A color pattern inhering in a bearer by virtue of the bearer's having one hue." [PATOC:GVG] subset: value_slim synonym: "evenly colored" EXACT [] synonym: "homogeneously colored" EXACT [] synonym: "homogenously pigmented" RELATED [] synonym: "uniformly colored" EXACT [] is_a: PATO:0000019 ! color pattern property_value: IAO:0000118 "uniformly colored" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/62136736 [Term] id: PATO:0001533 name: multi-colored namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's having two or more hues or degrees of saturation." [PATOC:GVG] subset: value_slim synonym: "variegated" EXACT [] is_a: PATO:0000019 ! color pattern property_value: seeAlso https://www.inaturalist.org/observations/61596659 [Term] id: PATO:0001534 name: motley namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's having 3 or more hues or degrees of saturations." [merriam-webster.:merriam-webster.] subset: value_slim is_a: PATO:0001533 ! multi-colored property_value: seeAlso https://www.inaturalist.org/observations/61876229 [Term] id: PATO:0001535 name: dappled namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's being marked with small spots, patches, or specks of hue or degree of saturation differing from that of the background." [merriam-webster.:merriam-webster.] subset: value_slim synonym: "speckled" RELATED [] is_a: PATO:0001533 ! multi-colored property_value: seeAlso https://www.inaturalist.org/observations/134980830 [Term] id: PATO:0001543 name: flexibility namespace: quality def: "A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster] def: "A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking." [] subset: attribute_slim subset: disposition_slim is_a: PATO:0001546 ! quality of a solid [Term] id: PATO:0001544 name: flexible namespace: quality def: "A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking." [] def: "A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster] subset: disposition_slim subset: value_slim synonym: "bendy" EXACT [] is_a: PATO:0001543 ! flexibility property_value: RO:0002604 PATO:0001545 [Term] id: PATO:0001546 name: quality of a solid namespace: quality 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." [Chemistry:http\://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm] subset: attribute_slim synonym: "solidity" EXACT [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001555 name: has number of namespace: quality def: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts." [PATOC:CJM] subset: attribute_slim subset: relational_slim synonym: "cardinality" RELATED [] synonym: "extra or missing physical or functional parts" EXACT [] synonym: "has or lacks parts of type" EXACT [] synonym: "mereological quality" EXACT [] synonym: "number" RELATED [] synonym: "number of" EXACT [] xref: OBO_REL:has_part is_a: PATO:0001241 ! physical object quality relationship: RO:0015012 PATO:0000070 ! reciprocal of amount [Term] id: PATO:0001577 name: increased permeability namespace: quality def: "A permeability which is relatively high." [PATO:GVG] subset: disposition_slim subset: value_slim synonym: "high permeability" EXACT [] is_a: PATO:0000982 ! permeable is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000982 ! permeable intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001578 [Term] id: PATO:0001591 name: curvature namespace: quality def: "A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending." [WordNet:WordNet] subset: attribute_slim is_a: PATO:0000052 ! shape [Term] id: PATO:0001592 name: increased curvature namespace: quality def: "A curvature which is relatively high." [PATO:GVG] subset: value_slim is_a: PATO:0000406 ! curved is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000406 ! curved intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001593 [Term] id: PATO:0001598 name: protruding namespace: quality alt_id: PATO:0001644 def: "A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary." [WordNet:WordNet] subset: value_slim synonym: "protruding" EXACT [] synonym: "relational protruding quality" EXACT [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001609 name: scattered name: sparse namespace: quality def: "A spatial pattern inhering in a bearer by virtue of the bearer's being scattered; spread irregularly, and at a distance from each other." [biology.lsu:biology.lsu] subset: mpath_slim subset: value_slim is_a: PATO:0000060 ! spatial pattern property_value: seeAlso https://www.inaturalist.org/observations/60738203 [Term] id: PATO:0001629 name: aggregated namespace: quality def: "A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole." [WordNet:WordNet] subset: mpath_slim subset: value_slim synonym: "clumped" EXACT [] synonym: "clustered" EXACT [] is_a: PATO:0000330 ! irregular spatial pattern property_value: seeAlso https://www.inaturalist.org/observations/135839958 [Term] id: PATO:0001662 name: fragility namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's disposition to being damaged or destroyed." [WordNet:WordNet] subset: attribute_slim subset: disposition_slim subset: scalar_slim is_a: PATO:0000141 ! structure [Term] id: PATO:0001708 name: 1-D extent namespace: quality def: "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." [PATOC:GVG] subset: attribute_slim synonym: "1-D size" EXACT [] is_a: PATO:0000117 ! size [Term] id: PATO:0001714 name: increased diameter namespace: quality def: "A diameter which is relatively large." [PATOC:GVG] subset: value_slim is_a: PATO:0000586 ! increased size is_a: PATO:0001334 ! diameter intersection_of: PATO:0001334 ! diameter intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001715 [Term] id: PATO:0001716 name: non-fragile namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's ability to withstand great strain without tearing or breaking." [thefreedictionary.com:thefreedictionary.com] subset: attribute_slim subset: disposition_slim synonym: "resilient" RELATED [] synonym: "strong" RELATED [] synonym: "tough" RELATED [] is_a: PATO:0001662 ! fragility property_value: RO:0002604 PATO:0001362 [Term] id: PATO:0001729 name: shedability namespace: quality def: "An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process." [PATOC:GVG] subset: attribute_slim subset: disposition_slim subset: relational_slim is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0001730 name: deciduous (generic) namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's disposition to shed body parts." [PATOC:GVG] subset: disposition_slim subset: relational_slim subset: value_slim is_a: PATO:0001729 ! shedability property_value: IAO:0000118 "detachable" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/34366055 [Term] id: PATO:0001732 name: non-deciduous name: non-deciduous (any body part) namespace: quality def: "A quality inhering in a plant by virtue of the bearer's disposition to not shed any body part." [PATOC:GVG] subset: disposition_slim subset: relational_slim subset: value_slim is_a: PATO:0001729 ! shedability property_value: IAO:0000118 "integral" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/64672768 [Term] id: PATO:0001764 name: increased age namespace: quality def: "An age which is high relative to the normal or average." [PATOC:GVG] subset: value_slim synonym: "high age" EXACT [] is_a: PATO:0000011 ! age is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000011 ! age intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001765 [Term] id: PATO:0001776 name: increased flexibility namespace: quality def: "A flexibility which is relatively high." [PATOC:GVG] subset: disposition_slim subset: value_slim synonym: "high flexibility" EXACT [] is_a: PATO:0001544 ! flexible is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0001544 ! flexible intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: RO:0002604 PATO:0001777 [Term] id: PATO:0001851 name: swollen namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's exhibiting transient abnormal enlargement, not due to cell proliferation." [thefreedictionary.com:thefreedictionary.com] subset: mpath_slim subset: value_slim synonym: "swelling" NARROW [] is_a: PATO:0000141 ! structure relationship: has_part PATO:0000586 ! increased size relationship: has_part PATO:0001598 ! protruding property_value: seeAlso https://www.inaturalist.org/observations/61503871 [Term] id: PATO:0001857 name: concave namespace: quality def: "A shape quality in a bearer by virtue of the bearer's curving inward." [WordNet:WordNet] subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001865 name: spheroid namespace: quality alt_id: PATO:0001864 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating an ellipse about one of its principal axes. Includes spheres and oblate/prolate spheroids." [Wikipedia:http\://en.wikipedia.org/wiki/Spheroid] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "sphericality" RELATED [] is_a: PATO:0002007 ! convex 3-D shape [Term] id: PATO:0001871 name: reniform namespace: quality def: "A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney." [ISBN:0881923214] subset: value_slim synonym: "bean shaped" RELATED [] synonym: "kidney-shaped" EXACT [] is_a: PATO:0002008 ! concave 3-D shape property_value: seeAlso https://www.inaturalist.org/observations/29748241 [Term] id: PATO:0001873 name: cylindrical namespace: quality alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim synonym: "rod-like" EXACT [] synonym: "rod-shaped" EXACT [] synonym: "tubulate" NARROW [] is_a: PATO:0002007 ! convex 3-D shape relationship: RO:0015011 PATO:0000411 ! has cross section circular property_value: seeAlso https://www.inaturalist.org/observations/111343832 [Term] id: PATO:0001874 name: discoid namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter." [PATOC:cjm] subset: cell_quality subset: value_slim synonym: "disc-shaped" EXACT [] synonym: "disk-shaped" EXACT [] is_a: PATO:0001873 ! cylindrical [Term] id: PATO:0001875 name: triangular namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's having three angles." [wordreference:wordreference] subset: cell_quality subset: value_slim synonym: "delta shaped" RELATED [] synonym: "deltoid" EXACT [] synonym: "triangle" RELATED [] synonym: "triangle-shaped" RELATED [] is_a: PATO:0002006 ! 2-D shape [Term] id: PATO:0001877 name: lanceolate namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle; attached at the broad end." [PATOC:GVG] def: "A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle; attached at the broad end." [] subset: cell_quality subset: value_slim synonym: "spear-shaped" EXACT [] is_a: PATO:0001419 ! sharp [Term] id: PATO:0001878 name: sigmoid namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped." [PATOC:CJM] subset: cell_quality subset: value_slim synonym: "S-shaped" EXACT [] synonym: "sigmoidal" EXACT [] is_a: PATO:0000052 ! shape property_value: IAO:0000118 "s-shaped" xsd:string property_value: IAO:0000118 "sigmoidal" xsd:string [Term] id: PATO:0001883 name: clavate namespace: quality alt_id: PATO:0001797 def: "A concave 3-D shape quality inhering in a bearer by virtue of the bearer's gradually becoming thicker towards the end." [MP:0000576] subset: value_slim synonym: "club-like" EXACT [] synonym: "club-shaped" EXACT [] synonym: "clubbed" EXACT [] is_a: PATO:0002008 ! concave 3-D shape property_value: IAO:0000118 "club-shaped" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/93643117 [Term] id: PATO:0001907 name: botryoidal namespace: quality def: "A surface feature shape quality inhering in a bearer by virtue of the bearer's being like the surface of a compact mass of grapes." [] def: "A surface feature shape quality inhering in a bearer by virtue of the bearer's being like the surface of a compact mass of grapes." [PATOC:cvs] subset: value_slim is_a: PATO:0001925 ! surface feature shape property_value: seeAlso https://www.inaturalist.org/observations/161485438 [Term] id: PATO:0001925 name: surface feature shape namespace: quality def: "A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell." [PATOC:CJM] comment: This quality either inheres directly in the surface, or in the entity that has the surface. For example, to say that a particular fly wing is curved is shorthand for saying the wing has a surface which is curved. subset: attribute_slim is_a: PATO:0000052 ! shape [Term] id: PATO:0001941 name: yellow green namespace: quality def: "A color consisting of yellow and green hues." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000320 ! green [Term] id: PATO:0001946 name: banded namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's exhibiting transverse stripes of one hue or degree of saturation crossing another." [ISBN:0881923214] subset: value_slim synonym: "striped" EXACT [] is_a: PATO:0001533 ! multi-colored property_value: seeAlso https://www.inaturalist.org/observations/61502856 [Term] id: PATO:0001947 name: netted namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's being covered with reticulated lines of a different hue or degree of saturation." [ISBN:0881923214] subset: value_slim synonym: "net-like" EXACT [] synonym: "reticulated" EXACT [] is_a: PATO:0001533 ! multi-colored property_value: seeAlso https://www.inaturalist.org/observations/106192928 [Term] id: PATO:0001949 name: pointleted namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly in a little point." [ISBN:0881923214] subset: value_slim is_a: PATO:0001419 ! sharp property_value: seeAlso https://www.inaturalist.org/observations/61595801 [Term] id: PATO:0001955 name: cuneate namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base." [wordreference:wordreference] subset: value_slim synonym: "wedge-shaped" EXACT [] is_a: PATO:0001875 ! triangular [Term] id: PATO:0001979 name: lobed namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions." [ISBN:0881923214] subset: mpath_slim subset: value_slim is_a: PATO:0000052 ! shape property_value: seeAlso https://www.inaturalist.org/observations/160895518 [Term] id: PATO:0001981 name: auriculate namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an ear." [url:http\://www.thefreedictionary.com/auriculate] subset: value_slim is_a: PATO:0000052 ! shape property_value: seeAlso https://www.inaturalist.org/observations/48456565 [Term] id: PATO:0001995 name: organismal quality namespace: quality def: "A quality that inheres in an entire organism or part of an organism." [PATOC:CJM] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001998 name: conspicuousness namespace: quality def: "A quality inhering in a bearer by virtue of its visibility." [PATOC:MAH] comment: This term was created as a grouping term for the 2 terms "conspicuous" and "inconspicuous". However, it is not clear if these terms should even remain in PATO. is_a: PATO:0000068 ! qualitative [Term] id: PATO:0002005 name: concavity namespace: quality def: "Surface shape that refers to the inward or outward curvature of the surface." [PATOC:MAH] subset: attribute_slim is_a: PATO:0000052 ! shape [Term] id: PATO:0002006 name: 2-D shape namespace: quality def: "A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity." [PATOC:CJM] subset: attribute_slim synonym: "2-D projection" RELATED [] synonym: "cross-sectional" RELATED [] is_a: PATO:0000052 ! shape [Term] id: PATO:0002007 name: convex 3-D shape namespace: quality def: "A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave." [PATOC:CJM] comment: Use this term or an is_a child of this term when the entire shape of the object is known. subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002008 name: concave 3-D shape namespace: quality def: "A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave." [PATOC:CJM] subset: attribute_slim xref: Image:http\://en.wikipedia.org/wiki/Image\:Convex_polygon_illustration2.png is_a: PATO:0002266 ! 3-D shape relationship: has_part PATO:0001857 ! concave property_value: RO:0002604 PATO:0002007 [Term] id: PATO:0002012 name: coating namespace: quality def: "A texture quality that exists through a liquid cover on the surface of the bearer." [Wikipedia:Wikipedia] subset: value_slim is_a: PATO:0000150 ! texture [Term] id: PATO:0002014 name: structure, cavities namespace: quality def: "A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas." [PATOC:GVG] subset: attribute_slim is_a: PATO:0000141 ! structure [Term] id: PATO:0002020 name: pale pink namespace: quality def: "Pink color having high brightness and low saturation." [PATOC:GVG] is_a: PATO:0000954 ! pink [Term] id: PATO:0002021 name: conical namespace: quality def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers)." [Wikipedia:http\://en.wikipedia.org/wiki/Cone_(geometry)] subset: value_slim synonym: "cone-shaped" EXACT [] xref: Image:http\://upload.wikimedia.org/wikipedia/commons/d/d2/Cone_3d.png is_a: PATO:0002007 ! convex 3-D shape property_value: seeAlso https://www.inaturalist.org/observations/61704917 [Term] id: PATO:0002055 name: increased fragility namespace: quality def: "A fragility which is relatively high." [PATOC:GVG] subset: disposition_slim subset: value_slim is_a: PATO:0001362 ! fragile is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0001362 ! fragile intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: RO:0002604 PATO:0002056 creation_date: 2009-03-26T04:01:37Z [Term] id: PATO:0002063 name: columnar namespace: quality def: "A shape inhering in a bearer by virtue of the bearer's being elongated and cylindrical." [PATOC:me] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/111432683 creation_date: 2009-07-01T01:44:06Z [Term] id: PATO:0002078 name: hollow namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: GALLONT:0000007 ! internal quality is_a: PATO:0002014 ! structure, cavities property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/117192961 creation_date: 2009-09-18T02:19:20Z [Term] id: PATO:0002108 name: papillary namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's resembling small nipple like projection." [PATO:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000052 {comment="probably not the right class for galls with nipple-like projections"} ! shape is_a: PATO:0000623 ! exserted property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/91418114 creation_date: 2009-10-05T03:04:52Z [Term] id: PATO:0002198 name: quality of a substance namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] id: PATO:0002215 name: falciform namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's having the shape of a scythe or sickle." [merriam-webster:http\://www.merriam-webster.com/dictionary/falciform] subset: value_slim synonym: "falcate" EXACT [] synonym: "hooked" EXACT [] synonym: "scythe-shaped" EXACT [] synonym: "sickle-shaped" EXACT [] synonym: "unciform" EXACT [] synonym: "uncinate" EXACT [] is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-08T01:57:46Z [Term] id: PATO:0002226 name: subcylindrical namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] id: PATO:0002228 name: acuminate namespace: quality def: "A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point." [url:http\://www.thefreedictionary.com/acuminate] subset: value_slim is_a: PATO:0001500 ! tapered property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/54845032 creation_date: 2010-07-15T09:03:18Z [Term] id: PATO:0002240 name: teardrop-shaped namespace: quality def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling falling drop." [url:wordnetweb.princeton.edu/perl/webwn] subset: value_slim synonym: "drop shaped" EXACT [] is_a: PATO:0002007 ! convex 3-D shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/34366055 creation_date: 2010-07-23T02:31:11Z [Term] id: PATO:0002266 name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] id: PATO:0002273 name: marbled namespace: quality def: "Multicolored quality inhering in a bearer by virtue of the bearer's being colored with a variegated pattern resembling marble,." [url:http\://www.oed.com/] subset: value_slim is_a: PATO:0001533 ! multi-colored property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/61596659 creation_date: 2010-11-16T11:17:32Z [Term] id: PATO:0002274 name: mottled namespace: quality def: "Multicolored quality inhering in a bearer by virtue of the bearer's being dappled with spots, patches, or blotches of different colors." [url:http\://www.oed.com/] subset: value_slim is_a: PATO:0001533 ! multi-colored property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/162989102 creation_date: 2010-11-16T11:22:57Z [Term] id: PATO:0002276 name: barred namespace: quality def: "A color pattern inhering in a bearer by virtue of bearer's exhibiting vertical bars of one hue or degree of saturation crossing another." [PATOC:WD] subset: value_slim is_a: PATO:0001533 ! multi-colored property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/45656874 creation_date: 2010-11-16T11:30:40Z [Term] id: PATO:0002299 name: tubular namespace: quality def: "A cylindrical shape that is hollow." [PATOC:GVG] synonym: "tube like" EXACT [] synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] id: PATO:0002300 name: increased quality namespace: quality def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] is_a: PATO:0000069 ! deviation (from_normal) intersection_of: PATO:0000001 ! quality intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal relationship: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: RO:0002604 PATO:0002301 creation_date: 2011-06-16T06:39:43Z [Term] id: PATO:0002305 name: increased object quality namespace: quality def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] is_a: PATO:0001241 ! physical object quality is_a: PATO:0002300 ! increased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: RO:0002604 PATO:0002303 creation_date: 2011-06-16T06:54:01Z [Term] id: PATO:0002311 name: fimbriated namespace: quality def: "Having a fringe or border of hairlike or fingerlike projections." [PATO:WS] subset: value_slim is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/14417106 creation_date: 2011-09-22T03:52:11Z [Term] id: PATO:0002318 name: superelliptic namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] id: PATO:0002335 name: tholiform namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being dome-shaped." [PATOC:dd] subset: value_slim is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: IAO:0000118 "dome-like" xsd:string property_value: IAO:0000118 "hemispheroid" xsd:string creation_date: 2012-01-31T02:32:14Z [Term] id: PATO:0002339 name: hispid namespace: quality def: "A quality of being covered with stiff or rough hairs." [PATOC:GVG] subset: value_slim is_a: PATO:0000454 ! hairy property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/64256556 creation_date: 2012-01-31T02:51:37Z [Term] id: PATO:0002340 name: hispidulous namespace: quality def: "A quality of being minutely hispid." [PATOC:DD] subset: value_slim is_a: PATO:0002339 ! hispid property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/27503910 creation_date: 2012-01-31T02:53:21Z [Term] id: PATO:0002344 name: arachnose namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's being characterized by fine, entangled hairs giving the appearance of cobweb." [PATOC:DD] subset: value_slim is_a: PATO:0000454 ! hairy property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/62631894 creation_date: 2012-01-31T03:49:00Z [Term] id: PATO:0002400 name: fusiform namespace: quality def: "Having a spindle-like shape that is wide in the middle and tapers at both ends." [wikipedia:wikipedia] subset: mpath_slim subset: value_slim is_a: PATO:0001409 ! spindle-shaped property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: seeAlso https://www.inaturalist.org/observations/47505522 creation_date: 2012-12-07T05:43:25Z [Term] id: PATO:0002411 name: yellow brown namespace: quality def: "A color consisting of yellow and brown hue." [PATOC:GVG] subset: value_slim is_a: PATO:0000952 ! brown property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T10:55:51Z [Term] id: PATO:0002427 name: knobbled namespace: quality def: "A surface feature shape having numerous very small circular rounded projections or protuberances." [] def: "A surface feature shape having numerous very small circular rounded projections or protuberances." [thefreedictionary.com:thefreedictionary.com] subset: value_slim is_a: PATO:0001925 ! surface feature shape disjoint_from: PATO:0002442 ! unornamented property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: IAO:0000118 "pebbled" xsd:string property_value: IAO:0000118 "tuberculose" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/118532452 creation_date: 2013-01-29T09:15:53Z [Term] id: PATO:0002440 name: ornamentation namespace: quality def: "A surface feature shape quality inhering in a bearer by virtue of the degree of the bearer's highly topographical with ridges, pits, rugosity or other surface structures." [PATOC:GVG] subset: disposition_slim is_a: PATO:0001925 ! surface feature shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-01-29T10:57:42Z [Term] id: PATO:0002442 name: unornamented namespace: quality def: "A surface feature shape in which the bearer's surface is lacking ridges, pits, rugosity or other surface structures." [] def: "A surface feature shape in which the bearer's surface is lacking ridges, pits, rugosity or other surface structures." [PATOC:AD] subset: value_slim is_a: PATO:0002440 ! ornamentation property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X property_value: RO:0002604 PATO:0002441 property_value: seeAlso https://www.inaturalist.org/observations/32783899 creation_date: 2013-01-29T11:00:20Z [Term] id: PATO:0005002 name: pear shaped name: pear-shaped namespace: quality def: "Having the shape of a pear; tapering near the top and bulging toward the base or bottom. From thefreedictionary.com" [PATOC:WD] subset: value_slim is_a: PATO:0002007 ! convex 3-D shape property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 creation_date: 2014-09-09T12:30:02Z [Term] id: PATO:0005004 name: subelliptical namespace: quality def: "A shape that is almost an ellipse." [PATOC:WD] subset: value_slim is_a: PATO:0002318 ! superelliptic property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 property_value: seeAlso https://www.inaturalist.org/observations/91487515 creation_date: 2014-09-09T12:36:15Z [Term] id: PATO:0005014 name: subspherical namespace: quality def: "A spheroid shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, spherical." [PATOC:WD] subset: value_slim is_a: PATO:0001865 ! spheroid property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 property_value: IAO:0000118 "globose" xsd:string property_value: IAO:0000118 "globular" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/84454407 creation_date: 2014-09-25T15:16:25Z [Term] id: PATO:0040022 name: flared namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer being expanded laterally and or opened outward in shape." [] is_a: PATO:0000052 ! shape property_value: http://purl.org/dc/elements/1.1/date "2018-11-19T21:49:07Z" xsd:dateTime property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 property_value: seeAlso https://www.inaturalist.org/observations/105016514 [Term] id: PATO:0070060 name: quality of interaction of a substance with electromagnetic radiation namespace: quality def: "A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength." [https://orcid.org/0000-0002-5111-7263] subset: attribute_slim is_a: PATO:0002198 ! quality of a substance [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, plural)" NARROW OMO:0003004 [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, plural)" NARROW OMO:0003004 [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: "shrub (narrow)" NARROW [] synonym: "sporophyte (narrow)" NARROW [] synonym: "suffrutex (narrow)" NARROW [FNA:99508f62-7116-4e2b-90c0-19ff55ebd967] synonym: "suffrutices (narrow, plural)" NARROW OMO:0003004 [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: FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 xref: FNA:99508f62-7116-4e2b-90c0-19ff55ebd967 xref: FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 xref: FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0 xref: FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba xref: FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b xref: FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8 xref: PO_GIT:538 xref: PO_GIT:69 is_a: PO:0009011 ! plant structure [Term] id: PO:0000017 name: vascular leaf primordium namespace: plant_anatomy def: "A phyllome primordium (PO:0025128) that develops from a vascular leaf anlagen (PO:0025431) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a vascular leaf (PO:0009025)." [POC:curators, POC:Laurel_Cooper] synonym: "leaf primordium (exact)" EXACT [] synonym: "portion of vascular leaf primordium tissue (exact)" EXACT [] synonym: "primordio de hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "vascular leaf primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "葉原基 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:466 is_a: PO:0025128 ! phyllome primordium relationship: develops_from PO:0025431 ! vascular leaf anlagen relationship: part_of PO:0025223 ! vegetative shoot apex [Term] id: PO:0000019 name: gynoecium primordium namespace: plant_anatomy def: "A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062)." [POC:curators] comment: Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030). synonym: "pistil primordium (exact)" EXACT [] synonym: "portion of gynoecium primordium tissue (exact)" EXACT [] synonym: "primordio de gineceo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "雌蕊原基(可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:465 is_a: PO:0025477 ! floral organ primordium [Term] id: PO:0000034 name: vascular system namespace: plant_anatomy def: "A maximal portion of vascular tissue (PO:0009015) in a whole plant (PO:0000003), collective plant structure (PO:0025497), multi-tissue plant structure (PO:0025496), or cardinal part of multi-tissue plant structure (PO:0025498)." [ISBN:0471245208, ISBN:0716710072, POC:curators] comment: A vascular system consist of the totality of the portions of vascular tissue in their specific arrangement in a plant structure. May include other portions of plant tissue or plant cells (PO:0009002) of other types, such as parenchyma (PO:0005421) or fiber cells (PO:0025407). subset: TraitNet synonym: "sistema vascular (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "vasculature (exact)" EXACT [FNA:caf918bf-f4c4-423c-8008-87c96e5399a0] synonym: "維管束系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:50 is_a: PO:0009015 ! portion of vascular tissue disjoint_from: PO:0009002 ! plant cell disjoint_from: PO:0009008 ! plant organ disjoint_from: PO:0025001 ! cardinal organ part disjoint_from: PO:0025007 ! collective plant organ structure relationship: part_of PO:0000003 ! whole plant relationship: participates_in PO:0028002 ! sporophyte development stage [Term] id: PO:0000036 name: leaf vascular system namespace: plant_anatomy def: "A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a vascular leaf (PO:0009025)." [POC:Ramona_Walls] subset: Maize synonym: "leaf venation (related)" RELATED [] synonym: "sistema vascular de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉維管系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:41 xref: PO_GIT:50 is_a: PO:0025206 ! phyllome vascular system relationship: part_of PO:0009025 ! vascular leaf [Term] id: PO:0000037 name: shoot axis apex namespace: plant_anatomy def: "A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127)." [POC:curators] subset: reference synonym: "ápice del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "シュート頂、茎頂 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:234 is_a: PO:0025029 ! shoot axis [Term] id: PO:0000047 name: leaf lamina epidermis namespace: plant_anatomy def: "A portion of leaf epidermis (PO:0006016) that is part of a leaf lamina (PO:0020039)." [POC:curators] comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. synonym: "epidermis de la lámina de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉身表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006016 ! leaf epidermis intersection_of: PO:0006016 ! leaf epidermis intersection_of: part_of PO:0020039 ! leaf lamina relationship: part_of PO:0020039 ! leaf lamina [Term] id: PO:0000048 name: leaf lamina vascular system namespace: plant_anatomy def: "A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a leaf lamina (PO:0020039)." [POC:Ramona_Walls] synonym: "sistema vascular de la lámina de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉身維管系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:41 is_a: PO:0000034 ! vascular system relationship: part_of PO:0000036 ! leaf vascular system relationship: part_of PO:0020039 ! leaf lamina [Term] id: PO:0000051 name: petiole epidermis namespace: plant_anatomy def: "A portion of leaf epidermis (PO:0006016) that is part of a petiole (PO:0020038)." [POC:Ramona_Walls, TAIR_curator:Katica_Ilic] comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. synonym: "epidermis del pecíolo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉柄表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006016 ! leaf epidermis intersection_of: PO:0006016 ! leaf epidermis intersection_of: part_of PO:0020038 ! petiole relationship: part_of PO:0020038 ! petiole [Term] id: PO:0000055 name: bud namespace: plant_anatomy def: "An undeveloped shoot system (PO:0009006)." [POC:curators] subset: TraitNet synonym: "adventitious bud (narrow)" NARROW [FNA:0eed275a-5dae-414a-bf36-81a08e6c6ba9] synonym: "yema (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "芽 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:0eed275a-5dae-414a-bf36-81a08e6c6ba9 xref: PO_GIT:124 is_a: PO:0009006 ! shoot system relationship: participates_in PO:0025528 ! bud development stage property_value: seeAlso https://www.inaturalist.org/observations/48455720 [Term] id: PO:0000112 name: shoot axis epidermis namespace: plant_anatomy def: "A portion of shoot system epidermis (PO:0006035) that is part of a shoot axis (PO:0025029)." [POC:curators, POC:Laurel_Cooper] comment: Can occur on a stem or branch. synonym: "branch epidermis (narrow)" NARROW [] synonym: "epidermis del eje del tallo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "シュート軸表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006035 ! shoot system epidermis intersection_of: PO:0006035 ! shoot system epidermis intersection_of: part_of PO:0025029 ! shoot axis relationship: part_of PO:0025029 ! shoot axis [Term] id: PO:0000146 name: abscission zone is_a: PO:0009007 ! portion of plant tissue [Term] id: PO:0000207 name: nectary epidermis namespace: plant_anatomy def: "A portion of shoot system epidermis (PO:0006035) that is part of a nectary (PO:0009035) ." [POC:Ramona_Walls] synonym: "epidermis del nectario (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "蜜腺表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006035 ! shoot system epidermis intersection_of: PO:0006035 ! shoot system epidermis intersection_of: part_of PO:0009035 ! nectary relationship: part_of PO:0009035 ! nectary [Term] id: PO:0000225 name: peripheral zone namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division." [ISBN:0521288959, TAIR_curator:Leonore_Reiser] synonym: "peripheral meristem (related)" RELATED [] synonym: "zona periférica (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "周辺帯 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009013 ! portion of meristem tissue relationship: part_of PO:0020148 ! shoot apical meristem [Term] id: PO:0000229 name: flower meristem namespace: plant_anatomy alt_id: PO:0006329 alt_id: PO:0006373 alt_id: PO:0006374 alt_id: PO:0025091 def: "A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395)." [Gramene:Pankaj_Jaiswal, POC:curators] comment: In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). synonym: "ear floret meristem (narrow)" NARROW [] synonym: "floral apical meristem (related)" RELATED [] synonym: "floral meristem (exact)" EXACT [] synonym: "floret meristem (narrow)" NARROW [] synonym: "mersitema floral (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "Poaceae floret meristem (narrow)" NARROW [] synonym: "tassel floret meristem (narrow)" NARROW [] synonym: "花芽分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0008028 ! reproductive shoot apical meristem [Term] id: PO:0000282 name: trichome namespace: plant_anatomy alt_id: PO:0004510 def: "A unicellular or multicellular plant structure (PO:0009011) that forms a non-sclerified outgrowth from the epidermis (PO:0005679)." [PMID:19939948, POC:curators] comment: This class is the union of unicellular trichome (PO:0025537) and multicellular trichome (PO:0025162). A trichome can vary in length and shape and may be branched or unbranched. It may be glandular or non-secretory. subset: TraitNet synonym: "barb trichome (broad)" BROAD [FNA:aa191087-e979-486f-ad87-0e050a83090f] synonym: "bristle (broad)" BROAD [FNA:78121d02-e7db-45eb-b1b7-011d5026beae] synonym: "capilli (narrow, plural)" NARROW OMO:0003004 [FNA:602c5ee8-6634-4093-bd2c-016dde8a350e] synonym: "capillus (narrow)" NARROW [FNA:43d66471-4955-4bc2-a70c-c88e33877c42] synonym: "cilia (narrow, plural)" NARROW OMO:0003004 [FNA:c358e298-5926-42d6-8d49-a918cdc72406] synonym: "cilium (narrow)" NARROW [FNA:12abd29b-5eae-47a2-baae-4059581e7eaa] synonym: "glochid (narrow)" NARROW [FNA:881fcb45-5dfd-4d06-8d6f-a111ba5e220a] synonym: "glochidia (narrow, plural)" NARROW OMO:0003004 [FNA:899a83bf-39bb-4128-b472-b0e27dcf5b35] synonym: "glochidium (narrow)" NARROW [FNA:99a6f711-b4da-4231-8dce-9ed171b87e9c] synonym: "hair (narrow)" NARROW [FNA:9ef3a0eb-f8e4-4a7b-911e-92952fc19956] synonym: "lepides (narrow, plural)" NARROW OMO:0003004 [FNA:e6a34ceb-a3e7-49f7-a4ac-cf0ea1552dc4] synonym: "lepis (narrow)" NARROW [FNA:bb12cad4-db12-4e59-a9fc-1676f2558a0a] synonym: "non-secretory trichome (narrow)" NARROW [] synonym: "scale (narrow)" NARROW [FNA:8c618dea-f3dd-434f-bb13-23273ea6c143] synonym: "seta (related)" RELATED [FNA:c751440c-a7b3-4997-aed8-47f8254fd05f] synonym: "setae (related)" RELATED [FNA:93b95b97-0f1a-4d26-9c86-ebede4157269] synonym: "squama (narrow)" NARROW [FNA:6cb9e7af-32a7-413a-8f80-9e40d3ae462a] synonym: "squamae (narrow, plural)" NARROW OMO:0003004 [FNA:cbb9ceb5-a404-4b5c-9c8f-4cf0ca6bade2] synonym: "squamella (narrow)" NARROW [FNA:ead20a1b-057b-4008-9466-bdb8e283aa82] synonym: "squamellae (narrow, plural)" NARROW OMO:0003004 [FNA:c5765385-917c-465e-83f8-b4fe5d693146] synonym: "squamule (narrow)" NARROW [FNA:f18da584-2b0b-4b03-a614-40140a1cb89e] synonym: "tricoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "毛茸、糸状体、毛 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:12abd29b-5eae-47a2-baae-4059581e7eaa xref: FNA:43d66471-4955-4bc2-a70c-c88e33877c42 xref: FNA:602c5ee8-6634-4093-bd2c-016dde8a350e xref: FNA:6cb9e7af-32a7-413a-8f80-9e40d3ae462a xref: FNA:78121d02-e7db-45eb-b1b7-011d5026beae xref: FNA:881fcb45-5dfd-4d06-8d6f-a111ba5e220a xref: FNA:899a83bf-39bb-4128-b472-b0e27dcf5b35 xref: FNA:8c618dea-f3dd-434f-bb13-23273ea6c143 xref: FNA:93b95b97-0f1a-4d26-9c86-ebede4157269 xref: FNA:99a6f711-b4da-4231-8dce-9ed171b87e9c xref: FNA:9ef3a0eb-f8e4-4a7b-911e-92952fc19956 xref: FNA:aa191087-e979-486f-ad87-0e050a83090f xref: FNA:bb12cad4-db12-4e59-a9fc-1676f2558a0a xref: FNA:c358e298-5926-42d6-8d49-a918cdc72406 xref: FNA:c5765385-917c-465e-83f8-b4fe5d693146 xref: FNA:c751440c-a7b3-4997-aed8-47f8254fd05f xref: FNA:cbb9ceb5-a404-4b5c-9c8f-4cf0ca6bade2 xref: FNA:e6a34ceb-a3e7-49f7-a4ac-cf0ea1552dc4 xref: FNA:ead20a1b-057b-4008-9466-bdb8e283aa82 xref: FNA:f18da584-2b0b-4b03-a614-40140a1cb89e xref: PO_GIT:207 is_a: PO:0009011 ! plant structure is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000349 ! plant epidermal initial cell relationship: part_of PO:0005679 ! plant epidermis [Term] id: PO:0000349 name: plant epidermal initial cell namespace: plant_anatomy def: "An initial cell (PO:0004011) that is part of an plant epidermis (PO:0005679) and gives rise to specialized cells." [PO:cooperl, TAIR_curator:Leonore_Reiser] subset: CL synonym: "célula inicial de la epidermis (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "epidermal initial (exact)" EXACT [] synonym: "表皮始原細胞 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0004011 ! initial cell relationship: part_of PO:0005679 ! plant epidermis [Term] id: PO:0001083 name: inflorescence development stage namespace: plant_structure_development_stage def: "A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049)." [POC:Laurel_Cooper] synonym: "panicle development (related)" RELATED [GRO:0007157] xref: GRO:0007157 xref: PO_GIT:517 is_a: PO:0025530 ! reproductive shoot system development stage [Term] id: PO:0004010 name: meristematic cell namespace: plant_anatomy def: "A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall." [ISBN:0471245208, POC:Laurel_Cooper] subset: CL synonym: "célula meristemática (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "stem cell (exact)" EXACT [] synonym: "分裂組織細胞 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: CL:0000034 xref: PO_GIT:272 is_a: PO:0025606 ! native plant cell [Term] id: PO:0004011 name: initial cell namespace: plant_anatomy alt_id: PO:0000070 def: "A meristematic cell (PO:0004010) that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body." [ISBN:0471245208] comment: Initial cells are often part of a portion of tissue that is composed mostly of somewhat older, differentiating cells. The division of an initial cell is often uneven, with the smaller daughter cell remaining meristematic. subset: CL synonym: "célula inicial (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "initial (exact)" EXACT [] synonym: "meristemoid (exact)" EXACT [] synonym: "stem cell (related)" RELATED [] synonym: "始原細胞 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:272 is_a: PO:0004010 ! meristematic cell [Term] id: PO:0005020 name: vascular bundle namespace: plant_anatomy def: "A portion of vascular tissue (PO:0009015) that is a unit strand of the vascular system (PO:0000034) and has as part xylem (PO:0005352) or phloem (PO:0005417)." [POC:curators] comment: May also contain portions of ground tissue (PO:0025059). The bundle sheath (PO:0006023) can also be part of a vascular bundle, if it is present. subset: Maize subset: TraitNet synonym: "haz vascular (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "vein (exact)" EXACT [] synonym: "維管束 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:431 is_a: PO:0009015 ! portion of vascular tissue [Term] id: PO:0005029 name: root primordium namespace: plant_anatomy def: "A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005)." [ISBN:0521288959, POC:curators] comment: A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). synonym: "portion of root primordium tissue (exact)" EXACT [] synonym: "primordio de raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "root primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "根原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:467 is_a: PO:0025127 ! primordium is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025433 ! root anlagen [Term] id: PO:0005421 name: parenchyma namespace: plant_anatomy def: "A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts." [POC:curators] comment: Parenchyma contains relatively unspecialized cells. subset: TraitNet synonym: "parénquima (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "portion of parenchyma tissue (exact)" EXACT [] synonym: "portion of parenchymatous tissue (exact)" EXACT [] synonym: "柔組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:107 is_a: PO:0025059 ! portion of ground tissue [Term] id: PO:0005597 name: cambium namespace: plant_anatomy def: "A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files." [ISBN:047125208] def: "A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files." [] comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599). subset: TraitNet synonym: "cambium (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "形成層 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:437 is_a: PO:0020145 ! lateral meristem [Term] id: PO:0005656 name: portion of secretory tissue namespace: plant_anatomy def: "A portion of plant tissue (PO:0009007) that form specialized structures producing a secretion." [Gramene:Pankaj_Jaiswal, ISBN:0471245208, POC:Laurel_Cooper] comment: The synonym gland does not imply non-secretory 'glands'. subset: TraitNet synonym: "gland (related)" RELATED [] synonym: "porción del tejido secretor (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "分泌組織の一部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:659 is_a: PO:0009007 ! portion of plant tissue [Term] id: PO:0005679 name: plant epidermis namespace: plant_anatomy def: "A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011)." [POC:curators] comment: The epidermis can be composed of one or more layers of cells. In some species of vascular plants, the epidermis, which is a primary tissue, is replaced by periderm, which is secondary tissue, later in development. The epidermis can also include trichomes, stomatal pores, root hairs, and rhizoids. subset: TraitNet synonym: "dermal tissue (exact)" EXACT [] synonym: "epidermal layer (exact)" EXACT [] synonym: "epidermides (exact, plural)" EXACT OMO:0003004 [FNA:35df04e5-fde5-465e-b79e-ae7d5e1537bb] synonym: "epidermis (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "epidermises (exact, plural)" EXACT OMO:0003004 [FNA:0d1bd0e6-c039-4de3-a162-68299a2f342a] synonym: "multiseriate epidermis (related)" RELATED [] synonym: "portion of epidermal tissue (exact)" EXACT [] synonym: "表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:109 is_a: PO:0009007 ! portion of plant tissue is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0006210 ! protoderm [Term] id: PO:0006001 name: phyllome namespace: plant_anatomy def: "A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148)." [POC:curators] subset: reference subset: TraitNet synonym: "filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム、葉(的）器官 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009008 ! plant organ is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025128 ! phyllome primordium relationship: part_of PO:0009006 ! shoot system [Term] id: PO:0006003 name: scale leaf namespace: plant_anatomy def: "A phyllome that is reduced in size relative to a vascular leaf on the same plant and is often associated with a perennating or dormant bud or a vegetatively propagating organ such as a rhizome." [ISBN:0080374913] comment: May be photosynthetic or non-photosynthetic. Some species have vascular leaves that are scale-like (such as Juniperus, Thuja, and Chamaecyparis). Annotations for scale-like leaves should go under vascular leaf (PO:0009025), not scale leaf. subset: reference subset: TraitNet synonym: "catáfila en escama (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "cataphyll (related)" RELATED [] synonym: "鱗片葉 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:273 is_a: PO:0006001 ! phyllome [Term] id: PO:0006016 name: leaf epidermis namespace: plant_anatomy def: "A portion of phyllome epidermis (PO:0025157) that is part of a leaf (PO:0025034)." [POC:curators] comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. synonym: "epidermis de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "foliage leaf epidermis (exact)" EXACT [] synonym: "phyllid epidermis (exact)" EXACT [] synonym: "葉表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0025157 ! phyllome epidermis intersection_of: PO:0025157 ! phyllome epidermis intersection_of: part_of PO:0025034 ! leaf relationship: part_of PO:0025034 ! leaf [Term] id: PO:0006018 name: adaxial leaf epidermis name: leaf adaxial epidermis namespace: plant_anatomy def: "A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf (PO:0025034)." [POC:Ramona_Walls] def: "A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf." [] comment: Used to refer to an adaxial epidermis of an entire leaf. More specific terms exist for leaf lamina adaxial epidermis and petiole adaxial epidermis. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. synonym: "epidermis adaxial de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "upper epidermis (related)" RELATED [] synonym: "upper leaf" RELATED [] synonym: "葉向軸側表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006016 ! leaf epidermis property_value: seeAlso https://www.inaturalist.org/observations/53324962 [Term] id: PO:0006019 name: abaxial leaf epidermis name: leaf abaxial epidermis namespace: plant_anatomy def: "A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf (PO:0025034)." [POC:curators, POC:Laurel_Cooper] def: "A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf." [] comment: Used to refer to an abaxial epidermis of an entire leaf. More specific terms exist for leaf lamina abaxial epidermis and petiole abaxial epidermis. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. synonym: "epidermis abaxial de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "leaf underside" EXACT [] synonym: "lower epidermis (related)" RELATED [] synonym: "lower leaf" RELATED [] synonym: "葉背軸側表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006016 ! leaf epidermis property_value: seeAlso https://www.inaturalist.org/observations/33275250 [Term] id: PO:0006035 name: shoot system epidermis namespace: plant_anatomy def: "A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020)." [ISBN:0471245208, POC:curators, POC:Laurel_Cooper] comment: Often interrupted by stomatal complexes (PO:0002000) and other structures. The shoot system epidermis is different from the root epidermis (PO:0006036) in its origin, function and structure. synonym: "epidermis del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "シュート表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:111 is_a: PO:0005679 ! plant epidermis intersection_of: PO:0005679 ! plant epidermis intersection_of: part_of PO:0009006 ! shoot system relationship: develops_from PO:0009020 ! meristem L1 layer relationship: part_of PO:0009006 ! shoot system [Term] id: PO:0006036 name: root epidermis namespace: plant_anatomy alt_id: PO:0006037 def: "A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005)." [ISBN:0080374913] comment: The root epidermis is different from the shoot epidermis in its origin, function and structure. synonym: "epiblem (related)" RELATED [] synonym: "epidermis de la raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "rhizodermis (related)" RELATED [] synonym: "根表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:111 is_a: PO:0005679 ! plant epidermis intersection_of: PO:0005679 ! plant epidermis intersection_of: part_of PO:0009005 ! root relationship: part_of PO:0009005 ! root [Term] id: PO:0006079 name: shoot system meristem namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006)." [Gramene:Pankaj_Jaiswal, POC:Laurel_Cooper] subset: TraitNet synonym: "meristema del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "シュート分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:472 xref: PO_GIT:583 is_a: PO:0009013 ! portion of meristem tissue relationship: part_of PO:0009006 ! shoot system [Term] id: PO:0006210 name: protoderm namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679)." [ISBN:0471245208, POC:Laurel_Cooper] comment: A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. synonym: "dermatogen cell (related)" RELATED [] synonym: "portion of protoderm tissue (exact)" EXACT [] synonym: "protodermis (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "前表皮、原表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:125 is_a: PO:0009013 ! portion of meristem tissue [Term] id: PO:0006504 name: leaf trichome namespace: plant_anatomy def: "A phyllome trichome that is part of a leaf epidermis." [POC:Ramona_Walls] comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. subset: TraitNet synonym: "phyllid trichome (narrow)" NARROW [] synonym: "tricoma de hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉毛（毛茸、糸状体） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:232 is_a: PO:0025186 ! phyllome trichome relationship: part_of PO:0006016 ! leaf epidermis [Term] id: PO:0007033 name: whole plant development stage namespace: plant_structure_development_stage def: "A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003)." [POC:curators] subset: TraitNet synonym: "cereal plant growth stage ontology (GRO:0007199) (related)" RELATED [] synonym: "maize growth stage (GRO:0007002) (related)" RELATED [] synonym: "plant growth stages in Arabidopsis (TAIR:0000021) (related)" RELATED [] synonym: "rice growth stage (GRO:0007040) (related)" RELATED [] synonym: "Solanaceae whole plant growth stages (SGN:0000001) (related)" RELATED [] synonym: "sorghum growth stage (GRO:0007124) (related)" RELATED [] synonym: "wheat, barley and oat growth stage (GRO:0007156) (related)" RELATED [] xref: PO_GIT:390 is_a: PO:0009012 ! plant structure development stage relationship: has_participant PO:0000003 ! whole plant [Term] id: PO:0008016 name: vegetative shoot apical meristem namespace: plant_anatomy def: "A shoot apical meristem (PO:0020148) that gives rise to the apical growth of vegetative tissues and organs." [Gramene:Chih-Wei_Tung] synonym: "meristema vegetativo apical del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "vegetative meristem (related)" RELATED [] synonym: "栄養シュート頂端分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:36 is_a: PO:0020148 ! shoot apical meristem [Term] id: PO:0008028 name: reproductive shoot apical meristem namespace: plant_anatomy def: "A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs." [Gramene:Chih-Wei_Tung] synonym: "meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "生殖シュート頂端 分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:36 is_a: PO:0020148 ! shoot apical meristem relationship: part_of PO:0025222 ! reproductive shoot apex [Term] id: PO:0008039 name: stem base namespace: plant_anatomy def: "The basal part of stem." [Gramene:Chih-Wei_Tung] synonym: "base del tallo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "gametophore stem base (exact)" EXACT [] synonym: "茎基部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0025001 ! cardinal organ part relationship: part_of PO:0009047 ! stem [Term] id: PO:0009001 name: fruit namespace: plant_anatomy alt_id: PO:0020067 alt_id: PO:0020068 alt_id: PO:0020069 alt_id: PO:0020070 alt_id: PO:0020071 alt_id: PO:0020072 alt_id: PO:0020073 alt_id: PO:0020074 alt_id: PO:0020076 alt_id: PO:0020077 alt_id: PO:0020078 alt_id: PO:0020079 alt_id: PO:0020080 alt_id: PO:0020082 alt_id: PO:0020083 alt_id: PO:0020087 alt_id: PO:0020107 def: "A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010)." [NYBG:Brandon_Sinn, NYBG:Dario_Cavaliere, POC:curators, POC:Laurel_Cooper] comment: A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. subset: Angiosperm subset: Arabidopsis subset: Maize subset: Poaceae subset: Rice subset: TraitNet synonym: "aggregate fruit (broad)" BROAD [] synonym: "coenocarp (narrow)" NARROW [FNA:c13b1312-1cc5-4ace-98e2-fde12aec09da] synonym: "compound fruit (broad)" BROAD [] synonym: "dehiscent fruit (broad)" BROAD [] synonym: "diaspore (broad)" BROAD [] synonym: "frucht (exact, German)" EXACT German [NYBG:Brandon_Sinn, NYBG:Dario_Cavaliere] synonym: "fruto (exact, Spanish)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "indehiscent fruit (broad)" BROAD [] synonym: "multiple fruit (broad)" BROAD [] synonym: "propagule (broad)" BROAD [] synonym: "syncarp (narrow)" NARROW [FNA:67fa41ae-b735-4d89-b5db-7631b873ef7a] synonym: "果実 (exact, Japanese)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:67fa41ae-b735-4d89-b5db-7631b873ef7a xref: FNA:c13b1312-1cc5-4ace-98e2-fde12aec09da xref: PO_GIT:76 is_a: PO:0025496 ! multi-tissue plant structure is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0009062 ! gynoecium property_value: seeAlso https://www.inaturalist.org/observations/138563159 [Term] id: PO:0009002 name: plant cell namespace: plant_anatomy def: "A cell which is a plant structure (PO:0009011)." [CL:0000000, POC:curators] comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. subset: CL subset: reference subset: TraitNet synonym: "célula vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "cell (broad)" BROAD [] synonym: "植物細胞 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: GO:0005623 xref: PO_GIT:56 is_a: PO:0009011 ! plant structure disjoint_from: PO:0009007 ! portion of plant tissue disjoint_from: PO:0009008 ! plant organ disjoint_from: PO:0025001 ! cardinal organ part disjoint_from: PO:0025007 ! collective plant organ structure [Term] id: PO:0009005 name: root namespace: plant_anatomy alt_id: PO:0003006 def: "A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately." [ISBN:978-0879015329, ISBN:9780964022157, NYBG:Brandon_Sinn, NYBG:Dario_Cavaliere, POC:curators, POC:Laurel_Cooper] comment: Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). subset: Angiosperm subset: Gymnosperms subset: Maize subset: Musa subset: Potato subset: reference subset: Rice subset: Tomato subset: TraitNet synonym: "aerial root (narrow)" NARROW [] synonym: "climbing root (narrow)" NARROW [FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f] synonym: "raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "radices (exact, plural)" EXACT OMO:0003004 [FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d] synonym: "radix (exact)" EXACT [FNA:e6315684-fc99-4976-b39d-b356c4b7e7fd] synonym: "根 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f xref: PO_GIT:578 is_a: PO:0025004 ! plant axis is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0005029 ! root primordium relationship: part_of PO:0025025 ! root system property_value: seeAlso https://www.inaturalist.org/observations/139148692 [Term] id: PO:0009006 name: shoot system namespace: plant_anatomy def: "A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them." [POC:curators, POC:Laurel_Cooper] comment: The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. subset: reference subset: TraitNet synonym: "Poaceae crown (related)" RELATED [] synonym: "shoot (related)" RELATED [] synonym: "sistema de epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "thalli (related, plural)" RELATED OMO:0003004 [FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85] synonym: "thallus (related)" RELATED [FNA:02756ad4-a09c-48d7-8754-903254e557a9] synonym: "tree crown (narrow)" NARROW [] synonym: "シュート系、苗条系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:02756ad4-a09c-48d7-8754-903254e557a9 xref: FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 xref: PO_GIT:135 is_a: PO:0025007 ! collective plant organ structure disjoint_from: PO:0025025 ! root system [Term] id: PO:0009007 name: portion of plant tissue namespace: plant_anatomy def: "A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types." [POC:curators, TAIR_curator:Leonore_Reiser] comment: A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. subset: reference subset: TraitNet synonym: "plant tissue (related)" RELATED [] synonym: "porción de un tejido vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "portion of tissue (broad)" BROAD [] synonym: "tissue (broad)" BROAD [] synonym: "植物組織の一部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:59 is_a: PO:0009011 ! plant structure disjoint_from: PO:0009008 ! plant organ disjoint_from: PO:0025001 ! cardinal organ part disjoint_from: PO:0025007 ! collective plant organ structure [Term] id: PO:0009008 name: plant organ namespace: plant_anatomy def: "A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path." [POC:curators] comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). subset: TraitNet synonym: "órgano vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "compound plant organ (related)" RELATED [] synonym: "organ (broad)" BROAD [] synonym: "simple plant organ (related)" RELATED [PATO:01503] synonym: "植物 器官 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PATO:01503 xref: PO_GIT:55 is_a: PO:0025496 ! multi-tissue 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, PO:cooperl, 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. comment: These terms (i.e., subclasses of plant structure) can be used to describe the location of a plant gall (e.g., on leaf or stem) and also the parts of a gall (e.g., nectary, larval chamber). {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-2119-4663"} 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:0009012 name: plant structure development stage namespace: plant_structure_development_stage alt_id: PO:0007021 def: "A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes." [BFO:0000003, GO:0032502, POC:curators] comment: Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. subset: TraitNet synonym: "Arabidopsis growth (related)" RELATED [TAIR:0000205] synonym: "etapa de desarrollo de estructura vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "plant growth and development stage (exact)" EXACT [] xref: PO_GIT:185 xref: TAIR:0000205 is_a: BFO:0000015 ! process [Term] id: PO:0009013 name: portion of meristem tissue namespace: plant_anatomy def: "A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth." [APweb:Glossary, Gramene:Pankaj_Jaiswal] subset: TraitNet synonym: "meristem (exact)" EXACT [] synonym: "meristema (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "meristematic tissue (exact)" EXACT [] synonym: "分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:472 is_a: PO:0009007 ! portion of plant tissue relationship: has_part PO:0004010 ! meristematic cell [Term] id: PO:0009015 name: portion of vascular tissue namespace: plant_anatomy def: "A portion of plant tissue (PO:0009007) that has as part one or more tracheary elements (PO:0000290) or sieve elements (PO:0025406)." [POC:curators] comment: Functions in conduction and support. In shoot axes (PO:0025029), vascular tissue is often found as part of a shoot axis stele (PO:0025198) or as scattered vascular bundles (PO:0005020). May include other types of tissues or cells, such as parenchyma (PO:0005421) or fiber cells (PO:0025407). subset: TraitNet synonym: "porción de tejido vascular (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "vascular system (related)" RELATED [] synonym: "vascular tissue (exact)" EXACT [] synonym: "維管束細胞の一部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: BTO:0001432 xref: PO_GIT:431 is_a: PO:0009007 ! portion of plant tissue [Term] id: PO:0009020 name: meristem L1 layer namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that is the outermost layer of a shoot apical meristem (PO:0020148) and gives rise to a shoot system epidermis (PO:0006035)." [Gramene:Pankaj_Jaiswal, PMID:11283725, PMID:12221985, POC:Laurel_Cooper] comment: The cells of the meristem L1 layer divide in a strictly anticlinical fashion. synonym: "meristema L1 (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "tunica (related)" RELATED [] synonym: "分裂組織 L1 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:150 xref: PO_GIT:576 is_a: PO:0009013 ! portion of meristem tissue relationship: part_of PO:0020148 ! shoot apical meristem [Term] id: PO:0009023 name: leaf axil namespace: plant_anatomy def: "An axil that is the space between a shoot axis and a leaf that branches from the shoot axis." [POC:Ramona_Walls] synonym: "hoja axilar (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉軸 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:104 is_a: PO:0025224 ! axil [Term] id: PO:0009025 name: vascular leaf namespace: plant_anatomy def: "A leaf (PO:0025034) in a vascular plant." [POC:curators] comment: Has vascular tissue. From APweb Glossary: In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud. Occurs in the sporophytic phase of a plant life cycle. subset: Angiosperm subset: Arabidopsis subset: Citrus subset: Gymnosperms subset: Maize subset: Musa subset: Potato subset: Pteridophytes subset: reference subset: Rice subset: Tomato subset: TraitNet synonym: "ascidia (narrow)" NARROW [FNA:06544712-db97-4208-b188-c4b756a53c72] synonym: "ascidium (narrow)" NARROW [FNA:a97f1513-7684-49d4-92f5-934d1c8b3e1c] synonym: "crozier (related)" RELATED [FNA:87e7efa9-89d7-4249-be74-bc22a0466a05] synonym: "fiddlehead (narrow)" NARROW [FNA:d894ba18-4523-484c-abab-26d1cac75bc4] synonym: "foliage leaf (exact)" EXACT [] synonym: "frond (narrow)" NARROW [] synonym: "hoja vascular (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "leaf, vascular (exact)" EXACT [] synonym: "macrophyll (related)" RELATED [FNA:c1142d9b-c42a-45e1-93ac-9cbe9575321e] synonym: "megaphyll (related)" RELATED [FNA:c26c826a-30d6-494e-a2f1-05540465c9fc] synonym: "needle-like leaf (narrow)" NARROW [] synonym: "pitcher (narrow)" NARROW [FNA:30d8bef3-ad1a-44ed-a995-24c3e342aefd] synonym: "pitcher blade (narrow)" NARROW [FNA:d3928bf3-1d8a-4fe5-a728-95c13c3a0f90] synonym: "pitcher-blade (narrow)" NARROW [FNA:30c47c20-f459-4518-8657-feed7eb92fe4] synonym: "scale-like leaf (narrow)" NARROW [] synonym: "sterile frond (narrow)" NARROW [FNA:a4dc40f4-92f9-4ba5-b616-a84564f63fed] synonym: "trophophyll (narrow)" NARROW [FNA:8654d268-1e4c-4edf-b937-82a965b4edef] synonym: "vascular leaves (exact, plural)" EXACT OMO:0003004 [FNA:c7d9d167-4121-43b0-b2fe-bb1ae9d6d3a6] synonym: "維管束のある葉, または維管束植物の葉 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:06544712-db97-4208-b188-c4b756a53c72 xref: FNA:30c47c20-f459-4518-8657-feed7eb92fe4 xref: FNA:30d8bef3-ad1a-44ed-a995-24c3e342aefd xref: FNA:8654d268-1e4c-4edf-b937-82a965b4edef xref: FNA:87e7efa9-89d7-4249-be74-bc22a0466a05 xref: FNA:a4dc40f4-92f9-4ba5-b616-a84564f63fed xref: FNA:a97f1513-7684-49d4-92f5-934d1c8b3e1c xref: FNA:c1142d9b-c42a-45e1-93ac-9cbe9575321e xref: FNA:c26c826a-30d6-494e-a2f1-05540465c9fc xref: FNA:d3928bf3-1d8a-4fe5-a728-95c13c3a0f90 xref: FNA:d894ba18-4523-484c-abab-26d1cac75bc4 xref: PO_GIT:137 is_a: PO:0025034 ! leaf relationship: develops_from PO:0000017 ! vascular leaf primordium relationship: participates_in PO:0028002 ! sporophyte development stage [Term] id: PO:0009035 name: nectary namespace: plant_anatomy def: "A portion of secretory tissue (PO:0005656) which is a multicellular glandular structure secreting a liquid containing organic substances, including sugars." [Gramene:Pankaj_Jaiswal, ISBN:0471245208, POC:Laurel_Cooper] def: "A portion of secretory tissue (PO:0005656) which is a multicellular glandular structure secreting a liquid containing organic substances, including sugars." [] subset: reference subset: TraitNet synonym: "nectario (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "蜜腺 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:659 is_a: PO:0005656 ! portion of secretory tissue relationship: part_of PO:0009006 ! shoot system [Term] id: PO:0009046 name: flower namespace: plant_anatomy alt_id: PO:0004541 def: "A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part." [POC:curators] comment: The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form. subset: Angiosperm subset: reference subset: TraitNet synonym: "Asteraceae floret (narrow)" NARROW [] synonym: "basal flower (narrow)" NARROW [CO_125:0000019] synonym: "double flower (narrow)" NARROW [] synonym: "flor (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "floret (related)" RELATED [] synonym: "hermaphrodite flower (narrow)" NARROW [CO_125:0000028] synonym: "monoclinous flower (narrow)" NARROW [] synonym: "perfect flower (narrow)" NARROW [] synonym: "花 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:160 xref: PO_GIT:259 is_a: PO:0025082 ! reproductive shoot system is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000229 ! flower meristem [Term] id: PO:0009047 name: stem namespace: plant_anatomy def: "A shoot axis (PO:0025029) that is the primary axis of a plant." [POC:curators] comment: A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic. subset: reference subset: TraitNet synonym: "bole (narrow)" NARROW [FNA:a5ba9e16-e0af-4430-a3a0-7aeb052fbffd] synonym: "caña (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "cane (narrow)" NARROW [] synonym: "caudex (narrow)" NARROW [FNA:cea24c10-d5ff-435f-aa40-db77dcbd27f0] synonym: "caudices (narrow, plural)" NARROW OMO:0003004 [FNA:3c0e37e8-e363-4962-847e-5f9f2906d0f8] synonym: "core (narrow)" NARROW [] synonym: "culm (exact)" EXACT [] synonym: "eje primario (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "primary axis (exact)" EXACT [] synonym: "primary stem (exact)" EXACT [FNA:e3b142f6-37cf-4c1f-be07-b64a90feb131] synonym: "primocane (narrow)" NARROW [FNA:58fb080c-dd6b-4172-b564-737091c72980] synonym: "scape (narrow)" NARROW [FNA:201dbd71-51cd-4138-8f61-3c3fdd55d02d] synonym: "stalk (narrow)" NARROW [] synonym: "tallo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "tronco (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "trunk (narrow)" NARROW [] synonym: "茎 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:201dbd71-51cd-4138-8f61-3c3fdd55d02d xref: FNA:3c0e37e8-e363-4962-847e-5f9f2906d0f8 xref: FNA:58fb080c-dd6b-4172-b564-737091c72980 xref: FNA:a5ba9e16-e0af-4430-a3a0-7aeb052fbffd xref: FNA:cea24c10-d5ff-435f-aa40-db77dcbd27f0 xref: PO_GIT:52 xref: PO_GIT:96 is_a: PO:0025029 ! shoot axis property_value: seeAlso https://www.inaturalist.org/observations/125859005 [Term] id: PO:0009049 name: inflorescence namespace: plant_anatomy alt_id: PO:0009048 alt_id: PO:0009050 alt_id: PO:0020088 alt_id: PO:0020111 alt_id: PO:0020112 alt_id: PO:0020113 alt_id: PO:0020114 alt_id: PO:0020115 alt_id: PO:0020116 alt_id: PO:0020117 alt_id: PO:0020118 alt_id: PO:0020119 alt_id: PO:0020120 def: "A reproductive shoot system (PO:0025082) that has as parts all of the shoot axes (PO:0025029) and flowers (PO:0009046; must have two or more) distal to the most distal leaf (PO:0009025)." [NYBG:Brandon_Sinn, NYBG:Dario_Cavaliere, POC:Laurel_Cooper, POC:Ramona_Walls] comment: An inflorescence is a reproductive shoot system from which at least two flowers develop. The growth pattern of an inflorescence may be monopodial (single main shoot axis), sympodial (growth only occurs from axillary meristems), or both. An inflorescence axis (PO:0020122) can be determinate or indeterminate. An inflorescence flower pedicel (PO:0009052) is the ultimate axis in an inflorescence. The flower (PO:0009046) of many plants, for example Magnolia spp., is solitary. subset: Angiosperm subset: reference subset: TraitNet synonym: "inflorescencia (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "Triticeae spike (narrow)" NARROW [] synonym: "花序 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:260 xref: PO_GIT:71 is_a: PO:0025082 ! reproductive shoot system is_a: PO:0025496 ! multi-tissue plant structure is_a: UBERON:0001062 ! anatomical entity relationship: has_part PO:0009046 ! flower relationship: participates_in PO:0001083 ! inflorescence development stage property_value: seeAlso https://www.inaturalist.org/observations/118434796 [Term] id: PO:0009062 name: gynoecium namespace: plant_anatomy alt_id: PO:0006317 alt_id: PO:0006357 alt_id: PO:0006365 alt_id: PO:0006384 alt_id: PO:0006391 alt_id: PO:0006394 alt_id: PO:0006403 alt_id: PO:0006404 alt_id: PO:0006423 alt_id: PO:0006424 alt_id: PO:0006425 alt_id: PO:0006426 alt_id: PO:0025089 def: "A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046)." [POC:curators] comment: If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). subset: reference subset: TraitNet synonym: "apocarpous gynoecium (narrow)" NARROW [] synonym: "ginoecio (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "gynaecium (exact)" EXACT [FNA:03f034c5-6bd6-4846-8ef7-c5190d09008c] synonym: "gynoecia (exact, plural)" EXACT OMO:0003004 [FNA:226a743c-7988-4b66-b163-2ce80d7c8a70] synonym: "gynoecium of ear floret (narrow)" NARROW [] synonym: "gynoecium of lower floret of pedicellate spikelet of ear (narrow)" NARROW [] synonym: "gynoecium of lower floret of pedicellate spikelet of tassel (narrow)" NARROW [] synonym: "gynoecium of lower floret of sessile spikelet of ear (narrow)" NARROW [] synonym: "gynoecium of lower floret of sessile spikelet of tassel (narrow)" NARROW [] synonym: "gynoecium of tassel floret (narrow)" NARROW [] synonym: "gynoecium of upper floret of pedicellate spikelet of ear (narrow)" NARROW [] synonym: "gynoecium of upper floret of pedicellate spikelet of tassel (narrow)" NARROW [] synonym: "gynoecium of upper floret of sessile spikelet of ear (narrow)" NARROW [] synonym: "gynoecium of upper floret of sessile spikelet of tassel (narrow)" NARROW [] synonym: "pistil (broad)" BROAD [] synonym: "Poaceae gynoecium (narrow)" NARROW [] synonym: "syncarpous gynoecium (narrow)" NARROW [] synonym: "Zea gynoecium (narrow)" NARROW [] synonym: "雌蕊群 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:470 xref: PO_GIT:71 xref: PO_GIT:98 is_a: PO:0025023 ! collective phyllome structure is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000019 ! gynoecium primordium relationship: part_of PO:0009046 ! flower [Term] id: PO:0020038 name: petiole namespace: plant_anatomy def: "A stalk (PO:0025066) of a vascular leaf (PO:0009025)." [APweb:Glossary, Gramene:Pankaj_Jaiswal] def: "A stalk (PO:0025066) of a vascular leaf (PO:0009025)." [] subset: TraitNet synonym: "pecíolo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉柄 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0025066 ! stalk relationship: part_of PO:0009025 ! vascular leaf property_value: seeAlso https://www.inaturalist.org/observations/32852385 [Term] id: PO:0020039 name: leaf lamina namespace: plant_anatomy def: "A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present." [POC:curators] comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. subset: TraitNet synonym: "lámina de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "leaf blade (related)" RELATED [] synonym: "葉身（葉片） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:428 xref: PO_GIT:70 is_a: PO:0025396 ! phyllome lamina relationship: part_of PO:0025034 ! leaf property_value: seeAlso https://www.inaturalist.org/observations/62631563 [Term] id: PO:0020043 name: compound leaf namespace: plant_anatomy def: "A leaf having two or more distinct leaflets that are evident as such from early in development." [APweb:Glossary] synonym: "hoja compuesta (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "複葉 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009025 ! vascular leaf [Term] id: PO:0020049 name: leaflet namespace: plant_anatomy def: "A cardinal organ part (PO:0025001) that is one of the ultimate segments of a compound leaf (PO:0020043)." [APweb:Glossary, POC:laurel_cooper] def: "A cardinal organ part (PO:0025001) that is one of the ultimate segments of a compound leaf (PO:0020043)." [] subset: TraitNet synonym: "folíolo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "pinna (narrow)" NARROW [FNA:9fc865bf-ac88-4ea9-a4e9-0d7b2b31cf44] synonym: "pinnae (narrow, plural)" NARROW OMO:0003004 [FNA:1d6bb560-f346-409b-b078-9bd2fd30e472] synonym: "pinnule (narrow)" NARROW [FNA:6e19c80b-c4a0-4d62-bf40-3206dce4af1c] synonym: "小葉 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:1d6bb560-f346-409b-b078-9bd2fd30e472 xref: FNA:6e19c80b-c4a0-4d62-bf40-3206dce4af1c xref: FNA:9fc865bf-ac88-4ea9-a4e9-0d7b2b31cf44 xref: PO_GIT:70 is_a: PO:0025001 ! cardinal organ part relationship: part_of PO:0020043 ! compound leaf property_value: seeAlso https://www.inaturalist.org/observations/90131758 [Term] id: PO:0020054 name: bud scale leaf namespace: plant_anatomy def: "A scale leaf that surrounds a dormant or perennating bud." [UMSL_curator:tk] synonym: "bud scale (exact)" EXACT [] synonym: "escama de la yema (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "芽鱗片葉 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006003 ! scale leaf [Term] id: PO:0020128 name: leaf margin namespace: plant_anatomy def: "A phyllome margin (PO:0025018) that is part of a leaf (PO:0025034)." [POC:curators] def: "A phyllome margin (PO:0025018) that is part of a leaf (PO:0025034)." [] comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. subset: TraitNet synonym: "margen de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉縁 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:85 is_a: PO:0025018 ! phyllome margin intersection_of: PO:0025018 ! phyllome margin intersection_of: part_of PO:0025034 ! leaf relationship: part_of PO:0025034 ! leaf [Term] id: PO:0020138 name: leaf lamina vein name: leaf vein namespace: plant_anatomy def: "A phyllome lamina vein (PO:0025348) that is part of a leaf lamina vascular system (PO:0000048)." [POC:curators] def: "A phyllome lamina vein (PO:0025348) that is part of a leaf lamina vascular system (PO:0000048)." [] subset: TraitNet synonym: "leaf lamina vascular bundle (exact)" EXACT [] synonym: "leaf lamina vein" EXACT [] synonym: "vena de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉身葉脈 ？ (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:410 xref: PO_GIT:435 is_a: PO:0025348 ! phyllome lamina vein relationship: part_of PO:0000048 ! leaf lamina vascular system property_value: seeAlso https://www.inaturalist.org/observations/54078107 [Term] id: PO:0020139 name: leaf midvein namespace: plant_anatomy def: "A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025)." [POC:curators] def: "A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025)." [] comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075). synonym: "mid rib" RELATED [] synonym: "mid rib (broad)" BROAD [] synonym: "mid-rib" RELATED [] synonym: "mid-rib (broad)" BROAD [] synonym: "midrib" RELATED [] synonym: "midrib (broad)" BROAD [] synonym: "vascular leaf costa (related)" RELATED [FNA:e05450e0-b820-465a-ba99-ced17c5a34b0] synonym: "vascular leaf costae (related, plural)" RELATED OMO:0003004 [FNA:d0ce6c67-625d-4187-bd50-3af01e6e68a6] synonym: "vascular leaf midvein" EXACT [] synonym: "vascular leaf midvein (exact)" EXACT [] synonym: "vena media" EXACT [] synonym: "vena media (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉主脈、中央脈、中脈 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:d0ce6c67-625d-4187-bd50-3af01e6e68a6 xref: FNA:e05450e0-b820-465a-ba99-ced17c5a34b0 xref: PO_GIT:435 is_a: PO:0025413 ! primary leaf vein property_value: seeAlso https://www.inaturalist.org/observations/62631219 [Term] id: PO:0020140 name: secondary leaf vein namespace: plant_anatomy def: "A leaf lamina vein (PO:0020138) arising from a primary leaf vein (PO:0025413)." [Gramene:Pankaj_Jaiswal] def: "A leaf lamina vein (PO:0020138) arising from a primary leaf vein (PO:0025413)." [] comment: Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as found in some ferns and gymnosperms. synonym: "cross-vein (narrow)" NARROW [FNA:dba43715-e71f-4192-87a2-489f5b9b4c82] synonym: "veinlet (related)" RELATED [] synonym: "vena secundaria (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "二次葉脈 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:dba43715-e71f-4192-87a2-489f5b9b4c82 xref: PO_GIT:435 is_a: PO:0020138 ! leaf lamina vein property_value: seeAlso https://www.inaturalist.org/observations/54078107 [Term] id: PO:0020144 name: apical meristem namespace: plant_anatomy def: "A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025)." [Gramene:Pankaj_Jaiswal, POC:curators, POC:Laurel_Cooper] subset: TraitNet synonym: "AM (exact)" EXACT [] synonym: "meristema apical (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "primary meristem (related)" RELATED [] synonym: "promeristem (broad)" BROAD [] synonym: "頂端分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:579 is_a: PO:0009013 ! portion of meristem tissue relationship: has_part PO:0006210 ! protoderm [Term] id: PO:0020145 name: lateral meristem namespace: plant_anatomy def: "A portion of meristem (PO:0009013) tissue located parallel to the sides of a shoot axis (PO:0025029) or root (PO:0009005) that participates in lateral growth." [ISBN:047125208] comment: A term for lateral growth has been requested in GO. Lateral meristems contribute to an increase in the cross-sectional area of a shoot axis or root. Examples of lateral meristems are: cambium (PO:0005597) (includes cork cambium (PO:0005599) and vascular cambium (PO:0005598)), shoot lateral meristem (PO:0006344) (includes primary thickening meristem (PO:0005039)), root lateral meristem (PO:0006308), and secondary thickening meristem (PO:0025414). Contrasts with apical meristem (PO:0020144), phyllome marginal meristem (PO:0025404), or intercalary meristem (PO:0006073). subset: TraitNet synonym: "lateral growth meristem (exact)" EXACT [] synonym: "meristema lateral (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "secondary meristem (related)" RELATED [] synonym: "側 分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:437 is_a: PO:0009013 ! portion of meristem tissue relationship: part_of PO:0025004 ! plant axis [Term] id: PO:0020148 name: shoot apical meristem namespace: plant_anatomy def: "A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232)." [POC:Laurel_Cooper, UMSL_curator:fz] subset: TraitNet synonym: "meristema apical del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "primary shoot meristem (related)" RELATED [] synonym: "promeristem (broad)" BROAD [] synonym: "SAM (exact)" EXACT [] synonym: "茎頂分裂組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:472 is_a: PO:0006079 ! shoot system meristem is_a: PO:0020144 ! apical meristem relationship: part_of PO:0000037 ! shoot axis apex [Term] id: PO:0025001 name: cardinal organ part namespace: plant_anatomy def: "A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types." [POC:curators] comment: Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs. subset: Arabidopsis subset: TraitNet synonym: "cardinal part of plant organ (exact)" EXACT [] synonym: "parte de un órgano cardinal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "基本的な（主要な）器官部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:52 xref: PO_GIT:60 is_a: PO:0025498 ! cardinal part of multi-tissue plant structure intersection_of: PO:0025498 ! cardinal part of multi-tissue plant structure intersection_of: part_of PO:0009008 ! plant organ relationship: part_of PO:0009008 ! plant organ created_by: rwalls creation_date: 2010-02-11T01:18:24Z [Term] id: PO:0025004 name: plant axis namespace: plant_anatomy def: "An axial plant organ (PO:0009008)." [POC:curators] comment: Includes roots and shoots. subset: TraitNet synonym: "eje de la planta (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "plant axes (exact, plural)" EXACT OMO:0003004 [FNA:2355281f-ab10-4ae2-a3d8-672cace068a8] synonym: "植物軸（軸柱） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009008 ! plant organ created_by: rwalls creation_date: 2010-07-01T03:44:41Z [Term] id: PO:0025005 name: plant organ margin namespace: plant_anatomy def: "A cardinal organ part (PO:0025001) that is the edge of a plant organ (PO:0009008) and the area immediately internally adjacent to it." [POC:curators, POC:laurel_cooper] comment: Only flattened or laminar plant organs or organ parts will have a margin. subset: TraitNet synonym: "margen de un órgano (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "器官縁 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:52 xref: PO_GIT:70 xref: PO_GIT:72 is_a: PO:0025001 ! cardinal organ part relationship: part_of PO:0025513 ! plant organ lamina created_by: rwalls creation_date: 2010-03-12T10:33:57Z [Term] id: PO:0025007 name: collective plant organ structure namespace: plant_anatomy def: "A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007)." [POC:curators] comment: Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. subset: TraitNet synonym: "estructura vegetal colectiva de órgano (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "集合植物器官構造 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:63 is_a: PO:0025497 ! collective plant structure relationship: has_part PO:0009008 ! plant organ created_by: rwalls creation_date: 2010-02-09T04:12:11Z [Term] id: PO:0025018 name: phyllome margin namespace: plant_anatomy def: "A plant organ margin (PO:0025005) that is part of a phyllome lamina (PO:0025396)." [POC:curators, POC:laurel_cooper] subset: TraitNet synonym: "margen del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム縁 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:70 is_a: PO:0025005 ! plant organ margin intersection_of: PO:0025005 ! plant organ margin intersection_of: part_of PO:0025396 ! phyllome lamina relationship: part_of PO:0025396 ! phyllome lamina created_by: rwalls creation_date: 2010-04-02T10:51:16Z [Term] id: PO:0025023 name: collective phyllome structure namespace: plant_anatomy alt_id: PO:0008033 def: "A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005)." [POC:curators] subset: TraitNet synonym: "cycle (broad)" BROAD [FNA:d42df0a9-60f4-4c24-9c0b-ba815272f2fe] synonym: "estructura colectiva del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "floral whorl (narrow)" NARROW [GO:0048438, GO:0048457, GO:0048458, GO:0048459] synonym: "phyllome whorl (related)" RELATED [] synonym: "verticil (broad)" BROAD [FNA:12607624-3d2a-4113-bd86-0e2557f2f473] synonym: "whorl (narrow)" NARROW [] synonym: "葉的器官が集まった構造 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:12607624-3d2a-4113-bd86-0e2557f2f473 xref: FNA:d42df0a9-60f4-4c24-9c0b-ba815272f2fe xref: GO:0048438 xref: GO:0048457 xref: GO:0048458 xref: GO:0048459 xref: PO_GIT:90 xref: PO_GIT:99 is_a: PO:0025007 ! collective plant organ structure created_by: Laurel_Cooper creation_date: 2010-04-28T11:04:34Z [Term] id: PO:0025025 name: root system namespace: plant_anatomy def: "A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof." [POC:curators, POC:Laurel_Cooper] comment: Generally the below ground portion of a vascular plant. subset: TraitNet synonym: "root (broad)" BROAD [FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9] synonym: "sistema de raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "根系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9 xref: PO_GIT:136 is_a: PO:0025007 ! collective plant organ structure relationship: participates_in PO:0028002 ! sporophyte development stage created_by: rwalls creation_date: 2010-07-01T02:11:26Z [Term] id: PO:0025029 name: shoot axis namespace: plant_anatomy def: "A plant axis (PO:0025004) that is part of a shoot system (PO:0009006)." [POC:curators] comment: Often bears leaves and branches. In vascular plants, has at least one node and one internode. subset: Angiosperm subset: Arabidopsis subset: Maize subset: Poaceae subset: Rice subset: TraitNet synonym: "caullome (exact)" EXACT [] synonym: "eje del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "shoot (related)" RELATED [] synonym: "シュート軸 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0025004 ! plant axis relationship: part_of PO:0009006 ! shoot system created_by: rwalls creation_date: 2010-07-01T03:46:35Z [Term] id: PO:0025034 name: leaf namespace: plant_anatomy def: "A phyllome (PO:0006001) that is not associated with a reproductive structure." [POC:curators] subset: TraitNet synonym: "hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "葉 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:274 xref: PO_GIT:301 is_a: PO:0006001 ! phyllome property_value: seeAlso https://www.inaturalist.org/observations/60861819 created_by: rwalls creation_date: 2010-07-12T01:31:44Z [Term] id: PO:0025059 name: portion of ground tissue namespace: plant_anatomy def: "Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015)." [ISBN:0471244554, ISBN:0716710072] comment: Develops from the ground meristem (PO:0025594). subset: TraitNet synonym: "fundamental tissue (exact)" EXACT [ISBN:0471244554] synonym: "porción del tejido fundamental (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "基本組織の一部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:106 is_a: PO:0009007 ! portion of plant tissue is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025594 ! ground meristem created_by: Laurel_Cooper creation_date: 2009-12-17T03:06:13Z [Term] id: PO:0025060 name: lamina namespace: plant_anatomy def: "A cardinal part of multi-tissue plant structure (PO:0025498) that is thin and flat." [POC:curators] comment: PATO:0000407 (flat) and PATO:0000592 (thin). subset: TraitNet synonym: "blade (exact)" EXACT [FNA:7dd0c248-f531-4cfe-b196-882e99f4c32b] synonym: "lámina (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "laminae (exact, plural)" EXACT OMO:0003004 [FNA:12cea564-84fd-40c9-9671-1db2ec4eac90] synonym: "葉身、葉片 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:428 xref: PO_GIT:70 is_a: PO:0025498 ! cardinal part of multi-tissue plant structure created_by: Laurel_Cooper creation_date: 2009-12-18T11:23:59Z [Term] id: PO:0025066 name: stalk namespace: plant_anatomy def: "A cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part." [POC:curators] comment: Some stalks may be ridged or grooved. subset: TraitNet synonym: "stipe (related)" RELATED [FNA:21cee2f5-016a-44c6-b7a5-1fff6adc7e35] synonym: "tallo de alto orden (secundario, terciario, etc) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "柄 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:21cee2f5-016a-44c6-b7a5-1fff6adc7e35 xref: PATO:0001873 xref: PATO:0002226 xref: PO_GIT:52 xref: PO_GIT:78 is_a: PO:0025001 ! cardinal organ part created_by: Laurel_Cooper creation_date: 2009-12-18T10:09:17Z [Term] id: PO:0025073 name: branch namespace: plant_anatomy def: "A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007)." [POC:curators] comment: In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants. subset: TraitNet synonym: "branchlet (narrow)" NARROW [FNA:32d32293-adee-47ae-b1ba-bd9bd22230c2] synonym: "higher order axis (narrow)" NARROW [] synonym: "ramificación (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "secondary axis (narrow)" NARROW [] synonym: "shoot axis branch (exact)" EXACT [POC:curators] synonym: "stem" RELATED [] synonym: "tertiary axis (narrow)" NARROW [] synonym: "twig" RELATED [] synonym: "twig (narrow)" NARROW [] synonym: "枝 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:32d32293-adee-47ae-b1ba-bd9bd22230c2 xref: PO_GIT:134 is_a: PO:0025029 ! shoot axis property_value: seeAlso https://www.inaturalist.org/observations/28377541 created_by: rwalls creation_date: 2010-07-01T04:21:46Z [Term] id: PO:0025082 name: reproductive shoot system namespace: plant_anatomy def: "A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094)." [POC:curators] subset: TraitNet synonym: "sistema de brote reproductivo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "生殖シュート 系、苗条系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009006 ! shoot system relationship: participates_in PO:0025530 ! reproductive shoot system development stage created_by: rwalls creation_date: 2010-09-17T09:49:10Z [Term] id: PO:0025092 name: dehiscence zone namespace: plant_anatomy def: "A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure." [POC:curators] synonym: "zona de dehiscencia (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "裂開帯 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: GO:0009900 is_a: PO:0009007 ! portion of plant tissue created_by: rwalls creation_date: 2010-10-27T11:07:17Z [Term] id: PO:0025117 name: plant anatomical space namespace: plant_anatomy def: "An anatomical space that is part of a plant." [CARO:0000005, PO:cooperl, POC:curators] comment: CARO:0000005 'anatomical space' is defined as: An immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes, and is bounded by an anatomical surface. synonym: "espacio anatómico vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "lacuna (narrow)" NARROW [FNA:8e5eb686-8308-4cd7-aaee-75fe9a36d042] synonym: "lacunae (narrow, plural)" NARROW OMO:0003004 [FNA:322646fb-30bf-422d-8373-9f91f48fd28b] synonym: "lumen (narrow)" NARROW [FNA:b069a022-2be0-43b4-8efa-4ad13ff17639] synonym: "lumina (narrow, plural)" NARROW OMO:0003004 [FNA:e3941c37-b2f0-468f-b857-0c3d095d71b1] synonym: "植物 解剖学（形態）的空間 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:322646fb-30bf-422d-8373-9f91f48fd28b xref: FNA:8e5eb686-8308-4cd7-aaee-75fe9a36d042 xref: FNA:b069a022-2be0-43b4-8efa-4ad13ff17639 xref: FNA:e3941c37-b2f0-468f-b857-0c3d095d71b1 xref: PO_GIT:203 is_a: PO:0025131 ! plant anatomical entity created_by: rwalls creation_date: 2010-11-10T11:57:16Z [Term] id: PO:0025127 name: primordium namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011)." [POC:curators] comment: A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. synonym: "portion of primordial tissue (exact)" EXACT [] synonym: "portion of primordium tissue (exact)" EXACT [] synonym: "primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "primordio (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:186 is_a: PO:0009013 ! portion of meristem tissue created_by: rwalls creation_date: 2010-11-15T09:10:22Z [Term] id: PO:0025128 name: phyllome primordium namespace: plant_anatomy def: "A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001)." [PMID:11572953, POC:curators] comment: The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop. synonym: "phyllome primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "portion of phyllome primordium tissue (exact)" EXACT [] synonym: "primordio del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:466 is_a: PO:0025127 ! primordium is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025430 ! phyllome anlagen relationship: part_of PO:0000037 ! shoot axis apex created_by: rwalls creation_date: 2010-11-15T09:27:11Z [Term] id: PO:0025129 name: petiole lamina namespace: plant_anatomy def: "A lamina (PO:0025060) that is part of a petiole (PO:0020038)." [POC:curators] comment: The entire petiole may be laminar, or the petiole may be more or less rounded in cross section with laminar extensions. subset: Musa synonym: "lámina (ala) del pecíolo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "petiole wing (narrow)" NARROW [CO_125:0000005] synonym: "葉柄葉身、葉片 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:428 is_a: PO:0025396 ! phyllome lamina intersection_of: PO:0025060 ! lamina intersection_of: part_of PO:0020038 ! petiole relationship: part_of PO:0020038 ! petiole created_by: rwalls creation_date: 2010-11-15T10:28:38Z [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, CAROC:Brownsville2014, 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'. 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: PO:0025157 name: phyllome epidermis namespace: plant_anatomy def: "A portion of shoot system epidermis (PO:0006035) that is part of a phyllome (PO:0006001)." [POC:curators, POC:Laurel_Cooper] synonym: "epidermis del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0006035 ! shoot system epidermis intersection_of: PO:0006035 ! shoot system epidermis intersection_of: part_of PO:0006001 ! phyllome relationship: part_of PO:0006001 ! phyllome created_by: rwalls creation_date: 2010-11-15T02:32:53Z [Term] id: PO:0025178 name: stem epidermis namespace: plant_anatomy def: "A portion of shoot axis epidermis (PO:0000112) that is part of a stem (PO:0009047)." [POC:Laurel_Cooper, POC:Ramona_Walls] synonym: "culm epidermis (related)" RELATED [] synonym: "epidermis del tallo (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "茎表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:111 is_a: PO:0000112 ! shoot axis epidermis intersection_of: PO:0000112 ! shoot axis epidermis intersection_of: part_of PO:0009047 ! stem relationship: part_of PO:0009047 ! stem created_by: rwalls creation_date: 2010-11-22T09:56:21Z [Term] id: PO:0025179 name: branch epidermis namespace: plant_anatomy def: "A portion of shoot axis epidermis (PO:0006035) that is part of a branch (PO:0025073)." [POC:Ramona_Walls] synonym: "epidermis de la ramificación (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "枝 表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0000112 ! shoot axis epidermis intersection_of: PO:0000112 ! shoot axis epidermis intersection_of: part_of PO:0025073 ! branch relationship: part_of PO:0025073 ! branch created_by: rwalls creation_date: 2010-11-22T09:58:06Z [Term] id: PO:0025186 name: phyllome trichome namespace: plant_anatomy def: "A trichome that is part of a phyllome epidermis." [POC:Ramona_Walls] synonym: "tricoma del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム毛（毛茸、糸状体） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0000282 ! trichome created_by: rwalls creation_date: 2010-12-06T01:17:31Z [Term] id: PO:0025205 name: shoot system vascular system namespace: plant_anatomy def: "A vascular system (PO:0000034) that is part of a shoot system (PO:0009006)." [POC:Ramona_Walls] synonym: "sistema vascular del sistema del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "シュート系維管系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:41 is_a: PO:0000034 ! vascular system relationship: part_of PO:0009006 ! shoot system created_by: rwalls creation_date: 2010-12-17T09:34:58Z [Term] id: PO:0025206 name: phyllome vascular system namespace: plant_anatomy def: "A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a phyllome (PO:0006001)." [POC:Ramona_Walls] synonym: "sistema vascular del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム維管系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:41 is_a: PO:0000034 ! vascular system relationship: part_of PO:0006001 ! phyllome relationship: part_of PO:0025205 ! shoot system vascular system created_by: rwalls creation_date: 2010-12-17T10:11:07Z [Term] id: PO:0025222 name: reproductive shoot apex namespace: plant_anatomy def: "A shoot apex that has as part a reproductive shoot apical meristem." [POC:Ramona_Walls] synonym: "ápice reproductivo del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "生殖シュート頂、茎頂 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0000037 ! shoot axis apex created_by: rwalls creation_date: 2010-12-20T08:47:03Z [Term] id: PO:0025223 name: vegetative shoot apex namespace: plant_anatomy def: "A shoot apex PO:0000037) that has as part a vegetative shoot apical meristem (PO:0008016)." [POC:Laurel_Cooper, POC:Ramona_Walls] synonym: "ápice vegetativo del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "栄養シュート頂、栄養枝頂 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:234 is_a: PO:0000037 ! shoot axis apex relationship: has_part PO:0008016 ! vegetative shoot apical meristem created_by: rwalls creation_date: 2010-12-20T08:47:03Z [Term] id: PO:0025224 name: axil namespace: plant_anatomy def: "A plant anatomical space that is the space between a shoot axis and a leaf, bract, or branch that branches from the shoot axis." [POC:curators] synonym: "axila (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "腋、軸 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0025117 ! plant anatomical space created_by: rwalls creation_date: 2010-12-20T08:59:45Z [Term] id: PO:0025337 name: life of whole plant stage namespace: plant_structure_development_stage def: "A maximal whole plant development stage." [POC:curators] comment: There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. synonym: "vida de la planta entera (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "植物体の一生 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:230 is_a: PO:0007033 ! whole plant development stage created_by: rwalls creation_date: 2011-10-19T10:54:37Z [Term] id: PO:0025338 name: collective plant organ structure development stage namespace: plant_structure_development_stage def: "A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497)." [POC:curators] comment: Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). synonym: "etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "集合的植物構造の発生過程 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:391 is_a: PO:0009012 ! plant structure development stage relationship: has_participant PO:0025007 ! collective plant organ structure created_by: rwalls creation_date: 2011-10-19T11:12:49Z [Term] id: PO:0025348 name: phyllome lamina vein namespace: plant_anatomy def: "A vascular bundle (PO:0005020) that is part of a phyllome lamina (PO:0025396)." [POC:Ramona_Walls] synonym: "vena del filoma laminar (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム葉身脈 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:462 is_a: PO:0005020 ! vascular bundle intersection_of: PO:0005020 ! vascular bundle intersection_of: part_of PO:0025396 ! phyllome lamina relationship: part_of PO:0025396 ! phyllome lamina created_by: rwalls creation_date: 2012-04-18T01:41:29Z [Term] id: PO:0025395 name: floral organ namespace: plant_anatomy def: "A plant organ (PO:0009008) that is part of a flower (PO:0009046)." [POC:curators] comment: Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores. synonym: "órgano floral (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "flower organ (exact)" EXACT [] synonym: "花器官 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:423 is_a: PO:0009008 ! plant organ intersection_of: PO:0009008 ! plant organ intersection_of: part_of PO:0009046 ! flower relationship: part_of PO:0009046 ! flower created_by: rwalls creation_date: 2012-01-19T11:44:36Z [Term] id: PO:0025396 name: phyllome lamina namespace: plant_anatomy def: "A plant organ lamina (PO:0025513) that is part of a phyllome (PO:0006001)." [POC:Ramona_Walls] synonym: "filoma laminar (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム葉身 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:428 is_a: PO:0025513 ! plant organ lamina intersection_of: PO:0025513 ! plant organ lamina intersection_of: part_of PO:0006001 ! phyllome relationship: part_of PO:0006001 ! phyllome created_by: rwalls creation_date: 2012-01-19T12:56:11Z [Term] id: PO:0025413 name: primary leaf vein namespace: plant_anatomy def: "A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039)." [POC:curators] comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as found in some ferns and gymnosperms. synonym: "vena primaria de la hoja (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "一次葉脈 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:435 is_a: PO:0020138 ! leaf lamina vein created_by: rwalls creation_date: 2012-02-01T04:24:58Z [Term] id: PO:0025430 name: phyllome anlagen namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128)." [POC:curators, POC:Laurel_Cooper] comment: The phyllome anlagen is only detectable by gene expression, not morphology. synonym: "phyllome meristem (broad)" BROAD [] synonym: "フィロム原基 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:427 is_a: PO:0009013 ! portion of meristem tissue relationship: part_of PO:0000225 ! peripheral zone created_by: Laurel_Cooper creation_date: 2012-02-07T08:20:10Z [Term] id: PO:0025431 name: vascular leaf anlagen namespace: plant_anatomy def: "A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148)." [PMID:14732442, POC:Laurel_Cooper] comment: This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied). synonym: "leaf meristem (broad)" BROAD [] synonym: "維管束系葉原基 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:407 is_a: PO:0025430 ! phyllome anlagen relationship: part_of PO:0008016 ! vegetative shoot apical meristem created_by: Laurel_Cooper creation_date: 2012-02-07T08:40:37Z [Term] id: PO:0025433 name: root anlagen namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029)." [POC:curators] comment: Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). synonym: "precursor de raí (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "根原基 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:427 is_a: PO:0009013 ! portion of meristem tissue created_by: Laurel_Cooper creation_date: 2012-02-08T01:00:56Z [Term] id: PO:0025477 name: floral organ primordium namespace: plant_anatomy def: "A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222)." [POC:curators] comment: If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089). subset: Angiosperm synonym: "floral structure primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "portion of floral structure primordium tissue (exact)" EXACT [] synonym: "primordio de organo floral (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "花器官原基 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:465 is_a: PO:0025127 ! primordium relationship: part_of PO:0025222 ! reproductive shoot apex created_by: rwalls creation_date: 2012-04-26T03:57:09Z [Term] id: PO:0025496 name: multi-tissue plant structure namespace: plant_anatomy def: "A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types." [CARO:0000055, POC:curators] comment: Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. synonym: "estructura vegetal con múltiples tejidos (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "複数の組織からなる植物構造 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:480 is_a: PO:0009011 ! plant structure created_by: Laurel_Cooper creation_date: 2012-06-11T14:57:00Z [Term] id: PO:0025497 name: collective plant structure namespace: plant_anatomy def: "A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007)." [POC:curators] comment: This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). synonym: "estructura vegetal colectiva (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "集合的植物構造 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:479 is_a: PO:0009011 ! plant structure created_by: Laurel_Cooper creation_date: 2012-06-11T15:09:20Z [Term] id: PO:0025498 name: cardinal part of multi-tissue plant structure namespace: plant_anatomy def: "A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types." [POC:curators] comment: Includes cardinal parts of plant organs (PO:0025001) as well as parts of other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Most cardinal parts of multi-tissue plant structures have both fiat and bona-fide boundaries, including parts with large fiat boundaries, such as leaf base (PO:0020040) or fruit distal end (PO:0008001), and parts with primarily bona-fide boundaries, such as leaflet (PO:0020049). synonym: "parte cardinal de estructura vegetal con múltiples tejidos (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:485 is_a: PO:0009011 ! plant structure relationship: part_of PO:0025496 ! multi-tissue plant structure created_by: Laurel_Cooper creation_date: 2012-06-11T15:28:44Z [Term] id: PO:0025513 name: plant organ lamina namespace: plant_anatomy def: "A lamina (PO:0025060) that is part of a plant organ (PO:0009008)." [POC:curators] synonym: "lámina órgano (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "器官 葉身 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:428 is_a: PO:0025001 ! cardinal organ part is_a: PO:0025060 ! lamina intersection_of: PO:0025060 ! lamina intersection_of: part_of PO:0009008 ! plant organ created_by: rwalls creation_date: 2012-10-17T15:51:02Z [Term] id: PO:0025527 name: shoot system development stage namespace: plant_structure_development_stage def: "A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death." [POC:Laurel_Cooper] comment: The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003). xref: PO_GIT:517 is_a: PO:0025338 ! collective plant organ structure development stage relationship: has_participant PO:0009006 ! shoot system created_by: Laurel_Cooper creation_date: 2012-12-13T18:21:19Z [Term] id: PO:0025528 name: bud development stage namespace: plant_structure_development_stage def: "A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006)." [POC:Laurel_Cooper] xref: PO_GIT:517 is_a: PO:0025527 ! shoot system development stage created_by: Laurel_Cooper creation_date: 2012-12-13T18:29:35Z [Term] id: PO:0025530 name: reproductive shoot system development stage namespace: plant_structure_development_stage def: "A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082)." [POC:Laurel_Cooper] xref: PO_GIT:517 is_a: PO:0025527 ! shoot system development stage created_by: Laurel_Cooper creation_date: 2012-12-13T19:01:14Z [Term] id: PO:0025594 name: ground meristem namespace: plant_anatomy def: "A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059)." [POC:curators, POC:Laurel_Cooper] xref: PO_GIT:584 is_a: PO:0009013 ! portion of meristem tissue created_by: Laurel_Cooper creation_date: 2013-11-18T11:14:03Z [Term] id: PO:0025606 name: native plant cell namespace: plant_anatomy def: "A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment)." [POC:Laurel_Cooper] comment: A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). xref: PO_GIT:586 is_a: PO:0009002 ! plant cell created_by: Laurel_Cooper creation_date: 2014-05-13T16:51:47Z [Term] id: PO:0028002 name: sporophyte development stage namespace: plant_structure_development_stage def: "A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death." [POC:curators] comment: A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. subset: TraitNet synonym: "fase esporofítica (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "sporophytic development stage (exact)" EXACT [] synonym: "sporophytic phase (exact)" EXACT [] synonym: "sporphyte phase (exact)" EXACT [] synonym: "胞子体発生過程 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:139 xref: PO_GIT:68 is_a: PO:0007033 ! whole plant development stage relationship: part_of PO:0025337 ! life of whole plant stage created_by: rwalls creation_date: 2010-07-15T02:56:11Z [Term] id: PO:0030119 name: catkin inflorescence namespace: plant_anatomy def: "An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of indeterminate, first order inflorescence axes (PO:0025104) and sessile, unisexual flowers (PO:0009046) that are each subtended by conspicuous inflorescence bracts (PO:0009054)." [NYBG:Brandon_Sinn, NYBG:Dario_Cavaliere, PO:cooperl] comment: Examples include poplars (including Populus trichocarpa, Salicaceae) and birches (Betula spp., Betulaceae). Catkin inflorescences are often pendulate. synonym: "ament" EXACT [] synonym: "ament (exact)" EXACT [] synonym: "catkin" EXACT [] synonym: "catkin (exact)" EXACT [] is_a: PO:0009049 ! inflorescence created_by: NYBG:Brandon_Sinn creation_date: 2017-04-20T12:48:27Z [Term] id: PO:0030121 name: capitulum inflorescence namespace: plant_anatomy def: "An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of a radially-enlarged, determinate, first order inflorescence axis (PO:0025104) with sessile flowers (PO:0009046)." [NYBG:Brandon_Sinn, NYBG:Dario_Cavaliere, PO:cooperl] comment: Many capitulum inflorescences have basal involucral bracts (PO:0009045) and are often discoid or globose in shape. Examples include sunflowers (Helianthus spp.; Asteraceae) and teasels (Dipsacus spp.; Dipsacaceae). synonym: "calathidium (exact)" EXACT [] synonym: "capitula (exact, plural)" EXACT OMO:0003004 [] synonym: "capitulum (exact)" EXACT [] synonym: "head (broad)" BROAD [] synonym: "hypanthodium (narrow)" NARROW [] is_a: PO:0009049 ! inflorescence created_by: NYBG:Brandon_Sinn creation_date: 2017-04-20T12:53:49Z [Term] id: UBERON:0001062 name: anatomical entity 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] is_a: BFO:0000004 ! independent continuant [Typedef] id: GALLONT:0000000 name: has associate comment: Relationship that specifies which organism is associated with a class. property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-24T01:49:45Z" xsd:string range: OBI:0100026 ! organism [Typedef] id: GALLONT:0000059 name: induced by is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: GALLONT:1000062 name: has seasonal maturity range: ENVO:03000096 ! season [Typedef] id: GALLONT:1000150 name: has seasonal emergence range: ENVO:03000096 ! season [Typedef] id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function [Typedef] id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: bearer_of ! bearer of [Typedef] id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: 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: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: 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 ! characteristic of [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: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by created_by: https://orcid.org/0000-0002-7073-9172 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: https://orcid.org/0000-0002-7073-9172 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: https://orcid.org/0000-0002-7073-9172 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="https://orcid.org/0000-0002-7073-9172"} is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates created_by: https://orcid.org/0000-0002-7073-9172 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." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates created_by: https://orcid.org/0000-0002-7073-9172 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." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates created_by: https://orcid.org/0000-0002-7073-9172 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." [https://orcid.org/0000-0002-7073-9172] 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: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002162 name: in taxon 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." [] range: OBI:0100026 ! organism holds_over_chain: capable_of RO:0002162 holds_over_chain: develops_from RO:0002162 holds_over_chain: has_part RO:0002162 holds_over_chain: part_of RO:0002162 holds_over_chain: RO:0002254 RO:0002162 is_a: RO:0002320 ! evolutionarily related to [Typedef] id: RO:0002203 name: develops into def: "inverse of develops from" [] is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into is_a: RO:0002388 ! has potential to directly develop into [Typedef] id: RO: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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent [Typedef] id: RO:0002254 name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity holds_over_chain: has_part develops_from is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to [Typedef] id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: part_of ! part_of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] [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: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI 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:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: part_of capable_of {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI 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 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: has_participant ! has participant is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002352 name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: participates_in ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 holds_over_chain: RO:0002409 RO:0002409 is_transitive: true is_a: positively_regulates ! positively regulates is_a: RO:0012012 ! indirectly regulates transitive_over: directly_positively_regulates ! directly positively regulates [Typedef] id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 is_transitive: true is_a: negatively_regulates ! negatively regulates is_a: RO:0012012 ! indirectly regulates transitive_over: directly_negatively_regulates ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO: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 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 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: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002434 name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true [Typedef] id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true is_a: RO:0002321 ! ecologically related to is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002440 name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 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:0002453 name: host of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002454 name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002464 name: helper property (not for use in curation) property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002481 name: is kinase activity property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002559 name: causally influenced by property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002574 name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: OBI:0100026 ! organism range: OBI:0100026 ! organism is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: 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 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: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] id: RO:0004035 name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_negative_effect is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences [Typedef] id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: causally_upstream_of ! causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] id: RO:0012012 name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: regulates ! regulates is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] id: RO:0015006 name: different in magnitude relative to def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] domain: PATO:0000001 ! quality range: PATO:0000001 ! quality [Typedef] id: RO:0015007 name: increased in magnitude relative to def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. domain: PATO:0000001 ! quality range: PATO:0000001 ! quality is_a: RO:0015006 ! different in magnitude relative to [Typedef] id: RO:0015011 name: has cross section def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [https://orcid.org/0000-0002-6601-2165] comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. [Typedef] id: RO:0015012 name: reciprocal of def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [https://orcid.org/0000-0002-6601-2165] comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. [Typedef] id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z [Typedef] id: bearer_of name: bearer of name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] id: capable_of name: capable of namespace: external 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: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of [Typedef] id: capable_of_part_of name: capable of part of namespace: external 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: capable_of part_of {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: causally_downstream_of name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded_by inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes [Typedef] id: causally_upstream_of name: causally upstream of namespace: external def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect name: causally upstream of, negative effect namespace: external def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect [Typedef] id: causally_upstream_of,_positive_effect name: causally upstream of, positive effect namespace: external def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: causally_upstream_of_or_within name: causally upstream of or within namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: developmentally_preceded_by name: developmentally preceded by name: developmentally_preceded_by namespace: plant_ontology 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" [] def: "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." [RO:0002258] xref: RO:0002258 domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by created_by: Laurel_Cooper creation_date: 2013-06-27T13:16:56Z [Typedef] id: develops_from name: develops from name: develops_from namespace: plant_ontology 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" [] xref: RO:0002202 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by is_a: RO:0002254 ! has developmental contribution from inverse_of: RO:0002203 ! develops into [Typedef] id: directly_negatively_regulates name: directly negatively regulates namespace: external def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002630 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 property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates namespace: external def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002629 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 property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates [Typedef] id: directly_regulates name: directly regulates namespace: external def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: regulates ! regulates [Typedef] id: has_component name: has component namespace: external 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: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part [Typedef] id: has_input name: has input namespace: external 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 xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process is_a: has_participant ! has participant inverse_of: RO:0002352 ! input of [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity namespace: external 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'. xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] id: has_part name: has part name: has_part namespace: external namespace: plant_ontology namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true is_a: overlaps ! overlaps [Typedef] id: has_participant name: has participant name: has_participant namespace: external namespace: plant_ontology def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: has_part has_participant [Typedef] id: has_regulatory_component_activity name: has regulatory component activity namespace: external 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." [] xref: RO:0002013 is_a: regulated_by ! regulated by is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] id: immediately_causally_upstream_of name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string is_a: preceded_by ! preceded_by inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes name: immediately precedes namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 is_a: precedes ! precedes [Typedef] id: negatively_regulated_by name: negatively regulated by namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates namespace: external def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect is_a: regulates ! regulates inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: negatively_regulates_characteristic name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic [Typedef] id: only_in_taxon name: only in taxon name: only_in_taxon namespace: plant_ontology 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: RO:0002162 ! in taxon [Typedef] id: overlaps name: overlaps namespace: external def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] id: part_of name: part of name: part_of namespace: external namespace: plant_ontology namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 property_value: RO:0040042 BFO:0000017 property_value: RO:0040042 BFO:0000019 property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part [Typedef] id: participates_in name: participates in name: participates_in namespace: external namespace: plant_ontology def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 property_value: IAO:0000111 "participates in" xsd:string property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant [Typedef] id: positively_regulated_by name: positively regulated by namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates namespace: external def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 holds_over_chain: negatively_regulates negatively_regulates is_transitive: true is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect is_a: regulates ! regulates inverse_of: positively_regulated_by ! positively regulated by [Typedef] id: positively_regulates_characteristic name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by name: preceded by name: preceded_by namespace: external namespace: plant_ontology def: "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." [POC:Laurel_Cooper] 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." [] comment: 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. subset: ro-eco xref: BFO:0000062 property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by is_transitive: true is_a: RO:0002086 ! ends after inverse_of: precedes ! precedes created_by: Laurel_Cooper creation_date: 2013-07-09T14:29:15Z [Typedef] id: precedes name: precedes namespace: external namespace: plant_ontology 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 domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to created_by: Laurel_Cooper creation_date: 2015-06-04T17:18:40Z [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: regulated_by name: regulated by namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates namespace: external def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates is_transitive: true is_a: causally_upstream_of ! causally upstream of inverse_of: regulated_by ! regulated by transitive_over: RO:0002025 ! has effector activity [Typedef] id: regulates_characteristic name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic is_a: RO:0002410 ! causally related to