format-version: 1.2 data-version: releases/2023-03-15 subsetdef: 1_STAR "" subsetdef: 2_STAR "" subsetdef: 3_STAR "" subsetdef: attribute_slim "" subsetdef: cell_quality "" subsetdef: core "CARO2 core class" subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_manually_annotate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" subsetdef: goslim_drosophila "" subsetdef: goslim_flybase_ribbon "" subsetdef: goslim_generic "" subsetdef: goslim_metagenomics "" subsetdef: goslim_mouse "" subsetdef: goslim_pir "" subsetdef: goslim_plant "" subsetdef: goslim_pombe "" subsetdef: goslim_synapse "" subsetdef: goslim_yeast "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: mpath_slim "" subsetdef: olfactory_system_draft "adult olfactory system model" subsetdef: plus "CARO2 plus class" subsetdef: prokaryote_subset "" subsetdef: relational_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: value_slim "" synonymtypedef: InChIKey "" synonymtypedef: INN "" synonymtypedef: IUPAC_NAME "" synonymtypedef: systematic_synonym "" EXACT remark: Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendel. ontology: caro property_value: dc-description "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies." xsd:string property_value: dc-title "Common Anatomy Reference Ontology" xsd:string property_value: dcterms-license https://creativecommons.org/licenses/by/4.0/ property_value: owl:versionInfo "2023-03-15" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string property_value: editor_note "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string property_value: editor_note "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: example_of_usage "Julius Caesar" xsd:string property_value: example_of_usage "the Second World War" xsd:string property_value: example_of_usage "Verdi’s Requiem" xsd:string property_value: example_of_usage "your body mass index" xsd:string property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 {all_only="true"} ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity relationship: part_of BFO:0000003 {all_only="true"} ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} property_value: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: example_of_usage "a chair" xsd:string property_value: example_of_usage "a heart" xsd:string property_value: example_of_usage "a leg" xsd:string property_value: example_of_usage "a molecule" xsd:string property_value: example_of_usage "a spatial region" xsd:string property_value: example_of_usage "an atom" xsd:string property_value: example_of_usage "an orchestra." xsd:string property_value: example_of_usage "an organism" xsd:string property_value: example_of_usage "the bottom right portion of a human torso" xsd:string property_value: example_of_usage "the interior of your mouth" xsd:string property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: editor_note "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string property_value: editor_note "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000009 name: two-dimensional spatial region is_a: BFO:0000006 ! spatial region property_value: BFO:0000179 "2d-s-region" xsd:string property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string property_value: example_of_usage "an infinitely thin plane in space." xsd:string property_value: example_of_usage "the surface of a sphere-shaped part of space" xsd:string property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: example_of_usage "a process of cell-division, \\ a beating of the heart" xsd:string property_value: example_of_usage "a process of meiosis" xsd:string property_value: example_of_usage "a process of sleeping" xsd:string property_value: example_of_usage "the course of a disease" xsd:string property_value: example_of_usage "the flight of a bird" xsd:string property_value: example_of_usage "the life of an organism" xsd:string property_value: example_of_usage "your process of aging." xsd:string property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role property_value: BFO:0000179 "disposition" xsd:string property_value: BFO:0000180 "Disposition" xsd:string property_value: editor_note "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string property_value: example_of_usage "an atom of element X has the disposition to decay to an atom of element Y" xsd:string property_value: example_of_usage "certain people have a predisposition to colon cancer" xsd:string property_value: example_of_usage "children are innately disposed to categorize objects in certain ways." xsd:string property_value: example_of_usage "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: example_of_usage "the disposition of this piece of metal to conduct electricity." xsd:string property_value: example_of_usage "the disposition of your blood to coagulate" xsd:string property_value: example_of_usage "the function of your reproductive organs" xsd:string property_value: example_of_usage "the role of being a doctor" xsd:string property_value: example_of_usage "the role of this boundary to delineate where Utah and Colorado meet" xsd:string property_value: IAO:0000117 "https://orcid.org/0000-0001-8815-0078" xsd:string property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000018 name: zero-dimensional spatial region is_a: BFO:0000006 ! spatial region property_value: BFO:0000179 "0d-s-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant relationship: part_of BFO:0000019 {all_only="true"} ! quality property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string property_value: example_of_usage "the ambient temperature of this portion of air" xsd:string property_value: example_of_usage "the color of a tomato" xsd:string property_value: example_of_usage "the length of the circumference of your waist" xsd:string property_value: example_of_usage "the mass of this piece of gold." xsd:string property_value: example_of_usage "the shape of your nose" xsd:string property_value: example_of_usage "the shape of your nostril" xsd:string property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: example_of_usage "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: example_of_usage "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string property_value: example_of_usage "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string property_value: example_of_usage "the disposition of this fish to decay" xsd:string property_value: example_of_usage "the function of this heart: to pump blood" xsd:string property_value: example_of_usage "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string property_value: example_of_usage "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string property_value: example_of_usage "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string property_value: example_of_usage "the role of being a doctor" xsd:string property_value: example_of_usage "the shape of this hole." xsd:string property_value: example_of_usage "the smell of this portion of mozzarella" xsd:string property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] is_a: CHEBI:50906 ! role equivalent_to: CHEBI:50906 ! role property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string property_value: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: example_of_usage "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string property_value: example_of_usage "the priest role" xsd:string property_value: example_of_usage "the role of a boundary to demarcate two neighboring administrative territories" xsd:string property_value: example_of_usage "the role of a building in serving as a military target" xsd:string property_value: example_of_usage "the role of a stone in marking a property boundary" xsd:string property_value: example_of_usage "the role of subject in a clinical trial" xsd:string property_value: example_of_usage "the student role" xsd:string property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000026 name: one-dimensional spatial region is_a: BFO:0000006 ! spatial region property_value: BFO:0000179 "1d-s-region" xsd:string property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string property_value: example_of_usage "an edge of a cube-shaped portion of space." xsd:string property_value: IAO:0000600 "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000029 name: site is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "site" xsd:string property_value: BFO:0000180 "Site" xsd:string property_value: example_of_usage "a hole in the interior of a portion of cheese" xsd:string property_value: example_of_usage "a rabbit hole" xsd:string property_value: example_of_usage "an air traffic control region defined in the airspace above an airport" xsd:string property_value: example_of_usage "Manhattan Canyon)" xsd:string property_value: example_of_usage "the cockpit of an aircraft" xsd:string property_value: example_of_usage "the Grand Canyon" xsd:string property_value: example_of_usage "the hold of a ship" xsd:string property_value: example_of_usage "the interior of a kangaroo pouch" xsd:string property_value: example_of_usage "the interior of the trunk of your car" xsd:string property_value: example_of_usage "the interior of your bedroom" xsd:string property_value: example_of_usage "the interior of your office" xsd:string property_value: example_of_usage "the interior of your refrigerator" xsd:string property_value: example_of_usage "the lumen of your gut" xsd:string property_value: example_of_usage "the Piazza San Marco" xsd:string property_value: example_of_usage "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition property_value: BFO:0000179 "function" xsd:string property_value: BFO:0000180 "Function" xsd:string property_value: editor_note "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string property_value: example_of_usage "the function of a hammer to drive in nails" xsd:string property_value: example_of_usage "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: example_of_usage "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 name: material entity def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string property_value: editor_note "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string property_value: editor_note "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string property_value: editor_note "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: example_of_usage "a flame" xsd:string property_value: example_of_usage "a forest fire" xsd:string property_value: example_of_usage "a human being" xsd:string property_value: example_of_usage "a hurricane" xsd:string property_value: example_of_usage "a photon" xsd:string property_value: example_of_usage "a puff of smoke" xsd:string property_value: example_of_usage "a sea wave" xsd:string property_value: example_of_usage "a tornado" xsd:string property_value: example_of_usage "an aggregate of human beings." xsd:string property_value: example_of_usage "an energy wave" xsd:string property_value: example_of_usage "an epidemic" xsd:string property_value: example_of_usage "the undetached arm of a human being" xsd:string property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string property_value: editor_note "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: CARO:0000000 name: anatomical entity def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [CAROC:Brownsville2014] comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. is_a: CARO:0030000 ! biological entity [Term] id: CARO:0000003 name: connected anatomical structure def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. subset: core is_a: CARO:0000006 ! material anatomical entity intersection_of: CARO:0000006 ! material anatomical entity intersection_of: bearer_of PATO:0002266 ! 3-D shape intersection_of: bearer_of PATO:0010000 ! maximally connected disjoint_from: CARO:0000004 ! organism substance relationship: bearer_of PATO:0002266 ! 3-D shape relationship: bearer_of PATO:0010000 ! maximally connected [Term] id: CARO:0000004 name: organism substance def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." [] comment: Note - CARO explicitly declares organisms substances to be part of (some) organism. synonym: "portion of organism substance" EXACT [] is_a: CARO:0001008 ! gross anatomical part property_value: example_of_usage "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." xsd:string [Term] id: CARO:0000005 name: anatomical space def: "An Immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes and that is bounded by an anatomical surface." [] comment: Original definition: "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." The last clause. "contains one or more organism substances or anatomical structures" was dropped from the definition because it was an unnecessary restriction. is_a: BFO:0000029 ! site is_a: CARO:0000007 ! immaterial anatomical entity intersection_of: BFO:0000029 ! site intersection_of: part_of CARO:0001010 ! organism disjoint_from: CARO:0000008 ! anatomical line disjoint_from: CARO:0000009 ! anatomical point disjoint_from: CARO:0001002 ! anatomical surface relationship: part_of CARO:0001010 ! organism [Term] id: CARO:0000006 name: material anatomical entity def: "An anatomical entity that has mass." [] subset: core is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity intersection_of: bearer_of PATO:0000125 ! mass disjoint_from: CARO:0000007 ! immaterial anatomical entity relationship: bearer_of PATO:0000125 ! mass [Term] id: CARO:0000007 name: immaterial anatomical entity def: "Anatomical entity that has no mass." [] subset: core is_a: BFO:0000141 ! immaterial entity is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0000008 name: anatomical line def: "A one dimensional, immaterial anatomical entity." [] is_a: BFO:0000026 ! one-dimensional spatial region is_a: CARO:0000007 ! immaterial anatomical entity disjoint_from: CARO:0000009 ! anatomical point disjoint_from: CARO:0001002 ! anatomical surface property_value: example_of_usage "A line between two points where these are typically used to measure some aspect of morphology, such as the distance between the eyes or the length of a leg. " xsd:string [Term] id: CARO:0000009 name: anatomical point def: "Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface." [] is_a: BFO:0000018 ! zero-dimensional spatial region is_a: CARO:0000007 ! immaterial anatomical entity disjoint_from: CARO:0001002 ! anatomical surface property_value: example_of_usage "The tip of the nose or other material anatomical entity, or the end of an anatomical line. " xsd:string [Term] id: CARO:0000010 name: anatomical boundary def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [] comment: Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. is_a: BFO:0000009 ! two-dimensional spatial region is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000011 name: connected anatomical system def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [] is_a: CARO:0010000 ! multicellular anatomical structure disjoint_from: CARO:0000032 ! organism subdivision [Term] id: CARO:0000012 name: multicellular organism def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. is_a: CARO:0010004 ! cellular organism disjoint_from: CARO:0000024 ! compound organ disjoint_from: CARO:0010001 ! cell cluster organ disjoint_from: CARO:0010002 ! compound cell cluster organ [Term] id: CARO:0000013 name: cell def: "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [] comment: deprecate and replace with CL or GO term? xref: CL:0000000 xref: GO:0005623 is_a: CARO:0000003 ! connected anatomical structure is_a: CARO:0020003 ! cellular anatomical structure disjoint_from: CARO:0000014 ! cell part disjoint_from: CARO:0000040 ! acellular anatomical structure disjoint_from: CARO:0000042 ! extraembryonic structure disjoint_from: CARO:0001000 ! multi-cell-part structure disjoint_from: CARO:0010000 ! multicellular anatomical structure [Term] id: CARO:0000014 name: cell part def: "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." [] comment: This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. is_a: CARO:0000003 ! connected anatomical structure disjoint_from: CARO:0000040 ! acellular anatomical structure disjoint_from: CARO:0000042 ! extraembryonic structure disjoint_from: CARO:0001000 ! multi-cell-part structure disjoint_from: CARO:0010000 ! multicellular anatomical structure relationship: part_of CARO:0000013 ! cell property_value: IAO:0000118 "cell component" xsd:string [Term] id: CARO:0000019 name: compound organ component def: "Multi-tissue structure that is part of a compound organ." [] is_a: CARO:0000055 ! multi-tissue structure relationship: part_of CARO:0000024 ! compound organ [Term] id: CARO:0000021 name: simple organ def: "An organ that consists of a single multi-tissue structure." [] is_a: CARO:0020004 ! organ intersection_of: CARO:0020004 ! organ intersection_of: has_component CARO:0000055 {cardinality="1"} ! multi-tissue structure relationship: has_component CARO:0000055 ! multi-tissue structure [Term] id: CARO:0000024 name: compound organ def: "An organ consisting of multiple, distinct multi-tissue structures." [] is_a: CARO:0000055 ! multi-tissue structure is_a: CARO:0020004 ! organ intersection_of: CARO:0020004 ! organ intersection_of: has_component CARO:0000055 {minCardinality="2"} ! multi-tissue structure disjoint_from: CARO:0010001 ! cell cluster organ disjoint_from: CARO:0010002 ! compound cell cluster organ relationship: has_component CARO:0000055 ! multi-tissue structure [Term] id: CARO:0000027 name: male organism def: "Gonochoristic organism that can produce male gametes." [] is_a: CARO:0000048 ! gonochoristic organism [Term] id: CARO:0000028 name: female organism def: "Gonochoristic organism that can produce female gametes." [] is_a: CARO:0000048 ! gonochoristic organism [Term] id: CARO:0000029 name: hermaphroditic organism def: "Multi-cellular organism that can produce both male and female gametes." [] is_a: CARO:0000012 ! multicellular organism property_value: IAO:0000118 "dioecious organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"} [Term] id: CARO:0000030 name: asexual multi-cellular organism def: "Multi-cellular organism that does not produce gametes." [] is_a: CARO:0000012 ! multicellular organism [Term] id: CARO:0000032 name: organism subdivision def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [] subset: core is_a: CARO:0010000 ! multicellular anatomical structure property_value: editor_note "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." xsd:string [Term] id: CARO:0000040 name: acellular anatomical structure def: "An anatomical structure that has no cells or cell parts as a part." [] comment: Example. Insect cuticle, eggshell, hair. is_a: CARO:0000003 ! connected anatomical structure is_a: CARO:0001008 ! gross anatomical part intersection_of: CARO:0000003 ! connected anatomical structure intersection_of: has_component CARO:0000013 {cardinality="0"} ! cell intersection_of: has_component CARO:0000014 {cardinality="0"} ! cell part disjoint_from: CARO:0000042 ! extraembryonic structure disjoint_from: CARO:0001000 ! multi-cell-part structure disjoint_from: CARO:0010000 ! multicellular anatomical structure [Term] id: CARO:0000041 name: anatomical cluster def: "Anatomical group that has its parts adjacent to one another." [FMA:49443, https://orcid.org/0000-0001-9114-8737] subset: plus is_obsolete: true replaced_by: CARO:0020001 [Term] id: CARO:0000042 name: extraembryonic structure def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [] comment: MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n subset: plus is_a: CARO:0000003 ! connected anatomical structure is_a: CARO:0001008 ! gross anatomical part disjoint_from: CARO:0001000 ! multi-cell-part structure disjoint_from: CARO:0010000 ! multicellular anatomical structure [Term] id: CARO:0000043 name: tissue def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [] is_a: CARO:0010000 ! multicellular anatomical structure property_value: editor_note "relabel 'tissue'?" xsd:string property_value: IAO:0000118 "portion of tissue" xsd:string [Term] id: CARO:0000045 name: sequential hermaphroditic organism def: "Hermaphroditic organism that produces gametes first of one sex, and then later of the other sex." [] is_a: CARO:0000029 ! hermaphroditic organism property_value: IAO:0000118 "consecutive hermaphroditic organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"} [Term] id: CARO:0000046 name: synchronous hermaphroditic organism def: "Hermaphroditic organism that produces both male and female gametes at the same time." [] is_a: CARO:0000029 ! hermaphroditic organism property_value: IAO:0000118 "serially hermaphroditic organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"} [Term] id: CARO:0000048 name: gonochoristic organism def: "Multi-cellular organism that has male and female sexes." [] is_a: CARO:0000012 ! multicellular organism property_value: IAO:0000118 "monoecious organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"} [Term] id: CARO:0000049 name: protandrous hermaphroditic organism def: "Sequential hermaphroditic organism that produces\\ngametes first of the male sex, and then later of the\\nfemale sex." [] is_a: CARO:0000045 ! sequential hermaphroditic organism [Term] id: CARO:0000050 name: protogynous hermaphroditic organism def: "Sequential hermaphroditic organism that produces\\ngametes first of the female sex, and then later of the\\nmale sex." [] is_a: CARO:0000045 ! sequential hermaphroditic organism [Term] id: CARO:0000054 name: anatomical group def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.\n" [https://orcid.org/0000-0001-9114-8737] comment: Obsoleted because the definition is too opaque. Also because this class was a subclass of 'anatomical structure' (CARO_0000003), but a similarly named class in the refactored caro (CARO_0020000) is a sibling of 'anatomical structure'. subset: core is_obsolete: true consider: CARO:0020000 [Term] id: CARO:0000055 name: multi-tissue structure def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [] is_a: CARO:0010000 ! multicellular anatomical structure relationship: has_component CARO:0000043 {minCardinality="2"} ! tissue [Term] id: CARO:0000062 name: cell space def: "Anatomical space that is part of a cell." [] is_a: CARO:0000005 ! anatomical space intersection_of: CARO:0000005 ! anatomical space intersection_of: part_of CARO:0000013 ! cell relationship: part_of CARO:0000013 ! cell [Term] id: CARO:0000063 name: portion of cell substance def: "Portion of organism substance located within a cell." [] comment: Deprecate this as better to leave it up to GO to define? is_a: CARO:0000004 ! organism substance [Term] id: CARO:0000064 name: unicellular organism def: "Organism that consists of a single cell for all of its life-cycle." [] is_a: CARO:0010004 ! cellular organism relationship: has_component CARO:0000013 {cardinality="1"} ! cell relationship: has_component CARO:0000013 {all_only="true"} ! cell property_value: IAO:0000118 "single-cell organism" xsd:string [Term] id: CARO:0000065 name: basal lamina def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [] is_obsolete: true [Term] id: CARO:0000066 name: epithelium def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina." [] is_a: CARO:0000043 ! tissue relationship: bearer_of PATO:0002124 ! laminar [Term] id: CARO:0000067 name: simple cuboidal epithelium def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000068 name: simple columnar epithlium def: "Unilaminar epithelium that consists of a single layer of columnar cells." [] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000069 name: multilaminar epithelium def: "Epithelium that consists of more than one layer of epithelial cells." [] is_a: CARO:0000066 ! epithelium disjoint_from: CARO:0000071 ! atypical epithelium disjoint_from: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000070 name: simple squamous epithelium def: "Unilaminar epithelium that consists of a single layer of squamous cells." [] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000071 name: atypical epithelium def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [] is_a: CARO:0000066 ! epithelium disjoint_from: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000072 name: cavitated compound organ def: "Compound organ that contains one or more macroscopic anatomical spaces." [] is_a: CARO:0000024 ! compound organ [Term] id: CARO:0000073 name: unilaminar epithelium def: "Epithelium that consists of a single layer of epithelial cells." [] is_a: CARO:0000066 ! epithelium [Term] id: CARO:0000074 name: solid compound organ def: "Compound organ that does not contain macroscopic anatomical spaces." [] is_a: CARO:0000024 ! compound organ [Term] id: CARO:0000077 name: epithelial cell def: "Cell which has as its part a cytoskeleton that allows for tight cell to cell contact and which has apical-basal cell polarity." [] is_obsolete: true [Term] id: CARO:0000081 name: circulating fluid def: "A fluid that is circulated around a multicellular organism carrying nutrients and carrying away waste products." [] comment: Examples: blood, lymph, hemolymph is_a: CARO:0000004 ! organism substance [Term] id: CARO:0000133 name: paired appendage def: "An appendage that is one of a bilateral pair." [] is_a: CARO:0010003 ! appendage disjoint_from: CARO:0000134 ! unpaired appendage [Term] id: CARO:0000134 name: unpaired appendage is_a: CARO:0010003 ! appendage [Term] id: CARO:0001000 name: multi-cell-part structure def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [] comment: Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. subset: core is_a: CARO:0001008 ! gross anatomical part disjoint_from: CARO:0010000 ! multicellular anatomical structure property_value: IAO:0000118 "multi-cell-component structure" xsd:string [Term] id: CARO:0001001 name: neuron projection bundle def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [] is_a: CARO:0001000 ! multi-cell-part structure relationship: bearer_of PATO:0002309 ! fiber shaped property_value: IAO:0000118 "nerve fiber bundle" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="EXACT"} [Term] id: CARO:0001002 name: anatomical surface def: "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.\n" [] comment: Old definition: "Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures." Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. is_a: CARO:0001007 ! morphological boundary [Term] id: CARO:0001003 name: fiat anatomical boundary def: "A two dimensional anatomical entity that does not correspond to any physical discontinuity." [] comment: Fiat anatomical boundaries are generally defined using external physical criteria as landmarks. One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) is_a: CARO:0000010 ! anatomical boundary [Term] id: CARO:0001004 name: bona-fide anatomical boundary def: "An anatomical boundary that corresponds to some physical discontinuity." [] comment: One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) is_a: CARO:0000010 ! anatomical boundary [Term] id: CARO:0001005 name: gene expression boundary def: "A two dimensional anatomical entity that is the boundary of a domain of expression of some gene." [] is_a: CARO:0001004 ! bona-fide anatomical boundary [Term] id: CARO:0001006 name: developmental compartment boundary def: "A two dimensional anatomical entity that is not a morphological boundary and that cells do not cross during development." [] is_a: CARO:0001004 ! bona-fide anatomical boundary [Term] id: CARO:0001007 name: morphological boundary def: "A two dimensional anatomical structure that corresponds to some structural discontinuity." [] is_a: CARO:0001004 ! bona-fide anatomical boundary [Term] id: CARO:0001008 name: gross anatomical part def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " [] subset: plus is_a: CARO:0000006 ! material anatomical entity union_of: CARO:0000004 ! organism substance union_of: CARO:0000032 ! organism subdivision union_of: CARO:0000040 ! acellular anatomical structure union_of: CARO:0000042 ! extraembryonic structure union_of: CARO:0001000 ! multi-cell-part structure union_of: CARO:0010000 ! multicellular anatomical structure relationship: part_of CARO:0000012 ! multicellular organism property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 [Term] id: CARO:0001009 name: obsolete anatomical chamber def: "Anatomical structure that surrounds an immaterial anatomical entity." [] comment: See CARO tracker #6, but essentially Chamber has connotations of space, rather than wall: see http://en.wiktionary.org/wiki/chamber\n\nThis term is extremely abstract as a genus - it specifies no granularity at all. It could refer to a chamber in a protein complex in a membrane as easily as some big multi-tissue structure like a segment of gut. subset: plus property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.10.2011" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 is_obsolete: true [Term] id: CARO:0001010 name: organism def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] synonym: "organism or virus or viroid" EXACT [] is_a: BFO:0000040 ! material entity property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string property_value: IAO:0000117 "Melissa Haendel" xsd:string [Term] id: CARO:0001013 name: anatomical plane comment: All anatomical planes are fiat anatomical boundaries - no morphological boundary could ever be a perfect plane. is_a: CARO:0001003 ! fiat anatomical boundary [Term] id: CARO:0001500 name: neuron projection bundle segment def: "A fiber-shaped subdivision of a neuron projection along its long axis." [] {http://purl.obolibrary.org/obo/IAO_0000117="https://orcid.org/0000-0002-7073-9172"} is_a: CARO:0001000 ! multi-cell-part structure relationship: bearer_of PATO:0002309 ! fiber shaped relationship: part_of CARO:0001001 ! neuron projection bundle [Term] id: CARO:0001501 name: neuron projection bundle subsegment def: "A subdivision of a neuron projection along its long axis that is as long as it is wide (and so does not qualify as fiber-shaped)." [] {http://purl.obolibrary.org/obo/IAO_0000117="https://orcid.org/0000-0002-7073-9172"} comment: This term was added in order to define fasciculation relations. It seems unlikely that it will be used directly in curation. is_a: CARO:0001000 ! multi-cell-part structure relationship: part_of CARO:0001001 ! neuron projection bundle [Term] id: CARO:0002000 name: epidermis def: "Epithelium of the integumentary system." [] is_a: CARO:0000066 ! epithelium intersection_of: CARO:0000066 ! epithelium intersection_of: part_of CARO:0002001 ! integumentary system relationship: part_of CARO:0002001 ! integumentary system [Term] id: CARO:0002001 name: integumentary system def: "Connected anatomical system that forms a barrier between an animal and its environment - generally consisting of an epidermis, which may be covered by some acellular structure." [] is_a: CARO:0000011 ! connected anatomical system [Term] id: CARO:0002002 name: aligned anatomical group def: "An anatomical group whose members are arranged in a line." [] comment: Examples include the rows of sense organs commonly found in the cuticles of insects. is_a: CARO:0020000 ! disconnected anatomical group [Term] id: CARO:0002003 name: clustered anatomical group def: "Anatomical group whose parts are close together, forming a cluster." [https://orcid.org/0000-0002-7073-9172] comment: Not to be confused with anatomical cluster, in the FMA sense. FMA anatomical structures are connected structures made up of heterologous parts. For example, joints are anatomical clusters in the FMA. The FMA definition on anatomical cluster, and the CARO1 definition that was based on it, are defined largely by exclusion. is_a: CARO:0020000 ! disconnected anatomical group [Term] id: CARO:0002004 name: segment body def: "One of a set of semi-repetitive organism subdivisions serially arranged along the anterior-posterior axis of an organism and excluding appendages if present." [] is_a: CARO:0000032 ! organism subdivision [Term] id: CARO:0002005 name: appendage subdivision def: "A subdivision of an appendage along its proximal-distal axis, consisting consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [] is_a: CARO:0000032 ! organism subdivision [Term] id: CARO:0002006 name: obsolete body cavity def: "A major anatomical space of an organism in which major organs are located." [] property_value: example_of_usage "Ceolom, cranial cavity, mammalian thoracic and abdominal body cavities, arthropod hemoceol." xsd:string is_obsolete: true [Term] id: CARO:0002100 name: anatomical system def: "An anatomical structure consisting of multiple cells, organs, tissues, distributed throught an organism, that act together to perform some physiological function." [] comment: Examples include connected systems such as the circulatory system - whose elements function together to perform the function or blood circulation - and disconected systems such as the immune system. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0002101 name: disconnected anatomical system def: "An anatomical system consisting of multiple disconnected parts." [https://orcid.org/0000-0002-7073-9172] comment: Examples include the immune system and the endocrine system. is_a: CARO:0002100 ! anatomical system intersection_of: CARO:0002100 ! anatomical system intersection_of: bearer_of PATO:0010001 ! disconnected intersection_of: has_component CARO:0000003 {minCardinality="2"} ! connected anatomical structure relationship: bearer_of PATO:0010001 ! disconnected relationship: has_component CARO:0000003 ! connected anatomical structure [Term] id: CARO:0010000 name: multicellular anatomical structure def: "An anatomical structure that has more than one cell as a part." [] subset: core is_a: CARO:0000003 ! connected anatomical structure is_a: CARO:0001008 ! gross anatomical part intersection_of: CARO:0000003 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! connected anatomical structure intersection_of: bearer_of PATO:0001993 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! multicellular relationship: bearer_of PATO:0001993 ! multicellular property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 10:53:00 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010001 name: cell cluster organ def: "A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function." [] comment: Examples include arthropod sensilla. is_a: CARO:0020002 ! cell cluster is_a: CARO:0020004 ! organ disjoint_from: CARO:0010002 ! compound cell cluster organ property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 11:00:35 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010002 name: compound cell cluster organ def: "An anatomical structure consisting of multiple cell cluster organs, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function." [] comment: Examples: compound eye; Johnston's organ. is_a: CARO:0020004 ! organ relationship: has_component CARO:0010001 {minCardinality="2"} ! cell cluster organ property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 11:13:17 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010003 name: appendage def: "An organism subdivision that protrudes from the body." [] is_a: CARO:0000032 ! organism subdivision disjoint_from: CARO:0010005 ! segment disjoint_from: CARO:0010006 ! tagma disjoint_from: CARO:0010007 ! appendage segment property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:09:17 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010004 name: cellular organism def: "An individual member of a clade of cellular organisms." [] comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0000003 ! connected anatomical structure is_a: CARO:0001010 ! organism property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 [Term] id: CARO:0010005 name: segment def: "One of a set of semi-repetitive organism subdivisions serially arranged along the anterior-posterior axis of an organism, including appendages if present." [https://orcid.org/0000-0002-7073-9172] synonym: "metamere" EXACT [] is_a: CARO:0000032 ! organism subdivision disjoint_from: CARO:0010006 ! tagma disjoint_from: CARO:0010007 ! appendage segment relationship: has_part CARO:0010006 ! tagma property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:13:46 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010006 name: tagma def: "A subdivision of the organism along the anterior-posterior axis that consists of multiple adjacent segments that are either fused, and/or share more structure with each other than with segments in adjacent tagmata." [] is_a: CARO:0000032 ! organism subdivision disjoint_from: CARO:0010007 ! appendage segment property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:14:57 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010007 name: appendage segment def: "One of a set of semi-repetitive organism subdivisions serially arranged along the proximal-distal axis of an appendage" [] is_a: CARO:0002005 ! appendage subdivision relationship: part_of CARO:0010003 ! appendage property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:16:21 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010009 name: epithelial tube def: "An epithelium that is rolled into a tube." [] is_a: CARO:0000066 ! epithelium intersection_of: CARO:0000066 ! epithelium intersection_of: bearer_of PATO:0001873 ! cylindrical intersection_of: bearer_of PATO:0002078 ! hollow relationship: bearer_of PATO:0001873 ! cylindrical relationship: bearer_of PATO:0002078 ! hollow property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 09 06:22:07 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0010010 name: epithelial sac is_a: CARO:0000066 ! epithelium intersection_of: CARO:0000066 ! epithelium intersection_of: bearer_of PATO:0001987 ! saccular relationship: bearer_of PATO:0001987 ! saccular property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 09 08:02:50 GMT 2011" xsd:string property_value: IAO:0000117 "djs93" xsd:string [Term] id: CARO:0020000 name: disconnected anatomical group def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [] subset: core is_a: CARO:0000006 ! material anatomical entity intersection_of: CARO:0000006 ! material anatomical entity intersection_of: bearer_of PATO:0010001 ! disconnected intersection_of: has_component CARO:0000003 {minCardinality="2"} ! connected anatomical structure relationship: bearer_of PATO:0010001 ! disconnected relationship: has_component CARO:0000003 ! connected anatomical structure [Term] id: CARO:0020001 name: multi organ part structure def: "A multicellular anatomical structure that has subparts of\nmultiple organs as a part." [] comment: Examples include joints of the vertebrate musculoskeletal system (each has (fiat) parts of multiple bone organs as a part). subset: plus synonym: "anatomical cluster" RELATED [] is_a: CARO:0010000 ! multicellular anatomical structure [Term] id: CARO:0020002 name: cell cluster def: "A cluster of cells, largely surrounded by a morphological boundary." [] {comment="https://orcid.org/0000-0002-7073-9172"} is_a: CARO:0010000 ! multicellular anatomical structure [Term] id: CARO:0020003 name: cellular anatomical structure def: "An anatomical structure consisting of one or more cells." [] is_a: CARO:0000006 ! material anatomical entity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2018-09-28T14:20:19Z [Term] id: CARO:0020004 name: organ def: "A multicellular anatomical structure largely delimited by a morphological boundary whose components work together to make the whole structure capable of a specific function." [] is_a: CARO:0010000 ! multicellular anatomical structure [Term] id: CARO:0020005 name: single tissue organ def: "An single tissue, largely surrounded by a morpholigical boundary, whose cells work together to make the whole structure capable of a specific function." [] is_a: CARO:0000043 ! tissue is_a: CARO:0020004 ! organ intersection_of: CARO:0020004 ! organ intersection_of: has_component CARO:0000043 {cardinality="1"} ! tissue relationship: has_component CARO:0000043 ! tissue [Term] id: CARO:0030000 name: biological entity def: "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." [] comment: Important for alignment with Darwin Core class "Organism". is_a: BFO:0000004 ! independent continuant [Term] id: CARO:0030002 name: expression pattern def: "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." [] is_a: CARO:0020003 ! cellular anatomical structure relationship: has_part CARO:0000013 ! cell [Term] id: CHEBI:10545 name: electron namespace: chebi_ontology def: "Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV." [] subset: 3_STAR synonym: "beta" RELATED [IUPAC] synonym: "beta(-)" RELATED [ChEBI] synonym: "beta-particle" RELATED [IUPAC] synonym: "e" RELATED [IUPAC] synonym: "e(-)" RELATED [UniProt] synonym: "e-" RELATED [KEGG_COMPOUND] synonym: "electron" EXACT [KEGG_COMPOUND] synonym: "electron" EXACT IUPAC_NAME [IUPAC] synonym: "electron" EXACT [ChEBI] synonym: "Elektron" RELATED [ChEBI] synonym: "negatron" RELATED [IUPAC] xref: KEGG:C05359 xref: PMID:21614077 {source="Europe PMC"} xref: Wikipedia:Electron is_a: CHEBI:36338 ! lepton property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "0.000548579903" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "0.0" xsd:string [Term] id: CHEBI:131604 name: Mycoplasma genitalium metabolite namespace: chebi_ontology def: "Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium." [] subset: 3_STAR synonym: "Mycoplasma genitalium metabolites" RELATED [ChEBI] is_a: CHEBI:76969 ! bacterial metabolite [Term] id: CHEBI:131927 name: dicarboxylic acids and O-substituted derivatives namespace: chebi_ontology def: "A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens." [] subset: 3_STAR synonym: "dicarboxylic acids and derivatives" RELATED [ChEBI] is_a: CHEBI:36586 ! carbonyl compound [Term] id: CHEBI:138675 name: gas molecular entity namespace: chebi_ontology def: "Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa)." [] subset: 3_STAR synonym: "gas molecular entities" RELATED [ChEBI] synonym: "gaseous molecular entities" RELATED [ChEBI] synonym: "gaseous molecular entity" RELATED [ChEBI] xref: Wikipedia:https\://en.wikipedia.org/wiki/Gas is_a: CHEBI:33579 ! main group molecular entity [Term] id: CHEBI:13941 name: carbamate namespace: chebi_ontology subset: 3_STAR synonym: "Carbamat" RELATED [ChEBI] synonym: "carbamate" EXACT [UniProt] synonym: "carbamate" EXACT IUPAC_NAME [IUPAC] synonym: "carbamate ion" RELATED [ChemIDplus] synonym: "carbamic acid, ion(1-)" RELATED [ChemIDplus] synonym: "Karbamat" RELATED [ChEBI] xref: Beilstein:3903503 {source="Beilstein"} xref: CAS:302-11-4 {source="ChemIDplus"} xref: Gmelin:239604 {source="Gmelin"} is_a: CHEBI:37022 ! amino-acid anion relationship: is_conjugate_base_of CHEBI:28616 ! carbamic acid property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CH2NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "KXDHJXZQYSOELW-UHFFFAOYSA-M" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "60.03212" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "60.00910" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC([O-])=O" xsd:string [Term] id: CHEBI:140601 name: fatty acid 4:0 namespace: chebi_ontology def: "Any saturated fatty acid containing 4 carbons." [] subset: 3_STAR is_a: CHEBI:26666 ! short-chain fatty acid relationship: is_conjugate_acid_of CHEBI:78115 ! fatty acid anion 4:0 property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CHO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "45.017" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "44.99765" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "*C(O)=O" xsd:string [Term] id: CHEBI:14321 name: glutamate(1-) namespace: chebi_ontology def: "An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group" [] subset: 3_STAR synonym: "2-ammoniopentanedioate" RELATED [IUPAC] synonym: "glutamate" RELATED [UniProt] synonym: "glutamate(1-)" EXACT [JCBN] synonym: "glutamic acid monoanion" RELATED [JCBN] synonym: "hydrogen glutamate" EXACT IUPAC_NAME [IUPAC] xref: Gmelin:327908 {source="Gmelin"} is_a: CHEBI:33558 ! alpha-amino-acid anion relationship: is_conjugate_acid_of CHEBI:29987 ! glutamate(2-) relationship: is_conjugate_base_of CHEBI:18237 ! glutamic acid relationship: RO:0000087 CHEBI:78675 ! has role fundamental metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C5H8NO4" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "WHUUTDBJXJRKMK-UHFFFAOYSA-M" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "146.12136" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "146.04588" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]C(CCC([O-])=O)C([O-])=O" xsd:string [Term] id: CHEBI:15339 name: acceptor namespace: chebi_ontology alt_id: CHEBI:13699 alt_id: CHEBI:2377 def: "A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity." [] subset: 3_STAR synonym: "A" RELATED [KEGG_COMPOUND] synonym: "accepteur" RELATED [ChEBI] synonym: "Acceptor" EXACT [KEGG_COMPOUND] synonym: "Akzeptor" RELATED [ChEBI] synonym: "Hydrogen-acceptor" RELATED [KEGG_COMPOUND] synonym: "Oxidized donor" RELATED [KEGG_COMPOUND] xref: KEGG:C00028 xref: KEGG:C16722 is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:15354 name: choline namespace: chebi_ontology alt_id: CHEBI:13985 alt_id: CHEBI:23212 alt_id: CHEBI:3665 alt_id: CHEBI:41524 def: "A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function." [] subset: 3_STAR synonym: "2-hydroxy-N,N,N-trimethylethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "Bilineurine" RELATED [KEGG_COMPOUND] synonym: "Choline" EXACT [KEGG_COMPOUND] synonym: "choline" EXACT [UniProt] synonym: "CHOLINE ION" RELATED [PDBeChem] synonym: "N,N,N-trimethylethanol-ammonium" RELATED [ChEBI] synonym: "N-trimethylethanolamine" RELATED [ChEBI] synonym: "trimethylethanolamine" RELATED [ChEBI] xref: Beilstein:1736748 {source="Beilstein"} xref: CAS:62-49-7 {source="ChemIDplus"} xref: CAS:62-49-7 {source="KEGG COMPOUND"} xref: Drug_Central:3097 {source="DrugCentral"} xref: DrugBank:DB00122 xref: ECMDB:ECMDB00097 xref: Gmelin:324597 {source="Gmelin"} xref: HMDB:HMDB0000097 xref: KEGG:C00114 xref: KEGG:D07690 xref: KNApSAcK:C00007298 xref: MetaCyc:CHOLINE xref: PDBeChem:CHT xref: PMID:10930630 {source="Europe PMC"} xref: PMID:12826235 {source="Europe PMC"} xref: PMID:12946691 {source="Europe PMC"} xref: PMID:14972364 {source="Europe PMC"} xref: PMID:16210714 {source="Europe PMC"} xref: PMID:17087106 {source="Europe PMC"} xref: PMID:17283071 {source="Europe PMC"} xref: PMID:17344490 {source="Europe PMC"} xref: PMID:18204095 {source="Europe PMC"} xref: PMID:18230680 {source="Europe PMC"} xref: PMID:18786517 {source="Europe PMC"} xref: PMID:18786520 {source="Europe PMC"} xref: PMID:19246089 {source="Europe PMC"} xref: PMID:20038853 {source="Europe PMC"} xref: PMID:20446114 {source="Europe PMC"} xref: PMID:22770225 {source="Europe PMC"} xref: PMID:22961562 {source="Europe PMC"} xref: PMID:23095202 {source="Europe PMC"} xref: PMID:23616508 {source="Europe PMC"} xref: PMID:23637565 {source="Europe PMC"} xref: PMID:23733158 {source="Europe PMC"} xref: PMID:6420466 {source="Europe PMC"} xref: PMID:7590654 {source="Europe PMC"} xref: PMID:9517478 {source="Europe PMC"} xref: Reaxys:1736748 {source="Reaxys"} xref: Wikipedia:Choline xref: YMDB:YMDB00227 is_a: CHEBI:23217 ! cholines relationship: RO:0000087 CHEBI:25512 ! has role neurotransmitter relationship: RO:0000087 CHEBI:33284 ! has role nutrient relationship: RO:0000087 CHEBI:50904 ! has role allergen relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:75772 ! has role Saccharomyces cerevisiae metabolite relationship: RO:0000087 CHEBI:76924 ! has role plant metabolite relationship: RO:0000087 CHEBI:76971 ! has role Escherichia coli metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite relationship: RO:0000087 CHEBI:83056 ! has role Daphnia magna metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C5H14NO" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "OEYIOHPDSNJKLS-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "104.17080" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "104.10699" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C[N+](C)(C)CCO" xsd:string [Term] id: CHEBI:15355 name: acetylcholine namespace: chebi_ontology alt_id: CHEBI:12686 alt_id: CHEBI:13715 alt_id: CHEBI:22197 alt_id: CHEBI:2416 alt_id: CHEBI:40559 def: "Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter." [ANON:ANON] subset: 3_STAR synonym: "2-acetyloxy-N,N,N-trimethylethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "2-acetyloxy-N,N,N-trimethylethanaminium" EXACT IUPAC_NAME [IUPAC:] synonym: "ACETYLCHOLINE" EXACT [PDBeChem:] synonym: "ACETYLCHOLINE" EXACT [PDBeChem] synonym: "Acetylcholine" EXACT [KEGG_COMPOUND] synonym: "Acetylcholine" EXACT [KEGG COMPOUND:] synonym: "acetylcholine" EXACT [UniProt] synonym: "ACh" RELATED [ChemIDplus] synonym: "ACh" RELATED [ChemIDplus:] synonym: "Azetylcholin" RELATED [ChEBI] synonym: "Azetylcholin" RELATED [ChEBI:] synonym: "C7H16NO2" RELATED FORMULA [KEGG COMPOUND:] synonym: "CC(=O)OCC[N+](C)(C)C" RELATED SMILES [ChEBI:] synonym: "choline acetate" RELATED [ChemIDplus] synonym: "choline acetate" RELATED [ChemIDplus:] synonym: "InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1" RELATED InChI [ChEBI:] synonym: "InChIKey=OIPILFWXSMYKGL-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "O-Acetylcholine" RELATED [KEGG COMPOUND:] synonym: "O-Acetylcholine" RELATED [KEGG_COMPOUND] xref: Beilstein:1764436 {source="ChemIDplus"} xref: CAS:51-84-3 {source="ChemIDplus"} xref: CAS:51-84-3 {source="KEGG COMPOUND"} xref: Drug_Central:65 {source="DrugCentral"} xref: DrugBank:DB03128 xref: Gmelin:326108 {source="Gmelin"} xref: KEGG:C01996 xref: LINCS:LSM-5888 xref: PDBeChem:ACH xref: PMID:14764638 {source="Europe PMC"} xref: PMID:15014918 {source="Europe PMC"} xref: PMID:15231705 {source="Europe PMC"} xref: PMID:15361288 {source="Europe PMC"} xref: PMID:18050502 {source="Europe PMC"} xref: PMID:18407448 {source="Europe PMC"} xref: PMID:19255787 {source="Europe PMC"} xref: PMID:20963497 {source="Europe PMC"} xref: PMID:21130809 {source="Europe PMC"} xref: PMID:21246223 {source="Europe PMC"} xref: PMID:21545631 {source="Europe PMC"} xref: PMID:21601579 {source="Europe PMC"} xref: Wikipedia:Acetylcholine is_a: CHEBI:35287 ! acylcholine is_a: CHEBI:47622 ! acetate ester relationship: RO:0000087 CHEBI:24621 ! has role hormone relationship: RO:0000087 CHEBI:25512 ! has role neurotransmitter relationship: RO:0000087 CHEBI:35620 ! has role vasodilator agent relationship: RO:0000087 CHEBI:38325 ! has role muscarinic agonist relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C7H16NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "OIPILFWXSMYKGL-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "146.20748" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "146.11756" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "CC(=O)OCC[N+](C)(C)C" xsd:string [Term] id: CHEBI:15366 name: acetic acid namespace: chebi_ontology alt_id: CHEBI:22169 alt_id: CHEBI:2387 alt_id: CHEBI:40486 def: "A simple monocarboxylic acid containing two carbons." [] subset: 3_STAR synonym: "ACETIC ACID" EXACT [PDBeChem] synonym: "Acetic acid" EXACT [KEGG_COMPOUND] synonym: "acetic acid" EXACT IUPAC_NAME [IUPAC] synonym: "acide acetique" RELATED [ChemIDplus] synonym: "AcOH" RELATED [ChEBI] synonym: "CH3-COOH" RELATED [IUPAC] synonym: "CH3CO2H" RELATED [ChEBI] synonym: "E 260" RELATED [ChEBI] synonym: "E-260" RELATED [ChEBI] synonym: "E260" RELATED [ChEBI] synonym: "Essigsaeure" RELATED [ChEBI] synonym: "Ethanoic acid" RELATED [KEGG_COMPOUND] synonym: "ethoic acid" RELATED [ChEBI] synonym: "Ethylic acid" RELATED [ChemIDplus] synonym: "HOAc" RELATED [ChEBI] synonym: "INS No. 260" RELATED [ChEBI] synonym: "MeCO2H" RELATED [ChEBI] synonym: "MeCOOH" RELATED [ChEBI] synonym: "Methanecarboxylic acid" RELATED [ChemIDplus] xref: Beilstein:506007 {source="Beilstein"} xref: CAS:64-19-7 {source="ChemIDplus"} xref: CAS:64-19-7 {source="NIST Chemistry WebBook"} xref: CAS:64-19-7 {source="KEGG COMPOUND"} xref: Drug_Central:4211 {source="DrugCentral"} xref: Gmelin:1380 {source="Gmelin"} xref: HMDB:HMDB0000042 xref: KEGG:C00033 xref: KEGG:D00010 xref: KNApSAcK:C00001176 xref: LIPID_MAPS_instance:LMFA01010002 {source="LIPID MAPS"} xref: MetaCyc:ACET xref: PDBeChem:ACT xref: PDBeChem:ACY xref: PMID:12005138 {source="Europe PMC"} xref: PMID:15107950 {source="Europe PMC"} xref: PMID:16630552 {source="Europe PMC"} xref: PMID:16774200 {source="Europe PMC"} xref: PMID:17190852 {source="Europe PMC"} xref: PMID:19416101 {source="Europe PMC"} xref: PMID:19469536 {source="Europe PMC"} xref: PMID:22153255 {source="Europe PMC"} xref: PMID:22173419 {source="Europe PMC"} xref: PPDB:1333 xref: Reaxys:506007 {source="Reaxys"} xref: Wikipedia:Acetic_acid is_a: CHEBI:25384 ! monocarboxylic acid relationship: is_conjugate_acid_of CHEBI:30089 ! acetate relationship: RO:0000087 CHEBI:48356 ! has role protic solvent relationship: RO:0000087 CHEBI:64049 ! has role food acidity regulator relationship: RO:0000087 CHEBI:65256 ! has role antimicrobial food preservative relationship: RO:0000087 CHEBI:83056 ! has role Daphnia magna metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4O2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QTBSBXVTEAMEQO-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "60.05200" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "60.02113" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "CC(O)=O" xsd:string [Term] id: CHEBI:15705 name: L-alpha-amino acid namespace: chebi_ontology alt_id: CHEBI:13072 alt_id: CHEBI:13243 alt_id: CHEBI:13797 alt_id: CHEBI:21224 alt_id: CHEBI:6175 def: "Any alpha-amino acid having L-configuration at the alpha-carbon." [] subset: 3_STAR synonym: "L-2-Amino acid" RELATED [KEGG_COMPOUND] synonym: "L-alpha-amino acid" EXACT [IUPAC] synonym: "L-alpha-amino acids" EXACT IUPAC_NAME [IUPAC] synonym: "L-alpha-amino acids" RELATED [ChEBI] synonym: "L-Amino acid" RELATED [KEGG_COMPOUND] xref: KEGG:C00151 is_a: CHEBI:33704 ! alpha-amino acid relationship: is_conjugate_acid_of CHEBI:59814 ! L-alpha-amino acid anion relationship: is_tautomer_of CHEBI:59869 ! L-alpha-amino acid zwitterion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "74.05870" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "74.02420" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "N[C@@H]([*])C(O)=O" xsd:string [Term] id: CHEBI:15841 name: polypeptide namespace: chebi_ontology alt_id: CHEBI:14860 alt_id: CHEBI:8314 def: "A peptide containing ten or more amino acid residues." [] subset: 3_STAR synonym: "polipeptido" RELATED [ChEBI] synonym: "Polypeptid" RELATED [ChEBI] synonym: "Polypeptide" EXACT [KEGG_COMPOUND] synonym: "polypeptides" EXACT IUPAC_NAME [IUPAC] xref: KEGG:C00403 is_a: CHEBI:16670 ! peptide is_a: CHEBI:33839 ! macromolecule property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H6N2O3R2(C2H2NOR)n" xsd:string [Term] id: CHEBI:15986 name: polynucleotide namespace: chebi_ontology alt_id: CHEBI:13672 alt_id: CHEBI:14859 alt_id: CHEBI:8312 def: "A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues." [] subset: 3_STAR synonym: "Polynucleotide" EXACT [KEGG_COMPOUND] synonym: "polynucleotides" RELATED [ChEBI] xref: KEGG:C00419 is_a: CHEBI:33695 ! information biomacromolecule is_a: CHEBI:61120 ! nucleobase-containing molecular entity relationship: has_part CHEBI:50319 ! nucleotide residue property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "(C5H8O6PR)n.C10H17O10PR2" xsd:string [Term] id: CHEBI:16134 name: ammonia namespace: chebi_ontology alt_id: CHEBI:13405 alt_id: CHEBI:13406 alt_id: CHEBI:13407 alt_id: CHEBI:13771 alt_id: CHEBI:22533 alt_id: CHEBI:44269 alt_id: CHEBI:44284 alt_id: CHEBI:44404 alt_id: CHEBI:7434 def: "An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms." [] subset: 3_STAR synonym: "[NH3]" RELATED [MolBase] synonym: "AMMONIA" EXACT [PDBeChem] synonym: "Ammonia" EXACT [KEGG_COMPOUND] synonym: "ammonia" EXACT IUPAC_NAME [IUPAC] synonym: "ammoniac" RELATED [ChEBI] synonym: "Ammoniak" RELATED [ChemIDplus] synonym: "amoniaco" RELATED [ChEBI] synonym: "azane" EXACT IUPAC_NAME [IUPAC] synonym: "NH3" RELATED [KEGG_COMPOUND] synonym: "NH3" RELATED [UniProt] synonym: "NH3" RELATED [IUPAC] synonym: "R-717" RELATED [ChEBI] synonym: "spirit of hartshorn" RELATED [ChemIDplus] xref: Beilstein:3587154 {source="Beilstein"} xref: CAS:7664-41-7 {source="ChemIDplus"} xref: CAS:7664-41-7 {source="NIST Chemistry WebBook"} xref: CAS:7664-41-7 {source="KEGG COMPOUND"} xref: Drug_Central:4625 {source="DrugCentral"} xref: Gmelin:79 {source="Gmelin"} xref: HMDB:HMDB0000051 xref: KEGG:C00014 xref: KEGG:D02916 xref: KNApSAcK:C00007267 xref: MetaCyc:AMMONIA xref: MolBase:930 xref: PDBeChem:NH3 xref: PMID:110589 {source="Europe PMC"} xref: PMID:11139349 {source="Europe PMC"} xref: PMID:11540049 {source="Europe PMC"} xref: PMID:11746427 {source="Europe PMC"} xref: PMID:11783653 {source="Europe PMC"} xref: PMID:13753780 {source="Europe PMC"} xref: PMID:14663195 {source="Europe PMC"} xref: PMID:15092448 {source="Europe PMC"} xref: PMID:15094021 {source="Europe PMC"} xref: PMID:15554424 {source="Europe PMC"} xref: PMID:15969015 {source="Europe PMC"} xref: PMID:16008360 {source="Europe PMC"} xref: PMID:16050680 {source="Europe PMC"} xref: PMID:16348008 {source="Europe PMC"} xref: PMID:16349403 {source="Europe PMC"} xref: PMID:16614889 {source="Europe PMC"} xref: PMID:16664306 {source="Europe PMC"} xref: PMID:16842901 {source="Europe PMC"} xref: PMID:17025297 {source="Europe PMC"} xref: PMID:17439666 {source="Europe PMC"} xref: PMID:17569513 {source="Europe PMC"} xref: PMID:17737668 {source="Europe PMC"} xref: PMID:18670398 {source="Europe PMC"} xref: PMID:22002069 {source="Europe PMC"} xref: PMID:22081570 {source="Europe PMC"} xref: PMID:22088435 {source="Europe PMC"} xref: PMID:22100291 {source="Europe PMC"} xref: PMID:22130175 {source="Europe PMC"} xref: PMID:22150211 {source="Europe PMC"} xref: PMID:22240068 {source="Europe PMC"} xref: PMID:22290316 {source="Europe PMC"} xref: PMID:22342082 {source="Europe PMC"} xref: PMID:22385337 {source="Europe PMC"} xref: PMID:22443779 {source="Europe PMC"} xref: PMID:22560242 {source="Europe PMC"} xref: Reaxys:3587154 {source="Reaxys"} xref: Wikipedia:Ammonia is_a: CHEBI:138675 ! gas molecular entity is_a: CHEBI:35107 ! azane is_a: CHEBI:37176 ! mononuclear parent hydride relationship: is_conjugate_acid_of CHEBI:29337 ! azanide relationship: is_conjugate_base_of CHEBI:28938 ! ammonium relationship: RO:0000087 CHEBI:50910 ! has role neurotoxin relationship: RO:0000087 CHEBI:59740 ! has role nucleophilic reagent relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:77941 ! has role EC 3.5.1.4 (amidase) inhibitor relationship: RO:0000087 CHEBI:78433 ! has role refrigerant property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "H3N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/H3N/h1H3" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QGZKDVFQNNGYKY-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "17.03056" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "17.02655" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[H]N([H])[H]" xsd:string [Term] id: CHEBI:16541 name: protein polypeptide chain namespace: chebi_ontology alt_id: CHEBI:8526 def: "A naturally occurring polypeptide synthesized at the ribosome." [] subset: 3_STAR synonym: "a protein" RELATED [UniProt] synonym: "polypeptide chain" RELATED [ChEBI] synonym: "Protein" RELATED [KEGG_COMPOUND] synonym: "protein polypeptide chains" RELATED [ChEBI] xref: KEGG:C00017 is_a: CHEBI:15841 ! polypeptide relationship: has_part CHEBI:33700 ! proteinogenic amino-acid residue [Term] id: CHEBI:16670 name: peptide namespace: chebi_ontology alt_id: CHEBI:14753 alt_id: CHEBI:25906 alt_id: CHEBI:7990 def: "Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid." [ANON:ANON] def: "Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc." [] subset: 3_STAR synonym: "C2H4NO2R(C2H2NOR)n" RELATED FORMULA [KEGG COMPOUND:] synonym: "Peptid" RELATED [ChEBI:] synonym: "Peptid" RELATED [ChEBI] synonym: "Peptide" EXACT [KEGG_COMPOUND] synonym: "Peptide" EXACT [KEGG COMPOUND:] synonym: "peptides" EXACT IUPAC_NAME [IUPAC:] synonym: "peptides" EXACT IUPAC_NAME [IUPAC] synonym: "peptido" RELATED [ChEBI] synonym: "peptido" RELATED [ChEBI:] synonym: "peptidos" RELATED [ChEBI:] synonym: "peptidos" RELATED [ChEBI] xref: KEGG:C00012 is_a: CHEBI:37622 ! carboxamide is_a: CHEBI:50047 ! organic amino compound relationship: has_part CHEBI:33708 ! amino-acid residue relationship: is_tautomer_of CHEBI:60466 ! peptide zwitterion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "(C2H2NOR)nC2H3NOR" xsd:string [Term] id: CHEBI:16765 name: tryptamine namespace: chebi_ontology alt_id: CHEBI:15274 alt_id: CHEBI:27161 alt_id: CHEBI:46157 alt_id: CHEBI:9767 def: "An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position." [] subset: 3_STAR synonym: "1H-indole-3-ethanamine" RELATED [NIST_Chemistry_WebBook] synonym: "2-(1H-INDOL-3-YL)ETHANAMINE" RELATED [PDBeChem] synonym: "2-(1H-indol-3-yl)ethanamine" EXACT IUPAC_NAME [IUPAC] synonym: "2-(3-indolyl)ethylamine" RELATED [ChemIDplus] synonym: "3-(2-Aminoethyl)indole" RELATED [KEGG_COMPOUND] synonym: "Tryptamine" EXACT [KEGG_COMPOUND] xref: Beilstein:125513 {source="Beilstein"} xref: CAS:61-54-1 {source="ChemIDplus"} xref: CAS:61-54-1 {source="NIST Chemistry WebBook"} xref: CAS:61-54-1 {source="KEGG COMPOUND"} xref: DrugBank:DB08653 xref: Gmelin:603448 {source="Gmelin"} xref: HMDB:HMDB0000303 xref: KEGG:C00398 xref: KNApSAcK:C00001434 xref: MetaCyc:TRYPTAMINE xref: PDBeChem:TSS xref: PMID:16126914 {source="Europe PMC"} xref: PMID:22770225 {source="Europe PMC"} xref: PMID:24345948 {source="Europe PMC"} xref: PMID:24558969 {source="Europe PMC"} xref: Reaxys:125513 {source="Reaxys"} xref: Wikipedia:Tryptamine is_a: CHEBI:27162 ! tryptamines is_a: CHEBI:38631 ! aminoalkylindole is_a: CHEBI:38958 ! indole alkaloid is_a: CHEBI:64365 ! aralkylamino compound relationship: is_conjugate_base_of CHEBI:57887 ! tryptaminium relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:76924 ! has role plant metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C10H12N2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "APJYDQYYACXCRM-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "160.21570" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "160.10005" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NCCc1c[nH]c2ccccc12" xsd:string [Term] id: CHEBI:16865 name: gamma-aminobutyric acid namespace: chebi_ontology alt_id: CHEBI:1786 alt_id: CHEBI:193777 alt_id: CHEBI:20318 alt_id: CHEBI:40483 def: "A gamma-amino acid that is butanoic acid with the amino substituent located at C-4." [] def: "An amino fatty acid composed of butanoic acid with the amino substituent at C-4." [ANON:ANON] subset: 3_STAR synonym: "4-Aminobutanoic acid" RELATED [KEGG COMPOUND:] synonym: "4-Aminobutanoic acid" RELATED [KEGG_COMPOUND] synonym: "4-aminobutanoic acid" EXACT IUPAC_NAME [IUPAC] synonym: "4-aminobutanoic acid" EXACT IUPAC_NAME [IUPAC:] synonym: "4-aminobutanoic acid" RELATED [UniProt:] synonym: "4-aminobutanoic acid" RELATED [ChEBI:] synonym: "4-aminobutanoic acid" RELATED [ChEBI] synonym: "4-Aminobutyric acid" RELATED [KEGG_COMPOUND] synonym: "4-Aminobutyric acid" RELATED [KEGG COMPOUND:] synonym: "4-aminobutyric acid" RELATED [ChEBI] synonym: "4-aminobutyric acid" RELATED [ChEBI:] synonym: "4Abu" RELATED [ChEBI] synonym: "C4H9NO2" RELATED FORMULA [KEGG COMPOUND:] synonym: "GABA" RELATED [IUPHAR:] synonym: "GABA" RELATED [KEGG_COMPOUND] synonym: "GABA" RELATED [IUPHAR] synonym: "GAMMA-AMINO-BUTANOIC ACID" RELATED [PDBeChem] synonym: "GAMMA-AMINO-BUTANOIC ACID" RELATED [PDBeChem:] synonym: "gamma-amino-n-butyric acid" RELATED [NIST_Chemistry_WebBook] synonym: "gamma-amino-n-butyric acid" RELATED [NIST Chemistry WebBook:] synonym: "gamma-aminobutanoic acid" RELATED [NIST_Chemistry_WebBook] synonym: "gamma-aminobutanoic acid" RELATED [NIST Chemistry WebBook:] synonym: "gamma-Aminobuttersaeure" RELATED [NIST Chemistry WebBook:] synonym: "gamma-Aminobuttersaeure" RELATED [NIST_Chemistry_WebBook] synonym: "gamma-Aminobutyric acid" EXACT [KEGG COMPOUND:] synonym: "gamma-Aminobutyric acid" EXACT [KEGG_COMPOUND] synonym: "gamma-aminobutyric acid" EXACT [NIST_Chemistry_WebBook] synonym: "gamma-aminobutyric acid" EXACT [NIST Chemistry WebBook:] synonym: "InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7)" RELATED InChI [ChEBI:] synonym: "InChIKey=BTCSSZJGUNDROE-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "NCCCC(O)=O" RELATED SMILES [ChEBI:] synonym: "omega-aminobutyric acid" RELATED [NIST_Chemistry_WebBook] synonym: "omega-aminobutyric acid" RELATED [NIST Chemistry WebBook:] synonym: "piperidic acid" RELATED [ChemIDplus:] synonym: "piperidic acid" RELATED [ChemIDplus] synonym: "piperidinic acid" RELATED [ChemIDplus:] synonym: "piperidinic acid" RELATED [ChemIDplus] xref: Beilstein:906818 {source="Beilstein"} xref: BPDB:2298 xref: CAS:56-12-2 {source="ChemIDplus"} xref: CAS:56-12-2 {source="NIST Chemistry WebBook"} xref: CAS:56-12-2 {source="KEGG COMPOUND"} xref: Drug_Central:1262 {source="DrugCentral"} xref: DrugBank:DB02530 xref: Gmelin:49775 {source="Gmelin"} xref: HMDB:HMDB0000112 xref: KEGG:C00334 xref: KEGG:D00058 xref: KNApSAcK:C00001337 xref: LIPID_MAPS_instance:LMFA01100039 {source="LIPID MAPS"} xref: MetaCyc:4-AMINO-BUTYRATE xref: PDBeChem:ABU xref: PMID:10630630 {source="Europe PMC"} xref: PMID:10930630 {source="Europe PMC"} xref: PMID:16276116 {source="Europe PMC"} xref: PMID:21614609 {source="Europe PMC"} xref: PMID:22770225 {source="Europe PMC"} xref: Reaxys:906818 {source="Reaxys"} xref: Wikipedia:Gamma-Aminobutyric_acid is_a: CHEBI:25384 ! monocarboxylic acid is_a: CHEBI:33707 ! gamma-amino acid relationship: has_functional_parent CHEBI:30772 ! butyric acid relationship: is_conjugate_acid_of CHEBI:30566 ! gamma-aminobutyrate relationship: is_tautomer_of CHEBI:59888 ! gamma-aminobutyric acid zwitterion relationship: RO:0000087 CHEBI:25512 ! has role neurotransmitter relationship: RO:0000087 CHEBI:62488 ! has role signalling molecule relationship: RO:0000087 CHEBI:75772 ! has role Saccharomyces cerevisiae metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H9NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "BTCSSZJGUNDROE-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "103.11980" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "103.06333" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NCCCC(O)=O" xsd:string [Term] id: CHEBI:17134 name: octopamine namespace: chebi_ontology alt_id: CHEBI:11191 alt_id: CHEBI:25655 alt_id: CHEBI:571 def: "A member of the class of phenylethanolamines that is phenol which is substituted at the para- position by a 2-amino-1-hydroxyethyl group. A biogenic phenylethanolamine which has been found to act as a neurotransmitter, neurohormone or neuromodulator in invertebrates." [] def: "Octopamine is a biogenic phenylethanolamine, which has been found to act as a neurotransmitter, neurohormone or neuromodulator in invertebrates." [ANON:ANON] subset: 3_STAR synonym: "1-(4-Hydroxyphenyl)-2-aminoethanol" RELATED [KEGG_COMPOUND] synonym: "1-(4-Hydroxyphenyl)-2-aminoethanol" RELATED [KEGG COMPOUND:] synonym: "1-(p-hydroxyphenyl)-2-aminoethanol" RELATED [ChemIDplus] synonym: "1-(p-hydroxyphenyl)-2-aminoethanol" RELATED [ChemIDplus:] synonym: "4-(2-amino-1-hydroxyethyl)phenol" EXACT IUPAC_NAME [IUPAC] synonym: "4-(2-amino-1-hydroxyethyl)phenol" EXACT IUPAC_NAME [IUPAC:] synonym: "alpha-(aminomethyl)-4-hydroxybenzenemethanol" RELATED [ChemIDplus] synonym: "alpha-(aminomethyl)-4-hydroxybenzenemethanol" RELATED [ChemIDplus:] synonym: "alpha-(aminomethyl)-p-hydroxybenzyl alcohol" RELATED [ChemIDplus] synonym: "alpha-(aminomethyl)-p-hydroxybenzyl alcohol" RELATED [ChemIDplus:] synonym: "beta-hydroxytyramine" RELATED [ChEBI:] synonym: "beta-hydroxytyramine" RELATED [ChEBI] synonym: "C8H11NO2" RELATED FORMULA [KEGG COMPOUND:] synonym: "InChI=1S/C8H11NO2/c9-5-8(11)6-1-3-7(10)4-2-6/h1-4,8,10-11H,5,9H2" RELATED InChI [ChEBI:] synonym: "InChIKey=QHGUCRYDKWKLMG-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "NCC(O)c1ccc(O)cc1" RELATED SMILES [ChEBI:] synonym: "norsynephrine" RELATED [ChemIDplus:] synonym: "norsynephrine" RELATED [ChemIDplus] synonym: "Octopamin" RELATED [ChEBI:] synonym: "Octopamin" RELATED [ChEBI] synonym: "Octopamine" EXACT [KEGG COMPOUND:] synonym: "Octopamine" EXACT [KEGG_COMPOUND] synonym: "octopaminum" RELATED [ChemIDplus] synonym: "octopaminum" RELATED [ChemIDplus:] synonym: "p-Hydroxyphenylethanolamine" RELATED [KEGG_COMPOUND] synonym: "p-Hydroxyphenylethanolamine" RELATED [KEGG COMPOUND:] xref: Beilstein:1211019 {source="ChemIDplus"} xref: CAS:104-14-3 {source="KEGG COMPOUND"} xref: CAS:104-14-3 {source="ChemIDplus"} xref: Drug_Central:3396 {source="DrugCentral"} xref: KEGG:C04227 xref: LINCS:LSM-4975 is_a: CHEBI:25990 ! phenylethanolamines is_a: CHEBI:27175 ! tyramines relationship: is_conjugate_base_of CHEBI:58025 ! octopaminium relationship: RO:0000087 CHEBI:25512 ! has role neurotransmitter property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C8H11NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C8H11NO2/c9-5-8(11)6-1-3-7(10)4-2-6/h1-4,8,10-11H,5,9H2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QHGUCRYDKWKLMG-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "153.17848" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "153.07898" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NCC(O)c1ccc(O)cc1" xsd:string [Term] id: CHEBI:17891 name: donor namespace: chebi_ontology alt_id: CHEBI:14202 alt_id: CHEBI:4697 def: "A molecular entity that can transfer (\"donate\") an electron, a pair of electrons, an atom or a group to another molecular entity." [] subset: 3_STAR synonym: "Donator" RELATED [ChEBI] synonym: "donneur" RELATED [ChEBI] synonym: "Donor" EXACT [KEGG_COMPOUND] xref: KEGG:C01351 is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:17968 name: butyrate namespace: chebi_ontology alt_id: CHEBI:13924 alt_id: CHEBI:22946 def: "A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group." [] subset: 3_STAR synonym: "1-butanoate" RELATED [ChEBI] synonym: "1-butyrate" RELATED [ChEBI] synonym: "1-propanecarboxylate" RELATED [ChEBI] synonym: "butanate" RELATED [ChEBI] synonym: "butanoate" EXACT IUPAC_NAME [IUPAC] synonym: "butanoate" RELATED [ChEBI] synonym: "butanoate" RELATED [UniProt] synonym: "butanoic acid, ion(1-)" RELATED [ChemIDplus] synonym: "butyrate" EXACT [IUPAC] synonym: "CH3-[CH2]2-COO(-)" RELATED [IUPAC] synonym: "n-butanoate" RELATED [ChEBI] synonym: "n-butyrate" RELATED [ChemIDplus] synonym: "propanecarboxylate" RELATED [ChEBI] synonym: "propylformate" RELATED [ChEBI] xref: Beilstein:3601060 {source="Beilstein"} xref: CAS:461-55-2 {source="ChemIDplus"} xref: Gmelin:324289 {source="Gmelin"} xref: KEGG:C00246 xref: MetaCyc:BUTYRIC_ACID xref: PMID:17190852 {source="Europe PMC"} xref: PMID:7496326 {source="Europe PMC"} xref: Reaxys:3601060 {source="Reaxys"} xref: UM-BBD_compID:c0035 {source="UM-BBD"} is_a: CHEBI:78115 ! fatty acid anion 4:0 relationship: is_conjugate_base_of CHEBI:30772 ! butyric acid relationship: RO:0000087 CHEBI:61115 ! has role EC 3.5.1.98 (histone deacetylase) inhibitor relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H7O2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)/p-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "FERIUCNNQQJTOY-UHFFFAOYSA-M" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "87.09718" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "87.04515" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "CCCC([O-])=O" xsd:string [Term] id: CHEBI:18059 name: lipid namespace: chebi_ontology alt_id: CHEBI:14517 alt_id: CHEBI:25054 alt_id: CHEBI:6486 def: "'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids." [ANON:ANON] subset: 3_STAR synonym: "Lipid" EXACT [KEGG_COMPOUND] synonym: "Lipid" EXACT [KEGG COMPOUND:] synonym: "lipid" EXACT [UniProt:] synonym: "lipids" EXACT IUPAC_NAME [IUPAC:] synonym: "lipids" EXACT IUPAC_NAME [IUPAC] xref: KEGG:C01356 is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:18237 name: glutamic acid namespace: chebi_ontology alt_id: CHEBI:24314 alt_id: CHEBI:5431 def: "An alpha-amino acid that has formula C5H9NO4." [ANON:ANON] def: "An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2." [] subset: 3_STAR synonym: "2-Aminoglutaric acid" RELATED [KEGG_COMPOUND] synonym: "2-Aminoglutaric acid" RELATED [KEGG COMPOUND:] synonym: "2-aminopentanedioic acid" EXACT IUPAC_NAME [IUPAC:] synonym: "2-aminopentanedioic acid" EXACT IUPAC_NAME [IUPAC] synonym: "C5H9NO4" RELATED FORMULA [KEGG COMPOUND:] synonym: "DL-Glutamic acid" RELATED [KEGG_DRUG] synonym: "DL-Glutaminic acid" RELATED [KEGG_COMPOUND] synonym: "E" RELATED [ChEBI] synonym: "Glu" RELATED [ChEBI] synonym: "Glutamate" RELATED [KEGG_COMPOUND] synonym: "Glutamic acid" EXACT [KEGG_COMPOUND] synonym: "glutamic acid" EXACT IUPAC_NAME [IUPAC:] synonym: "glutamic acid" EXACT IUPAC_NAME [IUPAC] synonym: "Glutaminic acid" RELATED [KEGG COMPOUND:] synonym: "Glutaminic acid" RELATED [KEGG_COMPOUND] synonym: "Glutaminsaeure" RELATED [ChEBI:] synonym: "Glutaminsaeure" RELATED [ChEBI] synonym: "InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)" RELATED InChI [ChEBI:] synonym: "InChIKey=WHUUTDBJXJRKMK-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "NC(CCC(O)=O)C(O)=O" RELATED SMILES [ChEBI:] xref: Beilstein:1723799 {source="Beilstein"} xref: CAS:617-65-2 {source="ChemIDplus"} xref: CAS:617-65-2 {source="NIST Chemistry WebBook"} xref: CAS:617-65-2 {source="KEGG COMPOUND"} xref: Gmelin:101971 {source="Gmelin"} xref: KEGG:C00302 xref: KEGG:D04341 xref: KNApSAcK:C00001358 xref: KNApSAcK:C00019577 xref: PMID:15739367 {source="Europe PMC"} xref: PMID:17190852 {source="Europe PMC"} xref: PMID:24616376 {source="Europe PMC"} xref: PMID:24984001 {source="Europe PMC"} xref: Reaxys:1723799 {source="Reaxys"} xref: Wikipedia:Glutamic_acid is_a: CHEBI:26167 ! polar amino acid is_a: CHEBI:33704 ! alpha-amino acid relationship: has_part CHEBI:50329 ! 2-carboxyethyl group relationship: is_conjugate_acid_of CHEBI:14321 ! glutamate(1-) relationship: RO:0000087 CHEBI:78675 ! has role fundamental metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C5H9NO4" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "WHUUTDBJXJRKMK-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "147.12930" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "147.05316" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC(CCC(O)=O)C(O)=O" xsd:string [Term] id: CHEBI:18243 name: dopamine namespace: chebi_ontology alt_id: CHEBI:11695 alt_id: CHEBI:11930 alt_id: CHEBI:14203 alt_id: CHEBI:1764 alt_id: CHEBI:23886 alt_id: CHEBI:43686 def: "Catechol in which the hydrogen at position 4 is substituted by a 2-aminoethyl group." [ANON:ANON] subset: 3_STAR synonym: "2-(3,4-Dihydroxyphenyl)ethylamine" RELATED [KEGG COMPOUND:] synonym: "2-(3,4-Dihydroxyphenyl)ethylamine" RELATED [KEGG_COMPOUND] synonym: "2-(3,4-dihydroxyphenyl)ethylamine" RELATED [ChEBI] synonym: "2-(3,4-dihydroxyphenyl)ethylamine" RELATED [ChEBI:] synonym: "3,4-Dihydroxyphenethylamine" RELATED [KEGG_COMPOUND] synonym: "3,4-Dihydroxyphenethylamine" RELATED [KEGG COMPOUND:] synonym: "3-Hydroxytyramine" RELATED [ChemIDplus] synonym: "3-Hydroxytyramine" RELATED [ChemIDplus:] synonym: "4-(2-Aminoethyl)-1,2-benzenediol" RELATED [KEGG_COMPOUND] synonym: "4-(2-Aminoethyl)-1,2-benzenediol" RELATED [KEGG COMPOUND:] synonym: "4-(2-aminoethyl)-1,2-benzenediol" RELATED [ChEBI] synonym: "4-(2-aminoethyl)-1,2-benzenediol" RELATED [ChEBI:] synonym: "4-(2-Aminoethyl)benzene-1,2-diol" RELATED [KEGG_COMPOUND] synonym: "4-(2-Aminoethyl)benzene-1,2-diol" RELATED [KEGG COMPOUND:] synonym: "4-(2-aminoethyl)benzene-1,2-diol" EXACT IUPAC_NAME [IUPAC] synonym: "4-(2-aminoethyl)benzene-1,2-diol" EXACT IUPAC_NAME [IUPAC:] synonym: "4-(2-aminoethyl)catechol" RELATED [ChemIDplus:] synonym: "4-(2-aminoethyl)catechol" RELATED [ChemIDplus] synonym: "4-(2-aminoethyl)pyrocatechol" RELATED [ChemIDplus] synonym: "4-(2-aminoethyl)pyrocatechol" RELATED [ChemIDplus:] synonym: "C8H11NO2" RELATED FORMULA [KEGG COMPOUND:] synonym: "Deoxyepinephrine" RELATED [DrugBank:] synonym: "Deoxyepinephrine" RELATED [DrugBank] synonym: "dopamina" RELATED INN [ChemIDplus:] synonym: "dopamina" RELATED INN [ChemIDplus] synonym: "Dopamine" EXACT [KEGG_COMPOUND] synonym: "Dopamine" EXACT [KEGG COMPOUND:] synonym: "dopamine" RELATED INN [ChEBI:] synonym: "dopamine" RELATED INN [ChEBI] synonym: "dopaminum" RELATED INN [ChemIDplus] synonym: "dopaminum" RELATED INN [ChemIDplus:] synonym: "Hydroxytyramin" RELATED [DrugBank:] synonym: "Hydroxytyramin" RELATED [DrugBank] synonym: "InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2" RELATED InChI [ChEBI:] synonym: "InChIKey=VYFYYTLLBUKUHU-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "NCCc1ccc(O)c(O)c1" RELATED SMILES [ChEBI:] xref: CAS:51-61-6 {source="ChemIDplus"} xref: Drug_Central:947 {source="DrugCentral"} xref: DrugBank:DB00988 xref: HMDB:HMDB0000073 xref: KEGG:C03758 xref: KEGG:D07870 xref: KNApSAcK:C00001408 xref: LINCS:LSM-4630 xref: MetaCyc:DOPAMINE xref: PMID:10629745 {source="Europe PMC"} xref: PMID:11149432 {source="Europe PMC"} xref: PMID:9422813 {source="Europe PMC"} xref: Reaxys:1072822 {source="Reaxys"} xref: Wikipedia:Dopamine is_a: CHEBI:33567 ! catecholamine relationship: is_conjugate_base_of CHEBI:59905 ! dopaminium(1+) relationship: RO:0000087 CHEBI:35522 ! has role beta-adrenergic agonist relationship: RO:0000087 CHEBI:35524 ! has role sympathomimetic agent relationship: RO:0000087 CHEBI:38147 ! has role cardiotonic drug relationship: RO:0000087 CHEBI:48560 ! has role dopaminergic agent relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:76971 ! has role Escherichia coli metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C8H11NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "VYFYYTLLBUKUHU-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "153.17840" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "153.07898" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NCCc1ccc(O)c(O)c1" xsd:string [Term] id: CHEBI:18282 name: nucleobase namespace: chebi_ontology alt_id: CHEBI:13873 alt_id: CHEBI:25598 alt_id: CHEBI:2995 def: "That part of DNA or RNA that may be involved in pairing." [] subset: 3_STAR synonym: "Base" RELATED [KEGG_COMPOUND] synonym: "nucleobases" RELATED [ChEBI] xref: KEGG:C00701 xref: Wikipedia:Nucleobase is_a: CHEBI:38101 ! organonitrogen heterocyclic compound [Term] id: CHEBI:18295 name: histamine namespace: chebi_ontology alt_id: CHEBI:14401 alt_id: CHEBI:24596 alt_id: CHEBI:43187 alt_id: CHEBI:817 def: "A member of the class of imidazoles that is 1H-imidazole substituted at position C-4 by a 2-aminoethyl group." [] def: "An aralkylamine that has formula C5H9N3." [ANON:ANON] subset: 3_STAR synonym: "1H-Imidazole-4-ethanamine" RELATED [KEGG COMPOUND:] synonym: "1H-Imidazole-4-ethanamine" RELATED [KEGG_COMPOUND] synonym: "2-(1H-imidazol-4-yl)ethanamine" EXACT IUPAC_NAME [IUPAC:] synonym: "2-(1H-imidazol-4-yl)ethanamine" EXACT IUPAC_NAME [IUPAC] synonym: "2-(4-Imidazolyl)ethylamine" RELATED [KEGG COMPOUND:] synonym: "2-(4-Imidazolyl)ethylamine" RELATED [KEGG_COMPOUND] synonym: "C5H9N3" RELATED FORMULA [KEGG COMPOUND:] synonym: "HISTAMINE" EXACT [PDBeChem:] synonym: "HISTAMINE" EXACT [PDBeChem] synonym: "Histamine" EXACT [KEGG COMPOUND:] synonym: "Histamine" EXACT [KEGG_COMPOUND] synonym: "InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8)" RELATED InChI [ChEBI:] synonym: "InChIKey=NTYJJOPFIAHURM-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "NCCc1c[nH]cn1" RELATED SMILES [ChEBI:] xref: Beilstein:2012 {source="Beilstein"} xref: CAS:51-45-6 {source="NIST Chemistry WebBook"} xref: CAS:51-45-6 {source="ChemIDplus"} xref: CAS:51-45-6 {source="KEGG COMPOUND"} xref: Drug_Central:1375 {source="DrugCentral"} xref: Gmelin:2968 {source="Gmelin"} xref: HMDB:HMDB0000870 xref: KEGG:C00388 xref: KEGG:D08040 xref: KNApSAcK:C00001414 xref: MetaCyc:HISTAMINE xref: PDBeChem:HSM xref: PMID:16399866 {source="Europe PMC"} xref: PMID:19547708 {source="Europe PMC"} xref: PMID:19843401 {source="Europe PMC"} xref: PMID:22770225 {source="Europe PMC"} xref: PMID:24101735 {source="Europe PMC"} xref: Reaxys:2012 {source="Reaxys"} xref: Wikipedia:Histamine is_a: CHEBI:24780 ! imidazoles is_a: CHEBI:64365 ! aralkylamino compound relationship: is_conjugate_base_of CHEBI:58432 ! histaminium relationship: RO:0000087 CHEBI:25512 ! has role neurotransmitter relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C5H9N3" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "NTYJJOPFIAHURM-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "111.14518" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "111.07965" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NCCc1c[nH]cn1" xsd:string [Term] id: CHEBI:22221 name: acyl group namespace: chebi_ontology def: "An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids." [] subset: 3_STAR synonym: "acyl group" EXACT [IUPAC] synonym: "acyl groups" RELATED [ChEBI] synonym: "alkanoyl" EXACT IUPAC_NAME [IUPAC] synonym: "alkanoyl group" RELATED [ChEBI] synonym: "groupe acyle" RELATED [IUPAC] is_a: CHEBI:33247 ! organic group [Term] id: CHEBI:22315 name: alkaloid namespace: chebi_ontology def: "Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids." [] subset: 3_STAR synonym: "alcaloide" RELATED [ChEBI] synonym: "alcaloides" RELATED [ChEBI] synonym: "Alkaloid" EXACT [ChEBI] synonym: "Alkaloide" RELATED [ChEBI] synonym: "alkaloids" EXACT IUPAC_NAME [IUPAC] xref: Wikipedia:Alkaloid is_a: CHEBI:35352 ! organonitrogen compound relationship: RO:0000087 CHEBI:25212 ! has role metabolite [Term] id: CHEBI:22331 name: alkylamines namespace: chebi_ontology def: "Any amine formally derived from ammonia by replacing one, two or three hydrogen atoms by alkyl groups." [] subset: 3_STAR is_a: CHEBI:32952 ! amine [Term] id: CHEBI:22478 name: amino alcohol namespace: chebi_ontology def: "An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group." [ANON:ANON] subset: 3_STAR synonym: "amino alcohols" RELATED [ChEBI:] synonym: "amino alcohols" RELATED [ChEBI] synonym: "aminoalcohol" RELATED [ChEBI:] synonym: "aminoalcohol" RELATED [ChEBI] synonym: "aminoalcohols" RELATED [ChEBI:] synonym: "aminoalcohols" RELATED [ChEBI] is_a: CHEBI:30879 ! alcohol is_a: CHEBI:50047 ! organic amino compound [Term] id: CHEBI:22563 name: anion namespace: chebi_ontology def: "A monoatomic or polyatomic species having one or more elementary charges of the electron." [] subset: 3_STAR synonym: "Anion" EXACT [ChEBI] synonym: "anion" EXACT IUPAC_NAME [IUPAC] synonym: "anion" EXACT [ChEBI] synonym: "Anionen" RELATED [ChEBI] synonym: "aniones" RELATED [ChEBI] synonym: "anions" RELATED [IUPAC] is_a: CHEBI:24870 ! ion [Term] id: CHEBI:22695 name: base namespace: chebi_ontology def: "A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base)." [] subset: 3_STAR synonym: "Base" EXACT [ChEBI] synonym: "base" EXACT [ChEBI] synonym: "base" EXACT IUPAC_NAME [IUPAC] synonym: "Base1" RELATED [KEGG_COMPOUND] synonym: "Base2" RELATED [KEGG_COMPOUND] synonym: "Basen" RELATED [ChEBI] synonym: "bases" RELATED [ChEBI] synonym: "Nucleobase" RELATED [KEGG_COMPOUND] xref: KEGG:C00701 is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:22728 name: benzopyrrole namespace: chebi_ontology subset: 3_STAR synonym: "benzopyrroles" RELATED [ChEBI:] synonym: "benzopyrroles" RELATED [ChEBI] is_a: CHEBI:27171 ! organic heterobicyclic compound is_a: CHEBI:38101 ! organonitrogen heterocyclic compound is_a: CHEBI:38180 ! polycyclic heteroarene [Term] id: CHEBI:23004 name: carbamoyl group namespace: chebi_ontology def: "The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid." [] subset: 3_STAR synonym: "-C(O)NH2" RELATED [ChEBI] synonym: "-CONH2" RELATED [IUPAC] synonym: "aminocarbonyl" RELATED [IUPAC] synonym: "carbamoyl" EXACT IUPAC_NAME [IUPAC] synonym: "carbamyl" RELATED [ChEBI] synonym: "carbamyl group" RELATED [ChEBI] synonym: "carboxamide" RELATED [IUPAC] xref: PMID:24168430 {source="Europe PMC"} is_a: CHEBI:27207 ! univalent carboacyl group relationship: is_substituent_group_from CHEBI:28616 ! carbamic acid property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CH2NO" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "44.03272" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "44.01364" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "*C(N)=O" xsd:string [Term] id: CHEBI:23019 name: carbonyl group namespace: chebi_ontology subset: 3_STAR synonym: ">C=O" RELATED [IUPAC] synonym: "carbonyl" EXACT IUPAC_NAME [IUPAC] synonym: "carbonyl group" EXACT [ChEBI] synonym: "carbonyl group" EXACT [UniProt] is_a: CHEBI:51422 ! organodiyl group property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CO" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "28.01010" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "27.99491" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "O=C(*)*" xsd:string [Term] id: CHEBI:23213 name: choline ester namespace: chebi_ontology alt_id: CHEBI:3666 subset: 3_STAR synonym: "choline esters" RELATED [ChEBI] synonym: "choline esters" RELATED [ChEBI:] is_a: CHEBI:35701 ! ester relationship: has_functional_parent CHEBI:15354 ! choline [Term] id: CHEBI:23217 name: cholines namespace: chebi_ontology def: "A quaternary ammonium ion based on the choline ion and its substituted derivatives thereof." [] subset: 3_STAR is_a: CHEBI:35267 ! quaternary ammonium ion [Term] id: CHEBI:23357 name: cofactor namespace: chebi_ontology def: "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group)." [] subset: 3_STAR synonym: "cofactor" EXACT [IUPAC] synonym: "cofactors" EXACT IUPAC_NAME [IUPAC] xref: Wikipedia:Cofactor_(biochemistry) is_a: CHEBI:52206 ! biochemical role [Term] id: CHEBI:23367 name: molecular entity namespace: chebi_ontology def: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." [ANON:ANON] subset: 3_STAR synonym: "entidad molecular" RELATED [IUPAC:] synonym: "entidad molecular" RELATED [IUPAC] synonym: "entidades moleculares" RELATED [IUPAC:] synonym: "entidades moleculares" RELATED [IUPAC] synonym: "entite moleculaire" RELATED [IUPAC] synonym: "entite moleculaire" RELATED [IUPAC:] synonym: "molecular entities" RELATED [IUPAC:] synonym: "molecular entities" RELATED [IUPAC] synonym: "molecular entity" EXACT IUPAC_NAME [IUPAC:] synonym: "molecular entity" EXACT IUPAC_NAME [IUPAC] synonym: "molekulare Entitaet" RELATED [ChEBI] synonym: "molekulare Entitaet" RELATED [ChEBI:] is_a: CHEBI:24431 ! chemical entity [Term] id: CHEBI:23677 name: diazole namespace: chebi_ontology def: "An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring." [] def: "Either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring." [ANON:ANON] subset: 3_STAR synonym: "diazoles" RELATED [ChEBI] synonym: "diazoles" RELATED [ChEBI:] is_a: CHEBI:68452 ! azole [Term] id: CHEBI:23824 name: diol namespace: chebi_ontology def: "A compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic. Aliphatic diols are also called glycols." [ANON:ANON] subset: 3_STAR synonym: "diols" EXACT IUPAC_NAME [IUPAC] synonym: "diols" EXACT IUPAC_NAME [IUPAC:] xref: Wikipedia:Diol is_a: CHEBI:26191 ! polyol [Term] id: CHEBI:23888 name: drug namespace: chebi_ontology def: "Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances." [] subset: 3_STAR synonym: "drugs" RELATED [ChEBI] synonym: "medicine" RELATED [ChEBI] is_a: CHEBI:52217 ! pharmaceutical [Term] id: CHEBI:23924 name: enzyme inhibitor namespace: chebi_ontology def: "A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction." [] subset: 3_STAR synonym: "enzyme inhibitor" EXACT IUPAC_NAME [IUPAC] synonym: "enzyme inhibitors" RELATED [ChEBI] synonym: "inhibidor enzimatico" RELATED [ChEBI] synonym: "inhibidores enzimaticos" RELATED [ChEBI] synonym: "inhibiteur enzymatique" RELATED [ChEBI] synonym: "inhibiteurs enzymatiques" RELATED [ChEBI] is_a: CHEBI:35222 ! inhibitor is_a: CHEBI:52206 ! biochemical role [Term] id: CHEBI:23981 name: ethanolamines namespace: chebi_ontology subset: 3_STAR synonym: "ethanolamine" RELATED [ChEBI] synonym: "ethanolamine" RELATED [ChEBI:] is_a: CHEBI:22478 ! amino alcohol [Term] id: CHEBI:24318 name: glutamine family amino acid namespace: chebi_ontology def: "An L-alpha-amino acid which is L-glutamic acid or any of the essential amino acids biosynthesised from it (glutamine, proline and arginine). A closed class." [] subset: 3_STAR synonym: "glutamine family amino acids" RELATED [ChEBI] xref: PMID:20716061 {source="Europe PMC"} is_a: CHEBI:15705 ! L-alpha-amino acid is_a: CHEBI:83813 ! proteinogenic amino acid [Term] id: CHEBI:24431 name: chemical entity namespace: chebi_ontology def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [ANON:ANON] subset: 3_STAR synonym: "chemical entity" EXACT [UniProt] is_a: BFO:0000040 ! material entity [Term] id: CHEBI:24432 name: biological role namespace: chebi_ontology def: "A role played by the molecular entity or part thereof within a biological context." [] subset: 3_STAR synonym: "biological function" RELATED [ChEBI] is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] id: CHEBI:24433 name: group namespace: chebi_ontology def: "A defined linked collection of atoms or a single atom within a molecular entity." [] subset: 3_STAR synonym: "group" EXACT IUPAC_NAME [IUPAC] synonym: "groupe" RELATED [IUPAC] synonym: "grupo" RELATED [IUPAC] synonym: "grupos" RELATED [IUPAC] synonym: "Gruppe" RELATED [ChEBI] synonym: "Rest" RELATED [ChEBI] is_a: CHEBI:24431 ! chemical entity relationship: has_part CHEBI:33250 ! atom [Term] id: CHEBI:24532 name: organic heterocyclic compound namespace: chebi_ontology def: "A cyclic compound having as ring members atoms of carbon and at least of one other element." [ANON:ANON] subset: 3_STAR synonym: "organic heterocycle" RELATED [ChEBI:] synonym: "organic heterocycle" RELATED [ChEBI] synonym: "organic heterocyclic compounds" RELATED [ChEBI] synonym: "organic heterocyclic compounds" RELATED [ChEBI:] is_a: CHEBI:33285 ! heteroorganic entity is_a: CHEBI:33832 ! organic cyclic compound is_a: CHEBI:5686 ! heterocyclic compound [Term] id: CHEBI:24621 name: hormone namespace: chebi_ontology def: "Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds." [] subset: 3_STAR synonym: "endocrine" RELATED [ChEBI] synonym: "hormones" RELATED [ChEBI] is_a: CHEBI:33280 ! molecular messenger is_a: CHEBI:48705 ! agonist [Term] id: CHEBI:24651 name: hydroxides namespace: chebi_ontology def: "Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-))." [ANON:ANON] subset: 3_STAR is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:33608 ! hydrogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity relationship: has_part CHEBI:43176 ! hydroxy group [Term] id: CHEBI:24780 name: imidazoles namespace: chebi_ontology def: "A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." [ANON:ANON] subset: 3_STAR is_a: CHEBI:23677 ! diazole [Term] id: CHEBI:24828 name: indoles namespace: chebi_ontology def: "Any compound containing an indole skeleton." [ANON:ANON] subset: 3_STAR is_a: CHEBI:22728 ! benzopyrrole [Term] id: CHEBI:24833 name: oxoacid namespace: chebi_ontology def: "A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [ANON:ANON] subset: 3_STAR synonym: "oxacids" RELATED [ChEBI] synonym: "oxacids" RELATED [ChEBI:] synonym: "oxiacids" RELATED [ChEBI:] synonym: "oxiacids" RELATED [ChEBI] synonym: "oxo acid" RELATED [ChEBI:] synonym: "oxo acid" RELATED [ChEBI] synonym: "oxoacid" EXACT IUPAC_NAME [IUPAC] synonym: "oxoacid" EXACT IUPAC_NAME [IUPAC:] synonym: "oxoacids" EXACT IUPAC_NAME [IUPAC:] synonym: "oxoacids" EXACT IUPAC_NAME [IUPAC] synonym: "oxy-acids" RELATED [ChEBI:] synonym: "oxy-acids" RELATED [ChEBI] synonym: "oxyacids" RELATED [ChEBI] synonym: "oxyacids" RELATED [ChEBI:] is_a: CHEBI:24651 ! hydroxides relationship: RO:0000087 CHEBI:39141 ! has role Bronsted acid [Term] id: CHEBI:24834 name: inorganic anion namespace: chebi_ontology subset: 3_STAR synonym: "inorganic anions" RELATED [ChEBI] is_a: CHEBI:22563 ! anion is_a: CHEBI:36914 ! inorganic ion [Term] id: CHEBI:24835 name: inorganic molecular entity namespace: chebi_ontology def: "A molecular entity that contains no carbon." [] subset: 3_STAR synonym: "anorganische Verbindungen" RELATED [ChEBI] synonym: "inorganic compounds" RELATED [ChEBI] synonym: "inorganic entity" RELATED [ChEBI] synonym: "inorganic molecular entities" RELATED [ChEBI] synonym: "inorganics" RELATED [ChEBI] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:24870 name: ion namespace: chebi_ontology def: "A molecular entity having a net electric charge." [ANON:ANON] subset: 3_STAR synonym: "Ion" EXACT [ChEBI] synonym: "Ion" EXACT [ChEBI:] synonym: "ion" EXACT IUPAC_NAME [IUPAC:] synonym: "ion" EXACT IUPAC_NAME [IUPAC] synonym: "ion" EXACT [ChEBI] synonym: "ion" EXACT [ChEBI:] synonym: "Ionen" RELATED [ChEBI:] synonym: "Ionen" RELATED [ChEBI] synonym: "iones" RELATED [ChEBI:] synonym: "iones" RELATED [ChEBI] synonym: "ions" RELATED [ChEBI:] synonym: "ions" RELATED [ChEBI] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:25212 name: metabolite namespace: chebi_ontology alt_id: CHEBI:26619 alt_id: CHEBI:35220 def: "Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites." [] subset: 3_STAR synonym: "metabolite" EXACT IUPAC_NAME [IUPAC] synonym: "metabolites" RELATED [ChEBI] synonym: "primary metabolites" RELATED [ChEBI] synonym: "secondary metabolites" RELATED [ChEBI] is_a: CHEBI:52206 ! biochemical role [Term] id: CHEBI:25367 name: molecule namespace: chebi_ontology def: "Any polyatomic entity that is an electrically neutral entity consisting of more than one atom." [] subset: 3_STAR synonym: "molecula" RELATED [IUPAC] synonym: "molecule" EXACT [IUPAC] synonym: "molecules" RELATED [IUPAC] synonym: "Molekuel" RELATED [ChEBI] synonym: "neutral molecular compounds" RELATED [IUPAC] is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:25375 name: monoamine molecular messenger namespace: chebi_ontology def: "A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan." [] subset: 3_STAR synonym: "monamines" RELATED [ChEBI] synonym: "monoamines" RELATED [ChEBI] is_a: CHEBI:63534 ! monoamine relationship: RO:0000087 CHEBI:33280 ! has role molecular messenger [Term] id: CHEBI:25384 name: monocarboxylic acid namespace: chebi_ontology def: "An oxoacid containing a single carboxy group." [ANON:ANON] subset: 3_STAR synonym: "monocarboxylic acid" EXACT [UniProt:] synonym: "monocarboxylic acids" RELATED [ChEBI] synonym: "monocarboxylic acids" RELATED [ChEBI:] is_a: CHEBI:33575 ! carboxylic acid relationship: is_conjugate_acid_of CHEBI:35757 ! monocarboxylic acid anion [Term] id: CHEBI:25512 name: neurotransmitter namespace: chebi_ontology def: "An endogenous compound that is used to transmit information across the synapse between a neuron and another cell." [] subset: 3_STAR synonym: "neurotransmitters" RELATED [ChEBI] xref: Wikipedia:Neurotransmitter is_a: CHEBI:33280 ! molecular messenger [Term] id: CHEBI:25555 name: nitrogen atom namespace: chebi_ontology subset: 3_STAR synonym: "7N" RELATED [IUPAC] synonym: "azote" RELATED [IUPAC] synonym: "N" RELATED [IUPAC] synonym: "nitrogen" EXACT IUPAC_NAME [IUPAC] synonym: "nitrogen" RELATED [ChEBI] synonym: "nitrogeno" RELATED [ChEBI] synonym: "Stickstoff" RELATED [ChEBI] xref: WebElements:N is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33300 ! pnictogen relationship: RO:0000087 CHEBI:33937 ! has role macronutrient property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "14.007" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "14.00307" xsd:string [Term] id: CHEBI:25585 name: nonmetal atom namespace: chebi_ontology subset: 3_STAR synonym: "Nichtmetall" RELATED [ChEBI] synonym: "Nichtmetalle" RELATED [ChEBI] synonym: "no metal" RELATED [ChEBI] synonym: "no metales" RELATED [ChEBI] synonym: "non-metal" RELATED [ChEBI] synonym: "non-metaux" RELATED [ChEBI] synonym: "nonmetal" EXACT IUPAC_NAME [IUPAC] synonym: "nonmetal" RELATED [ChEBI] synonym: "nonmetals" RELATED [ChEBI] is_a: CHEBI:33250 ! atom [Term] id: CHEBI:25693 name: organic heteromonocyclic compound namespace: chebi_ontology subset: 3_STAR synonym: "organic heteromonocyclic compounds" RELATED [ChEBI:] synonym: "organic heteromonocyclic compounds" RELATED [ChEBI] is_a: CHEBI:24532 ! organic heterocyclic compound is_a: CHEBI:33670 ! heteromonocyclic compound [Term] id: CHEBI:25696 name: organic anion namespace: chebi_ontology def: "Any organic ion with a net negative charge." [] subset: 3_STAR synonym: "organic anions" RELATED [ChEBI] is_a: CHEBI:22563 ! anion is_a: CHEBI:25699 ! organic ion [Term] id: CHEBI:25697 name: organic cation namespace: chebi_ontology def: "Any organic ion with a net positive charge." [] subset: 3_STAR synonym: "organic cations" RELATED [ChEBI] is_a: CHEBI:25699 ! organic ion is_a: CHEBI:36916 ! cation [Term] id: CHEBI:25699 name: organic ion namespace: chebi_ontology subset: 3_STAR synonym: "organic ions" RELATED [ChEBI] is_a: CHEBI:24870 ! ion is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:25741 name: oxide namespace: chebi_ontology def: "An oxide is a chemical compound of oxygen with other chemical elements." [] subset: 3_STAR synonym: "oxide" EXACT [ChEBI] synonym: "oxides" RELATED [ChEBI] is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:25805 name: oxygen atom namespace: chebi_ontology subset: 3_STAR synonym: "8O" RELATED [IUPAC] synonym: "O" RELATED [IUPAC] synonym: "oxigeno" RELATED [ChEBI] synonym: "oxygen" EXACT IUPAC_NAME [IUPAC] synonym: "oxygen" RELATED [ChEBI] synonym: "oxygene" RELATED [ChEBI] synonym: "Sauerstoff" RELATED [ChEBI] xref: KEGG:C00007 xref: WebElements:O is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33303 ! chalcogen relationship: RO:0000087 CHEBI:33937 ! has role macronutrient property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QVGXLLKOCUKJST-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "15.99940" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "15.99491" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O]" xsd:string [Term] id: CHEBI:25806 name: oxygen molecular entity namespace: chebi_ontology subset: 3_STAR synonym: "oxygen molecular entities" RELATED [ChEBI] synonym: "oxygen molecular entities" RELATED [ChEBI:] synonym: "oxygen molecular entity" EXACT [ChEBI:] synonym: "oxygen molecular entity" EXACT [ChEBI] is_a: CHEBI:33304 ! chalcogen molecular entity relationship: has_part CHEBI:25805 ! oxygen atom [Term] id: CHEBI:25990 name: phenylethanolamines namespace: chebi_ontology def: "An ethanolamine compound having a phenyl (substituted or unsubstituted) group on the carbon bearing the hydroxy substituent." [ANON:ANON] subset: 3_STAR is_a: CHEBI:23981 ! ethanolamines [Term] id: CHEBI:26167 name: polar amino acid namespace: chebi_ontology alt_id: CHEBI:8283 def: "Any amino acid whose side chain is capable of forming one or more hydrogen bonds." [] subset: 3_STAR synonym: "polar amino acid" EXACT [ChEBI] synonym: "polar amino acids" RELATED [ChEBI] synonym: "polar amino-acid" RELATED [ChEBI] synonym: "polar amino-acids" RELATED [ChEBI] xref: MetaCyc:Polar-amino-acids xref: PMID:12016058 {source="Europe PMC"} is_a: CHEBI:33709 ! amino acid relationship: is_tautomer_of CHEBI:62031 ! polar amino acid zwitterion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "74.059" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "74.02420" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "OC(C(*)N)=O" xsd:string [Term] id: CHEBI:26191 name: polyol namespace: chebi_ontology def: "A compound that contains two or more hydroxy groups." [] subset: 3_STAR synonym: "polyols" RELATED [ChEBI] is_a: CHEBI:33822 ! organic hydroxy compound [Term] id: CHEBI:26469 name: quaternary nitrogen compound namespace: chebi_ontology def: "A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen." [] subset: 3_STAR is_a: CHEBI:35352 ! organonitrogen compound relationship: has_part CHEBI:35267 ! quaternary ammonium ion [Term] id: CHEBI:26607 name: saturated fatty acid namespace: chebi_ontology def: "Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess." [ANON:ANON] subset: 3_STAR synonym: "saturated fatty acid" EXACT [ChEBI:] synonym: "saturated fatty acid" EXACT [ChEBI] synonym: "saturated fatty acids" RELATED [ChEBI:] synonym: "saturated fatty acids" RELATED [ChEBI] synonym: "SFA" RELATED [ChEBI] synonym: "SFA" RELATED [ChEBI:] synonym: "SFAs" RELATED [ChEBI:] synonym: "SFAs" RELATED [ChEBI] xref: PMID:16492686 {source="Europe PMC"} xref: PMID:19763019 {source="Europe PMC"} xref: PMID:20237329 {source="Europe PMC"} is_a: CHEBI:35366 ! fatty acid [Term] id: CHEBI:26666 name: short-chain fatty acid namespace: chebi_ontology def: "An aliphatic monocarboxylic acid with a chain length of less than C6." [ANON:ANON] def: "An aliphatic monocarboxylic acid with a chain length of less than C6. If any non-hydrocarbon substituent is present, the compound is not normally regarded as a short-chain fatty acid." [] subset: 3_STAR synonym: "SCFA" RELATED [ChEBI] synonym: "SCFA" RELATED [ChEBI:] synonym: "SCFAs" RELATED [ChEBI:] synonym: "SCFAs" RELATED [ChEBI] synonym: "short-chain fatty acids" RELATED [ChEBI:] synonym: "short-chain fatty acids" RELATED [ChEBI] xref: PMID:16633129 {source="Europe PMC"} xref: PMID:16870803 {source="Europe PMC"} xref: PMID:18203540 {source="Europe PMC"} xref: PMID:20148677 {source="Europe PMC"} is_a: CHEBI:35366 ! fatty acid relationship: is_conjugate_acid_of CHEBI:58951 ! short-chain fatty acid anion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CH2OR" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "45.017" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "44.99765" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "OC([*])=O" xsd:string [Term] id: CHEBI:27162 name: tryptamines namespace: chebi_ontology def: "Tryptamine and its substitution derivatives." [ANON:ANON] subset: 3_STAR is_a: CHEBI:24828 ! indoles [Term] id: CHEBI:27171 name: organic heterobicyclic compound namespace: chebi_ontology subset: 3_STAR synonym: "heterobicyclic compounds" RELATED [ChEBI:] synonym: "heterobicyclic compounds" RELATED [ChEBI] synonym: "organic heterobicyclic compounds" RELATED [ChEBI] synonym: "organic heterobicyclic compounds" RELATED [ChEBI:] is_a: CHEBI:33672 ! heterobicyclic compound is_a: CHEBI:38166 ! organic heteropolycyclic compound [Term] id: CHEBI:27175 name: tyramines namespace: chebi_ontology def: "Aralkylamino compounds which contain a tyramine skeleton." [] subset: 3_STAR is_a: CHEBI:33853 ! phenols is_a: CHEBI:64365 ! aralkylamino compound [Term] id: CHEBI:27207 name: univalent carboacyl group namespace: chebi_ontology def: "A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid." [] subset: 3_STAR synonym: "univalent acyl group" RELATED [ChEBI] synonym: "univalent carboacyl groups" RELATED [ChEBI] synonym: "univalent carboxylic acyl groups" RELATED [ChEBI] is_a: CHEBI:37838 ! carboacyl group [Term] id: CHEBI:27369 name: zwitterion namespace: chebi_ontology def: "A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer)." [] subset: 3_STAR synonym: "compose zwitterionique" RELATED [IUPAC] synonym: "compuestos zwitterionicos" RELATED [IUPAC] synonym: "zwitterion" EXACT IUPAC_NAME [IUPAC] synonym: "zwitteriones" RELATED [IUPAC] synonym: "zwitterionic compounds" RELATED [IUPAC] synonym: "zwitterions" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:51151 ! dipolar compound [Term] id: CHEBI:27594 name: carbon atom namespace: chebi_ontology alt_id: CHEBI:23009 alt_id: CHEBI:3399 subset: 3_STAR synonym: "6C" RELATED [IUPAC] synonym: "C" RELATED [KEGG_COMPOUND] synonym: "C" RELATED [IUPAC] synonym: "Carbon" RELATED [KEGG_COMPOUND] synonym: "carbon" EXACT IUPAC_NAME [IUPAC] synonym: "carbon" RELATED [ChEBI] synonym: "carbone" RELATED [ChEBI] synonym: "carbonium" RELATED [ChEBI] synonym: "carbono" RELATED [ChEBI] synonym: "Kohlenstoff" RELATED [ChEBI] xref: CAS:7440-44-0 {source="ChemIDplus"} xref: CAS:7440-44-0 {source="KEGG COMPOUND"} xref: KEGG:C06265 xref: WebElements:C is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33306 ! carbon group element atom relationship: RO:0000087 CHEBI:33937 ! has role macronutrient property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "OKTJSMMVPCPJKN-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "12.01070" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "12.00000" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[C]" xsd:string [Term] id: CHEBI:28616 name: carbamic acid namespace: chebi_ontology alt_id: CHEBI:22504 alt_id: CHEBI:23002 alt_id: CHEBI:3386 alt_id: CHEBI:44573 def: "A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised." [] subset: 3_STAR synonym: "Aminoameisensaeure" RELATED [ChEBI] synonym: "Aminoformic acid" RELATED [KEGG_COMPOUND] synonym: "Carbamate" RELATED [KEGG_COMPOUND] synonym: "CARBAMIC ACID" EXACT [PDBeChem] synonym: "Carbamic acid" EXACT [KEGG_COMPOUND] synonym: "carbamic acid" EXACT IUPAC_NAME [IUPAC] synonym: "Carbamidsaeure" RELATED [ChEBI] xref: Beilstein:1734754 {source="Beilstein"} xref: CAS:463-77-4 {source="KEGG COMPOUND"} xref: CAS:463-77-4 {source="ChemIDplus"} xref: DrugBank:DB04261 xref: Gmelin:130345 {source="Gmelin"} xref: KEGG:C01563 xref: PDBeChem:OUT xref: Wikipedia:Carbamic_acid is_a: CHEBI:35352 ! organonitrogen compound is_a: CHEBI:35605 ! carbon oxoacid is_a: CHEBI:64708 ! one-carbon compound relationship: is_conjugate_acid_of CHEBI:13941 ! carbamate relationship: RO:0000087 CHEBI:76971 ! has role Escherichia coli metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CH3NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "KXDHJXZQYSOELW-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "61.04006" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "61.01638" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC(O)=O" xsd:string [Term] id: CHEBI:28790 name: serotonin namespace: chebi_ontology alt_id: CHEBI:1420 alt_id: CHEBI:26652 alt_id: CHEBI:49894 def: "A primary amino compound that is the 5-hydroxy derivative of tryptamine." [] def: "The 5-hydroxy derivative of tryptamine." [ANON:ANON] subset: 3_STAR synonym: "3-(2-Aminoethyl)-1H-indol-5-ol" RELATED [KEGG COMPOUND:] synonym: "3-(2-Aminoethyl)-1H-indol-5-ol" RELATED [KEGG_COMPOUND] synonym: "3-(2-aminoethyl)-1H-indol-5-ol" EXACT IUPAC_NAME [IUPAC:] synonym: "3-(2-aminoethyl)-1H-indol-5-ol" EXACT IUPAC_NAME [IUPAC] synonym: "5-HT" RELATED [IUPHAR:] synonym: "5-HT" RELATED [IUPHAR] synonym: "5-Hydroxytryptamine" RELATED [KEGG COMPOUND:] synonym: "5-Hydroxytryptamine" RELATED [KEGG_COMPOUND] synonym: "C10H12N2O" RELATED FORMULA [KEGG COMPOUND:] synonym: "Enteramine" RELATED [KEGG COMPOUND:] synonym: "Enteramine" RELATED [KEGG_COMPOUND] synonym: "InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2" RELATED InChI [ChEBI:] synonym: "InChIKey=QZAYGJVTTNCVMB-UHFFFAOYSA-N" RELATED InChIKey [ChEBI:] synonym: "NCCc1c[nH]c2ccc(O)cc12" RELATED SMILES [ChEBI:] synonym: "SEROTONIN" EXACT [PDBeChem:] synonym: "SEROTONIN" EXACT [PDBeChem] synonym: "Serotonin" EXACT [KEGG COMPOUND:] synonym: "Serotonin" EXACT [KEGG_COMPOUND] synonym: "serotonine" RELATED [ChEBI:] synonym: "serotonine" RELATED [ChEBI] synonym: "thrombocytin" RELATED [ChemIDplus:] synonym: "thrombocytin" RELATED [ChemIDplus] synonym: "thrombotonin" RELATED [ChemIDplus] synonym: "thrombotonin" RELATED [ChemIDplus:] xref: Beilstein:143524 {source="Beilstein"} xref: CAS:50-67-9 {source="KEGG COMPOUND"} xref: CAS:50-67-9 {source="ChemIDplus"} xref: Gmelin:1861995 {source="Gmelin"} xref: HMDB:HMDB0000259 xref: KEGG:C00780 xref: KNApSAcK:C00001429 xref: LINCS:LSM-6589 xref: MetaCyc:SEROTONIN xref: PDBeChem:SRO xref: PMID:18593914 {source="Europe PMC"} xref: PMID:22770225 {source="Europe PMC"} xref: PMID:24136337 {source="Europe PMC"} xref: Reaxys:143524 {source="Reaxys"} xref: Wikipedia:Serotonin is_a: CHEBI:25375 ! monoamine molecular messenger is_a: CHEBI:27162 ! tryptamines is_a: CHEBI:33853 ! phenols is_a: CHEBI:50994 ! primary amino compound is_a: CHEBI:84729 ! hydroxyindoles relationship: has_functional_parent CHEBI:16765 ! tryptamine relationship: is_conjugate_base_of CHEBI:350546 ! serotonin(1+) relationship: RO:0000087 CHEBI:25512 ! has role neurotransmitter relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C10H12N2O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QZAYGJVTTNCVMB-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "176.215" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "176.09496" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C1=CC(=CC=2C(=CNC12)CCN)O" xsd:string [Term] id: CHEBI:28868 name: fatty acid anion namespace: chebi_ontology alt_id: CHEBI:13634 alt_id: CHEBI:24022 alt_id: CHEBI:4985 def: "The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid." [] subset: 3_STAR synonym: "a fatty acid" RELATED [UniProt] synonym: "acido graso anionico" RELATED [ChEBI] synonym: "acidos grasos anionicos" RELATED [ChEBI] synonym: "Alkanate" RELATED [KEGG_COMPOUND] synonym: "anion de l'acide gras" RELATED [ChEBI] synonym: "Fatty acid anion" EXACT [KEGG_COMPOUND] synonym: "fatty acid anions" RELATED [ChEBI] synonym: "Fettsaeureanion" RELATED [ChEBI] synonym: "Fettsaeureanionen" RELATED [ChEBI] xref: KEGG:C02403 xref: PMID:18628202 {source="Europe PMC"} is_a: CHEBI:18059 ! lipid is_a: CHEBI:35757 ! monocarboxylic acid anion relationship: is_conjugate_base_of CHEBI:35366 ! fatty acid property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "44.00950" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "43.98983" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-]C([*])=O" xsd:string [Term] id: CHEBI:28938 name: ammonium namespace: chebi_ontology alt_id: CHEBI:22534 alt_id: CHEBI:49783 alt_id: CHEBI:7435 def: "An onium cation obtained by protonation of ammonia." [] subset: 3_STAR synonym: "[NH4](+)" RELATED [MolBase] synonym: "ammonium" EXACT IUPAC_NAME [IUPAC] synonym: "ammonium" EXACT [ChEBI] synonym: "ammonium cation" RELATED [ChemIDplus] synonym: "ammonium ion" RELATED [PDBeChem] synonym: "Ammonium(1+)" RELATED [ChemIDplus] synonym: "azanium" EXACT IUPAC_NAME [IUPAC] synonym: "NH4(+)" RELATED [UniProt] synonym: "NH4(+)" RELATED [IUPAC] synonym: "NH4+" RELATED [KEGG_COMPOUND] xref: CAS:14798-03-9 {source="NIST Chemistry WebBook"} xref: CAS:14798-03-9 {source="ChemIDplus"} xref: Gmelin:84 {source="Gmelin"} xref: KEGG:C01342 xref: MetaCyc:AMMONIUM xref: MolBase:929 xref: PDBeChem:NH4 xref: PMID:11319011 {source="Europe PMC"} xref: PMID:11341317 {source="Europe PMC"} xref: PMID:12096804 {source="Europe PMC"} xref: PMID:14512268 {source="Europe PMC"} xref: PMID:14879753 {source="Europe PMC"} xref: PMID:16345391 {source="Europe PMC"} xref: PMID:16903292 {source="Europe PMC"} xref: PMID:17392693 {source="Europe PMC"} xref: PMID:18515490 {source="Europe PMC"} xref: PMID:19199063 {source="Europe PMC"} xref: PMID:19596600 {source="Europe PMC"} xref: PMID:19682559 {source="Europe PMC"} xref: PMID:19716251 {source="Europe PMC"} xref: PMID:21993530 {source="Europe PMC"} xref: PMID:22265469 {source="Europe PMC"} xref: PMID:22524020 {source="Europe PMC"} xref: PMID:22562341 {source="Europe PMC"} xref: PMID:22631217 {source="Europe PMC"} xref: Reaxys:16093784 {source="Reaxys"} xref: Wikipedia:Ammonium is_a: CHEBI:35106 ! nitrogen hydride is_a: CHEBI:50313 ! onium cation is_a: CHEBI:60242 ! monovalent inorganic cation relationship: is_conjugate_acid_of CHEBI:16134 ! ammonia relationship: RO:0000087 CHEBI:23357 ! has role cofactor relationship: RO:0000087 CHEBI:75772 ! has role Saccharomyces cerevisiae metabolite relationship: RO:0000087 CHEBI:76971 ! has role Escherichia coli metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "H4N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/H3N/h1H3/p+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QGZKDVFQNNGYKY-UHFFFAOYSA-O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "18.03850" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "18.03383" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[H][N+]([H])([H])[H]" xsd:string [Term] id: CHEBI:28965 name: dicarboxylic acid dianion namespace: chebi_ontology alt_id: CHEBI:13632 alt_id: CHEBI:23688 alt_id: CHEBI:23689 alt_id: CHEBI:38711 def: "A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid." [] subset: 3_STAR synonym: "a dicarboxylate" RELATED [UniProt] synonym: "dicarboxylate" RELATED [ChEBI] synonym: "dicarboxylates" RELATED [ChEBI] synonym: "dicarboxylic acid dianion" EXACT [ChEBI] synonym: "dicarboxylic acid dianions" RELATED [ChEBI] is_a: CHEBI:35693 ! dicarboxylic acid anion is_a: CHEBI:38716 ! carboxylic acid dianion property_value: http://purl.obolibrary.org/obo/chebi/charge "-2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2O4R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "88.019" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "87.97966" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-]C(=O)[*]C([O-])=O" xsd:string [Term] id: CHEBI:29067 name: carboxylic acid anion namespace: chebi_ontology alt_id: CHEBI:13626 alt_id: CHEBI:13945 alt_id: CHEBI:23026 alt_id: CHEBI:58657 def: "The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated." [] subset: 3_STAR synonym: "a carboxylate" RELATED [UniProt] synonym: "carboxylic acid anions" RELATED [ChEBI] synonym: "carboxylic anions" RELATED [ChEBI] is_a: CHEBI:25696 ! organic anion is_a: CHEBI:35406 ! oxoanion relationship: is_conjugate_base_of CHEBI:33575 ! carboxylic acid property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "44.00950" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "43.98983" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-]C([*])=O" xsd:string [Term] id: CHEBI:29337 name: azanide namespace: chebi_ontology subset: 3_STAR synonym: "amide" EXACT IUPAC_NAME [IUPAC] synonym: "azanide" EXACT IUPAC_NAME [IUPAC] synonym: "dihydridonitrate(1-)" EXACT IUPAC_NAME [IUPAC] synonym: "NH2(-)" RELATED [IUPAC] is_a: CHEBI:35106 ! nitrogen hydride is_a: CHEBI:79389 ! monovalent inorganic anion relationship: is_conjugate_acid_of CHEBI:29340 ! hydridonitrate(2-) relationship: is_conjugate_base_of CHEBI:16134 ! ammonia property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "H2N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/H2N/h1H2/q-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "HYGWNUKOUCZBND-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "16.02262" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "16.01927" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[H][N-][H]" xsd:string [Term] id: CHEBI:29340 name: hydridonitrate(2-) namespace: chebi_ontology def: "A divalent inorganic anion resulting from the removal of two protons from ammonia." [] subset: 3_STAR synonym: "azanediide" EXACT IUPAC_NAME [IUPAC] synonym: "hydridonitrate(2-)" EXACT IUPAC_NAME [IUPAC] synonym: "imide" RELATED [IUPAC] synonym: "NH(2-)" RELATED [IUPAC] is_a: CHEBI:35106 ! nitrogen hydride is_a: CHEBI:79388 ! divalent inorganic anion relationship: is_conjugate_base_of CHEBI:29337 ! azanide property_value: http://purl.obolibrary.org/obo/chebi/charge "-2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "HN" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/HN/h1H/q-2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "DZQYTNGKSBCIOE-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "15.01468" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "15.01200" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[N--][H]" xsd:string [Term] id: CHEBI:29987 name: glutamate(2-) namespace: chebi_ontology def: "A dicarboxylic acid dianion that is the conjugate base of glutamate(1-)." [] subset: 3_STAR synonym: "2-aminopentanedioate" EXACT IUPAC_NAME [IUPAC] synonym: "glutamate" EXACT IUPAC_NAME [IUPAC] synonym: "glutamate(2-)" EXACT [JCBN] synonym: "glutamic acid dianion" RELATED [JCBN] xref: Beilstein:4134100 {source="Beilstein"} xref: Gmelin:327903 {source="Gmelin"} xref: Reaxys:4134100 {source="Reaxys"} is_a: CHEBI:28965 ! dicarboxylic acid dianion relationship: is_conjugate_base_of CHEBI:14321 ! glutamate(1-) relationship: RO:0000087 CHEBI:78675 ! has role fundamental metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "-2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C5H7NO4" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "WHUUTDBJXJRKMK-UHFFFAOYSA-L" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "145.11342" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "145.03860" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC(CCC([O-])=O)C([O-])=O" xsd:string [Term] id: CHEBI:30089 name: acetate namespace: chebi_ontology alt_id: CHEBI:13704 alt_id: CHEBI:22165 alt_id: CHEBI:40480 def: "A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid." [] subset: 3_STAR synonym: "acetate" EXACT [UniProt] synonym: "acetate" EXACT IUPAC_NAME [IUPAC] synonym: "ACETATE ION" RELATED [PDBeChem] synonym: "acetic acid, ion(1-)" RELATED [ChemIDplus] synonym: "Azetat" RELATED [ChEBI] synonym: "CH3-COO(-)" RELATED [IUPAC] synonym: "Ethanoat" RELATED [ChEBI] synonym: "ethanoate" RELATED [ChEBI] synonym: "MeCO2 anion" RELATED [NIST_Chemistry_WebBook] xref: Beilstein:1901470 {source="Beilstein"} xref: CAS:71-50-1 {source="ChemIDplus"} xref: CAS:71-50-1 {source="NIST Chemistry WebBook"} xref: DrugBank:DB03166 xref: Gmelin:1379 {source="Gmelin"} xref: KEGG:C00033 xref: MetaCyc:ACET xref: PDBeChem:ACT xref: PMID:17190852 {source="Europe PMC"} xref: PMID:22211106 {source="Europe PMC"} xref: PMID:22371380 {source="Europe PMC"} xref: Reaxys:1901470 {source="Reaxys"} xref: UM-BBD_compID:c0050 {source="UM-BBD"} xref: Wikipedia:Acetate is_a: CHEBI:35757 ! monocarboxylic acid anion relationship: is_conjugate_base_of CHEBI:15366 ! acetic acid relationship: RO:0000087 CHEBI:75772 ! has role Saccharomyces cerevisiae metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H3O2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QTBSBXVTEAMEQO-UHFFFAOYSA-M" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "59.04402" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "59.01385" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "CC([O-])=O" xsd:string [Term] id: CHEBI:30566 name: gamma-aminobutyrate namespace: chebi_ontology alt_id: CHEBI:11961 alt_id: CHEBI:20317 def: "An gamma-amino acid anion resulting from the deprotonation of the carboxy group of gamma-aminobutyric acid." [] subset: 3_STAR synonym: "4-Amino-butyrat" RELATED [ChEBI] synonym: "4-aminobutanoate" EXACT IUPAC_NAME [IUPAC] synonym: "4-aminobutanoic acid ion (1-)" RELATED [ChEBI] synonym: "4-Aminobutylate" RELATED [KEGG_COMPOUND] synonym: "4-aminobutyrate" RELATED [ChEBI] synonym: "gamma-aminobutanoate" RELATED [ChEBI] synonym: "gamma-aminobutyrate anion" RELATED [ChEBI] xref: Beilstein:3536873 {source="Beilstein"} xref: Gmelin:559138 {source="Gmelin"} xref: KEGG:C00334 xref: PMID:12509893 {source="Europe PMC"} xref: Reaxys:3536873 {source="Reaxys"} is_a: CHEBI:71666 ! gamma-amino acid anion relationship: has_functional_parent CHEBI:17968 ! butyrate relationship: is_conjugate_base_of CHEBI:16865 ! gamma-aminobutyric acid relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H8NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7)/p-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "BTCSSZJGUNDROE-UHFFFAOYSA-M" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "102.11186" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "102.05605" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NCCCC([O-])=O" xsd:string [Term] id: CHEBI:30772 name: butyric acid namespace: chebi_ontology alt_id: CHEBI:113450 alt_id: CHEBI:22948 alt_id: CHEBI:3234 alt_id: CHEBI:41208 def: "A straight-chain saturated fatty acid that is butane in which one of the terminal methyl groups has been oxidised to a carboxy group." [] subset: 3_STAR synonym: "1-butanoic acid" RELATED [HMDB] synonym: "1-butyric acid" RELATED [HMDB] synonym: "1-propanecarboxylic acid" RELATED [MetaCyc] synonym: "4:0" RELATED [ChEBI] synonym: "acide butanoique" RELATED [IUPAC] synonym: "acide butyrique" RELATED [ChEBI] synonym: "butanic acid" RELATED [ChEBI] synonym: "Butanoate" RELATED [KEGG_COMPOUND] synonym: "BUTANOIC ACID" RELATED [PDBeChem] synonym: "Butanoic acid" RELATED [KEGG_COMPOUND] synonym: "butanoic acid" EXACT IUPAC_NAME [IUPAC] synonym: "butoic acid" RELATED [ChEBI] synonym: "Buttersaeure" RELATED [ChEBI] synonym: "Butyric acid" EXACT [KEGG_COMPOUND] synonym: "butyric acid" EXACT [IUPAC] synonym: "C4:0" RELATED [ChEBI] synonym: "CH3-[CH2]2-COOH" RELATED [IUPAC] synonym: "ethylacetic acid" RELATED [NIST_Chemistry_WebBook] synonym: "n-butanoic acid" RELATED [NIST_Chemistry_WebBook] synonym: "n-butyric acid" RELATED [NIST_Chemistry_WebBook] synonym: "propanecarboxylic acid" RELATED [HMDB] synonym: "propylformic acid" RELATED [MetaCyc] xref: Beilstein:906770 {source="Beilstein"} xref: CAS:107-92-6 {source="ChemIDplus"} xref: CAS:107-92-6 {source="NIST Chemistry WebBook"} xref: CAS:107-92-6 {source="KEGG COMPOUND"} xref: DrugBank:DB03568 xref: Gmelin:26242 {source="Gmelin"} xref: HMDB:HMDB0000039 xref: KEGG:C00246 xref: KNApSAcK:C00001180 xref: LIPID_MAPS_instance:LMFA01010004 {source="LIPID MAPS"} xref: MetaCyc:BUTYRIC_ACID xref: PDBeChem:BUA xref: PMID:10736622 {source="Europe PMC"} xref: PMID:10956204 {source="ChEMBL"} xref: PMID:11201044 {source="Europe PMC"} xref: PMID:11208715 {source="Europe PMC"} xref: PMID:11238216 {source="Europe PMC"} xref: PMID:11305323 {source="Europe PMC"} xref: PMID:12068484 {source="Europe PMC"} xref: PMID:13678314 {source="Europe PMC"} xref: PMID:14962641 {source="Europe PMC"} xref: PMID:1542095 {source="ChEMBL"} xref: PMID:15809727 {source="Europe PMC"} xref: PMID:15810631 {source="Europe PMC"} xref: PMID:15938880 {source="Europe PMC"} xref: PMID:19318247 {source="Europe PMC"} xref: PMID:19366864 {source="Europe PMC"} xref: PMID:19703412 {source="Europe PMC"} xref: PMID:21699495 {source="Europe PMC"} xref: PMID:22038864 {source="Europe PMC"} xref: PMID:22194341 {source="Europe PMC"} xref: PMID:22322557 {source="Europe PMC"} xref: PMID:22339023 {source="Europe PMC"} xref: PMID:22466881 {source="Europe PMC"} xref: Reaxys:906770 {source="Reaxys"} xref: Wikipedia:Butyric_acid is_a: CHEBI:140601 ! fatty acid 4:0 is_a: CHEBI:39418 ! straight-chain saturated fatty acid relationship: is_conjugate_acid_of CHEBI:17968 ! butyrate relationship: RO:0000087 CHEBI:131604 ! has role Mycoplasma genitalium metabolite relationship: RO:0000087 CHEBI:84087 ! has role human urinary metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H8O2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "FERIUCNNQQJTOY-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "88.10510" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "88.05243" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "CCCC(O)=O" xsd:string [Term] id: CHEBI:30879 name: alcohol namespace: chebi_ontology alt_id: CHEBI:13804 alt_id: CHEBI:22288 alt_id: CHEBI:2553 def: "A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom." [ANON:ANON] subset: 3_STAR synonym: "Alcohol" EXACT [KEGG COMPOUND:] synonym: "Alcohol" EXACT [KEGG_COMPOUND] synonym: "alcohols" EXACT IUPAC_NAME [IUPAC] synonym: "alcohols" EXACT IUPAC_NAME [IUPAC:] synonym: "an alcohol" RELATED [UniProt] synonym: "CHOR3" RELATED FORMULA [ChEBI:] synonym: "HOR" RELATED FORMULA [KEGG COMPOUND:] synonym: "OC([*])([*])[*]" RELATED SMILES [ChEBI:] xref: KEGG:C00069 is_a: CHEBI:33822 ! organic hydroxy compound property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "HOR" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "17.007" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "17.00274" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "O[*]" xsd:string [Term] id: CHEBI:32877 name: primary amine namespace: chebi_ontology alt_id: CHEBI:26263 alt_id: CHEBI:26265 alt_id: CHEBI:8407 alt_id: CHEBI:8409 def: "A compound formally derived from ammonia by replacing one hydrogen atom by a hydrocarbyl group." [ANON:ANON] subset: 3_STAR synonym: "H2NR" RELATED FORMULA [KEGG COMPOUND:] synonym: "N[*]" RELATED SMILES [ChEBI:] synonym: "primaeres Amin" RELATED [ChEBI] synonym: "primaeres Amin" RELATED [ChEBI:] synonym: "Primary amine" EXACT [KEGG_COMPOUND] synonym: "Primary amine" EXACT [KEGG COMPOUND:] synonym: "primary amines" EXACT IUPAC_NAME [IUPAC] synonym: "primary amines" EXACT IUPAC_NAME [IUPAC:] synonym: "Primary monoamine" RELATED [KEGG_COMPOUND] synonym: "Primary monoamine" RELATED [KEGG COMPOUND:] synonym: "R-NH2" RELATED [IUPAC:] synonym: "R-NH2" RELATED [IUPAC] synonym: "RCH2NH2" RELATED [KEGG_COMPOUND] xref: KEGG:C00375 xref: KEGG:C00893 xref: KEGG:C02580 is_a: CHEBI:32952 ! amine is_a: CHEBI:50994 ! primary amino compound property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "H2NR" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "16.02260" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "16.01872" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "N[*]" xsd:string [Term] id: CHEBI:32952 name: amine namespace: chebi_ontology alt_id: CHEBI:13814 alt_id: CHEBI:22474 alt_id: CHEBI:2641 def: "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups." [ANON:ANON] subset: 3_STAR synonym: "Amin" RELATED [ChEBI] synonym: "Amin" RELATED [ChEBI:] synonym: "Amine" EXACT [KEGG_COMPOUND] synonym: "Amine" EXACT [KEGG COMPOUND:] synonym: "amines" EXACT IUPAC_NAME [IUPAC:] synonym: "amines" EXACT IUPAC_NAME [IUPAC] synonym: "an amine" RELATED [UniProt:] synonym: "Substituted amine" RELATED [KEGG_COMPOUND] xref: KEGG:C00706 is_a: CHEBI:50047 ! organic amino compound [Term] id: CHEBI:32988 name: amide namespace: chebi_ontology alt_id: CHEBI:22473 alt_id: CHEBI:2633 def: "An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [ANON:ANON] subset: 3_STAR synonym: "Amide" EXACT [KEGG_COMPOUND] synonym: "Amide" EXACT [KEGG COMPOUND:] synonym: "amides" EXACT IUPAC_NAME [IUPAC] synonym: "amides" EXACT IUPAC_NAME [IUPAC:] xref: KEGG:C00241 is_a: CHEBI:51143 ! nitrogen molecular entity [Term] id: CHEBI:33232 name: application namespace: chebi_ontology def: "Intended use of the molecular entity or part thereof by humans." [] subset: 3_STAR is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] id: CHEBI:33233 name: fundamental particle namespace: chebi_ontology def: "A particle not known to have substructure." [] subset: 3_STAR synonym: "elementary particle" EXACT IUPAC_NAME [IUPAC] synonym: "elementary particles" RELATED [ChEBI] is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:33242 name: inorganic hydride namespace: chebi_ontology subset: 3_STAR synonym: "inorganic hydrides" RELATED [ChEBI] is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:33692 ! hydrides [Term] id: CHEBI:33246 name: inorganic group namespace: chebi_ontology def: "Any substituent group which does not contain carbon." [] subset: 3_STAR synonym: "inorganic groups" RELATED [ChEBI] is_a: CHEBI:24433 ! group [Term] id: CHEBI:33247 name: organic group namespace: chebi_ontology def: "Any substituent group or skeleton containing carbon." [] subset: 3_STAR synonym: "organic groups" RELATED [ChEBI] is_a: CHEBI:24433 ! group relationship: is_substituent_group_from CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33249 name: organyl group namespace: chebi_ontology def: "Any organic substituent group, regardless of functional type, having one free valence at a carbon atom." [] subset: 3_STAR synonym: "groupe organyle" RELATED [IUPAC] synonym: "grupo organilo" RELATED [IUPAC] synonym: "grupos organilo" RELATED [IUPAC] synonym: "organyl group" EXACT IUPAC_NAME [IUPAC] synonym: "organyl groups" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:51447 ! organic univalent group [Term] id: CHEBI:33250 name: atom namespace: chebi_ontology alt_id: CHEBI:22671 alt_id: CHEBI:23907 def: "A chemical entity constituting the smallest component of an element having the chemical properties of the element." [] subset: 3_STAR synonym: "atom" EXACT IUPAC_NAME [IUPAC] synonym: "atome" RELATED [IUPAC] synonym: "atomo" RELATED [IUPAC] synonym: "atoms" RELATED [ChEBI] synonym: "atomus" RELATED [ChEBI] synonym: "element" RELATED [ChEBI] synonym: "elements" RELATED [ChEBI] is_a: CHEBI:24431 ! chemical entity relationship: has_part CHEBI:10545 ! electron relationship: has_part CHEBI:33252 ! atomic nucleus [Term] id: CHEBI:33252 name: atomic nucleus namespace: chebi_ontology def: "A nucleus is the positively charged central portion of an atom, excluding the orbital electrons." [] subset: 3_STAR synonym: "Atomkern" RELATED [ChEBI] synonym: "Kern" RELATED [ChEBI] synonym: "noyau" RELATED [IUPAC] synonym: "noyau atomique" RELATED [ChEBI] synonym: "nuclei" RELATED [ChEBI] synonym: "nucleo" RELATED [IUPAC] synonym: "nucleo atomico" RELATED [ChEBI] synonym: "nucleus" EXACT IUPAC_NAME [IUPAC] synonym: "nucleus atomi" RELATED [ChEBI] is_a: CHEBI:36347 ! nuclear particle relationship: has_part CHEBI:33253 ! nucleon [Term] id: CHEBI:33253 name: nucleon namespace: chebi_ontology def: "Heavy nuclear particle: proton or neutron." [] subset: 3_STAR synonym: "nucleon" EXACT [IUPAC] synonym: "nucleon" EXACT IUPAC_NAME [IUPAC] synonym: "nucleons" RELATED [ChEBI] synonym: "Nukleon" RELATED [ChEBI] synonym: "Nukleonen" RELATED [ChEBI] is_a: CHEBI:36339 ! baryon is_a: CHEBI:36347 ! nuclear particle [Term] id: CHEBI:33256 name: primary amide namespace: chebi_ontology def: "A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [ANON:ANON] subset: 3_STAR synonym: "primary amide" EXACT [IUPAC:] synonym: "primary amide" EXACT [IUPAC] synonym: "primary amides" EXACT IUPAC_NAME [IUPAC] synonym: "primary amides" EXACT IUPAC_NAME [IUPAC:] is_a: CHEBI:32988 ! amide [Term] id: CHEBI:33273 name: polyatomic anion namespace: chebi_ontology def: "An anion consisting of more than one atom." [] subset: 3_STAR synonym: "polyatomic anions" RELATED [ChEBI] is_a: CHEBI:22563 ! anion is_a: CHEBI:36358 ! polyatomic ion [Term] id: CHEBI:33280 name: molecular messenger namespace: chebi_ontology subset: 3_STAR synonym: "chemical messenger" RELATED [ChEBI] is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:33281 name: antimicrobial agent namespace: chebi_ontology alt_id: CHEBI:22582 def: "A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans." [] subset: 3_STAR synonym: "antibiotic" RELATED [ChEBI] synonym: "antibiotics" RELATED [ChEBI] synonym: "Antibiotika" RELATED [ChEBI] synonym: "Antibiotikum" RELATED [ChEBI] synonym: "antibiotique" RELATED [IUPAC] synonym: "antimicrobial" RELATED [ChEBI] synonym: "antimicrobial agents" RELATED [ChEBI] synonym: "antimicrobials" RELATED [ChEBI] synonym: "microbicide" RELATED [ChEBI] synonym: "microbicides" RELATED [ChEBI] xref: PMID:12964249 {source="Europe PMC"} xref: PMID:22117953 {source="Europe PMC"} xref: PMID:22439833 {source="Europe PMC"} xref: PMID:22849268 {source="Europe PMC"} xref: PMID:22849276 {source="Europe PMC"} xref: PMID:22958833 {source="Europe PMC"} is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:33284 name: nutrient namespace: chebi_ontology def: "A nutrient is a food component that an organism uses to survive and grow." [] subset: 3_STAR synonym: "nutrients" RELATED [ChEBI] is_a: CHEBI:78295 ! food component [Term] id: CHEBI:33285 name: heteroorganic entity namespace: chebi_ontology def: "A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms." [ANON:ANON] subset: 3_STAR synonym: "heteroorganic entities" RELATED [ChEBI:] synonym: "heteroorganic entities" RELATED [ChEBI] synonym: "organoelement compounds" RELATED [ChEBI:] synonym: "organoelement compounds" RELATED [ChEBI] is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33300 name: pnictogen namespace: chebi_ontology def: "Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth." [] subset: 3_STAR synonym: "group 15 elements" RELATED [ChEBI] synonym: "group V elements" RELATED [ChEBI] synonym: "nitrogenoideos" RELATED [ChEBI] synonym: "nitrogenoides" RELATED [ChEBI] synonym: "pnictogene" RELATED [ChEBI] synonym: "pnictogenes" RELATED [ChEBI] synonym: "pnictogens" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33302 name: pnictogen molecular entity namespace: chebi_ontology def: "A p-block molecular entity containing any pnictogen." [] subset: 3_STAR synonym: "pnictogen molecular entities" RELATED [ChEBI:] synonym: "pnictogen molecular entities" RELATED [ChEBI] synonym: "pnictogen molecular entity" EXACT [ChEBI] synonym: "pnictogen molecular entity" EXACT [ChEBI:] is_a: CHEBI:33675 ! p-block molecular entity relationship: has_part CHEBI:33300 ! pnictogen [Term] id: CHEBI:33303 name: chalcogen namespace: chebi_ontology def: "Any p-block element belonging to the group 16 family of the periodic table." [] subset: 3_STAR synonym: "anfigeno" RELATED [ChEBI] synonym: "anfigenos" RELATED [ChEBI] synonym: "calcogeno" RELATED [ChEBI] synonym: "calcogenos" RELATED [ChEBI] synonym: "chalcogen" EXACT IUPAC_NAME [IUPAC] synonym: "chalcogene" RELATED [ChEBI] synonym: "chalcogenes" RELATED [ChEBI] synonym: "chalcogens" EXACT IUPAC_NAME [IUPAC] synonym: "Chalkogen" RELATED [ChEBI] synonym: "Chalkogene" RELATED [ChEBI] synonym: "group 16 elements" RELATED [ChEBI] synonym: "group VI elements" RELATED [ChEBI] xref: PMID:17084588 {source="Europe PMC"} is_a: CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33304 name: chalcogen molecular entity namespace: chebi_ontology def: "Any p-block molecular entity containing a chalcogen." [ANON:ANON] subset: 3_STAR synonym: "chalcogen compounds" RELATED [ChEBI:] synonym: "chalcogen compounds" RELATED [ChEBI] synonym: "chalcogen molecular entities" RELATED [ChEBI:] synonym: "chalcogen molecular entities" RELATED [ChEBI] synonym: "chalcogen molecular entity" EXACT [ChEBI] synonym: "chalcogen molecular entity" EXACT [ChEBI:] is_a: CHEBI:33675 ! p-block molecular entity relationship: has_part CHEBI:33303 ! chalcogen [Term] id: CHEBI:33306 name: carbon group element atom namespace: chebi_ontology subset: 3_STAR synonym: "carbon group element" RELATED [ChEBI] synonym: "carbon group elements" RELATED [ChEBI] synonym: "carbonoides" RELATED [ChEBI] synonym: "cristallogene" RELATED [ChEBI] synonym: "cristallogenes" RELATED [ChEBI] synonym: "group 14 elements" EXACT IUPAC_NAME [IUPAC] synonym: "group IV elements" RELATED [ChEBI] is_a: CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33308 name: carboxylic ester namespace: chebi_ontology alt_id: CHEBI:13204 alt_id: CHEBI:23028 alt_id: CHEBI:3408 def: "An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl." [] def: "An ester of a carboxylic acid." [ANON:ANON] subset: 3_STAR synonym: "a carboxylic ester" RELATED [UniProt] synonym: "carboxylic acid esters" RELATED [ChEBI] synonym: "carboxylic acid esters" RELATED [ChEBI:] synonym: "Carboxylic ester" EXACT [KEGG_COMPOUND] synonym: "Carboxylic ester" EXACT [KEGG COMPOUND:] synonym: "carboxylic ester" EXACT [UniProt:] synonym: "carboxylic esters" EXACT IUPAC_NAME [IUPAC:] synonym: "carboxylic esters" EXACT IUPAC_NAME [IUPAC] synonym: "CO2R2" RELATED FORMULA [KEGG COMPOUND:] xref: KEGG:C02391 xref: Wikipedia:Ester is_a: CHEBI:35701 ! ester is_a: CHEBI:36586 ! carbonyl compound property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2R2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "44.010" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "43.98983" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[*]C(=O)O[*]" xsd:string [Term] id: CHEBI:33318 name: main group element atom namespace: chebi_ontology def: "An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table." [] subset: 3_STAR synonym: "Hauptgruppenelement" RELATED [ChEBI] synonym: "Hauptgruppenelemente" RELATED [ChEBI] synonym: "main group element" RELATED [ChEBI] synonym: "main group elements" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:33250 ! atom [Term] id: CHEBI:33558 name: alpha-amino-acid anion namespace: chebi_ontology def: "An amino-acid anion obtained by deprotonation of any alpha-amino acid." [] subset: 3_STAR synonym: "alpha-amino acid anions" RELATED [ChEBI] synonym: "alpha-amino-acid anion" EXACT [ChEBI] synonym: "alpha-amino-acid anions" RELATED [ChEBI] is_a: CHEBI:37022 ! amino-acid anion relationship: is_conjugate_base_of CHEBI:33704 ! alpha-amino acid [Term] id: CHEBI:33559 name: s-block element atom namespace: chebi_ontology subset: 3_STAR synonym: "s-block element" RELATED [ChEBI] synonym: "s-block elements" RELATED [ChEBI] is_a: CHEBI:33250 ! atom [Term] id: CHEBI:33560 name: p-block element atom namespace: chebi_ontology def: "Any main group element atom belonging to the p-block of the periodic table." [] subset: 3_STAR synonym: "p-block element" RELATED [ChEBI] synonym: "p-block elements" RELATED [ChEBI] is_a: CHEBI:33318 ! main group element atom [Term] id: CHEBI:33566 name: catechols namespace: chebi_ontology alt_id: CHEBI:134187 alt_id: CHEBI:13628 alt_id: CHEBI:18862 def: "Any compound containing an o-diphenol component." [] subset: 3_STAR synonym: "1,2-benzenediols" RELATED [ChEBI] synonym: "a catechol" RELATED [UniProt] synonym: "benzene-1,2-diols" RELATED [ChEBI] xref: KEGG:C15571 is_a: CHEBI:33570 ! benzenediols property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C6H2O2R4" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "106.079" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "106.00548" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "OC1=C(O)C(*)=C(*)C(*)=C1*" xsd:string [Term] id: CHEBI:33567 name: catecholamine namespace: chebi_ontology alt_id: CHEBI:23056 alt_id: CHEBI:3468 def: "4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution." [ANON:ANON] subset: 3_STAR synonym: "C8H9NO2R2" RELATED FORMULA [KEGG COMPOUND:] synonym: "Catecholamine" EXACT [KEGG_COMPOUND] synonym: "Catecholamine" EXACT [KEGG COMPOUND:] synonym: "catecholamines" EXACT IUPAC_NAME [IUPAC] synonym: "catecholamines" EXACT IUPAC_NAME [IUPAC:] synonym: "catecholamines" RELATED [ChEBI] synonym: "catecholamines" RELATED [ChEBI:] xref: KEGG:C02012 is_a: CHEBI:25375 ! monoamine molecular messenger is_a: CHEBI:33566 ! catechols property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C8H9NO2R2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "151.163" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "151.06333" xsd:string [Term] id: CHEBI:33570 name: benzenediols namespace: chebi_ontology alt_id: CHEBI:22705 alt_id: CHEBI:22711 subset: 3_STAR is_a: CHEBI:33853 ! phenols [Term] id: CHEBI:33575 name: carboxylic acid namespace: chebi_ontology alt_id: CHEBI:13428 alt_id: CHEBI:13627 alt_id: CHEBI:23027 def: "A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid." [] def: "An oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid." [ANON:ANON] subset: 3_STAR synonym: "acide carboxylique" RELATED [IUPAC] synonym: "acide carboxylique" RELATED [IUPAC:] synonym: "acides carboxyliques" RELATED [IUPAC] synonym: "acides carboxyliques" RELATED [IUPAC:] synonym: "acido carboxilico" RELATED [IUPAC:] synonym: "acido carboxilico" RELATED [IUPAC] synonym: "acidos carboxilicos" RELATED [IUPAC] synonym: "acidos carboxilicos" RELATED [IUPAC:] synonym: "Carbonsaeure" RELATED [ChEBI] synonym: "Carbonsaeure" RELATED [ChEBI:] synonym: "Carbonsaeuren" RELATED [ChEBI:] synonym: "Carbonsaeuren" RELATED [ChEBI] synonym: "carboxylic acid" EXACT IUPAC_NAME [IUPAC:] synonym: "carboxylic acid" EXACT IUPAC_NAME [IUPAC] synonym: "carboxylic acids" EXACT IUPAC_NAME [IUPAC:] synonym: "carboxylic acids" EXACT IUPAC_NAME [IUPAC] synonym: "CHO2R" RELATED FORMULA [ChEBI:] synonym: "Karbonsaeure" RELATED [ChEBI] synonym: "Karbonsaeure" RELATED [ChEBI:] synonym: "OC([*])=O" RELATED SMILES [ChEBI:] synonym: "RC(=O)OH" RELATED [IUPAC] synonym: "RC(=O)OH" RELATED [IUPAC:] xref: PMID:17147560 {source="Europe PMC"} xref: PMID:18433345 {source="Europe PMC"} xref: Wikipedia:Carboxylic_acid is_a: CHEBI:35605 ! carbon oxoacid is_a: CHEBI:36586 ! carbonyl compound is_a: CHEBI:64709 ! organic acid relationship: has_part CHEBI:46883 ! carboxy group relationship: is_conjugate_acid_of CHEBI:29067 ! carboxylic acid anion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CHO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "45.01740" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "44.99765" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "OC([*])=O" xsd:string [Term] id: CHEBI:33579 name: main group molecular entity namespace: chebi_ontology def: "A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table." [ANON:ANON] subset: 3_STAR synonym: "main group compounds" RELATED [ChEBI:] synonym: "main group compounds" RELATED [ChEBI] synonym: "main group molecular entities" RELATED [ChEBI:] synonym: "main group molecular entities" RELATED [ChEBI] is_a: CHEBI:23367 ! molecular entity relationship: has_part CHEBI:33318 ! main group element atom [Term] id: CHEBI:33582 name: carbon group molecular entity namespace: chebi_ontology subset: 3_STAR synonym: "carbon group molecular entities" RELATED [ChEBI:] synonym: "carbon group molecular entities" RELATED [ChEBI] synonym: "carbon group molecular entity" EXACT [ChEBI] synonym: "carbon group molecular entity" EXACT [ChEBI:] is_a: CHEBI:33675 ! p-block molecular entity relationship: has_part CHEBI:33306 ! carbon group element atom [Term] id: CHEBI:33595 name: cyclic compound namespace: chebi_ontology def: "Any molecule that consists of a series of atoms joined together to form a ring." [] subset: 3_STAR synonym: "cyclic compounds" RELATED [ChEBI] synonym: "cyclic compounds" RELATED [ChEBI:] xref: Wikipedia:Cyclic_compound is_a: CHEBI:25367 ! molecule [Term] id: CHEBI:33608 name: hydrogen molecular entity namespace: chebi_ontology subset: 3_STAR synonym: "hydrogen compounds" RELATED [ChEBI:] synonym: "hydrogen compounds" RELATED [ChEBI] synonym: "hydrogen molecular entities" RELATED [ChEBI] synonym: "hydrogen molecular entities" RELATED [ChEBI:] is_a: CHEBI:33674 ! s-block molecular entity relationship: has_part CHEBI:49637 ! hydrogen atom [Term] id: CHEBI:33635 name: polycyclic compound namespace: chebi_ontology subset: 3_STAR synonym: "polycyclic compounds" RELATED [ChEBI] is_a: CHEBI:33595 ! cyclic compound [Term] id: CHEBI:33636 name: bicyclic compound namespace: chebi_ontology def: "A molecule that features two fused rings." [ANON:ANON] subset: 3_STAR synonym: "bicyclic compounds" RELATED [ChEBI] synonym: "bicyclic compounds" RELATED [ChEBI:] is_a: CHEBI:33595 ! cyclic compound [Term] id: CHEBI:33655 name: aromatic compound namespace: chebi_ontology def: "A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character." [ANON:ANON] subset: 3_STAR synonym: "aromatic compounds" EXACT IUPAC_NAME [IUPAC:] synonym: "aromatic compounds" EXACT IUPAC_NAME [IUPAC] synonym: "aromatic molecular entity" EXACT IUPAC_NAME [IUPAC] synonym: "aromatic molecular entity" EXACT IUPAC_NAME [IUPAC:] synonym: "aromatics" RELATED [ChEBI] synonym: "aromatics" RELATED [ChEBI:] synonym: "aromatische Verbindungen" RELATED [ChEBI:] synonym: "aromatische Verbindungen" RELATED [ChEBI] is_a: CHEBI:33595 ! cyclic compound [Term] id: CHEBI:33659 name: organic aromatic compound namespace: chebi_ontology subset: 3_STAR synonym: "organic aromatic compounds" RELATED [ChEBI] synonym: "organic aromatic compounds" RELATED [ChEBI:] is_a: CHEBI:33655 ! aromatic compound is_a: CHEBI:33832 ! organic cyclic compound [Term] id: CHEBI:33661 name: monocyclic compound namespace: chebi_ontology subset: 3_STAR synonym: "monocyclic compounds" RELATED [ChEBI] synonym: "monocyclic compounds" RELATED [ChEBI:] is_a: CHEBI:33595 ! cyclic compound [Term] id: CHEBI:33670 name: heteromonocyclic compound namespace: chebi_ontology subset: 3_STAR synonym: "heteromonocyclic compound" EXACT IUPAC_NAME [IUPAC] synonym: "heteromonocyclic compound" EXACT IUPAC_NAME [IUPAC:] synonym: "heteromonocyclic compounds" EXACT IUPAC_NAME [IUPAC] synonym: "heteromonocyclic compounds" EXACT IUPAC_NAME [IUPAC:] is_a: CHEBI:33661 ! monocyclic compound is_a: CHEBI:5686 ! heterocyclic compound [Term] id: CHEBI:33671 name: heteropolycyclic compound namespace: chebi_ontology def: "A polycyclic compound in which at least one of the rings contains at least one non-carbon atom." [] subset: 3_STAR synonym: "heteropolycyclic compounds" EXACT IUPAC_NAME [IUPAC] synonym: "polyheterocyclic compounds" RELATED [ChEBI] is_a: CHEBI:33635 ! polycyclic compound is_a: CHEBI:5686 ! heterocyclic compound [Term] id: CHEBI:33672 name: heterobicyclic compound namespace: chebi_ontology def: "A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom." [ANON:ANON] subset: 3_STAR synonym: "heterobicyclic compounds" EXACT IUPAC_NAME [IUPAC] synonym: "heterobicyclic compounds" EXACT IUPAC_NAME [IUPAC:] is_a: CHEBI:33636 ! bicyclic compound is_a: CHEBI:5686 ! heterocyclic compound [Term] id: CHEBI:33674 name: s-block molecular entity namespace: chebi_ontology def: "An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element." [ANON:ANON] subset: 3_STAR synonym: "s-block compounds" RELATED [ChEBI] synonym: "s-block compounds" RELATED [ChEBI:] synonym: "s-block molecular entities" RELATED [ChEBI] synonym: "s-block molecular entities" RELATED [ChEBI:] synonym: "s-block molecular entity" EXACT [ChEBI:] synonym: "s-block molecular entity" EXACT [ChEBI] is_a: CHEBI:33579 ! main group molecular entity relationship: has_part CHEBI:33559 ! s-block element atom [Term] id: CHEBI:33675 name: p-block molecular entity namespace: chebi_ontology def: "A main group molecular entity that contains one or more atoms of a p-block element." [] def: "A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element." [ANON:ANON] subset: 3_STAR synonym: "p-block compounds" RELATED [ChEBI] synonym: "p-block compounds" RELATED [ChEBI:] synonym: "p-block molecular entities" RELATED [ChEBI:] synonym: "p-block molecular entities" RELATED [ChEBI] synonym: "p-block molecular entitiy" RELATED [ChEBI] synonym: "p-block molecular entitiy" RELATED [ChEBI:] is_a: CHEBI:33579 ! main group molecular entity relationship: has_part CHEBI:33560 ! p-block element atom [Term] id: CHEBI:33692 name: hydrides namespace: chebi_ontology def: "Hydrides are chemical compounds of hydrogen with other chemical elements." [] subset: 3_STAR is_a: CHEBI:33608 ! hydrogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:33694 name: biomacromolecule namespace: chebi_ontology def: "A macromolecule formed by a living organism." [] subset: 3_STAR synonym: "biomacromolecules" RELATED [ChEBI] synonym: "biopolymer" EXACT IUPAC_NAME [IUPAC] synonym: "Biopolymere" RELATED [ChEBI] synonym: "biopolymers" RELATED [ChEBI] is_a: CHEBI:33839 ! macromolecule is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33695 name: information biomacromolecule namespace: chebi_ontology subset: 3_STAR synonym: "genetically encoded biomacromolecules" RELATED [ChEBI] synonym: "genetically encoded biopolymers" RELATED [ChEBI] synonym: "information biomacromolecules" RELATED [ChEBI] synonym: "information biopolymers" RELATED [ChEBI] synonym: "information macromolecule" RELATED [ChEBI] synonym: "information macromolecules" RELATED [ChEBI] is_a: CHEBI:33694 ! biomacromolecule [Term] id: CHEBI:33696 name: nucleic acid namespace: chebi_ontology def: "A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid." [] subset: 3_STAR synonym: "acide nucleique" RELATED [ChEBI] synonym: "acides nucleiques" RELATED [ChEBI] synonym: "acido nucleico" RELATED [ChEBI] synonym: "acidos nucleicos" RELATED [ChEBI] synonym: "NA" RELATED [ChEBI] synonym: "nucleic acids" EXACT IUPAC_NAME [IUPAC] synonym: "Nukleinsaeure" RELATED [ChEBI] synonym: "Nukleinsaeuren" RELATED [ChEBI] is_a: CHEBI:15986 ! polynucleotide relationship: has_part CHEBI:33791 ! canonical nucleoside residue relationship: has_part CHEBI:50297 ! canonical nucleotide residue [Term] id: CHEBI:33697 name: ribonucleic acid namespace: chebi_ontology def: "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins." [] subset: 3_STAR synonym: "pentosenucleic acids" RELATED [ChemIDplus] synonym: "ribonucleic acid" EXACT [IUPAC] synonym: "ribonucleic acids" EXACT IUPAC_NAME [IUPAC] synonym: "ribonucleic acids" RELATED [ChEBI] synonym: "Ribonukleinsaeure" RELATED [ChEBI] synonym: "ribose nucleic acid" RELATED [ChEBI] synonym: "RNA" RELATED [UniProt] synonym: "RNA" RELATED [IUPAC] synonym: "RNS" RELATED [ChEBI] synonym: "yeast nucleic acid" RELATED [ChEBI] xref: CAS:63231-63-0 {source="ChemIDplus"} is_a: CHEBI:33696 ! nucleic acid relationship: has_part CHEBI:33792 ! canonical ribonucleoside residue relationship: has_part CHEBI:50299 ! canonical ribonucleotide residue [Term] id: CHEBI:33700 name: proteinogenic amino-acid residue namespace: chebi_ontology subset: 3_STAR synonym: "canonical amino-acid residue" RELATED [ChEBI] synonym: "canonical amino-acid residues" RELATED [ChEBI] synonym: "common amino acid residues" RELATED [ChEBI] synonym: "proteinogenic amino-acid residues" RELATED [ChEBI] synonym: "standard amino acid residues" RELATED [ChEBI] synonym: "standard amino-acid residues" RELATED [ChEBI] is_a: CHEBI:33710 ! alpha-amino-acid residue [Term] id: CHEBI:33702 name: polyatomic cation namespace: chebi_ontology def: "A cation consisting of more than one atom." [ANON:ANON] subset: 3_STAR synonym: "polyatomic cations" RELATED [ChEBI:] synonym: "polyatomic cations" RELATED [ChEBI] is_a: CHEBI:36358 ! polyatomic ion is_a: CHEBI:36916 ! cation [Term] id: CHEBI:33704 name: alpha-amino acid namespace: chebi_ontology alt_id: CHEBI:10208 alt_id: CHEBI:13779 alt_id: CHEBI:22442 alt_id: CHEBI:2642 def: "An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group." [] subset: 3_STAR synonym: "alpha-amino acid" EXACT IUPAC_NAME [IUPAC:] synonym: "alpha-amino acid" EXACT IUPAC_NAME [IUPAC] synonym: "alpha-amino acids" RELATED [JCBN:] synonym: "alpha-amino acids" RELATED [ChEBI] synonym: "alpha-amino acids" RELATED [ChEBI:] synonym: "alpha-amino acids" RELATED [JCBN] synonym: "alpha-amino carboxylic acids" RELATED [IUPAC:] synonym: "alpha-amino carboxylic acids" RELATED [IUPAC] synonym: "Amino acid" RELATED [KEGG_COMPOUND] synonym: "Amino acid" RELATED [KEGG COMPOUND:] synonym: "Amino acids" RELATED [KEGG_COMPOUND] synonym: "an alpha-amino acid" RELATED [UniProt:] xref: KEGG:C00045 xref: KEGG:C05167 is_a: CHEBI:33709 ! amino acid relationship: is_conjugate_acid_of CHEBI:33558 ! alpha-amino-acid anion relationship: is_tautomer_of CHEBI:78608 ! alpha-amino acid zwitterion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "74.05870" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "74.02420" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "NC([*])C(O)=O" xsd:string [Term] id: CHEBI:33707 name: gamma-amino acid namespace: chebi_ontology def: "A non-proteinogenic amino-acid in which the amino group is located on the carbon atom at the position gamma to the carboxy group." [] subset: 3_STAR synonym: "gamma-amino acid" EXACT [ChEBI] synonym: "gamma-amino acid" EXACT [ChEBI:] synonym: "gamma-amino acids" RELATED [ChEBI:] synonym: "gamma-amino acids" RELATED [ChEBI] is_a: CHEBI:83820 ! non-proteinogenic amino acid relationship: is_conjugate_acid_of CHEBI:71666 ! gamma-amino acid anion [Term] id: CHEBI:33708 name: amino-acid residue namespace: chebi_ontology def: "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue." [] subset: 3_STAR synonym: "amino acid residue" RELATED [ChEBI] synonym: "amino-acid residue" EXACT IUPAC_NAME [IUPAC] synonym: "amino-acid residues" RELATED [JCBN] is_a: CHEBI:33247 ! organic group relationship: is_substituent_group_from CHEBI:33709 ! amino acid [Term] id: CHEBI:33709 name: amino acid namespace: chebi_ontology alt_id: CHEBI:13815 alt_id: CHEBI:22477 def: "A carboxylic acid containing one or more amino groups." [ANON:ANON] subset: 3_STAR synonym: "amino acids" RELATED [ChEBI] synonym: "amino acids" RELATED [ChEBI:] synonym: "Aminocarbonsaeure" RELATED [ChEBI:] synonym: "Aminocarbonsaeure" RELATED [ChEBI] synonym: "Aminokarbonsaeure" RELATED [ChEBI] synonym: "Aminokarbonsaeure" RELATED [ChEBI:] synonym: "Aminosaeure" RELATED [ChEBI] synonym: "Aminosaeure" RELATED [ChEBI:] xref: Wikipedia:Amino_acid is_a: CHEBI:33575 ! carboxylic acid is_a: CHEBI:50047 ! organic amino compound relationship: is_conjugate_acid_of CHEBI:37022 ! amino-acid anion [Term] id: CHEBI:33710 name: alpha-amino-acid residue namespace: chebi_ontology subset: 3_STAR synonym: "alpha-amino-acid residues" RELATED [ChEBI] is_a: CHEBI:33708 ! amino-acid residue relationship: is_substituent_group_from CHEBI:33704 ! alpha-amino acid [Term] id: CHEBI:33791 name: canonical nucleoside residue namespace: chebi_ontology subset: 3_STAR synonym: "canonical nucleoside residues" RELATED [ChEBI] synonym: "common nucleoside residues" RELATED [CBN] synonym: "nucleoside residue" RELATED [CBN] synonym: "standard nucleoside residues" RELATED [ChEBI] is_a: CHEBI:50320 ! nucleoside residue [Term] id: CHEBI:33792 name: canonical ribonucleoside residue namespace: chebi_ontology subset: 3_STAR synonym: "canonical ribonucleoside residues" RELATED [ChEBI] synonym: "common ribonucleoside residue" RELATED [CBN] synonym: "common ribonucleoside residues" RELATED [CBN] synonym: "N" RELATED [CBN] synonym: "Nuc" RELATED [CBN] synonym: "standard ribonucleoside residues" RELATED [ChEBI] is_a: CHEBI:33791 ! canonical nucleoside residue [Term] id: CHEBI:33822 name: organic hydroxy compound namespace: chebi_ontology alt_id: CHEBI:64710 def: "An organic compound having at least one hydroxy group attached to a carbon atom." [ANON:ANON] subset: 3_STAR synonym: "hydroxy compounds" EXACT IUPAC_NAME [IUPAC] synonym: "hydroxy compounds" EXACT IUPAC_NAME [IUPAC:] synonym: "organic alcohol" RELATED [ChEBI] synonym: "organic hydroxy compounds" RELATED [ChEBI:] synonym: "organic hydroxy compounds" RELATED [ChEBI] is_a: CHEBI:24651 ! hydroxides is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33832 name: organic cyclic compound namespace: chebi_ontology def: "Any organic molecule that consists of atoms connected in the form of a ring." [] subset: 3_STAR synonym: "organic cyclic compounds" RELATED [ChEBI:] synonym: "organic cyclic compounds" RELATED [ChEBI] is_a: CHEBI:33595 ! cyclic compound is_a: CHEBI:72695 ! organic molecule [Term] id: CHEBI:33833 name: heteroarene namespace: chebi_ontology def: "A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2)." [ANON:ANON] subset: 3_STAR synonym: "hetarenes" RELATED [IUPAC:] synonym: "hetarenes" RELATED [IUPAC] synonym: "heteroarenes" EXACT IUPAC_NAME [IUPAC:] synonym: "heteroarenes" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:24532 ! organic heterocyclic compound is_a: CHEBI:33659 ! organic aromatic compound [Term] id: CHEBI:33839 name: macromolecule namespace: chebi_ontology def: "A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [] subset: 3_STAR synonym: "macromolecule" EXACT IUPAC_NAME [IUPAC] synonym: "macromolecules" RELATED [ChEBI] synonym: "polymer" RELATED [ChEBI] synonym: "polymer molecule" RELATED [IUPAC] synonym: "polymers" RELATED [ChEBI] xref: Wikipedia:Macromolecule is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:33853 name: phenols namespace: chebi_ontology alt_id: CHEBI:13664 alt_id: CHEBI:13825 alt_id: CHEBI:25969 alt_id: CHEBI:2857 def: "Compounds having one or more hydroxy groups attached to a benzene or other arene ring." [ANON:ANON] def: "Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring." [] subset: 3_STAR synonym: "a phenol" RELATED [UniProt] synonym: "arenols" RELATED [IUPAC] synonym: "arenols" RELATED [IUPAC:] synonym: "Aryl alcohol" RELATED [KEGG COMPOUND:] synonym: "Aryl alcohol" RELATED [KEGG_COMPOUND] synonym: "aryl alcohol" RELATED [UniProt:] synonym: "phenols" EXACT IUPAC_NAME [IUPAC] synonym: "phenols" EXACT IUPAC_NAME [IUPAC:] xref: KEGG:C15584 xref: MetaCyc:Phenols xref: Wikipedia:Phenols is_a: CHEBI:33659 ! organic aromatic compound is_a: CHEBI:33822 ! organic hydroxy compound property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C6HOR5" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "89.072" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "89.00274" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C1(=C(C(=C(C(=C1*)*)*)*)*)O" xsd:string [Term] id: CHEBI:33893 name: reagent namespace: chebi_ontology def: "A substance used in a chemical reaction to detect, measure, examine, or produce other substances." [] subset: 3_STAR synonym: "reactif" RELATED [IUPAC] synonym: "reactivo" RELATED [IUPAC] synonym: "reagent" EXACT IUPAC_NAME [IUPAC] synonym: "reagents" RELATED [ChEBI] is_a: CHEBI:33232 ! application [Term] id: CHEBI:33937 name: macronutrient namespace: chebi_ontology def: "Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals." [] subset: 3_STAR synonym: "macronutrients" RELATED [ChEBI] is_a: CHEBI:33284 ! nutrient [Term] id: CHEBI:350546 name: serotonin(1+) namespace: chebi_ontology def: "An ammonium ion that is the conjugate acid of serotonin; major species at pH 7.3." [] subset: 3_STAR synonym: "2-(5-hydroxy-1H-indol-3-yl)ethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "serotonin" RELATED [UniProt] synonym: "serotonin cation" RELATED [ChEBI] is_a: CHEBI:35274 ! ammonium ion derivative relationship: is_conjugate_acid_of CHEBI:28790 ! serotonin relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C10H13N2O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2/p+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QZAYGJVTTNCVMB-UHFFFAOYSA-O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "177.22250" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "177.10224" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]CCc1c[nH]c2ccc(O)cc12" xsd:string [Term] id: CHEBI:35106 name: nitrogen hydride namespace: chebi_ontology subset: 3_STAR synonym: "nitrogen hydrides" RELATED [ChEBI] is_a: CHEBI:35881 ! pnictogen hydride is_a: CHEBI:51143 ! nitrogen molecular entity [Term] id: CHEBI:35107 name: azane namespace: chebi_ontology def: "Saturated acyclic nitrogen hydrides having the general formula NnHn+2." [] subset: 3_STAR synonym: "azanes" RELATED [ChEBI] is_a: CHEBI:35106 ! nitrogen hydride [Term] id: CHEBI:35222 name: inhibitor namespace: chebi_ontology def: "A substance that diminishes the rate of a chemical reaction." [] subset: 3_STAR synonym: "inhibidor" RELATED [ChEBI] synonym: "inhibiteur" RELATED [ChEBI] synonym: "inhibitor" EXACT IUPAC_NAME [IUPAC] synonym: "inhibitors" RELATED [ChEBI] is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:35238 name: amino acid zwitterion namespace: chebi_ontology def: "The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group." [] subset: 3_STAR synonym: "amino acid zwitterion" EXACT [ChEBI] is_a: CHEBI:27369 ! zwitterion [Term] id: CHEBI:35267 name: quaternary ammonium ion namespace: chebi_ontology alt_id: CHEBI:26470 alt_id: CHEBI:8693 def: "A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually hydrocarbyl) groups." [ANON:ANON] def: "A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups." [] subset: 3_STAR synonym: "[*][N+]([*])([*])[*]" RELATED SMILES [ChEBI:] synonym: "a quaternary ammonium" RELATED [UniProt] synonym: "NR4" RELATED FORMULA [ChEBI:] synonym: "Quaternary amine" RELATED [KEGG COMPOUND:] synonym: "Quaternary amine" RELATED [KEGG_COMPOUND] synonym: "quaternary ammonium ion" EXACT IUPAC_NAME [IUPAC] synonym: "quaternary ammonium ion" EXACT IUPAC_NAME [IUPAC:] synonym: "quaternary ammonium ions" RELATED [ChEBI:] synonym: "quaternary ammonium ions" RELATED [ChEBI] xref: KEGG:C06703 is_a: CHEBI:25697 ! organic cation is_a: CHEBI:35274 ! ammonium ion derivative property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "NR4" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "14.00670" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "14.00307" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[*][N+]([*])([*])[*]" xsd:string [Term] id: CHEBI:35274 name: ammonium ion derivative namespace: chebi_ontology def: "A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc)." [] def: "Ammonium, NH4(+), and derivatives formed by substitution by univalent groups." [ANON:ANON] subset: 3_STAR synonym: "ammonium ion derivatives" RELATED [ChEBI] synonym: "ammonium ions" RELATED [ChEBI:] synonym: "azanium ion derivative" RELATED [ChEBI] synonym: "azanium ion derivatives" RELATED [ChEBI] synonym: "azanium ions" RELATED [ChEBI:] is_a: CHEBI:33702 ! polyatomic cation is_a: CHEBI:51143 ! nitrogen molecular entity relationship: has_parent_hydride CHEBI:28938 ! ammonium [Term] id: CHEBI:35287 name: acylcholine namespace: chebi_ontology alt_id: CHEBI:13245 alt_id: CHEBI:22227 alt_id: CHEBI:2463 def: "A choline ester formed from choline and a carboxylic acid." [ANON:ANON] subset: 3_STAR synonym: "acylcholine" EXACT [UniProt:] synonym: "acylcholines" RELATED [ChEBI:] synonym: "acylcholines" RELATED [ChEBI] synonym: "an acylcholine" RELATED [UniProt] synonym: "C6H13NO2R" RELATED FORMULA [KEGG COMPOUND:] synonym: "C[N+](C)(C)CCOC([*])=O" RELATED SMILES [ChEBI:] xref: KEGG:C01777 is_a: CHEBI:35267 ! quaternary ammonium ion property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C6H13NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "131.17290" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "131.09463" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C[N+](C)(C)CCOC([*])=O" xsd:string [Term] id: CHEBI:35352 name: organonitrogen compound namespace: chebi_ontology def: "Any heteroorganic entity containing at least one carbon-nitrogen bond." [ANON:ANON] subset: 3_STAR synonym: "organonitrogen compounds" EXACT IUPAC_NAME [IUPAC:] synonym: "organonitrogen compounds" EXACT IUPAC_NAME [IUPAC] synonym: "organonitrogens" RELATED [ChEBI:] synonym: "organonitrogens" RELATED [ChEBI] is_a: CHEBI:33285 ! heteroorganic entity is_a: CHEBI:51143 ! nitrogen molecular entity [Term] id: CHEBI:35366 name: fatty acid namespace: chebi_ontology alt_id: CHEBI:13633 alt_id: CHEBI:24024 alt_id: CHEBI:4984 def: "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax." [ANON:ANON] def: "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids." [] subset: 3_STAR synonym: "acide gras" RELATED [ChEBI:] synonym: "acide gras" RELATED [ChEBI] synonym: "acides gras" RELATED [ChemIDplus] synonym: "acides gras" RELATED [ChemIDplus:] synonym: "acido graso" RELATED [ChEBI:] synonym: "acido graso" RELATED [ChEBI] synonym: "acidos grasos" RELATED [ChEBI:] synonym: "acidos grasos" RELATED [ChEBI] synonym: "CHO2R" RELATED FORMULA [KEGG COMPOUND:] synonym: "Fatty acid" EXACT [KEGG COMPOUND:] synonym: "Fatty acid" EXACT [KEGG_COMPOUND] synonym: "fatty acids" EXACT IUPAC_NAME [IUPAC] synonym: "fatty acids" EXACT IUPAC_NAME [IUPAC:] synonym: "fatty acids" RELATED [ChEBI:] synonym: "fatty acids" RELATED [ChEBI] synonym: "Fettsaeure" RELATED [ChEBI:] synonym: "Fettsaeure" RELATED [ChEBI] synonym: "Fettsaeuren" RELATED [ChEBI:] synonym: "Fettsaeuren" RELATED [ChEBI] synonym: "OC([*])=O" RELATED SMILES [ChEBI:] xref: KEGG:C00162 xref: PMID:14287444 {source="Europe PMC"} xref: PMID:14300208 {source="Europe PMC"} xref: PMID:14328676 {source="Europe PMC"} xref: Wikipedia:Fatty_acid is_a: CHEBI:18059 ! lipid is_a: CHEBI:25384 ! monocarboxylic acid relationship: is_conjugate_acid_of CHEBI:28868 ! fatty acid anion property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CHO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "45.01740" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "44.99765" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "OC([*])=O" xsd:string [Term] id: CHEBI:35406 name: oxoanion namespace: chebi_ontology alt_id: CHEBI:33274 alt_id: CHEBI:33436 def: "An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen." [] subset: 3_STAR synonym: "oxoacid anions" RELATED [ChEBI] synonym: "oxoanion" EXACT [ChEBI] synonym: "oxoanions" RELATED [ChEBI] is_a: CHEBI:25741 ! oxide is_a: CHEBI:33273 ! polyatomic anion [Term] id: CHEBI:35522 name: beta-adrenergic agonist namespace: chebi_ontology def: "An agent that selectively binds to and activates beta-adrenergic receptors." [] subset: 3_STAR synonym: "beta-adrenergic agonists" RELATED [ChEBI] synonym: "beta-adrenergic receptor agonist" RELATED [ChEBI] synonym: "beta-adrenoceptor agonists" RELATED [IUPHAR] is_a: CHEBI:37886 ! adrenergic agonist is_a: CHEBI:48540 ! beta-adrenergic drug [Term] id: CHEBI:35524 name: sympathomimetic agent namespace: chebi_ontology def: "A drug that mimics the effects of stimulating postganglionic adrenergic sympathetic nerves. Included in this class are drugs that directly stimulate adrenergic receptors and drugs that act indirectly by provoking the release of adrenergic transmitters." [] subset: 3_STAR synonym: "sympathomimetic" RELATED [ChEBI] synonym: "sympathomimetics" RELATED [ChEBI] is_a: CHEBI:37962 ! adrenergic agent [Term] id: CHEBI:35554 name: cardiovascular drug namespace: chebi_ontology def: "A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume." [] subset: 3_STAR synonym: "cardiovascular agent" RELATED [ChEBI] synonym: "cardiovascular drugs" RELATED [ChEBI] is_a: CHEBI:23888 ! drug [Term] id: CHEBI:35605 name: carbon oxoacid namespace: chebi_ontology subset: 3_STAR synonym: "carbon oxoacids" RELATED [ChEBI] synonym: "oxoacids of carbon" RELATED [ChEBI] is_a: CHEBI:24833 ! oxoacid is_a: CHEBI:36963 ! organooxygen compound [Term] id: CHEBI:35620 name: vasodilator agent namespace: chebi_ontology def: "A drug used to cause dilation of the blood vessels." [] subset: 3_STAR synonym: "vasodilator" RELATED [ChEBI] synonym: "vasodilator agents" RELATED [ChEBI] is_a: CHEBI:35554 ! cardiovascular drug [Term] id: CHEBI:35692 name: dicarboxylic acid namespace: chebi_ontology alt_id: CHEBI:23692 alt_id: CHEBI:36172 alt_id: CHEBI:4501 def: "Any carboxylic acid containing two carboxy groups." [] subset: 3_STAR synonym: "Dicarboxylic acid" EXACT [KEGG_COMPOUND] synonym: "dicarboxylic acids" RELATED [ChEBI] xref: KEGG:C02028 is_a: CHEBI:131927 ! dicarboxylic acids and O-substituted derivatives is_a: CHEBI:33575 ! carboxylic acid relationship: is_conjugate_acid_of CHEBI:35693 ! dicarboxylic acid anion [Term] id: CHEBI:35693 name: dicarboxylic acid anion namespace: chebi_ontology subset: 3_STAR synonym: "dicarboxylic acid anion" EXACT [ChEBI] synonym: "dicarboxylic acid anions" RELATED [ChEBI] is_a: CHEBI:29067 ! carboxylic acid anion relationship: is_conjugate_base_of CHEBI:35692 ! dicarboxylic acid [Term] id: CHEBI:35701 name: ester namespace: chebi_ontology alt_id: CHEBI:23960 alt_id: CHEBI:4859 def: "A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter." [ANON:ANON] subset: 3_STAR synonym: "Ester" EXACT [KEGG_COMPOUND] synonym: "Ester" EXACT [KEGG COMPOUND:] synonym: "esters" RELATED [ChEBI:] synonym: "esters" RELATED [ChEBI] xref: KEGG:C00287 xref: Wikipedia:Ester is_a: CHEBI:36963 ! organooxygen compound [Term] id: CHEBI:35757 name: monocarboxylic acid anion namespace: chebi_ontology alt_id: CHEBI:13657 alt_id: CHEBI:25382 alt_id: CHEBI:3407 def: "A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated." [] subset: 3_STAR synonym: "a monocarboxylate" RELATED [UniProt] synonym: "Carboxylate" RELATED [KEGG_COMPOUND] synonym: "Monocarboxylate" RELATED [KEGG_COMPOUND] synonym: "monocarboxylates" RELATED [ChEBI] synonym: "monocarboxylic acid anions" RELATED [ChEBI] xref: KEGG:C00060 is_a: CHEBI:29067 ! carboxylic acid anion relationship: is_conjugate_base_of CHEBI:25384 ! monocarboxylic acid property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "44.01000" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "43.98983" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-]C([*])=O" xsd:string [Term] id: CHEBI:35881 name: pnictogen hydride namespace: chebi_ontology subset: 3_STAR synonym: "pnictogen hydride" EXACT [ChEBI] synonym: "pnictogen hydrides" RELATED [ChEBI] is_a: CHEBI:33242 ! inorganic hydride is_a: CHEBI:33302 ! pnictogen molecular entity [Term] id: CHEBI:35942 name: neurotransmitter agent namespace: chebi_ontology def: "A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function." [] subset: 3_STAR synonym: "neurotransmitter agents" RELATED [ChEBI] is_a: CHEBI:23888 ! drug is_a: CHEBI:52210 ! pharmacological role [Term] id: CHEBI:36080 name: protein namespace: chebi_ontology alt_id: CHEBI:13677 alt_id: CHEBI:14911 def: "A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome." [] subset: 3_STAR synonym: "proteins" EXACT IUPAC_NAME [IUPAC] is_a: PR:000000001 ! protein equivalent_to: PR:000000001 ! protein [Term] id: CHEBI:36338 name: lepton namespace: chebi_ontology def: "Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin)." [] subset: 3_STAR synonym: "leptons" RELATED [ChEBI] is_a: CHEBI:33233 ! fundamental particle is_a: CHEBI:36340 ! fermion [Term] id: CHEBI:36339 name: baryon namespace: chebi_ontology def: "Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy)." [] subset: 3_STAR synonym: "baryons" RELATED [ChEBI] is_a: CHEBI:36340 ! fermion is_a: CHEBI:36344 ! hadron [Term] id: CHEBI:36340 name: fermion namespace: chebi_ontology def: "Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi." [] subset: 3_STAR synonym: "fermion" EXACT IUPAC_NAME [IUPAC] synonym: "fermions" RELATED [ChEBI] is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:36342 name: subatomic particle namespace: chebi_ontology def: "A particle smaller than an atom." [] subset: 3_STAR synonym: "subatomic particles" RELATED [ChEBI] xref: Wikipedia:Subatomic_particle [Term] id: CHEBI:36343 name: composite particle namespace: chebi_ontology def: "A subatomic particle known to have substructure (i.e. consisting of smaller particles)." [] subset: 3_STAR synonym: "composite particles" RELATED [ChEBI] is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:36344 name: hadron namespace: chebi_ontology def: "Hadron is a subatomic particle which experiences the strong force." [] subset: 3_STAR synonym: "hadrons" RELATED [ChEBI] is_a: CHEBI:36343 ! composite particle [Term] id: CHEBI:36347 name: nuclear particle namespace: chebi_ontology def: "A nucleus or any of its constituents in any of their energy states." [] subset: 3_STAR synonym: "nuclear particle" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:36342 ! subatomic particle [Term] id: CHEBI:36357 name: polyatomic entity namespace: chebi_ontology def: "Any molecular entity consisting of more than one atom." [ANON:ANON] subset: 3_STAR synonym: "polyatomic entities" RELATED [ChEBI:] synonym: "polyatomic entities" RELATED [ChEBI] is_a: CHEBI:23367 ! molecular entity relationship: has_part CHEBI:24433 ! group [Term] id: CHEBI:36358 name: polyatomic ion namespace: chebi_ontology def: "An ion consisting of more than one atom." [ANON:ANON] subset: 3_STAR synonym: "polyatomic ions" RELATED [ChEBI] synonym: "polyatomic ions" RELATED [ChEBI:] is_a: CHEBI:24870 ! ion is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:36586 name: carbonyl compound namespace: chebi_ontology def: "Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives." [ANON:ANON] subset: 3_STAR synonym: "carbonyl compounds" EXACT IUPAC_NAME [IUPAC:] synonym: "carbonyl compounds" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:36587 ! organic oxo compound is_a: CHEBI:36963 ! organooxygen compound relationship: has_part CHEBI:23019 ! carbonyl group [Term] id: CHEBI:36587 name: organic oxo compound namespace: chebi_ontology def: "Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element." [ANON:ANON] subset: 3_STAR synonym: "organic oxo compounds" RELATED [ChEBI] synonym: "organic oxo compounds" RELATED [ChEBI:] synonym: "oxo compounds" EXACT IUPAC_NAME [IUPAC:] synonym: "oxo compounds" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:72695 ! organic molecule relationship: has_part CHEBI:46629 ! oxo group [Term] id: CHEBI:36914 name: inorganic ion namespace: chebi_ontology subset: 3_STAR synonym: "inorganic ions" RELATED [ChEBI] is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:24870 ! ion [Term] id: CHEBI:36915 name: inorganic cation namespace: chebi_ontology subset: 3_STAR synonym: "inorganic cations" RELATED [ChEBI] is_a: CHEBI:36914 ! inorganic ion is_a: CHEBI:36916 ! cation [Term] id: CHEBI:36916 name: cation namespace: chebi_ontology alt_id: CHEBI:23058 alt_id: CHEBI:3473 def: "A monoatomic or polyatomic species having one or more elementary charges of the proton." [ANON:ANON] subset: 3_STAR synonym: "Cation" EXACT [KEGG_COMPOUND] synonym: "Cation" EXACT [KEGG COMPOUND:] synonym: "cation" EXACT IUPAC_NAME [IUPAC] synonym: "cation" EXACT [ChEBI:] synonym: "cation" EXACT [ChEBI] synonym: "cation" EXACT IUPAC_NAME [IUPAC:] synonym: "cationes" RELATED [ChEBI] synonym: "cationes" RELATED [ChEBI:] synonym: "cations" RELATED [ChEBI] synonym: "cations" RELATED [ChEBI:] synonym: "Kation" RELATED [ChEBI:] synonym: "Kation" RELATED [ChEBI] synonym: "Kationen" RELATED [ChEBI:] synonym: "Kationen" RELATED [ChEBI] xref: KEGG:C01373 is_a: CHEBI:24870 ! ion [Term] id: CHEBI:36962 name: organochalcogen compound namespace: chebi_ontology def: "An organochalcogen compound is a compound containing at least one carbon-chalcogen bond." [ANON:ANON] subset: 3_STAR synonym: "organochalcogen compound" EXACT [ChEBI] synonym: "organochalcogen compound" EXACT [ChEBI:] synonym: "organochalcogen compounds" RELATED [ChEBI] synonym: "organochalcogen compounds" RELATED [ChEBI:] is_a: CHEBI:33285 ! heteroorganic entity is_a: CHEBI:33304 ! chalcogen molecular entity [Term] id: CHEBI:36963 name: organooxygen compound namespace: chebi_ontology def: "An organochalcogen compound containing at least one carbon-oxygen bond." [ANON:ANON] subset: 3_STAR synonym: "organooxygen compound" EXACT [ChEBI:] synonym: "organooxygen compound" EXACT [ChEBI] synonym: "organooxygen compounds" RELATED [ChEBI] synonym: "organooxygen compounds" RELATED [ChEBI:] xref: PMID:17586126 {source="Europe PMC"} is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:36962 ! organochalcogen compound [Term] id: CHEBI:37022 name: amino-acid anion namespace: chebi_ontology subset: 3_STAR synonym: "amino acid anions" RELATED [ChEBI] synonym: "amino-acid anion" EXACT [ChEBI] synonym: "amino-acid anions" RELATED [ChEBI] is_a: CHEBI:29067 ! carboxylic acid anion is_a: CHEBI:35352 ! organonitrogen compound relationship: is_conjugate_base_of CHEBI:33709 ! amino acid [Term] id: CHEBI:37176 name: mononuclear parent hydride namespace: chebi_ontology subset: 3_STAR synonym: "mononuclear hydride" RELATED [ChEBI] synonym: "mononuclear hydrides" RELATED [IUPAC] synonym: "mononuclear parent hydrides" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:33692 ! hydrides [Term] id: CHEBI:37527 name: acid namespace: chebi_ontology alt_id: CHEBI:13800 alt_id: CHEBI:13801 alt_id: CHEBI:22209 alt_id: CHEBI:2426 def: "An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid)." [] subset: 3_STAR synonym: "Acid" EXACT [KEGG_COMPOUND] synonym: "acid" EXACT IUPAC_NAME [IUPAC] synonym: "acide" RELATED [IUPAC] synonym: "acido" RELATED [ChEBI] synonym: "acids" RELATED [ChEBI] synonym: "Saeure" RELATED [ChEBI] synonym: "Saeuren" RELATED [ChEBI] xref: KEGG:C00174 is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:37577 name: heteroatomic molecular entity namespace: chebi_ontology def: "A molecular entity consisting of two or more chemical elements." [ANON:ANON] subset: 3_STAR synonym: "chemical compound" RELATED [ChEBI] synonym: "chemical compound" RELATED [ChEBI:] synonym: "heteroatomic molecular entities" RELATED [ChEBI] synonym: "heteroatomic molecular entities" RELATED [ChEBI:] is_a: CHEBI:36357 ! polyatomic entity [Term] id: CHEBI:37622 name: carboxamide namespace: chebi_ontology alt_id: CHEBI:35354 alt_id: CHEBI:35355 def: "An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom." [ANON:ANON] subset: 3_STAR synonym: "[*]C(=O)N([*])[*]" RELATED SMILES [ChEBI:] synonym: "carboxamides" EXACT IUPAC_NAME [IUPAC:] synonym: "carboxamides" EXACT IUPAC_NAME [IUPAC] synonym: "carboxamides" RELATED [ChEBI] synonym: "carboxamides" RELATED [ChEBI:] synonym: "primary carboxamide" RELATED [ChEBI] synonym: "primary carboxamide" RELATED [ChEBI:] is_a: CHEBI:33256 ! primary amide is_a: CHEBI:35352 ! organonitrogen compound is_a: CHEBI:36963 ! organooxygen compound relationship: has_part CHEBI:23004 ! carbamoyl group property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CNOR3" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "42.01680" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "41.99799" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[*]C(=O)N([*])[*]" xsd:string [Term] id: CHEBI:37838 name: carboacyl group namespace: chebi_ontology def: "A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid." [] subset: 3_STAR synonym: "carboacyl groups" EXACT IUPAC_NAME [IUPAC] synonym: "carboxylic acyl group" EXACT IUPAC_NAME [IUPAC] synonym: "carboxylic acyl groups" RELATED [IUPAC] is_a: CHEBI:22221 ! acyl group relationship: is_substituent_group_from CHEBI:33575 ! carboxylic acid [Term] id: CHEBI:37886 name: adrenergic agonist namespace: chebi_ontology def: "An agent that selectively binds to and activates adrenergic receptors." [] subset: 3_STAR synonym: "adrenergic agonists" RELATED [ChEBI] synonym: "adrenergic receptor agonist" RELATED [ChEBI] synonym: "adrenoceptor agonists" RELATED [IUPHAR] synonym: "adrenomimetic" RELATED [ChEBI] synonym: "adrenomimetics" RELATED [ChEBI] is_a: CHEBI:37962 ! adrenergic agent [Term] id: CHEBI:37962 name: adrenergic agent namespace: chebi_ontology def: "Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter." [] subset: 3_STAR synonym: "adrenergic agents" RELATED [ChEBI] synonym: "adrenergic drug" RELATED [ChEBI] synonym: "adrenergic drugs" RELATED [ChEBI] synonym: "adrenergic neuron agents" RELATED [ChEBI] synonym: "adrenergics" RELATED [ChEBI] is_a: CHEBI:35942 ! neurotransmitter agent [Term] id: CHEBI:38101 name: organonitrogen heterocyclic compound namespace: chebi_ontology def: "Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms." [ANON:ANON] subset: 3_STAR synonym: "heterocyclic organonitrogen compounds" RELATED [ChEBI:] synonym: "heterocyclic organonitrogen compounds" RELATED [ChEBI] synonym: "organonitrogen heterocyclic compounds" RELATED [ChEBI] synonym: "organonitrogen heterocyclic compounds" RELATED [ChEBI:] is_a: CHEBI:24532 ! organic heterocyclic compound is_a: CHEBI:35352 ! organonitrogen compound [Term] id: CHEBI:38147 name: cardiotonic drug namespace: chebi_ontology def: "A drug that has a strengthening effect on the heart or that can increase cardiac output." [] subset: 3_STAR synonym: "cardiotonic drugs" RELATED [ChEBI] is_a: CHEBI:35554 ! cardiovascular drug [Term] id: CHEBI:38166 name: organic heteropolycyclic compound namespace: chebi_ontology alt_id: CHEBI:25429 alt_id: CHEBI:38075 subset: 3_STAR synonym: "organic heteropolycyclic compounds" RELATED [ChEBI] is_a: CHEBI:24532 ! organic heterocyclic compound is_a: CHEBI:33671 ! heteropolycyclic compound [Term] id: CHEBI:38179 name: monocyclic heteroarene namespace: chebi_ontology subset: 3_STAR synonym: "monocyclic heteroarenes" RELATED [ChEBI] is_a: CHEBI:33833 ! heteroarene [Term] id: CHEBI:38180 name: polycyclic heteroarene namespace: chebi_ontology subset: 3_STAR synonym: "polycyclic heteroarenes" RELATED [ChEBI] synonym: "polycyclic heteroarenes" RELATED [ChEBI:] is_a: CHEBI:33833 ! heteroarene [Term] id: CHEBI:38323 name: cholinergic drug namespace: chebi_ontology def: "Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons." [] subset: 3_STAR synonym: "cholinergic agent" RELATED [ChEBI] synonym: "cholinergic drugs" RELATED [ChEBI] synonym: "cholinomimetic" RELATED [ChEBI] is_a: CHEBI:35942 ! neurotransmitter agent [Term] id: CHEBI:38324 name: cholinergic agonist namespace: chebi_ontology def: "Any drug that binds to and activates cholinergic receptors." [] subset: 3_STAR synonym: "acetylcholine agonist" RELATED [ChEBI] synonym: "acetylcholine agonists" RELATED [ChEBI] synonym: "acetylcholine receptor agonist" RELATED [IUPHAR] synonym: "cholinergic agonists" RELATED [ChEBI] synonym: "cholinomimetic" RELATED [ChEBI] synonym: "cholinomimetics" RELATED [ChEBI] is_a: CHEBI:38323 ! cholinergic drug [Term] id: CHEBI:38325 name: muscarinic agonist namespace: chebi_ontology def: "Any drug that binds to and activates a muscarinic cholinergic receptor." [] subset: 3_STAR synonym: "muscarinic acetylcholine receptor agonist" RELATED [ChEBI] synonym: "muscarinic agonists" RELATED [ChEBI] synonym: "muscarinic cholinergic agonist" RELATED [ChEBI] synonym: "muscarinic cholinergic agonists" RELATED [ChEBI] is_a: CHEBI:38324 ! cholinergic agonist [Term] id: CHEBI:38631 name: aminoalkylindole namespace: chebi_ontology alt_id: CHEBI:22503 alt_id: CHEBI:24792 subset: 3_STAR synonym: "aminoalkylindoles" RELATED [ChEBI] is_a: CHEBI:24828 ! indoles [Term] id: CHEBI:38716 name: carboxylic acid dianion namespace: chebi_ontology def: "Any dianion containing at least one carboxy group." [] subset: 3_STAR synonym: "carboxylic acid dianion" EXACT [ChEBI] synonym: "carboxylic acid dianions" RELATED [ChEBI] is_a: CHEBI:29067 ! carboxylic acid anion [Term] id: CHEBI:38958 name: indole alkaloid namespace: chebi_ontology alt_id: CHEBI:24795 alt_id: CHEBI:5901 def: "An alkaloid containing an indole skeleton." [] subset: 3_STAR synonym: "Indole alkaloid" EXACT [KEGG_COMPOUND] synonym: "indole alkaloids" RELATED [ChEBI] xref: KEGG:C06073 xref: Wikipedia:Indole_alkaloid is_a: CHEBI:22315 ! alkaloid relationship: has_part CHEBI:73398 ! indole skeleton [Term] id: CHEBI:39141 name: Bronsted acid namespace: chebi_ontology def: "A molecular entity capable of donating a hydron to an acceptor (Bronsted base)." [] subset: 3_STAR synonym: "acide de Bronsted" RELATED [IUPAC] synonym: "Bronsted acid" EXACT IUPAC_NAME [IUPAC] synonym: "Bronsted-Saeure" RELATED [ChEBI] synonym: "donneur d'hydron" RELATED [IUPAC] synonym: "hydron donor" RELATED [IUPAC] is_a: CHEBI:17891 ! donor is_a: CHEBI:37527 ! acid [Term] id: CHEBI:39142 name: Bronsted base namespace: chebi_ontology def: "A molecular entity capable of accepting a hydron from a donor (Bronsted acid)." [] subset: 3_STAR synonym: "accepteur d'hydron" RELATED [IUPAC] synonym: "base de Bronsted" RELATED [IUPAC] synonym: "Bronsted base" EXACT IUPAC_NAME [IUPAC] synonym: "Bronsted-Base" RELATED [ChEBI] synonym: "hydron acceptor" RELATED [IUPAC] is_a: CHEBI:15339 ! acceptor is_a: CHEBI:22695 ! base [Term] id: CHEBI:39144 name: Lewis base namespace: chebi_ontology def: "A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct." [] subset: 3_STAR synonym: "base de Lewis" RELATED [IUPAC] synonym: "donneur d'une paire d'electrons" RELATED [ChEBI] synonym: "electron donor" RELATED [ChEBI] synonym: "Lewis base" EXACT IUPAC_NAME [IUPAC] synonym: "Lewis-Base" RELATED [ChEBI] is_a: CHEBI:17891 ! donor is_a: CHEBI:22695 ! base [Term] id: CHEBI:39418 name: straight-chain saturated fatty acid namespace: chebi_ontology def: "Any saturated fatty acid lacking a carbon side-chain." [ANON:ANON] def: "Any saturated fatty acid lacking a side-chain." [] subset: 3_STAR synonym: "straight-chain saturated fatty acid" EXACT [ChEBI:] synonym: "straight-chain saturated fatty acid" EXACT [ChEBI] synonym: "straight-chain saturated fatty acids" RELATED [ChEBI:] synonym: "straight-chain saturated fatty acids" RELATED [ChEBI] xref: PMID:15644336 {source="Europe PMC"} is_a: CHEBI:26607 ! saturated fatty acid is_a: CHEBI:59202 ! straight-chain fatty acid relationship: is_conjugate_acid_of CHEBI:58954 ! straight-chain saturated fatty acid anion [Term] id: CHEBI:43176 name: hydroxy group namespace: chebi_ontology alt_id: CHEBI:24706 alt_id: CHEBI:43171 subset: 3_STAR synonym: "-OH" RELATED [IUPAC] synonym: "hydroxy" EXACT IUPAC_NAME [IUPAC] synonym: "HYDROXY GROUP" EXACT [PDBeChem] synonym: "hydroxy group" EXACT [UniProt] synonym: "hydroxyl" RELATED [ChEBI] synonym: "hydroxyl group" RELATED [ChEBI] xref: PDBeChem:OH is_a: CHEBI:33246 ! inorganic group property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "HO" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "17.00734" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "17.00274" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "*O[H]" xsd:string [Term] id: CHEBI:46629 name: oxo group namespace: chebi_ontology alt_id: CHEBI:29353 alt_id: CHEBI:44607 subset: 3_STAR synonym: "=O" RELATED [IUPAC] synonym: "oxo" EXACT IUPAC_NAME [IUPAC] synonym: "OXO GROUP" EXACT [PDBeChem] xref: PDBeChem:O is_a: CHEBI:33246 ! inorganic group property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "15.99940" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "15.99491" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "O=*" xsd:string [Term] id: CHEBI:46787 name: solvent namespace: chebi_ontology def: "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." [] subset: 3_STAR synonym: "Loesungsmittel" RELATED [ChEBI] synonym: "solvant" RELATED [ChEBI] synonym: "solvents" RELATED [ChEBI] xref: Wikipedia:Solvent is_a: CHEBI:33232 ! application is_a: CHEBI:51086 ! chemical role [Term] id: CHEBI:46883 name: carboxy group namespace: chebi_ontology alt_id: CHEBI:23025 alt_id: CHEBI:41420 subset: 3_STAR synonym: "-C(O)OH" RELATED [IUPAC] synonym: "-CO2H" RELATED [ChEBI] synonym: "-COOH" RELATED [IUPAC] synonym: "carboxy" EXACT IUPAC_NAME [IUPAC] synonym: "CARBOXY GROUP" EXACT [PDBeChem] synonym: "carboxyl group" RELATED [ChEBI] xref: PDBeChem:FMT is_a: CHEBI:33249 ! organyl group property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CHO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "45.01744" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "44.99765" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "*C(=O)O" xsd:string [Term] id: CHEBI:47622 name: acetate ester namespace: chebi_ontology alt_id: CHEBI:13244 alt_id: CHEBI:13799 alt_id: CHEBI:22189 alt_id: CHEBI:2406 def: "Any carboxylic ester where the carboxylic acid component is acetic acid." [ANON:ANON] subset: 3_STAR synonym: "acetate" RELATED [ChEBI] synonym: "acetate" RELATED [ChEBI:] synonym: "acetate esters" RELATED [ChEBI:] synonym: "acetate esters" RELATED [ChEBI] synonym: "acetates" RELATED [ChEBI:] synonym: "acetates" RELATED [ChEBI] synonym: "Acetic ester" RELATED [KEGG COMPOUND:] synonym: "Acetic ester" RELATED [KEGG_COMPOUND] synonym: "Acetyl ester" RELATED [KEGG_COMPOUND] synonym: "Acetyl ester" RELATED [KEGG COMPOUND:] synonym: "acetyl ester" RELATED [UniProt:] synonym: "acetyl esters" RELATED [ChEBI] synonym: "acetyl esters" RELATED [ChEBI:] synonym: "an acetyl ester" RELATED [UniProt] synonym: "C2H3O2R" RELATED FORMULA [KEGG COMPOUND:] xref: KEGG:C01883 xref: Wikipedia:Acetate#Esters is_a: CHEBI:33308 ! carboxylic ester relationship: has_functional_parent CHEBI:15366 ! acetic acid property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H3O2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "59.04400" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "59.01330" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "CC(=O)O[*]" xsd:string [Term] id: CHEBI:48354 name: polar solvent namespace: chebi_ontology def: "A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds." [] subset: 3_STAR synonym: "polar solvent" EXACT IUPAC_NAME [IUPAC] synonym: "polar solvents" RELATED [ChEBI] is_a: CHEBI:46787 ! solvent [Term] id: CHEBI:48356 name: protic solvent namespace: chebi_ontology def: "A polar solvent that is capable of acting as a hydron (proton) donor." [] subset: 3_STAR synonym: "protogenic solvent" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:39141 ! Bronsted acid is_a: CHEBI:48354 ! polar solvent [Term] id: CHEBI:48540 name: beta-adrenergic drug namespace: chebi_ontology def: "Any of the drugs that act on beta-adrenergic receptors." [] subset: 3_STAR synonym: "beta-adrenergic drugs" RELATED [ChEBI] is_a: CHEBI:37962 ! adrenergic agent [Term] id: CHEBI:48560 name: dopaminergic agent namespace: chebi_ontology def: "A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons." [] subset: 3_STAR synonym: "dopamine agent" RELATED [ChEBI] synonym: "dopamine agents" RELATED [ChEBI] synonym: "dopamine drug" RELATED [ChEBI] synonym: "dopamine drugs" RELATED [ChEBI] synonym: "dopaminergic agents" RELATED [ChEBI] is_a: CHEBI:35942 ! neurotransmitter agent [Term] id: CHEBI:48705 name: agonist namespace: chebi_ontology def: "Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own." [] subset: 3_STAR synonym: "agonist" EXACT IUPAC_NAME [IUPAC] synonym: "agonista" RELATED [ChEBI] synonym: "agoniste" RELATED [ChEBI] synonym: "agonists" RELATED [ChEBI] is_a: CHEBI:52210 ! pharmacological role [Term] id: CHEBI:49637 name: hydrogen atom namespace: chebi_ontology alt_id: CHEBI:24634 alt_id: CHEBI:49636 subset: 3_STAR synonym: "1H" RELATED [IUPAC] synonym: "H" RELATED [IUPAC] synonym: "hidrogeno" RELATED [ChEBI] synonym: "hydrogen" EXACT IUPAC_NAME [IUPAC] synonym: "hydrogen" RELATED [ChEBI] synonym: "hydrogene" RELATED [ChEBI] synonym: "Wasserstoff" RELATED [ChEBI] xref: WebElements:H is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33559 ! s-block element atom relationship: RO:0000087 CHEBI:33937 ! has role macronutrient property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "H" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/H" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "YZCKVEUIGOORGS-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "1.00794" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "1.00783" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[H]" xsd:string [Term] id: CHEBI:50047 name: organic amino compound namespace: chebi_ontology def: "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups." [ANON:ANON] subset: 3_STAR synonym: "organic amino compounds" RELATED [ChEBI] synonym: "organic amino compounds" RELATED [ChEBI:] is_a: CHEBI:35352 ! organonitrogen compound relationship: has_parent_hydride CHEBI:16134 ! ammonia relationship: RO:0000087 CHEBI:39142 ! has role Bronsted base [Term] id: CHEBI:50297 name: canonical nucleotide residue namespace: chebi_ontology subset: 3_STAR synonym: "canonical nucleotide residues" RELATED [ChEBI] is_a: CHEBI:50319 ! nucleotide residue [Term] id: CHEBI:50299 name: canonical ribonucleotide residue namespace: chebi_ontology subset: 3_STAR synonym: "canonical ribonucleotide residues" RELATED [ChEBI] is_a: CHEBI:50297 ! canonical nucleotide residue [Term] id: CHEBI:50312 name: onium compound namespace: chebi_ontology subset: 1_STAR is_a: CHEBI:37577 ! heteroatomic molecular entity [Term] id: CHEBI:50313 name: onium cation namespace: chebi_ontology def: "Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families." [] subset: 3_STAR synonym: "onium cations" EXACT IUPAC_NAME [IUPAC] synonym: "onium cations" RELATED [ChEBI] synonym: "onium ion" RELATED [ChEBI] synonym: "onium ions" RELATED [ChEBI] is_a: CHEBI:50312 ! onium compound [Term] id: CHEBI:50319 name: nucleotide residue namespace: chebi_ontology subset: 3_STAR synonym: "nucleotide residues" RELATED [ChEBI] is_a: CHEBI:33247 ! organic group [Term] id: CHEBI:50320 name: nucleoside residue namespace: chebi_ontology subset: 3_STAR synonym: "nucleoside residues" RELATED [ChEBI] is_a: CHEBI:33247 ! organic group [Term] id: CHEBI:50325 name: proteinogenic amino-acid side-chain group namespace: chebi_ontology def: "A univalent organyl group obtained by cleaving the bond from C-2 to the side chain of a proteinogenic amino-acid." [] subset: 3_STAR synonym: "canonical amino-acid side-chain" RELATED [ChEBI] synonym: "canonical amino-acid side-chains" RELATED [ChEBI] synonym: "proteinogenic amino-acid side-chain" RELATED [ChEBI] synonym: "proteinogenic amino-acid side-chain groups" RELATED [ChEBI] synonym: "proteinogenic amino-acid side-chains" RELATED [ChEBI] is_a: CHEBI:33249 ! organyl group [Term] id: CHEBI:50329 name: 2-carboxyethyl group namespace: chebi_ontology subset: 3_STAR synonym: "2-carboxyethyl" EXACT IUPAC_NAME [IUPAC] synonym: "glutamic acid side-chain" RELATED [ChEBI] is_a: CHEBI:50325 ! proteinogenic amino-acid side-chain group property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C3H5O2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "73.07060" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "73.02895" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C(CC(=O)O)*" xsd:string [Term] id: CHEBI:50860 name: organic molecular entity namespace: chebi_ontology alt_id: CHEBI:25700 alt_id: CHEBI:33244 def: "Any molecular entity that contains carbon." [ANON:ANON] subset: 3_STAR synonym: "organic compounds" RELATED [ChEBI] synonym: "organic compounds" RELATED [ChEBI:] synonym: "organic entity" RELATED [ChEBI] synonym: "organic entity" RELATED [ChEBI:] synonym: "organic molecular entities" RELATED [ChEBI:] synonym: "organic molecular entities" RELATED [ChEBI] is_a: CHEBI:33582 ! carbon group molecular entity relationship: has_part CHEBI:27594 ! carbon atom [Term] id: CHEBI:50904 name: allergen namespace: chebi_ontology def: "A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy." [] subset: 3_STAR synonym: "alergeno" RELATED [ChEBI] synonym: "allergene" RELATED [ChEBI] synonym: "allergenic agent" RELATED [ChEBI] xref: Wikipedia:Allergen is_a: CHEBI:52209 ! aetiopathogenetic role [Term] id: CHEBI:50906 name: role namespace: chebi_ontology def: "A role is particular behaviour which a material entity may exhibit." [] subset: 3_STAR is_a: BFO:0000023 ! role [Term] id: CHEBI:50910 name: neurotoxin namespace: chebi_ontology alt_id: CHEBI:50911 def: "A poison that interferes with the functions of the nervous system." [] subset: 3_STAR synonym: "agente neurotoxico" RELATED [ChEBI] synonym: "nerve poison" RELATED [ChEBI] synonym: "nerve poisons" RELATED [ChEBI] synonym: "neurotoxic agent" RELATED [ChEBI] synonym: "neurotoxic agents" RELATED [ChEBI] synonym: "neurotoxicant" RELATED [ChEBI] synonym: "neurotoxins" RELATED [ChEBI] xref: Wikipedia:Neurotoxin is_a: CHEBI:52209 ! aetiopathogenetic role is_a: CHEBI:64909 ! poison [Term] id: CHEBI:50994 name: primary amino compound namespace: chebi_ontology def: "A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group." [ANON:ANON] subset: 3_STAR synonym: "primary amino compounds" RELATED [ChEBI] synonym: "primary amino compounds" RELATED [ChEBI:] is_a: CHEBI:50047 ! organic amino compound relationship: is_conjugate_base_of CHEBI:65296 ! primary ammonium ion [Term] id: CHEBI:51086 name: chemical role namespace: chebi_ontology def: "A role played by the molecular entity or part thereof within a chemical context." [] subset: 3_STAR is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] id: CHEBI:51143 name: nitrogen molecular entity namespace: chebi_ontology alt_id: CHEBI:25556 alt_id: CHEBI:7594 subset: 3_STAR synonym: "nitrogen compounds" RELATED [ChEBI:] synonym: "nitrogen compounds" RELATED [ChEBI] synonym: "nitrogen molecular entities" RELATED [ChEBI] synonym: "nitrogen molecular entities" RELATED [ChEBI:] synonym: "Nitrogenous compounds" RELATED [KEGG COMPOUND:] synonym: "Nitrogenous compounds" RELATED [KEGG_COMPOUND] xref: KEGG:C06061 is_a: CHEBI:33302 ! pnictogen molecular entity relationship: has_part CHEBI:25555 ! nitrogen atom [Term] id: CHEBI:51151 name: dipolar compound namespace: chebi_ontology def: "An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case." [] subset: 3_STAR synonym: "dipolar compounds" RELATED [ChEBI] is_a: CHEBI:72695 ! organic molecule [Term] id: CHEBI:51422 name: organodiyl group namespace: chebi_ontology def: "Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s)." [] subset: 3_STAR synonym: "organodiyl groups" RELATED [ChEBI] is_a: CHEBI:51446 ! organic divalent group [Term] id: CHEBI:51446 name: organic divalent group namespace: chebi_ontology subset: 1_STAR is_a: CHEBI:33247 ! organic group [Term] id: CHEBI:51447 name: organic univalent group namespace: chebi_ontology subset: 1_STAR is_a: CHEBI:33247 ! organic group [Term] id: CHEBI:52206 name: biochemical role namespace: chebi_ontology def: "A biological role played by the molecular entity or part thereof within a biochemical context." [] subset: 3_STAR is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:52209 name: aetiopathogenetic role namespace: chebi_ontology def: "A role played by the molecular entity or part thereof which causes the development of a pathological process." [] subset: 3_STAR synonym: "etiopathogenetic agent" RELATED [ChEBI] synonym: "etiopathogenetic role" RELATED [ChEBI] is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:52210 name: pharmacological role namespace: chebi_ontology def: "A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties." [] subset: 3_STAR is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:52211 name: physiological role namespace: chebi_ontology subset: 1_STAR is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:52217 name: pharmaceutical namespace: chebi_ontology alt_id: CHEBI:33293 alt_id: CHEBI:33294 def: "Any substance introduced into a living organism with therapeutic or diagnostic purpose." [] subset: 3_STAR synonym: "farmaco" RELATED [ChEBI] synonym: "medicament" RELATED [ChEBI] synonym: "pharmaceuticals" RELATED [ChEBI] is_a: CHEBI:33232 ! application [Term] id: CHEBI:52845 name: cyclic organic group namespace: chebi_ontology def: "An organic group that consists of a closed ring. It may be a substituent or a skeleton." [] subset: 3_STAR synonym: "cyclic organic groups" RELATED [ChEBI] is_a: CHEBI:33247 ! organic group [Term] id: CHEBI:5686 name: heterocyclic compound namespace: chebi_ontology def: "A cyclic compound having as ring members atoms of at least two different elements." [ANON:ANON] subset: 3_STAR synonym: "compuesto heterociclico" RELATED [IUPAC] synonym: "compuesto heterociclico" RELATED [IUPAC:] synonym: "compuestos heterociclicos" RELATED [IUPAC:] synonym: "compuestos heterociclicos" RELATED [IUPAC] synonym: "heterocycle" RELATED [ChEBI:] synonym: "heterocycle" RELATED [ChEBI] synonym: "Heterocyclic compound" EXACT [KEGG COMPOUND:] synonym: "Heterocyclic compound" EXACT [KEGG_COMPOUND] synonym: "heterocyclic compounds" RELATED [ChEBI:] synonym: "heterocyclic compounds" RELATED [ChEBI] is_a: CHEBI:33595 ! cyclic compound [Term] id: CHEBI:57887 name: tryptaminium namespace: chebi_ontology def: "An ammonium ion that is the conjugate acid of tryptamine arising from protonation of the primary amino group; major species at pH 7.3." [] subset: 3_STAR synonym: "2-(1H-indol-3-yl)ethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "tryptamine" RELATED [UniProt] synonym: "tryptaminium cation" RELATED [ChEBI] synonym: "tryptaminium(1+)" RELATED [ChEBI] xref: Gmelin:533978 {source="Gmelin"} is_a: CHEBI:65296 ! primary ammonium ion relationship: is_conjugate_acid_of CHEBI:16765 ! tryptamine relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:76924 ! has role plant metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C10H13N2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2/p+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "APJYDQYYACXCRM-UHFFFAOYSA-O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "161.22310" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "161.10732" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]CCc1c[nH]c2ccccc12" xsd:string [Term] id: CHEBI:58025 name: octopaminium namespace: chebi_ontology def: "The conjugate acid of octopamine; major species at pH 7.3." [] subset: 3_STAR synonym: "2-hydroxy-2-(4-hydroxyphenyl)ethan-1-aminium" RELATED [ChEBI] synonym: "2-hydroxy-2-(4-hydroxyphenyl)ethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "4-(2-ammonio-1-hydroxyethyl)phenol" RELATED [ChEBI] synonym: "4-(2-azaniumyl-1-hydroxyethyl)phenol" RELATED [ChEBI] synonym: "octopamine" RELATED [UniProt] synonym: "octopaminium cation" RELATED [ChEBI] synonym: "octopaminium(1+)" RELATED [ChEBI] is_a: CHEBI:25697 ! organic cation is_a: CHEBI:35274 ! ammonium ion derivative relationship: is_conjugate_acid_of CHEBI:17134 ! octopamine property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C8H12NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C8H11NO2/c9-5-8(11)6-1-3-7(10)4-2-6/h1-4,8,10-11H,5,9H2/p+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "QHGUCRYDKWKLMG-UHFFFAOYSA-O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "154.18640" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "154.08626" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]CC(O)c1ccc(O)cc1" xsd:string [Term] id: CHEBI:58432 name: histaminium namespace: chebi_ontology def: "An ammonium ion that is the conjugate acid of histamine protonated on the side-chain nitrogen." [] subset: 3_STAR synonym: "2-(1H-imidazol-4-yl)ethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "histamine" RELATED [UniProt] synonym: "histaminium cation" RELATED [ChEBI] is_a: CHEBI:35274 ! ammonium ion derivative relationship: is_conjugate_acid_of CHEBI:18295 ! histamine relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C5H10N3" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8)/p+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "NTYJJOPFIAHURM-UHFFFAOYSA-O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "112.15300" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "112.08692" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]CCc1c[nH]cn1" xsd:string [Term] id: CHEBI:58951 name: short-chain fatty acid anion namespace: chebi_ontology def: "Any fatty acid anion obtained by removal of a proton from the carboxy group of a short-chain fatty acid (chain length of less than C6)." [] subset: 3_STAR synonym: "a short-chain fatty acid" RELATED [UniProt] synonym: "short-chain fatty acid anions" RELATED [ChEBI] is_a: CHEBI:28868 ! fatty acid anion relationship: is_conjugate_base_of CHEBI:26666 ! short-chain fatty acid property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "44.010" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "43.98983" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-]C([*])=O" xsd:string [Term] id: CHEBI:58953 name: saturated fatty acid anion namespace: chebi_ontology def: "Any fatty acid anion in which there is no C-C unsaturation." [] subset: 3_STAR synonym: "saturated fatty acid anions" RELATED [ChEBI] is_a: CHEBI:28868 ! fatty acid anion [Term] id: CHEBI:58954 name: straight-chain saturated fatty acid anion namespace: chebi_ontology def: "Any saturated fatty acid anion lacking a carbon side-chain." [] subset: 3_STAR synonym: "straight-chain saturated fatty acid anions" RELATED [ChEBI] is_a: CHEBI:58953 ! saturated fatty acid anion relationship: is_conjugate_base_of CHEBI:39418 ! straight-chain saturated fatty acid [Term] id: CHEBI:59202 name: straight-chain fatty acid namespace: chebi_ontology def: "Any fatty acid whose skeletal carbon atoms form an unbranched open chain." [] subset: 3_STAR synonym: "straight-chain fatty acids" RELATED [ChEBI] is_a: CHEBI:35366 ! fatty acid relationship: is_conjugate_acid_of CHEBI:59203 ! straight-chain fatty acid anion [Term] id: CHEBI:59203 name: straight-chain fatty acid anion namespace: chebi_ontology def: "A fatty acid anion formed by deprotonation of the carboxylic acid functional group of a straight-chain fatty acid." [] subset: 3_STAR synonym: "straight-chain FA anion" RELATED [ChEBI] synonym: "straight-chain FA anions" RELATED [ChEBI] synonym: "straight-chain fatty acid anions" RELATED [ChEBI] is_a: CHEBI:28868 ! fatty acid anion relationship: is_conjugate_base_of CHEBI:59202 ! straight-chain fatty acid [Term] id: CHEBI:59650 name: amino fatty acid namespace: chebi_ontology def: "A fatty acid containing at least one amino substituent." [ANON:ANON] subset: 3_STAR synonym: "amino FA" RELATED [ChEBI] synonym: "amino FA" RELATED [ChEBI:] synonym: "amino fatty acids" RELATED [ChEBI:] synonym: "amino fatty acids" RELATED [ChEBI] synonym: "carboxylated base" RELATED [ChEBI] synonym: "carboxylated base" RELATED [ChEBI:] synonym: "carboxylated bases" RELATED [ChEBI] synonym: "carboxylated bases" RELATED [ChEBI:] synonym: "lipoamino acid" RELATED [ChEBI] synonym: "lipoamino acids" RELATED [ChEBI] is_a: CHEBI:32952 ! amine is_a: CHEBI:33709 ! amino acid is_a: CHEBI:60690 ! nitrogen-containing fatty acid relationship: is_conjugate_acid_of CHEBI:61007 ! amino fatty acid anion [Term] id: CHEBI:59740 name: nucleophilic reagent namespace: chebi_ontology def: "A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons." [] subset: 3_STAR synonym: "nucleophile" RELATED [ChEBI] synonym: "nucleophiles" RELATED [ChEBI] synonym: "nucleophilic reagents" RELATED [ChEBI] is_a: CHEBI:33893 ! reagent is_a: CHEBI:39144 ! Lewis base [Term] id: CHEBI:59814 name: L-alpha-amino acid anion namespace: chebi_ontology def: "Conjugate base of an L-alpha-amino acid arising from deprotonation of the C-1 carboxy group." [] subset: 3_STAR synonym: "L-alpha-amino carboxylate" RELATED [ChEBI] is_a: CHEBI:33558 ! alpha-amino-acid anion relationship: is_conjugate_base_of CHEBI:15705 ! L-alpha-amino acid property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H3NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "73.051" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "73.01638" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[C@H](C(=O)[O-])(N)*" xsd:string [Term] id: CHEBI:59869 name: L-alpha-amino acid zwitterion namespace: chebi_ontology def: "Zwitterionic form of an L-alpha-amino acid having an anionic carboxy group and a protonated amino group." [] subset: 3_STAR synonym: "an L-alpha-amino acid" RELATED [UniProt] synonym: "L-alpha-amino acid zwitterions" RELATED [ChEBI] is_a: CHEBI:78608 ! alpha-amino acid zwitterion relationship: is_tautomer_of CHEBI:15705 ! L-alpha-amino acid property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "74.059" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "74.02420" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+][C@@H]([*])C([O-])=O" xsd:string [Term] id: CHEBI:59888 name: gamma-aminobutyric acid zwitterion namespace: chebi_ontology def: "Zwitterionic form of gamma-aminobutyric acid having an anionic carboxy group and a protonated amino group." [] subset: 3_STAR synonym: "4-aminobutanoate" RELATED [UniProt] synonym: "4-ammoniobutanoate" RELATED [ChEBI] synonym: "4-azaniumylbutanoate" EXACT IUPAC_NAME [IUPAC] xref: Gmelin:1041559 {source="Gmelin"} is_a: CHEBI:35238 ! amino acid zwitterion relationship: is_tautomer_of CHEBI:16865 ! gamma-aminobutyric acid property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H9NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7)" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "BTCSSZJGUNDROE-UHFFFAOYSA-N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "103.11980" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "103.06333" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]CCCC([O-])=O" xsd:string [Term] id: CHEBI:59905 name: dopaminium(1+) namespace: chebi_ontology def: "An ammonium ion that is the conjugate acid of dopamine; major species at pH 7.3." [] subset: 3_STAR synonym: "2-(3,4-dihydroxyphenyl)ethan-1-aminium" RELATED [ChEBI] synonym: "2-(3,4-dihydroxyphenyl)ethanaminium" EXACT IUPAC_NAME [IUPAC] synonym: "dopamine" RELATED [UniProt] synonym: "dopaminium cation" RELATED [ChEBI] xref: Gmelin:328863 {source="Gmelin"} is_a: CHEBI:35274 ! ammonium ion derivative relationship: is_conjugate_acid_of CHEBI:18243 ! dopamine relationship: RO:0000087 CHEBI:77746 ! has role human metabolite property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C8H12NO2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2/p+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/inchikey "VYFYYTLLBUKUHU-UHFFFAOYSA-O" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "154.18640" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "154.08626" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]CCc1ccc(O)c(O)c1" xsd:string [Term] id: CHEBI:60242 name: monovalent inorganic cation namespace: chebi_ontology def: "An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one." [] subset: 3_STAR synonym: "a monovalent cation" RELATED [UniProt] is_a: CHEBI:36915 ! inorganic cation [Term] id: CHEBI:60466 name: peptide zwitterion namespace: chebi_ontology def: "Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged." [] subset: 3_STAR synonym: "a peptide" RELATED [UniProt] synonym: "peptide zwitterions" RELATED [ChEBI] is_a: CHEBI:27369 ! zwitterion relationship: is_tautomer_of CHEBI:16670 ! peptide property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R(C2H2NOR)n" xsd:string [Term] id: CHEBI:60690 name: nitrogen-containing fatty acid namespace: chebi_ontology def: "Any fatty acid containing nitrogen as either a substituent or a replacement for a methylene carbon." [ANON:ANON] subset: 3_STAR synonym: "N-containing fatty acid" RELATED [ChEBI] synonym: "N-containing fatty acid" RELATED [ChEBI:] synonym: "N-containing fatty acids" RELATED [ChEBI] synonym: "N-containing fatty acids" RELATED [ChEBI:] synonym: "nitrogen-containing fatty acids" RELATED [ChEBI] synonym: "nitrogen-containing fatty acids" RELATED [ChEBI:] is_a: CHEBI:35366 ! fatty acid relationship: is_conjugate_acid_of CHEBI:61008 ! nitrogen-containing fatty acid anion [Term] id: CHEBI:61007 name: amino fatty acid anion namespace: chebi_ontology def: "A nitrogen-containing fatty acid anion arising from deprotonation of the carboxy group of any amino fatty acid." [] subset: 3_STAR synonym: "amino FA anion" RELATED [ChEBI] synonym: "amino FA anions" RELATED [ChEBI] synonym: "amino fatty acid anions" RELATED [ChEBI] synonym: "NH2-FA anion" RELATED [ChEBI] synonym: "NH2-FA anions" RELATED [ChEBI] synonym: "NH2-fatty acid anion" RELATED [ChEBI] synonym: "NH2-fatty acid anions" RELATED [ChEBI] is_a: CHEBI:37022 ! amino-acid anion is_a: CHEBI:61008 ! nitrogen-containing fatty acid anion relationship: is_conjugate_base_of CHEBI:59650 ! amino fatty acid [Term] id: CHEBI:61008 name: nitrogen-containing fatty acid anion namespace: chebi_ontology def: "A fatty acid anion arising from deprotonation of the carboxylic acid group of any nitrogen-containing fatty acid." [] subset: 3_STAR synonym: "N-containing FA anion" RELATED [ChEBI] synonym: "N-containing FA anions" RELATED [ChEBI] synonym: "N-containing fatty acid anions" RELATED [ChEBI] synonym: "nitrogen-containing FA anion" RELATED [ChEBI] synonym: "nitrogen-containing FA anions" RELATED [ChEBI] synonym: "nitrogen-containing fatty acid anion" EXACT [ChEBI] synonym: "nitrogen-containing fatty acid anions" RELATED [ChEBI] is_a: CHEBI:28868 ! fatty acid anion relationship: is_conjugate_base_of CHEBI:60690 ! nitrogen-containing fatty acid [Term] id: CHEBI:61115 name: EC 3.5.1.98 (histone deacetylase) inhibitor namespace: chebi_ontology def: "An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the function of histone deacetylase (EC 3.5.1.98)." [] subset: 3_STAR synonym: "EC 3.5.1.98 (histone deacetylase) inhibitors" RELATED [ChEBI] synonym: "EC 3.5.1.98 inhibitor" RELATED [ChEBI] synonym: "EC 3.5.1.98 inhibitors" RELATED [ChEBI] synonym: "HDAC inhibitor" RELATED [ChEBI] synonym: "HDAC inhibitors" RELATED [ChEBI] synonym: "HDACi" RELATED [ChEBI] synonym: "HDACis" RELATED [ChEBI] synonym: "HDI" RELATED [ChEBI] synonym: "HDIs" RELATED [ChEBI] synonym: "histone amidohydrolase inhibitor" RELATED [ChEBI] synonym: "histone amidohydrolase inhibitors" RELATED [ChEBI] synonym: "histone deacetylase (EC 3.5.1.98) inhibitor" RELATED [ChEBI] synonym: "histone deacetylase (EC 3.5.1.98) inhibitors" RELATED [ChEBI] synonym: "histone deacetylase inhibitor" RELATED [ChEBI] synonym: "histone deacetylase inhibitors" RELATED [ChEBI] xref: Wikipedia:Histone_deacetylase_inhibitor is_a: CHEBI:76807 ! EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor [Term] id: CHEBI:61120 name: nucleobase-containing molecular entity namespace: chebi_ontology def: "Any compound that has a nucleobase as a part." [] subset: 3_STAR synonym: "nucleobase-containing compound" RELATED [SUBMITTER] synonym: "nucleobase-containing compounds" RELATED [ChEBI] synonym: "nucleobase-containing molecular entities" RELATED [ChEBI] is_a: CHEBI:33833 ! heteroarene is_a: CHEBI:51143 ! nitrogen molecular entity relationship: has_functional_parent CHEBI:18282 ! nucleobase [Term] id: CHEBI:62031 name: polar amino acid zwitterion namespace: chebi_ontology def: "Zwitterionic form of a polar amino acid having an anionic carboxy group and a protonated amino group." [] subset: 2_STAR synonym: "a polar amino acid" RELATED [UniProt] xref: MetaCyc:Polar-amino-acids {source="SUBMITTER"} is_a: CHEBI:35238 ! amino acid zwitterion relationship: is_tautomer_of CHEBI:26167 ! polar amino acid property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "74.059" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "74.02420" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C(C([O-])=O)(*)[NH3+]" xsd:string [Term] id: CHEBI:62488 name: signalling molecule namespace: chebi_ontology def: "A molecular messenger in which the molecule is specifically involved in transmitting information between cells. Such molecules are released from the cell sending the signal, cross over the gap between cells by diffusion, and interact with specific receptors in another cell, triggering a response in that cell by activating a series of enzyme controlled reactions which lead to changes inside the cell." [] subset: 3_STAR synonym: "signal molecule" RELATED [ChEBI] synonym: "signal molecules" RELATED [ChEBI] synonym: "signaling molecule" RELATED [ChEBI] synonym: "signaling molecules" RELATED [ChEBI] synonym: "signalling molecules" RELATED [ChEBI] is_a: CHEBI:33280 ! molecular messenger [Term] id: CHEBI:63534 name: monoamine namespace: chebi_ontology def: "An aralylamino compound which contains one amino group connected to an aromatic ring by a two-carbon chain. Monoamines are derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by the action of aromatic amino acid decarboxylase enzymes." [] subset: 3_STAR synonym: "monoamines" RELATED [ChEBI] synonym: "naturally occurring monoamine" RELATED [ChEBI] synonym: "naturally occurring monoamines" RELATED [ChEBI] xref: PMID:21822758 {source="Europe PMC"} xref: PMID:21993877 {source="Europe PMC"} xref: PMID:22005599 {source="Europe PMC"} xref: PMID:22082101 {source="Europe PMC"} xref: PMID:22153577 {source="Europe PMC"} xref: PMID:22213370 {source="Europe PMC"} xref: PMID:22218931 {source="Europe PMC"} xref: PMID:22342987 {source="Europe PMC"} xref: PMID:22371656 {source="Europe PMC"} is_a: CHEBI:64365 ! aralkylamino compound [Term] id: CHEBI:64047 name: food additive namespace: chebi_ontology def: "Any substance which is added to food to preserve or enhance its flavour and/or appearance." [] subset: 3_STAR synonym: "food additives" RELATED [ChEBI] xref: Wikipedia:Food_additive is_a: CHEBI:33232 ! application is_a: CHEBI:78295 ! food component [Term] id: CHEBI:64049 name: food acidity regulator namespace: chebi_ontology def: "A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents." [] subset: 3_STAR synonym: "acidity regulator" RELATED [ChEBI] synonym: "acidity regulators" RELATED [ChEBI] synonym: "food acidity regulators" RELATED [ChEBI] synonym: "pH control agent" RELATED [ChEBI] synonym: "pH control agents" RELATED [ChEBI] xref: Wikipedia:Acidity_regulator is_a: CHEBI:64047 ! food additive [Term] id: CHEBI:64365 name: aralkylamino compound namespace: chebi_ontology def: "An organic amino compound in which an aminoalkyl group is linked to an arene." [] subset: 3_STAR synonym: "aralkylamino compounds" RELATED [ChEBI] is_a: CHEBI:50047 ! organic amino compound [Term] id: CHEBI:64708 name: one-carbon compound namespace: chebi_ontology def: "An organic molecular entity containing a single carbon atom (C1)." [] subset: 3_STAR synonym: "one-carbon compounds" RELATED [ChEBI] is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:64709 name: organic acid namespace: chebi_ontology def: "Any organic molecular entity that is acidic and contains carbon in covalent linkage." [] subset: 3_STAR synonym: "organic acids" RELATED [ChEBI] is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:64909 name: poison namespace: chebi_ontology def: "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism." [] subset: 3_STAR synonym: "poisonous agent" RELATED [ChEBI] synonym: "poisonous agents" RELATED [ChEBI] synonym: "poisonous substance" RELATED [ChEBI] synonym: "poisonous substances" RELATED [ChEBI] synonym: "poisons" RELATED [ChEBI] synonym: "toxic agent" RELATED [ChEBI] synonym: "toxic agents" RELATED [ChEBI] synonym: "toxic substance" RELATED [ChEBI] synonym: "toxic substances" RELATED [ChEBI] xref: Wikipedia:Poison is_a: CHEBI:24432 ! biological role [Term] id: CHEBI:65255 name: food preservative namespace: chebi_ontology def: "Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes." [] subset: 3_STAR synonym: "food preservatives" RELATED [ChEBI] is_a: CHEBI:64047 ! food additive [Term] id: CHEBI:65256 name: antimicrobial food preservative namespace: chebi_ontology def: "A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299)." [] subset: 3_STAR synonym: "antimicrobial food preservatives" RELATED [ChEBI] synonym: "antimicrobial preservative" RELATED [ChEBI] synonym: "antimicrobial preservatives" RELATED [ChEBI] is_a: CHEBI:33281 ! antimicrobial agent is_a: CHEBI:65255 ! food preservative [Term] id: CHEBI:65296 name: primary ammonium ion namespace: chebi_ontology def: "An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3." [] subset: 3_STAR synonym: "a primary amine" RELATED [UniProt] synonym: "substituted ammonium" RELATED [ChEBI] is_a: CHEBI:25697 ! organic cation is_a: CHEBI:35274 ! ammonium ion derivative relationship: is_conjugate_acid_of CHEBI:50994 ! primary amino compound property_value: http://purl.obolibrary.org/obo/chebi/charge "+1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "H3NR" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "17.031" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "17.02655" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+][*]" xsd:string [Term] id: CHEBI:68452 name: azole namespace: chebi_ontology def: "Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen." [] subset: 3_STAR synonym: "azoles" RELATED [ChEBI] xref: Wikipedia:Azole is_a: CHEBI:38101 ! organonitrogen heterocyclic compound is_a: CHEBI:38179 ! monocyclic heteroarene [Term] id: CHEBI:71666 name: gamma-amino acid anion namespace: chebi_ontology def: "An amino-acid anion in which the amino group is situated gamma- to the carboxylate group." [] subset: 3_STAR synonym: "gamma-amino acid anions" RELATED [ChEBI] is_a: CHEBI:37022 ! amino-acid anion relationship: is_conjugate_base_of CHEBI:33707 ! gamma-amino acid [Term] id: CHEBI:72695 name: organic molecule namespace: chebi_ontology def: "Any molecule that consists of at least one carbon atom as part of the electrically neutral entity." [] subset: 3_STAR synonym: "organic compound" RELATED [ChEBI] synonym: "organic compounds" RELATED [ChEBI] synonym: "organic molecules" RELATED [ChEBI] is_a: CHEBI:25367 ! molecule is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:73398 name: indole skeleton namespace: chebi_ontology def: "A mancude heterobicyclic organic group consisting of a benzene ring fused to a pyrrole ring." [] subset: 3_STAR is_a: CHEBI:73541 ! organic heterobicyclic ring property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C8N" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "110.09230" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "110.00307" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "C1(=C(C(=C2C(=C1*)N(C(=C2*)*)*)*)*)*" xsd:string [Term] id: CHEBI:73541 name: organic heterobicyclic ring namespace: chebi_ontology def: "A bicyclic organic group that contains both carbon and hetero atoms." [] subset: 3_STAR synonym: "organic heterobicyclic rings" RELATED [ChEBI] is_a: CHEBI:52845 ! cyclic organic group [Term] id: CHEBI:75763 name: eukaryotic metabolite namespace: chebi_ontology def: "Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms." [] subset: 3_STAR synonym: "eukaryotic metabolites" RELATED [ChEBI] is_a: CHEBI:25212 ! metabolite [Term] id: CHEBI:75767 name: animal metabolite namespace: chebi_ontology alt_id: CHEBI:77721 alt_id: CHEBI:77743 def: "Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals." [] subset: 3_STAR synonym: "animal metabolites" RELATED [ChEBI] is_a: CHEBI:75763 ! eukaryotic metabolite [Term] id: CHEBI:75768 name: mammalian metabolite namespace: chebi_ontology alt_id: CHEBI:77464 alt_id: CHEBI:77744 def: "Any animal metabolite produced during a metabolic reaction in mammals." [] subset: 3_STAR synonym: "mammalian metabolites" RELATED [ChEBI] is_a: CHEBI:75767 ! animal metabolite [Term] id: CHEBI:75771 name: mouse metabolite namespace: chebi_ontology def: "Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus)." [] subset: 3_STAR synonym: "mouse metabolites" RELATED [ChEBI] synonym: "Mus musculus metabolite" RELATED [ChEBI] synonym: "Mus musculus metabolites" RELATED [ChEBI] is_a: CHEBI:75768 ! mammalian metabolite [Term] id: CHEBI:75772 name: Saccharomyces cerevisiae metabolite namespace: chebi_ontology alt_id: CHEBI:76949 alt_id: CHEBI:76951 def: "Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae)." [] subset: 3_STAR synonym: "baker's yeast metabolite" RELATED [ChEBI] synonym: "baker's yeast metabolites" RELATED [ChEBI] synonym: "baker's yeast secondary metabolite" RELATED [ChEBI] synonym: "baker's yeast secondary metabolites" RELATED [ChEBI] synonym: "S. cerevisiae metabolite" RELATED [ChEBI] synonym: "S. cerevisiae metabolites" RELATED [ChEBI] synonym: "S. cerevisiae secondary metabolite" RELATED [ChEBI] synonym: "S. cerevisiae secondary metabolites" RELATED [ChEBI] synonym: "Saccharomyces cerevisiae metabolites" RELATED [ChEBI] synonym: "Saccharomyces cerevisiae secondary metabolites" RELATED [ChEBI] is_a: CHEBI:76946 ! fungal metabolite [Term] id: CHEBI:75787 name: prokaryotic metabolite namespace: chebi_ontology def: "Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea." [] subset: 3_STAR synonym: "prokaryotic metabolites" RELATED [ChEBI] is_a: CHEBI:25212 ! metabolite [Term] id: CHEBI:76759 name: EC 3.* (hydrolase) inhibitor namespace: chebi_ontology def: "Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*)." [] subset: 3_STAR synonym: "EC 3.* (hydrolase) inhibitors" RELATED [ChEBI] synonym: "EC 3.* inhibitor" RELATED [ChEBI] synonym: "EC 3.* inhibitors" RELATED [ChEBI] synonym: "EC 3.*.*.* inhibitor" RELATED [ChEBI] synonym: "EC 3.*.*.* inhibitors" RELATED [ChEBI] synonym: "hydrolase (EC 3.*) inhibitor" RELATED [ChEBI] synonym: "hydrolase (EC 3.*) inhibitors" RELATED [ChEBI] synonym: "hydrolase inhibitor" RELATED [ChEBI] synonym: "hydrolase inhibitors" RELATED [ChEBI] xref: Wikipedia:Hydrolase is_a: CHEBI:23924 ! enzyme inhibitor [Term] id: CHEBI:76764 name: EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor namespace: chebi_ontology def: "Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*)." [] subset: 3_STAR synonym: "EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor" RELATED [ChEBI] synonym: "EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors" RELATED [ChEBI] synonym: "EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor" RELATED [ChEBI] synonym: "EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors" RELATED [ChEBI] synonym: "EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors" RELATED [ChEBI] synonym: "EC 3.5.* inhibitor" RELATED [ChEBI] synonym: "EC 3.5.* inhibitors" RELATED [ChEBI] is_a: CHEBI:76759 ! EC 3.* (hydrolase) inhibitor [Term] id: CHEBI:76807 name: EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor namespace: chebi_ontology def: "An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*)." [] subset: 3_STAR synonym: "EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors" RELATED [ChEBI] synonym: "EC 3.5.1.* inhibitor" RELATED [ChEBI] synonym: "EC 3.5.1.* inhibitors" RELATED [ChEBI] synonym: "non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor" RELATED [ChEBI] synonym: "non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors" RELATED [ChEBI] is_a: CHEBI:76764 ! EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor [Term] id: CHEBI:76924 name: plant metabolite namespace: chebi_ontology alt_id: CHEBI:75766 alt_id: CHEBI:76925 def: "Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms." [] subset: 3_STAR synonym: "plant metabolites" RELATED [ChEBI] synonym: "plant secondary metabolites" RELATED [ChEBI] is_a: CHEBI:75763 ! eukaryotic metabolite [Term] id: CHEBI:76946 name: fungal metabolite namespace: chebi_ontology alt_id: CHEBI:75765 alt_id: CHEBI:76947 def: "Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds." [] subset: 3_STAR synonym: "fungal metabolites" RELATED [ChEBI] is_a: CHEBI:75763 ! eukaryotic metabolite [Term] id: CHEBI:76969 name: bacterial metabolite namespace: chebi_ontology alt_id: CHEBI:75760 alt_id: CHEBI:76970 def: "Any prokaryotic metabolite produced during a metabolic reaction in bacteria." [] subset: 3_STAR is_a: CHEBI:75787 ! prokaryotic metabolite [Term] id: CHEBI:76971 name: Escherichia coli metabolite namespace: chebi_ontology def: "Any bacterial metabolite produced during a metabolic reaction in Escherichia coli." [] subset: 3_STAR synonym: "E.coli metabolite" RELATED [ChEBI] synonym: "E.coli metabolites" RELATED [ChEBI] synonym: "Escherichia coli metabolites" RELATED [ChEBI] is_a: CHEBI:76969 ! bacterial metabolite [Term] id: CHEBI:77746 name: human metabolite namespace: chebi_ontology alt_id: CHEBI:75770 alt_id: CHEBI:77123 def: "Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens)." [] subset: 3_STAR synonym: "H. sapiens metabolite" RELATED [ChEBI] synonym: "H. sapiens metabolites" RELATED [ChEBI] synonym: "Homo sapiens metabolite" RELATED [ChEBI] synonym: "Homo sapiens metabolites" RELATED [ChEBI] is_a: CHEBI:75768 ! mammalian metabolite [Term] id: CHEBI:77941 name: EC 3.5.1.4 (amidase) inhibitor namespace: chebi_ontology def: "An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4)." [] subset: 3_STAR synonym: "acylamidase inhibitor" RELATED [ChEBI] synonym: "acylamidase inhibitors" RELATED [ChEBI] synonym: "acylamide amidohydrolase inhibitor" RELATED [ChEBI] synonym: "acylamide amidohydrolase inhibitors" RELATED [ChEBI] synonym: "amidase (EC 3.5.1.4) inhibitor" RELATED [ChEBI] synonym: "amidase (EC 3.5.1.4) inhibitors" RELATED [ChEBI] synonym: "amidase inhibitor" RELATED [ChEBI] synonym: "amidase inhibitors" RELATED [ChEBI] synonym: "amidohydrolase inhibitor" RELATED [ChEBI] synonym: "amidohydrolase inhibitors" RELATED [ChEBI] synonym: "deaminase inhibitor" RELATED [ChEBI] synonym: "deaminase inhibitors" RELATED [ChEBI] synonym: "EC 3.5.1.4 (amidase) inhibitors" RELATED [ChEBI] synonym: "EC 3.5.1.4 inhibitor" RELATED [ChEBI] synonym: "EC 3.5.1.4 inhibitors" RELATED [ChEBI] synonym: "fatty acylamidase inhibitor" RELATED [ChEBI] synonym: "fatty acylamidase inhibitors" RELATED [ChEBI] synonym: "N-acetylaminohydrolase inhibitor" RELATED [ChEBI] synonym: "N-acetylaminohydrolase inhibitors" RELATED [ChEBI] xref: Wikipedia:Amidase is_a: CHEBI:76807 ! EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor [Term] id: CHEBI:78115 name: fatty acid anion 4:0 namespace: chebi_ontology def: "Any saturated fatty acid anion containing 4 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3." [] subset: 3_STAR synonym: "fatty acid 4:0" RELATED [UniProt] is_a: CHEBI:58951 ! short-chain fatty acid anion is_a: CHEBI:58953 ! saturated fatty acid anion relationship: is_conjugate_base_of CHEBI:140601 ! fatty acid 4:0 property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C4H7O2" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "87.09718" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "87.04460" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-]C([*])=O" xsd:string [Term] id: CHEBI:78295 name: food component namespace: chebi_ontology def: "A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants." [] subset: 3_STAR synonym: "dietary component" RELATED [ChEBI] synonym: "dietary components" RELATED [ChEBI] synonym: "food components" RELATED [ChEBI] is_a: CHEBI:52211 ! physiological role [Term] id: CHEBI:78433 name: refrigerant namespace: chebi_ontology def: "A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a \"R\" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure." [] subset: 3_STAR synonym: "refrigerants" RELATED [ChEBI] xref: Wikipedia:Refrigerant is_a: CHEBI:33232 ! application [Term] id: CHEBI:78608 name: alpha-amino acid zwitterion namespace: chebi_ontology alt_id: CHEBI:83409 def: "An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3." [] subset: 3_STAR synonym: "an alpha-amino acid" RELATED [UniProt] xref: MetaCyc:Alpha-Amino-Acids {source="SUBMITTER"} is_a: CHEBI:35238 ! amino acid zwitterion relationship: is_tautomer_of CHEBI:33704 ! alpha-amino acid property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/formula "C2H4NO2R" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/mass "74.059" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "74.02420" xsd:string property_value: http://purl.obolibrary.org/obo/chebi/smiles "[NH3+]C([*])C([O-])=O" xsd:string [Term] id: CHEBI:78675 name: fundamental metabolite namespace: chebi_ontology def: "Any metabolite produced by all living cells." [] subset: 3_STAR synonym: "essential metabolite" RELATED [ChEBI] synonym: "essential metabolites" RELATED [ChEBI] synonym: "fundamental metabolites" RELATED [ChEBI] is_a: CHEBI:25212 ! metabolite [Term] id: CHEBI:79388 name: divalent inorganic anion namespace: chebi_ontology def: "Any inorganic anion with a valency of two." [] subset: 3_STAR synonym: "divalent inorganic anions" RELATED [ChEBI] is_a: CHEBI:24834 ! inorganic anion [Term] id: CHEBI:79389 name: monovalent inorganic anion namespace: chebi_ontology def: "Any inorganic anion with a valency of one." [] subset: 3_STAR synonym: "monovalent inorganic anions" RELATED [ChEBI] is_a: CHEBI:24834 ! inorganic anion [Term] id: CHEBI:83039 name: crustacean metabolite namespace: chebi_ontology def: "An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill." [] subset: 3_STAR synonym: "crustacean metabolites" RELATED [ChEBI] is_a: CHEBI:75767 ! animal metabolite [Term] id: CHEBI:83056 name: Daphnia magna metabolite namespace: chebi_ontology def: "A Daphnia metabolite produced by the species Daphnia magna." [] subset: 3_STAR synonym: "Daphnia magna metabolites" RELATED [ChEBI] is_a: CHEBI:83057 ! Daphnia metabolite [Term] id: CHEBI:83057 name: Daphnia metabolite namespace: chebi_ontology def: "A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia" [] subset: 3_STAR synonym: "Daphnia metabolites" RELATED [ChEBI] xref: Wikipedia:Daphnia is_a: CHEBI:83039 ! crustacean metabolite [Term] id: CHEBI:83813 name: proteinogenic amino acid namespace: chebi_ontology def: "Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration." [] subset: 3_STAR synonym: "canonical amino acid" RELATED [ChEBI] synonym: "canonical amino acids" RELATED [ChEBI] synonym: "proteinogenic amino acids" RELATED [ChEBI] xref: Wikipedia:Proteinogenic_amino_acid is_a: CHEBI:33575 ! carboxylic acid is_a: CHEBI:35352 ! organonitrogen compound [Term] id: CHEBI:83820 name: non-proteinogenic amino acid namespace: chebi_ontology def: "Any amino-acid that is not naturally encoded in the genetic code of any organism." [] subset: 3_STAR synonym: "non-canonical amino acid" RELATED [ChEBI] synonym: "non-canonical amino acids" RELATED [ChEBI] synonym: "non-canonical amino-acid" RELATED [ChEBI] synonym: "non-canonical amino-acids" RELATED [ChEBI] synonym: "non-coded amino acid" RELATED [ChEBI] synonym: "non-coded amino acids" RELATED [ChEBI] synonym: "non-coded amino-acid" RELATED [ChEBI] synonym: "non-coded amino-acids" RELATED [ChEBI] synonym: "non-proteinogenic amino acids" RELATED [ChEBI] synonym: "non-proteinogenic amino-acid" RELATED [ChEBI] synonym: "non-proteinogenic amino-acids" RELATED [ChEBI] xref: Wikipedia:Non-proteinogenic_amino_acids is_a: CHEBI:33709 ! amino acid [Term] id: CHEBI:84087 name: human urinary metabolite namespace: chebi_ontology def: "Any metabolite (endogenous or exogenous) found in human urine samples." [] subset: 3_STAR synonym: "human urinary metabolites" RELATED [ChEBI] is_a: CHEBI:77746 ! human metabolite [Term] id: CHEBI:84729 name: hydroxyindoles namespace: chebi_ontology def: "Any member of the class of indoles carrying at least one hydroxy group." [] subset: 3_STAR is_a: CHEBI:24828 ! indoles is_a: CHEBI:33822 ! organic hydroxy compound [Term] id: CL:0000000 disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! nucleus relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! nucleus [Term] id: GO:0000035 name: acyl binding namespace: molecular_function def: "Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid." [GOC:curators, ISBN:0198506732] synonym: "acyl-CoA or acyl binding" BROAD [] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:22221 ! acyl group relationship: has_input CHEBI:22221 ! acyl group [Term] id: GO:0001505 name: regulation of neurotransmitter levels namespace: biological_process def: "Any process that modulates levels of neurotransmitter." [GOC:jl] [Term] id: GO:0001677 name: formation of translation initiation ternary complex namespace: biological_process def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd] synonym: "translation initiation ternary complex assembly" EXACT [] is_a: GO:0022618 ! ribonucleoprotein complex assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0044207 ! translation initiation ternary complex relationship: part_of GO:0006413 ! translational initiation relationship: results_in_assembly_of GO:0044207 ! translation initiation ternary complex [Term] id: GO:0001692 name: histamine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172] synonym: "histamine metabolism" EXACT [] is_a: GO:0006576 ! biogenic amine metabolic process is_a: GO:0052803 ! imidazole-containing compound metabolic process is_a: GO:0097164 ! ammonium ion metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:58432 ! histaminium relationship: has_primary_input_or_output CHEBI:58432 ! histaminium [Term] id: GO:0001694 name: histamine biosynthetic process namespace: biological_process alt_id: GO:0001693 def: "The chemical reactions and pathways resulting in the formation of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172] synonym: "histamine anabolism" EXACT [] synonym: "histamine biosynthesis" EXACT [] synonym: "histamine formation" EXACT [] synonym: "histamine synthesis" EXACT [] is_a: GO:0001692 ! histamine metabolic process is_a: GO:0042401 ! biogenic amine biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:58432 ! histaminium relationship: has_primary_output CHEBI:58432 ! histaminium [Term] id: GO:0002054 name: nucleobase binding namespace: molecular_function def: "Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases." [GOC:hjd] subset: goslim_pir is_a: GO:0036094 ! small molecule binding is_a: GO:0097159 ! organic cyclic compound binding is_a: GO:1901363 ! heterocyclic compound binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:18282 ! nucleobase relationship: has_input CHEBI:18282 ! nucleobase [Term] id: GO:0003674 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 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. 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:0005575 ! cellular_component disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function alt_id: GO:0000496 def: "Binding to a nucleic acid." [GOC:jl] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "base pairing" NARROW [] is_a: GO:0097159 ! organic cyclic compound binding is_a: GO:1901363 ! heterocyclic compound binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:33696 ! nucleic acid relationship: has_input CHEBI:33696 ! nucleic acid [Term] id: GO:0003723 name: RNA binding namespace: molecular_function alt_id: GO:0000498 alt_id: GO:0044822 def: "Binding to an RNA molecule or a portion thereof." [GOC:jl, GOC:mah] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_plant subset: goslim_yeast subset: prokaryote_subset synonym: "base pairing with RNA" NARROW [] synonym: "poly(A) RNA binding" RELATED [] synonym: "poly(A)-RNA binding" RELATED [] synonym: "poly-A RNA binding" RELATED [] xref: Reactome:R-HSA-203922 "Exportin-5 recognizes 3' overhang of pre-miRNA" is_a: GO:0003676 ! nucleic acid binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:33697 ! ribonucleic acid relationship: has_input CHEBI:33697 ! ribonucleic acid [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:0004857 name: enzyme inhibitor activity namespace: molecular_function alt_id: GO:0048551 def: "Binds to and stops, prevents or reduces the activity of an enzyme." [GOC:ai, GOC:ebc] comment: This term should only be used in cases when the regulator directly interacts with the enzyme. synonym: "metalloenzyme inhibitor activity" NARROW [] is_a: GO:0030234 ! enzyme regulator activity is_a: GO:0140678 ! molecular function inhibitor activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_negatively_regulates GO:0003824 ! catalytic activity relationship: directly_negatively_regulates GO:0003824 ! catalytic activity [Term] id: GO:0005488 name: binding namespace: molecular_function def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. subset: gocheck_do_not_annotate subset: goslim_pir subset: goslim_plant synonym: "ligand" NARROW [] xref: Wikipedia:Binding_(molecular) is_a: GO:0003674 ! molecular_function [Term] id: GO:0005504 name: fatty acid binding namespace: molecular_function def: "Binding to a fatty acid, an aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198506732] is_a: GO:0008289 ! lipid binding is_a: GO:0033293 ! monocarboxylic acid binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:28868 ! fatty acid anion relationship: has_input CHEBI:28868 ! fatty acid anion [Term] id: GO:0005515 name: protein binding namespace: molecular_function alt_id: GO:0001948 alt_id: GO:0045308 def: "Binding to a protein." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "glycoprotein binding" NARROW [] synonym: "protein amino acid binding" EXACT [] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input PR:000000001 ! protein relationship: has_input PR:000000001 ! protein [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao1337158144] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell or subcellular entity" EXACT [] synonym: "cellular component" EXACT [] synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] xref: NIF_Subcellular:sao1337158144 is_a: BFO:0000040 ! material entity disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0005622 name: intracellular anatomical structure namespace: cellular_component def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant synonym: "internal to cell" EXACT [] synonym: "intracellular" EXACT [] synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI [Term] id: GO:0005634 name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell nucleus" EXACT [] synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm relationship: in_taxon NCBITaxon:2759 {all_only="true"} relationship: only_in_taxon NCBITaxon:2759 [Term] id: GO:0005635 name: nuclear envelope namespace: cellular_component alt_id: GO:0005636 def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] subset: goslim_chembl subset: goslim_generic subset: goslim_plant xref: Wikipedia:Nuclear_envelope is_a: GO:0031967 ! organelle envelope relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0012505 ! endomembrane system [Term] id: GO:0005737 name: cytoplasm namespace: cellular_component def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: prokaryote_subset xref: Wikipedia:Cytoplasm is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI [Term] id: GO:0005773 name: vacuole namespace: cellular_component def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "vacuolar carboxypeptidase Y" RELATED [] xref: Wikipedia:Vacuole is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component alt_id: GO:0005887 alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_plant subset: goslim_yeast subset: prokaryote_subset synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645] synonym: "cytoplasmic membrane" EXACT [] synonym: "inner endospore membrane" NARROW [] synonym: "integral component of plasma membrane" NARROW [] synonym: "integral to plasma membrane" NARROW [] synonym: "juxtamembrane" BROAD [] synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah] synonym: "plasmalemma" EXACT [] xref: NIF_Subcellular:sao1663586795 xref: Wikipedia:Cell_membrane is_a: GO:0016020 ! membrane relationship: part_of GO:0071944 ! cell periphery [Term] id: GO:0005938 name: cell cortex namespace: cellular_component def: "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins." [GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_yeast synonym: "cell periphery" RELATED [] synonym: "peripheral cytoplasm" RELATED [] xref: Wikipedia:Cell_cortex is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0071944 ! cell periphery relationship: part_of GO:0071944 ! cell periphery [Term] id: GO:0006066 name: alcohol metabolic process namespace: biological_process def: "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [ISBN:0198506732] subset: goslim_drosophila subset: goslim_pir synonym: "alcohol metabolism" EXACT [] is_a: GO:0044281 ! small molecule metabolic process is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:30879 ! alcohol relationship: has_primary_input_or_output CHEBI:30879 ! alcohol [Term] id: GO:0006082 name: organic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] subset: goslim_pir synonym: "organic acid metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process is_a: GO:0044281 ! small molecule metabolic process is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:64709 ! organic acid relationship: has_primary_input_or_output CHEBI:64709 ! organic acid [Term] id: GO:0006083 name: acetate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving acetate, the anion of acetic acid." [GOC:go_curators] synonym: "acetate metabolism" EXACT [] is_a: GO:0032787 ! monocarboxylic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:30089 ! acetate relationship: has_primary_input_or_output CHEBI:30089 ! acetate [Term] id: GO:0006139 name: nucleobase-containing compound metabolic process namespace: biological_process alt_id: GO:0055134 def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_pir subset: goslim_plant synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:61120 ! nucleobase-containing molecular entity relationship: has_primary_input_or_output CHEBI:61120 ! nucleobase-containing molecular entity [Term] id: GO:0006412 name: translation namespace: biological_process alt_id: GO:0006416 alt_id: GO:0006453 alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: prokaryote_subset synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein biosynthetic process" EXACT [] synonym: "protein formation" EXACT [] synonym: "protein synthesis" EXACT [] synonym: "protein translation" EXACT [] xref: Wikipedia:Translation_(genetics) is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0019538 ! protein metabolic process is_a: GO:0043043 ! peptide biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:16541 ! protein polypeptide chain intersection_of: part_of GO:0010467 ! gene expression relationship: ends_with GO:0006415 ! translational termination relationship: has_part GO:0006414 ! translational elongation relationship: has_primary_output CHEBI:16541 ! protein polypeptide chain relationship: part_of GO:0010467 ! gene expression relationship: starts_with GO:0006413 ! translational initiation [Term] id: GO:0006413 name: translational initiation namespace: biological_process alt_id: GO:0006440 alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] is_a: GO:0044237 ! cellular metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex [Term] id: GO:0006414 name: translational elongation namespace: biological_process alt_id: GO:0006442 alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] synonym: "translation elongation" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process relationship: part_of GO:0006412 ! translation [Term] id: GO:0006415 name: translational termination namespace: biological_process alt_id: GO:0006443 alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] synonym: "translational complex disassembly" EXACT [] is_a: GO:0032984 ! protein-containing complex disassembly relationship: part_of GO:0006412 ! translation [Term] id: GO:0006518 name: peptide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:go_curators] subset: goslim_pir synonym: "peptide metabolism" EXACT [] is_a: GO:0043603 ! amide metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:16670 ! peptide relationship: has_primary_input_or_output CHEBI:16670 ! peptide [Term] id: GO:0006520 name: amino acid metabolic process namespace: biological_process alt_id: GO:0006519 def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups." [ISBN:0198506732] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: prokaryote_subset synonym: "amino acid and derivative metabolism" RELATED [] synonym: "cellular amino acid and derivative metabolic process" RELATED [] synonym: "cellular amino acid metabolic process" EXACT [] synonym: "cellular amino acid metabolism" EXACT [] is_a: GO:0019752 ! carboxylic acid metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:37022 ! amino-acid anion relationship: has_primary_input_or_output CHEBI:37022 ! amino-acid anion property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI [Term] id: GO:0006536 name: glutamate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators] synonym: "glutamate metabolism" EXACT [] synonym: "glutamic acid metabolic process" EXACT [] synonym: "glutamic acid metabolism" EXACT [] xref: Wikipedia:Glutamic_acid is_a: GO:0009064 ! glutamine family amino acid metabolic process is_a: GO:0043648 ! dicarboxylic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:14321 ! glutamate(1-) relationship: has_primary_input_or_output CHEBI:14321 ! glutamate(1-) [Term] id: GO:0006537 name: glutamate biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators] synonym: "glutamate anabolism" EXACT [] synonym: "glutamate biosynthesis" EXACT [] synonym: "glutamate biosynthesis, using glutamate dehydrogenase (NAD(P)+)" NARROW [] synonym: "glutamate biosynthesis, using glutamate synthase (NADPH)" NARROW [] synonym: "glutamate biosynthetic process, using glutamate dehydrogenase (NAD(P)+)" NARROW [] synonym: "glutamate biosynthetic process, using glutamate synthase (NADPH)" NARROW [] synonym: "glutamate formation" EXACT [] synonym: "glutamate synthesis" EXACT [] synonym: "glutamic acid biosynthesis" EXACT [] synonym: "glutamic acid biosynthetic process" EXACT [] is_a: GO:0006536 ! glutamate metabolic process is_a: GO:0008652 ! amino acid biosynthetic process is_a: GO:0009084 ! glutamine family amino acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:14321 ! glutamate(1-) relationship: has_primary_output CHEBI:14321 ! glutamate(1-) [Term] id: GO:0006576 name: biogenic amine metabolic process namespace: biological_process def: "The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:jl, ISBN:0395825172] synonym: "biogenic amine metabolism" EXACT [] synonym: "cellular biogenic amine metabolic process" EXACT [] is_a: GO:0009308 ! amine metabolic process [Term] id: GO:0006584 name: catecholamine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:jl, ISBN:0198506732] synonym: "catecholamine metabolism" EXACT [] is_a: GO:0006576 ! biogenic amine metabolic process is_a: GO:0009712 ! catechol-containing compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33567 ! catecholamine relationship: has_primary_input_or_output CHEBI:33567 ! catecholamine [Term] id: GO:0006586 name: indolalkylamine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group." [GOC:curators] synonym: "indolalkylamine metabolism" EXACT [] synonym: "indolamine metabolic process" BROAD [] synonym: "indolamine metabolism" BROAD [] is_a: GO:0006576 ! biogenic amine metabolic process is_a: GO:0042430 ! indole-containing compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:38631 ! aminoalkylindole relationship: has_primary_input_or_output CHEBI:38631 ! aminoalkylindole [Term] id: GO:0006589 name: octopamine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of octopamine, 1-(p-hydroxyphenyl)-2-aminoethanol. The D enantiomer is about one-tenth as active as norepinephrine and is found in the salivary glands of Octopus and Eledone species." [ISBN:0198506732] synonym: "octopamine anabolism" EXACT [] synonym: "octopamine biosynthesis" EXACT [] synonym: "octopamine formation" EXACT [] synonym: "octopamine synthesis" EXACT [] is_a: GO:0042136 ! neurotransmitter biosynthetic process is_a: GO:0042401 ! biogenic amine biosynthetic process is_a: GO:0046333 ! octopamine metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:58025 ! octopaminium relationship: has_primary_output CHEBI:58025 ! octopaminium [Term] id: GO:0006629 name: lipid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma] subset: goslim_agr 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_pombe subset: goslim_yeast subset: prokaryote_subset synonym: "lipid metabolism" EXACT [] xref: Wikipedia:Lipid_metabolism is_a: GO:0044238 ! primary metabolic process is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:18059 ! lipid relationship: has_primary_input_or_output CHEBI:18059 ! lipid [Term] id: GO:0006631 name: fatty acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198547684] synonym: "fatty acid metabolism" EXACT [] xref: Wikipedia:Fatty_acid_metabolism is_a: GO:0032787 ! monocarboxylic acid metabolic process is_a: GO:0044255 ! cellular lipid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:28868 ! fatty acid anion relationship: has_primary_input_or_output CHEBI:28868 ! fatty acid anion [Term] id: GO:0006633 name: fatty acid biosynthetic process namespace: biological_process alt_id: GO:0000037 def: "The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes." [GOC:mah, ISBN:0198506732] synonym: "fatty acid anabolism" EXACT [] synonym: "fatty acid biosynthesis" EXACT [] synonym: "fatty acid formation" EXACT [] synonym: "fatty acid synthesis" EXACT [] xref: MetaCyc:FASYN-INITIAL-PWY xref: MetaCyc:PWY-4381 xref: MetaCyc:PWY-5156 xref: Wikipedia:Fatty_acid_synthesis is_a: GO:0006631 ! fatty acid metabolic process is_a: GO:0008610 ! lipid biosynthetic process is_a: GO:0072330 ! monocarboxylic acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28868 ! fatty acid anion relationship: has_primary_output CHEBI:28868 ! fatty acid anion [Term] id: GO:0006725 name: cellular aromatic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732] subset: goslim_pir synonym: "aromatic compound metabolism" EXACT [] synonym: "aromatic hydrocarbon metabolic process" NARROW [] synonym: "aromatic hydrocarbon metabolism" NARROW [] is_a: GO:0044237 ! cellular metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33655 ! aromatic compound relationship: has_primary_input_or_output CHEBI:33655 ! aromatic compound [Term] id: GO:0006807 name: nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen." [GOC:jl, ISBN:0198506732] subset: goslim_metagenomics subset: goslim_pir synonym: "nitrogen compound metabolism" EXACT [] is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:51143 ! nitrogen molecular entity relationship: has_primary_input_or_output CHEBI:51143 ! nitrogen molecular entity [Term] id: GO:0006996 name: organelle organization namespace: biological_process alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] subset: goslim_candida subset: goslim_pir synonym: "organelle organisation" EXACT [] synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah] synonym: "single organism organelle organization" EXACT [GOC:TermGenie] synonym: "single-organism organelle organization" RELATED [] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] id: GO:0006997 name: nucleus organization namespace: biological_process alt_id: GO:0048287 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] subset: goslim_candida subset: goslim_drosophila subset: goslim_pir subset: goslim_yeast synonym: "nuclear morphology" RELATED [] synonym: "nuclear organisation" EXACT [] synonym: "nuclear organization" EXACT [] synonym: "nuclear organization and biogenesis" RELATED [GOC:mah] synonym: "nucleus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005634 ! nucleus relationship: results_in_organization_of GO:0005634 ! nucleus [Term] id: GO:0006998 name: nuclear envelope organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] synonym: "nuclear envelope organisation" EXACT [GOC:mah] synonym: "nuclear envelope organization and biogenesis" RELATED [GOC:mah] is_a: GO:0061024 ! membrane organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005635 ! nuclear envelope relationship: part_of GO:0006997 ! nucleus organization relationship: part_of GO:0010256 ! endomembrane system organization relationship: results_in_organization_of GO:0005635 ! nuclear envelope [Term] id: GO:0007009 name: plasma membrane organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl synonym: "plasma membrane organisation" EXACT [] synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] is_a: GO:0061024 ! membrane organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005886 ! plasma membrane relationship: part_of GO:0010256 ! endomembrane system organization relationship: results_in_organization_of GO:0005886 ! plasma membrane [Term] id: GO:0007028 name: cytoplasm organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GOC:curators, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "cytoplasm organisation" EXACT [] synonym: "cytoplasm organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005737 ! cytoplasm relationship: results_in_organization_of GO:0005737 ! cytoplasm [Term] id: GO:0007033 name: vacuole organization namespace: biological_process alt_id: GO:0044086 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole." [GOC:mah] subset: goslim_drosophila subset: goslim_pir subset: goslim_yeast synonym: "vacuolar assembly" NARROW [GOC:mah] synonym: "vacuole biogenesis" RELATED [GOC:mah] synonym: "vacuole organisation" EXACT [] synonym: "vacuole organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005773 ! vacuole relationship: results_in_organization_of GO:0005773 ! vacuole [Term] id: GO:0008047 name: enzyme activator activity namespace: molecular_function alt_id: GO:0010577 def: "Binds to and increases the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb] comment: This term should only be used in cases when the regulator directly interacts with the enzyme. synonym: "metalloenzyme activator activity" NARROW [] is_a: GO:0030234 ! enzyme regulator activity is_a: GO:0140677 ! molecular function activator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_positively_regulates GO:0003824 ! catalytic activity relationship: directly_positively_regulates GO:0003824 ! catalytic activity [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process alt_id: GO:0044236 alt_id: GO:0044710 def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_manually_annotate subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] synonym: "multicellular organism metabolic process" NARROW [] synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0008289 name: lipid binding namespace: molecular_function def: "Binding to a lipid." [GOC:ai] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: prokaryote_subset is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:18059 ! lipid relationship: has_input CHEBI:18059 ! lipid [Term] id: GO:0008291 name: acetylcholine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." [GOC:jl, GOC:nln, ISBN:0192800752] synonym: "acetylcholine metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0042133 ! neurotransmitter metabolic process is_a: GO:1900619 ! acetate ester metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:15355 ! acetylcholine relationship: has_primary_input_or_output CHEBI:15355 ! acetylcholine [Term] id: GO:0008292 name: acetylcholine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of acetylcholine, the acetic acid ester of the organic base choline." [GOC:jl, ISBN:0192800752] synonym: "acetylcholine anabolism" EXACT [] synonym: "acetylcholine biosynthesis" EXACT [] synonym: "acetylcholine formation" EXACT [] synonym: "acetylcholine synthesis" EXACT [] is_a: GO:0008291 ! acetylcholine metabolic process is_a: GO:0042136 ! neurotransmitter biosynthetic process is_a: GO:1900620 ! acetate ester biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:15355 ! acetylcholine relationship: has_primary_output CHEBI:15355 ! acetylcholine [Term] id: GO:0008610 name: lipid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators] synonym: "lipid anabolism" EXACT [] synonym: "lipid biosynthesis" EXACT [] synonym: "lipid formation" EXACT [] synonym: "lipid synthesis" EXACT [] synonym: "lipogenesis" EXACT [GOC:sl] is_a: GO:0006629 ! lipid metabolic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:18059 ! lipid relationship: has_primary_output CHEBI:18059 ! lipid [Term] id: GO:0008652 name: amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN:0198506732] synonym: "amino acid anabolism" EXACT [] synonym: "amino acid biosynthesis" EXACT [] synonym: "amino acid formation" EXACT [] synonym: "amino acid synthesis" EXACT [] synonym: "cellular amino acid biosynthetic process" EXACT [] xref: Wikipedia:Amino_acid_synthesis is_a: GO:0006520 ! amino acid metabolic process is_a: GO:0046394 ! carboxylic acid biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:37022 ! amino-acid anion relationship: has_primary_output CHEBI:37022 ! amino-acid anion property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process alt_id: GO:0044274 alt_id: GO:0044711 def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" BROAD [] synonym: "multicellular organismal biosynthetic process" NARROW [] synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: goslim_pir synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33694 ! biomacromolecule relationship: has_primary_output CHEBI:33694 ! biomacromolecule property_value: IAO:0000233 "http://amigo.geneontology.org/amigo/term/GO:0070589" xsd:anyURI [Term] id: GO:0009064 name: glutamine family amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai] synonym: "glutamine family amino acid metabolism" EXACT [] is_a: GO:1901605 ! alpha-amino acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24318 ! glutamine family amino acid relationship: has_primary_input_or_output CHEBI:24318 ! glutamine family amino acid [Term] id: GO:0009084 name: glutamine family amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai] synonym: "glutamine family amino acid anabolism" EXACT [] synonym: "glutamine family amino acid biosynthesis" EXACT [] synonym: "glutamine family amino acid formation" EXACT [] synonym: "glutamine family amino acid synthesis" EXACT [] is_a: GO:0009064 ! glutamine family amino acid metabolic process is_a: GO:0016053 ! organic acid biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:24318 ! glutamine family amino acid relationship: has_primary_output CHEBI:24318 ! glutamine family amino acid [Term] id: GO:0009112 name: nucleobase metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine." [GOC:ma] synonym: "nucleobase metabolism" EXACT [] is_a: GO:0055086 ! nucleobase-containing small molecule metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:18282 ! nucleobase relationship: has_primary_input_or_output CHEBI:18282 ! nucleobase [Term] id: GO:0009308 name: amine metabolic process namespace: biological_process alt_id: GO:0044106 def: "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732] subset: goslim_chembl subset: goslim_pir synonym: "amine metabolism" EXACT [] synonym: "cellular amine metabolic process" EXACT [] is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:32952 ! amine relationship: has_primary_input_or_output CHEBI:32952 ! amine created_by: jl creation_date: 2009-07-15T11:55:44Z [Term] id: GO:0009309 name: amine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732] synonym: "amine anabolism" EXACT [] synonym: "amine biosynthesis" EXACT [] synonym: "amine formation" EXACT [] synonym: "amine synthesis" EXACT [] is_a: GO:0009308 ! amine metabolic process is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:32952 ! amine relationship: has_primary_output CHEBI:32952 ! amine [Term] id: GO:0009448 name: gamma-aminobutyric acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [ISBN:0198506732] comment: See also the biological process term 'neurotransmitter metabolic process ; GO:0042133'. synonym: "4-aminobutanoate metabolic process" EXACT [] synonym: "4-aminobutanoate metabolism" EXACT [] synonym: "4-aminobutyrate metabolic process" EXACT [] synonym: "4-aminobutyrate metabolism" EXACT [] synonym: "GABA metabolic process" EXACT [] synonym: "GABA metabolism" EXACT [] synonym: "gamma-aminobutyric acid metabolism" EXACT [] is_a: GO:0006520 ! amino acid metabolic process is_a: GO:0032787 ! monocarboxylic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:59888 ! gamma-aminobutyric acid zwitterion relationship: has_primary_input_or_output CHEBI:59888 ! gamma-aminobutyric acid zwitterion [Term] id: GO:0009449 name: gamma-aminobutyric acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [GOC:ai] comment: See also the biological process term 'neurotransmitter biosynthetic process ; GO:0042136'. synonym: "4-aminobutanoate biosynthesis" EXACT [] synonym: "4-aminobutanoate biosynthetic process" EXACT [] synonym: "4-aminobutyrate biosynthesis" EXACT [] synonym: "4-aminobutyrate biosynthetic process" EXACT [] synonym: "GABA biosynthesis" EXACT [] synonym: "GABA biosynthetic process" EXACT [] synonym: "gamma-aminobutyric acid anabolism" EXACT [] synonym: "gamma-aminobutyric acid biosynthesis" EXACT [] synonym: "gamma-aminobutyric acid formation" EXACT [] synonym: "gamma-aminobutyric acid synthesis" EXACT [] is_a: GO:0009448 ! gamma-aminobutyric acid metabolic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:59888 ! gamma-aminobutyric acid zwitterion relationship: has_primary_output CHEBI:59888 ! gamma-aminobutyric acid zwitterion [Term] id: GO:0009712 name: catechol-containing compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent." [GOC:sm, ISBN:0198547684] synonym: "catechol metabolic process" RELATED [] synonym: "catechol metabolism" RELATED [] is_a: GO:0018958 ! phenol-containing compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33566 ! catechols relationship: has_primary_input_or_output CHEBI:33566 ! catechols [Term] id: GO:0009713 name: catechol-containing compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." [GOC:go_curators] synonym: "catechol anabolism" RELATED [] synonym: "catechol biosynthesis" RELATED [] synonym: "catechol biosynthetic process" RELATED [] synonym: "catechol formation" RELATED [] synonym: "catechol synthesis" RELATED [] is_a: GO:0009712 ! catechol-containing compound metabolic process is_a: GO:0046189 ! phenol-containing compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33566 ! catechols relationship: has_primary_output CHEBI:33566 ! catechols [Term] id: GO:0009820 name: alkaloid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases)." [GOC:lr, ISBN:0122146743] subset: goslim_chembl synonym: "alkaloid metabolism" EXACT [] is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:22315 ! alkaloid relationship: has_primary_input_or_output CHEBI:22315 ! alkaloid [Term] id: GO:0009821 name: alkaloid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases)." [GOC:lr, ISBN:0122146743] synonym: "alkaloid anabolism" EXACT [] synonym: "alkaloid biosynthesis" EXACT [] synonym: "alkaloid formation" EXACT [] synonym: "alkaloid synthesis" EXACT [] xref: UM-BBD_enzymeID:e0711 is_a: GO:0009820 ! alkaloid metabolic process is_a: GO:0044550 ! secondary metabolite biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:22315 ! alkaloid relationship: has_primary_output CHEBI:22315 ! alkaloid [Term] id: GO:0009987 name: cellular process namespace: biological_process alt_id: GO:0008151 alt_id: GO:0044763 alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate subset: goslim_plant synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] id: GO:0010256 name: endomembrane system organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system." [GOC:mah, GOC:sm] subset: goslim_drosophila synonym: "endomembrane organization" EXACT [] synonym: "endomembrane system organisation" EXACT [GOC:mah] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0012505 ! endomembrane system relationship: results_in_organization_of GO:0012505 ! endomembrane system [Term] id: GO:0010467 name: gene expression namespace: biological_process def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes." [GOC:txnOH-2018, PMID:25934543, PMID:31580950] subset: goslim_flybase_ribbon xref: Wikipedia:Gene_expression is_a: GO:0043170 ! macromolecule metabolic process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22557" xsd:anyURI [Term] id: GO:0012505 name: endomembrane system namespace: cellular_component def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh] subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast xref: Wikipedia:Endomembrane_system is_a: GO:0110165 ! cellular anatomical entity relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 [Term] id: GO:0016020 name: membrane namespace: cellular_component alt_id: GO:0016021 alt_id: GO:0098589 alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "integral component of membrane" NARROW [] synonym: "integral to membrane" NARROW [] synonym: "membrane region" NARROW [] synonym: "region of membrane" NARROW [] synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein is_a: GO:0110165 ! cellular anatomical entity creation_date: 2014-03-06T11:37:54Z [Term] id: GO:0016043 name: cellular component organization namespace: biological_process alt_id: GO:0044235 alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: goslim_agr subset: goslim_mouse subset: goslim_pir subset: goslim_plant synonym: "cell organisation" EXACT [] synonym: "cell organization and biogenesis" RELATED [GOC:mah] synonym: "cellular component organisation at cellular level" EXACT [GOC:mah] synonym: "cellular component organisation in other organism" EXACT [GOC:mah] synonym: "cellular component organization at cellular level" EXACT [] synonym: "cellular component organization in other organism" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis intersection_of: GO:0009987 ! cellular process intersection_of: results_in_organization_of GO:0005575 ! cellular_component relationship: results_in_organization_of GO:0005575 ! cellular_component [Term] id: GO:0016053 name: organic acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] synonym: "organic acid anabolism" EXACT [] synonym: "organic acid biosynthesis" EXACT [] synonym: "organic acid formation" EXACT [] synonym: "organic acid synthesis" EXACT [] is_a: GO:0006082 ! organic acid metabolic process is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0044283 ! small molecule biosynthetic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:64709 ! organic acid relationship: has_primary_output CHEBI:64709 ! organic acid [Term] id: GO:0016070 name: RNA metabolic process namespace: biological_process def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir subset: prokaryote_subset synonym: "RNA metabolism" EXACT [] is_a: GO:0090304 ! nucleic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33697 ! ribonucleic acid relationship: has_primary_input_or_output CHEBI:33697 ! ribonucleic acid [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:0016595 name: glutamate binding namespace: molecular_function def: "Binding to glutamate, the anion of 2-aminopentanedioic acid." [GOC:ai] synonym: "glutamic acid binding" EXACT [] is_a: GO:0031406 ! carboxylic acid binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:14321 ! glutamate(1-) relationship: has_input CHEBI:14321 ! glutamate(1-) [Term] id: GO:0016597 name: amino acid binding namespace: molecular_function def: "Binding to an amino acid, organic acids containing one or more amino substituents." [GOC:ai] subset: goslim_metagenomics subset: goslim_pir is_a: GO:0043177 ! organic acid binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:33709 ! amino acid relationship: has_input CHEBI:33709 ! amino acid [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_yeast subset: prokaryote_subset 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: GO:0018130 name: heterocycle biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198547684] synonym: "heterocycle anabolism" EXACT [] synonym: "heterocycle biosynthesis" EXACT [] synonym: "heterocycle formation" EXACT [] synonym: "heterocycle synthesis" EXACT [] is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0046483 ! heterocycle metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:5686 ! heterocyclic compound relationship: has_primary_output CHEBI:5686 ! heterocyclic compound [Term] id: GO:0018958 name: phenol-containing compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." [ISBN:0198506732] comment: Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds. synonym: "carbolic acid metabolic process" EXACT [] synonym: "carbolic acid metabolism" EXACT [] synonym: "hydroxybenzene metabolic process" EXACT [] synonym: "hydroxybenzene metabolism" EXACT [] synonym: "phenol-containing compound metabolism" EXACT [] xref: UM-BBD_pathwayID:phe is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33853 ! phenols relationship: has_primary_input_or_output CHEBI:33853 ! phenols [Term] id: GO:0019207 name: kinase regulator activity namespace: molecular_function def: "Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] is_a: GO:0030234 ! enzyme regulator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_regulates GO:0016301 ! kinase activity relationship: directly_regulates GO:0016301 ! kinase activity [Term] id: GO:0019209 name: kinase activator activity namespace: molecular_function def: "Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] is_a: GO:0008047 ! enzyme activator activity is_a: GO:0019207 ! kinase regulator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_positively_regulates GO:0016301 ! kinase activity relationship: directly_positively_regulates GO:0016301 ! kinase activity [Term] id: GO:0019210 name: kinase inhibitor activity namespace: molecular_function def: "Binds to and stops, prevents or reduces the activity of a kinase." [GOC:mah] is_a: GO:0004857 ! enzyme inhibitor activity is_a: GO:0019207 ! kinase regulator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_negatively_regulates GO:0016301 ! kinase activity relationship: directly_negatively_regulates GO:0016301 ! kinase activity [Term] id: GO:0019413 name: acetate biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid." [GOC:go_curators] synonym: "acetate anabolism" EXACT [] synonym: "acetate biosynthesis" EXACT [] synonym: "acetate formation" EXACT [] synonym: "acetate synthesis" EXACT [] is_a: GO:0006083 ! acetate metabolic process is_a: GO:0072330 ! monocarboxylic acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:30089 ! acetate relationship: has_primary_output CHEBI:30089 ! acetate [Term] id: GO:0019438 name: aromatic compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] synonym: "aromatic compound anabolism" EXACT [] synonym: "aromatic compound biosynthesis" EXACT [] synonym: "aromatic compound formation" EXACT [] synonym: "aromatic compound synthesis" EXACT [] synonym: "aromatic hydrocarbon biosynthesis" NARROW [] synonym: "aromatic hydrocarbon biosynthetic process" NARROW [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0044249 ! cellular biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33655 ! aromatic compound relationship: has_primary_output CHEBI:33655 ! aromatic compound [Term] id: GO:0019538 name: protein metabolic process namespace: biological_process alt_id: GO:0006411 alt_id: GO:0044267 alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir subset: goslim_plant synonym: "cellular protein metabolic process" EXACT [] synonym: "cellular protein metabolism" EXACT [] synonym: "multicellular organismal protein metabolic process" NARROW [] synonym: "protein metabolic process and modification" EXACT [] synonym: "protein metabolism" EXACT [] synonym: "protein metabolism and modification" EXACT [] xref: Wikipedia:Protein_metabolism is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output PR:000000001 ! protein relationship: has_primary_input_or_output PR:000000001 ! protein property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI [Term] id: GO:0019605 name: butyrate metabolic process namespace: biological_process alt_id: GO:0043437 def: "The chemical reactions and pathways involving any butyrate, the anions of butyric acid (butanoic acid), a saturated, unbranched aliphatic acid." [ISBN:0198506732] synonym: "butanoic acid metabolic process" EXACT [] synonym: "butanoic acid metabolism" EXACT [] synonym: "butyrate metabolism" EXACT [] synonym: "butyric acid metabolic process" EXACT [] synonym: "butyric acid metabolism" EXACT [] is_a: GO:0046459 ! short-chain fatty acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:17968 ! butyrate relationship: has_primary_input_or_output CHEBI:17968 ! butyrate [Term] id: GO:0019695 name: choline metabolic process namespace: biological_process def: "The chemical reactions and pathways involving choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine." [GOC:jl, ISBN:0192801023] synonym: "choline metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process is_a: GO:0097164 ! ammonium ion metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:15354 ! choline relationship: has_primary_input_or_output CHEBI:15354 ! choline [Term] id: GO:0019748 name: secondary metabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators] subset: goslim_chembl subset: goslim_pir subset: goslim_plant subset: goslim_pombe synonym: "secondary metabolism" EXACT [] synonym: "secondary metabolite metabolic process" EXACT [] synonym: "secondary metabolite metabolism" EXACT [] xref: Wikipedia:Secondary_metabolism is_a: GO:0008152 ! metabolic process [Term] id: GO:0019751 name: polyol metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms." [PMID:30240188] synonym: "polyhydric alcohol metabolic process" EXACT [] synonym: "polyol metabolism" EXACT [] is_a: GO:0006066 ! alcohol metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:26191 ! polyol relationship: has_primary_input_or_output CHEBI:26191 ! polyol [Term] id: GO:0019752 name: carboxylic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [ISBN:0198506732] synonym: "carboxylic acid metabolism" EXACT [] is_a: GO:0043436 ! oxoacid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:29067 ! carboxylic acid anion relationship: has_primary_input_or_output CHEBI:29067 ! carboxylic acid anion [Term] id: GO:0022411 name: cellular component disassembly namespace: biological_process alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] subset: goslim_pir synonym: "cell structure disassembly" EXACT [] synonym: "cellular component disassembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0009987 ! cellular process intersection_of: results_in_disassembly_of GO:0005575 ! cellular_component disjoint_from: GO:0022607 ! cellular component assembly relationship: results_in_disassembly_of GO:0005575 ! cellular_component [Term] id: GO:0022607 name: cellular component assembly namespace: biological_process alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_pir synonym: "cell structure assembly" EXACT [] synonym: "cellular component assembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0009987 ! cellular process intersection_of: results_in_assembly_of GO:0005575 ! cellular_component relationship: part_of GO:0044085 ! cellular component biogenesis relationship: results_in_assembly_of GO:0005575 ! cellular_component [Term] id: GO:0022613 name: ribonucleoprotein complex biogenesis namespace: biological_process def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex." [GOC:isa_complete, GOC:mah] synonym: "ribonucleoprotein complex biogenesis and assembly" EXACT [GOC:mah] synonym: "RNA-protein complex biogenesis" EXACT [GOC:mah] is_a: GO:0044085 ! cellular component biogenesis [Term] id: GO:0022618 name: ribonucleoprotein complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl] subset: goslim_chembl synonym: "protein-RNA complex assembly" EXACT [] synonym: "RNA-protein complex assembly" EXACT [] synonym: "RNP complex assembly" EXACT [] is_a: GO:0065003 ! protein-containing complex assembly is_a: GO:0071826 ! ribonucleoprotein complex subunit organization intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex [Term] id: GO:0030234 name: enzyme regulator activity namespace: molecular_function alt_id: GO:0010576 def: "Binds to and modulates the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb] comment: This term should only be used in cases when the regulator directly interacts with the enzyme. subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "catalytic regulator activity" EXACT [GOC:dph] synonym: "enzyme modulator" EXACT [] synonym: "metalloenzyme regulator activity" NARROW [] is_a: GO:0098772 ! molecular function regulator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_regulates GO:0003824 ! catalytic activity relationship: directly_regulates GO:0003824 ! catalytic activity [Term] id: GO:0030397 name: membrane disassembly namespace: biological_process def: "The controlled breakdown of any cell membrane in the context of a normal process such as autophagy." [GOC:mah] synonym: "membrane breakdown" EXACT [] synonym: "membrane catabolism" EXACT [] synonym: "membrane degradation" EXACT [] is_a: GO:0022411 ! cellular component disassembly is_a: GO:0061024 ! membrane organization intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0016020 ! membrane relationship: results_in_disassembly_of GO:0016020 ! membrane [Term] id: GO:0031090 name: organelle membrane namespace: cellular_component def: "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle." [GOC:dos, GOC:mah] synonym: "intracellular membrane" RELATED [NIF_Subcellular:sao830981606] xref: NIF_Subcellular:sao830981606 is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0043227 ! membrane-bounded organelle relationship: part_of GO:0043227 ! membrane-bounded organelle [Term] id: GO:0031406 name: carboxylic acid binding namespace: molecular_function def: "Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732] subset: goslim_pir is_a: GO:0043168 ! anion binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:29067 ! carboxylic acid anion relationship: has_input CHEBI:29067 ! carboxylic acid anion [Term] id: GO:0031965 name: nuclear membrane namespace: cellular_component def: "Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space." [GOC:mah, GOC:pz] xref: NIF_Subcellular:sao1687101204 is_a: GO:0031090 ! organelle membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005635 ! nuclear envelope [Term] id: GO:0031967 name: organelle envelope namespace: cellular_component def: "A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes." [GOC:mah, GOC:pz] subset: goslim_mouse is_a: GO:0031975 ! envelope relationship: part_of GO:0043227 ! membrane-bounded organelle relationship: part_of GO:0043229 ! intracellular organelle [Term] id: GO:0031975 name: envelope namespace: cellular_component def: "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers." [GOC:mah, GOC:pz] is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 [Term] id: GO:0032774 name: RNA biosynthetic process namespace: biological_process alt_id: GO:0062103 def: "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication." [GOC:mah, GOC:txnOH] comment: Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. subset: gocheck_do_not_annotate synonym: "double-stranded RNA biosynthesis" NARROW [] synonym: "double-stranded RNA biosynthetic process" NARROW [] synonym: "dsRNA biosynthesis" NARROW [] synonym: "dsRNA biosynthetic process" NARROW [GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:rl] synonym: "RNA anabolism" EXACT [] synonym: "RNA biosynthesis" EXACT [] synonym: "RNA formation" EXACT [] synonym: "RNA synthesis" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016070 ! RNA metabolic process is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33697 ! ribonucleic acid relationship: has_primary_output CHEBI:33697 ! ribonucleic acid [Term] id: GO:0032787 name: monocarboxylic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-)." [GOC:vk] subset: goslim_yeast synonym: "monocarboxylate metabolic process" EXACT [] synonym: "monocarboxylic acid metabolism" EXACT [] is_a: GO:0019752 ! carboxylic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:35757 ! monocarboxylic acid anion relationship: has_primary_input_or_output CHEBI:35757 ! monocarboxylic acid anion [Term] id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process alt_id: GO:0034623 alt_id: GO:0043241 alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] synonym: "macromolecule complex disassembly" RELATED [] synonym: "protein complex disassembly" EXACT [] is_a: GO:0022411 ! cellular component disassembly is_a: GO:0043933 ! protein-containing complex organization intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0032991 ! protein-containing complex relationship: results_in_disassembly_of GO:0032991 ! protein-containing complex property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI [Term] id: GO:0032988 name: ribonucleoprotein complex disassembly namespace: biological_process def: "The disaggregation of a protein-RNA complex into its constituent components." [GOC:mah] synonym: "protein-RNA complex disassembly" EXACT [] synonym: "RNA-protein complex disassembly" EXACT [] synonym: "RNP complex disassembly" EXACT [] is_a: GO:0032984 ! protein-containing complex disassembly is_a: GO:0071826 ! ribonucleoprotein complex subunit organization intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_disassembly_of GO:1990904 ! ribonucleoprotein complex [Term] id: GO:0032991 name: protein-containing complex namespace: cellular_component alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir synonym: "macromolecular complex" EXACT [] synonym: "macromolecule complex" EXACT [] synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity [Term] id: GO:0033218 name: amide binding namespace: molecular_function def: "Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:mah] subset: goslim_pir is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:32988 ! amide relationship: has_input CHEBI:32988 ! amide [Term] id: GO:0033265 name: choline binding namespace: molecular_function def: "Binding to choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium." [GOC:mlg] is_a: GO:0043169 ! cation binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:15354 ! choline relationship: has_input CHEBI:15354 ! choline [Term] id: GO:0033293 name: monocarboxylic acid binding namespace: molecular_function def: "Binding to a monocarboxylic acid, any organic acid containing one carboxyl (COOH) group or anion (COO-)." [GOC:mah] is_a: GO:0031406 ! carboxylic acid binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:35757 ! monocarboxylic acid anion relationship: has_input CHEBI:35757 ! monocarboxylic acid anion [Term] id: GO:0034311 name: diol metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a diol, a compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic." [GOC:curators] synonym: "dihydric alcohol metabolic process" RELATED [] synonym: "diol metabolism" EXACT [] is_a: GO:0019751 ! polyol metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:23824 ! diol relationship: has_primary_input_or_output CHEBI:23824 ! diol [Term] id: GO:0034312 name: diol biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a diol, any alcohol containing two hydroxyl groups attached to saturated carbon atoms." [GOC:mah] synonym: "dihydric alcohol biosynthetic process" EXACT [] synonym: "diol anabolism" EXACT [] synonym: "diol biosynthesis" EXACT [] synonym: "diol formation" EXACT [] synonym: "diol synthesis" EXACT [] is_a: GO:0034311 ! diol metabolic process is_a: GO:0046173 ! polyol biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:23824 ! diol relationship: has_primary_output CHEBI:23824 ! diol [Term] id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] subset: goslim_chembl synonym: "cellular nitrogen compound metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0034654 name: nucleobase-containing compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid anabolism" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid formation" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid synthesis" NARROW [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0018130 ! heterocycle biosynthetic process is_a: GO:0019438 ! aromatic compound biosynthetic process is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process is_a: GO:1901362 ! organic cyclic compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:61120 ! nucleobase-containing molecular entity relationship: has_primary_output CHEBI:61120 ! nucleobase-containing molecular entity [Term] id: GO:0035240 name: dopamine binding namespace: molecular_function def: "Binding to dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine." [ISBN:0198506732] is_a: GO:0043169 ! cation binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:59905 ! dopaminium(1+) relationship: has_input CHEBI:59905 ! dopaminium(1+) [Term] id: GO:0035834 name: indole alkaloid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an indole alkaloid, an alkaloid containing an indole skeleton." [GOC:yaf] synonym: "indole alkaloid metabolism" EXACT [GOC:bf] is_a: GO:0009820 ! alkaloid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:38958 ! indole alkaloid relationship: has_primary_input_or_output CHEBI:38958 ! indole alkaloid created_by: bf creation_date: 2011-05-04T03:17:44Z [Term] id: GO:0035835 name: indole alkaloid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an indole alkaloid, an alkaloid containing an indole skeleton." [GOC:yaf] synonym: "indole alkaloid anabolism" EXACT [GOC:bf] synonym: "indole alkaloid biosynthesis" EXACT [GOC:bf] synonym: "indole alkaloid formation" EXACT [GOC:bf] synonym: "indole alkaloid synthesis" EXACT [GOC:bf] is_a: GO:0009821 ! alkaloid biosynthetic process is_a: GO:0035834 ! indole alkaloid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:38958 ! indole alkaloid relationship: has_primary_output CHEBI:38958 ! indole alkaloid created_by: bf creation_date: 2011-05-04T03:18:31Z [Term] id: GO:0036094 name: small molecule binding namespace: molecular_function def: "Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:pm] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. subset: goslim_agr subset: goslim_flybase_ribbon is_a: GO:0005488 ! binding created_by: bf creation_date: 2012-01-17T04:20:34Z [Term] id: GO:0042133 name: neurotransmitter metabolic process namespace: biological_process def: "The chemical reactions and pathways involving neurotransmitters, any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell." [GOC:jl] subset: goslim_pir synonym: "neurotransmitter metabolism" EXACT [] is_a: GO:0001505 ! regulation of neurotransmitter levels is_a: GO:0044237 ! cellular metabolic process property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0042136 name: neurotransmitter biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell." [GOC:jl] subset: goslim_synapse synonym: "neurotransmitter anabolism" EXACT [] synonym: "neurotransmitter biosynthesis" EXACT [] synonym: "neurotransmitter biosynthesis and storage" BROAD [] synonym: "neurotransmitter biosynthetic process and storage" BROAD [] synonym: "neurotransmitter formation" EXACT [] synonym: "neurotransmitter synthesis" EXACT [] is_a: GO:0042133 ! neurotransmitter metabolic process is_a: GO:0044249 ! cellular biosynthetic process [Term] id: GO:0042165 name: neurotransmitter binding namespace: molecular_function def: "Binding to a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [ISBN:0198506732] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0042166 name: acetylcholine binding namespace: molecular_function def: "Binding to acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai] is_a: GO:0042165 ! neurotransmitter binding is_a: GO:0043169 ! cation binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:15355 ! acetylcholine relationship: has_input CHEBI:15355 ! acetylcholine [Term] id: GO:0042277 name: peptide binding namespace: molecular_function def: "Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds." [GOC:jl] subset: goslim_chembl subset: goslim_pir is_a: GO:0033218 ! amide binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:16670 ! peptide relationship: has_input CHEBI:16670 ! peptide [Term] id: GO:0042401 name: biogenic amine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:jl, ISBN:0395825172] synonym: "biogenic amine anabolism" EXACT [] synonym: "biogenic amine biosynthesis" EXACT [] synonym: "biogenic amine formation" EXACT [] synonym: "biogenic amine synthesis" EXACT [] synonym: "cellular biogenic amine biosynthetic process" EXACT [] is_a: GO:0006576 ! biogenic amine metabolic process is_a: GO:0009309 ! amine biosynthetic process [Term] id: GO:0042416 name: dopamine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." [GOC:jl, ISBN:0198506732] synonym: "dopamine anabolism" EXACT [] synonym: "dopamine biosynthesis" EXACT [] synonym: "dopamine formation" EXACT [] synonym: "dopamine synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0042417 ! dopamine metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:59905 ! dopaminium(1+) relationship: has_primary_output CHEBI:59905 ! dopaminium(1+) [Term] id: GO:0042417 name: dopamine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." [GOC:jl, ISBN:0198506732] synonym: "dopamine metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:59905 ! dopaminium(1+) relationship: has_primary_input_or_output CHEBI:59905 ! dopaminium(1+) [Term] id: GO:0042423 name: catecholamine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:jl, ISBN:0198506732] synonym: "catecholamine anabolism" EXACT [] synonym: "catecholamine biosynthesis" EXACT [] synonym: "catecholamine formation" EXACT [] synonym: "catecholamine synthesis" EXACT [] xref: Wikipedia:Catecholamines is_a: GO:0006584 ! catecholamine metabolic process is_a: GO:0009713 ! catechol-containing compound biosynthetic process is_a: GO:0042401 ! biogenic amine biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33567 ! catecholamine relationship: has_primary_output CHEBI:33567 ! catecholamine [Term] id: GO:0042425 name: choline biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine." [GOC:jl, ISBN:0192801023] synonym: "choline anabolism" EXACT [] synonym: "choline biosynthesis" EXACT [] synonym: "choline formation" EXACT [] synonym: "choline synthesis" EXACT [] xref: MetaCyc:PWY-4762 is_a: GO:0019695 ! choline metabolic process is_a: GO:0042401 ! biogenic amine biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:15354 ! choline relationship: has_primary_output CHEBI:15354 ! choline [Term] id: GO:0042427 name: serotonin biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:jl, ISBN:0198506732] synonym: "serotonin anabolism" EXACT [] synonym: "serotonin biosynthesis" EXACT [] synonym: "serotonin formation" EXACT [] synonym: "serotonin synthesis" EXACT [] xref: Wikipedia:Serotonin is_a: GO:0009058 ! biosynthetic process is_a: GO:0042428 ! serotonin metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:350546 ! serotonin(1+) relationship: has_primary_output CHEBI:350546 ! serotonin(1+) [Term] id: GO:0042428 name: serotonin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:jl, ISBN:0198506732] synonym: "serotonin metabolism" EXACT [] is_a: GO:0018958 ! phenol-containing compound metabolic process is_a: GO:0042430 ! indole-containing compound metabolic process is_a: GO:0097164 ! ammonium ion metabolic process is_a: GO:1901160 ! primary amino compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:350546 ! serotonin(1+) relationship: has_primary_input_or_output CHEBI:350546 ! serotonin(1+) [Term] id: GO:0042430 name: indole-containing compound metabolic process namespace: biological_process alt_id: GO:0042434 def: "The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton." [GOC:jl, GOC:mah] synonym: "indole and derivative metabolic process" EXACT [] synonym: "indole and derivative metabolism" EXACT [] synonym: "indole derivative metabolic process" NARROW [] synonym: "indole derivative metabolism" NARROW [] synonym: "indole-containing compound metabolism" EXACT [] synonym: "ketole metabolic process" EXACT [] synonym: "ketole metabolism" EXACT [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24828 ! indoles relationship: has_primary_input_or_output CHEBI:24828 ! indoles [Term] id: GO:0042435 name: indole-containing compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton." [GOC:jl] synonym: "indole derivative biosynthesis" EXACT [] synonym: "indole derivative biosynthetic process" EXACT [] synonym: "indole-containing compound anabolism" EXACT [] synonym: "indole-containing compound biosynthesis" EXACT [] synonym: "indole-containing compound formation" EXACT [] synonym: "indole-containing compound synthesis" EXACT [] is_a: GO:0018130 ! heterocycle biosynthetic process is_a: GO:0019438 ! aromatic compound biosynthetic process is_a: GO:0042430 ! indole-containing compound metabolic process is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process is_a: GO:1901362 ! organic cyclic compound biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:24828 ! indoles relationship: has_primary_output CHEBI:24828 ! indoles [Term] id: GO:0042439 name: ethanolamine-containing compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving ethanolamine (2-aminoethanol) and compounds derived from it." [GOC:mah] synonym: "ethanolamine and derivative metabolic process" EXACT [] synonym: "ethanolamine and derivative metabolism" EXACT [] synonym: "ethanolamine-containing compound metabolism" EXACT [GOC:mah] is_a: GO:0006066 ! alcohol metabolic process is_a: GO:0006576 ! biogenic amine metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:23981 ! ethanolamines relationship: has_primary_input_or_output CHEBI:23981 ! ethanolamines [Term] id: GO:0043021 name: ribonucleoprotein complex binding namespace: molecular_function def: "Binding to a complex of RNA and protein." [GOC:bf, GOC:go_curators, GOC:vk] subset: goslim_pir synonym: "protein-RNA complex binding" EXACT [GOC:bf, GOC:vk] synonym: "ribonucleoprotein binding" EXACT [GOC:bf, GOC:vk] synonym: "RNP binding" EXACT [] is_a: GO:0044877 ! protein-containing complex binding intersection_of: GO:0005488 ! binding intersection_of: has_input GO:1990904 ! ribonucleoprotein complex relationship: has_input GO:1990904 ! ribonucleoprotein complex [Term] id: GO:0043043 name: peptide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide." [GOC:dph, GOC:jl] synonym: "peptide anabolism" EXACT [] synonym: "peptide biosynthesis" EXACT [] synonym: "peptide formation" EXACT [] synonym: "peptide synthesis" EXACT [] is_a: GO:0006518 ! peptide metabolic process is_a: GO:0043604 ! amide biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:16670 ! peptide relationship: has_primary_output CHEBI:16670 ! peptide [Term] id: GO:0043167 name: ion binding namespace: molecular_function def: "Binding to an ion, a charged atoms or groups of atoms." [GOC:jl] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast synonym: "atom binding" RELATED [] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:24870 ! ion relationship: has_input CHEBI:24870 ! ion [Term] id: GO:0043168 name: anion binding namespace: molecular_function def: "Binding to an anion, a charged atom or group of atoms with a net negative charge." [GOC:jl] is_a: GO:0043167 ! ion binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:22563 ! anion relationship: has_input CHEBI:22563 ! anion [Term] id: GO:0043169 name: cation binding namespace: molecular_function def: "Binding to a cation, a charged atom or group of atoms with a net positive charge." [GOC:jl] is_a: GO:0043167 ! ion binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:36916 ! cation relationship: has_input CHEBI:36916 ! cation [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0034960 alt_id: GO:0043283 alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: goslim_pir synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] synonym: "multicellular organismal macromolecule metabolic process" NARROW [] synonym: "organismal macromolecule metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33694 ! biomacromolecule relationship: has_primary_input_or_output CHEBI:33694 ! biomacromolecule [Term] id: GO:0043176 name: amine binding namespace: molecular_function def: "Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group." [GOC:jl] subset: goslim_pir is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:32952 ! amine relationship: has_input CHEBI:32952 ! amine [Term] id: GO:0043177 name: organic acid binding namespace: molecular_function def: "Binding to an organic acid, any acidic compound containing carbon in covalent linkage." [GOC:jl, ISBN:0198506732] is_a: GO:0036094 ! small molecule binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:64709 ! organic acid relationship: has_input CHEBI:64709 ! organic acid [Term] id: GO:0043178 name: alcohol binding namespace: molecular_function def: "Binding to an alcohol, any of a class of alkyl compounds containing a hydroxyl group." [GOC:jl, ISBN:0198506732] subset: goslim_pir is_a: GO:0036094 ! small molecule binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:30879 ! alcohol relationship: has_input CHEBI:30879 ! alcohol [Term] id: GO:0043226 name: organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: prokaryote_subset xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane relationship: has_part GO:0016020 ! membrane [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043231 name: intracellular membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_pir synonym: "intracellular membrane-enclosed organelle" EXACT [] is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0043229 ! intracellular organelle intersection_of: GO:0043227 ! membrane-bounded organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043436 name: oxoacid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [Wikipedia:Oxyacid] synonym: "keto acid metabolic process" EXACT [] synonym: "keto acid metabolism" EXACT [] synonym: "ketoacid metabolic process" EXACT [] synonym: "ketoacid metabolism" EXACT [] synonym: "oxo acid metabolic process" EXACT [] synonym: "oxo acid metabolism" EXACT [] synonym: "oxoacid metabolism" EXACT [] is_a: GO:0006082 ! organic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:35406 ! oxoanion relationship: has_primary_input_or_output CHEBI:35406 ! oxoanion [Term] id: GO:0043603 name: amide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." [GOC:curators] subset: goslim_pir synonym: "amide metabolism" EXACT [] synonym: "cellular amide metabolic process" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:32988 ! amide relationship: has_primary_input_or_output CHEBI:32988 ! amide [Term] id: GO:0043604 name: amide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:curators] is_a: GO:0043603 ! amide metabolic process is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:32988 ! amide relationship: has_primary_output CHEBI:32988 ! amide [Term] id: GO:0043648 name: dicarboxylic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-)." [ISBN:0198506732] synonym: "dicarboxylate metabolic process" EXACT [] synonym: "dicarboxylate metabolism" EXACT [] synonym: "dicarboxylic acid metabolism" EXACT [] is_a: GO:0019752 ! carboxylic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:35693 ! dicarboxylic acid anion relationship: has_primary_input_or_output CHEBI:35693 ! dicarboxylic acid anion [Term] id: GO:0043650 name: dicarboxylic acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups." [ISBN:0198506732] synonym: "dicarboxylate biosynthesis" EXACT [] synonym: "dicarboxylate biosynthetic process" EXACT [] synonym: "dicarboxylic acid anabolism" EXACT [] synonym: "dicarboxylic acid biosynthesis" EXACT [] synonym: "dicarboxylic acid formation" EXACT [] synonym: "dicarboxylic acid synthesis" EXACT [] is_a: GO:0043648 ! dicarboxylic acid metabolic process is_a: GO:0046394 ! carboxylic acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:35693 ! dicarboxylic acid anion relationship: has_primary_output CHEBI:35693 ! dicarboxylic acid anion [Term] id: GO:0043933 name: protein-containing complex organization namespace: biological_process alt_id: GO:0034600 alt_id: GO:0034621 alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] synonym: "cellular macromolecular complex subunit organization" RELATED [] synonym: "macromolecular complex organization" RELATED [] synonym: "macromolecular complex subunit organisation" RELATED [] synonym: "macromolecular complex subunit organization" RELATED [] synonym: "protein complex subunit organisation" EXACT [GOC:mah] synonym: "protein complex subunit organization" EXACT [] synonym: "protein-containing complex subunit organization" RELATED [] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis [Term] id: GO:0044091 name: membrane biogenesis namespace: biological_process def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane." [GOC:jl] is_a: GO:0044085 ! cellular component biogenesis intersection_of: GO:0044085 ! cellular component biogenesis intersection_of: has_output GO:0016020 ! membrane relationship: has_output GO:0016020 ! membrane [Term] id: GO:0044207 name: translation initiation ternary complex namespace: cellular_component def: "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:jl] synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm created_by: jl creation_date: 2009-10-22T02:38:55Z [Term] id: GO:0044237 name: cellular metabolic process namespace: biological_process def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate synonym: "cellular metabolism" EXACT [] synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] subset: goslim_pir synonym: "primary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0044249 name: cellular biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] synonym: "cellular anabolism" EXACT [] synonym: "cellular biosynthesis" EXACT [] synonym: "cellular formation" EXACT [] synonym: "cellular synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044255 name: cellular lipid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving lipids, as carried out by individual cells." [GOC:jl] subset: goslim_pir synonym: "cellular lipid metabolism" EXACT [] is_a: GO:0006629 ! lipid metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044271 name: cellular nitrogen compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] synonym: "nitrogen compound anabolism" BROAD [] synonym: "nitrogen compound biosynthesis" BROAD [] synonym: "nitrogen compound formation" BROAD [] synonym: "nitrogen compound synthesis" BROAD [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044249 ! cellular biosynthetic process [Term] id: GO:0044281 name: small molecule metabolic process namespace: biological_process def: "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_metagenomics synonym: "small molecule metabolism" EXACT [] is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2010-01-26T12:05:20Z [Term] id: GO:0044283 name: small molecule biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. subset: prokaryote_subset synonym: "small molecule biosynthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044281 ! small molecule metabolic process created_by: jl creation_date: 2010-01-26T12:06:49Z [Term] id: GO:0044550 name: secondary metabolite biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon." [GOC:jl] subset: prokaryote_subset synonym: "secondary metabolite biosynthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0019748 ! secondary metabolic process created_by: jl creation_date: 2012-03-29T01:55:18Z [Term] id: GO:0044877 name: protein-containing complex binding namespace: molecular_function alt_id: GO:0032403 def: "Binding to a macromolecular complex." [GOC:jl] subset: goslim_chembl synonym: "macromolecular complex binding" RELATED [] synonym: "protein complex binding" EXACT [] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input GO:0032991 ! protein-containing complex relationship: has_input GO:0032991 ! protein-containing complex created_by: jl creation_date: 2014-12-16T11:38:58Z [Term] id: GO:0046112 name: nucleobase biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid." [GOC:ai] synonym: "nucleobase anabolism" EXACT [] synonym: "nucleobase biosynthesis" EXACT [] synonym: "nucleobase formation" EXACT [] synonym: "nucleobase synthesis" EXACT [] is_a: GO:0009112 ! nucleobase metabolic process is_a: GO:0018130 ! heterocycle biosynthetic process is_a: GO:1901362 ! organic cyclic compound biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:18282 ! nucleobase relationship: has_primary_output CHEBI:18282 ! nucleobase [Term] id: GO:0046165 name: alcohol biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [GOC:ai] synonym: "alcohol anabolism" EXACT [] synonym: "alcohol biosynthesis" EXACT [] synonym: "alcohol formation" EXACT [] synonym: "alcohol synthesis" EXACT [] is_a: GO:0006066 ! alcohol metabolic process is_a: GO:0044283 ! small molecule biosynthetic process is_a: GO:1901617 ! organic hydroxy compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:30879 ! alcohol relationship: has_primary_output CHEBI:30879 ! alcohol [Term] id: GO:0046173 name: polyol biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms." [GOC:curators] synonym: "polyhydric alcohol biosynthetic process" EXACT [] synonym: "polyol anabolism" EXACT [] synonym: "polyol biosynthesis" EXACT [] synonym: "polyol formation" EXACT [] synonym: "polyol synthesis" EXACT [] is_a: GO:0019751 ! polyol metabolic process is_a: GO:0046165 ! alcohol biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:26191 ! polyol relationship: has_primary_output CHEBI:26191 ! polyol [Term] id: GO:0046189 name: phenol-containing compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." [GOC:ai] synonym: "phenol-containing compound anabolism" EXACT [] synonym: "phenol-containing compound biosynthesis" EXACT [] synonym: "phenol-containing compound formation" EXACT [] synonym: "phenol-containing compound synthesis" EXACT [] is_a: GO:0018958 ! phenol-containing compound metabolic process is_a: GO:0019438 ! aromatic compound biosynthetic process is_a: GO:1901362 ! organic cyclic compound biosynthetic process is_a: GO:1901617 ! organic hydroxy compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33853 ! phenols relationship: has_primary_output CHEBI:33853 ! phenols [Term] id: GO:0046219 name: indolalkylamine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group." [GOC:curators] synonym: "indolalkylamine anabolism" EXACT [] synonym: "indolalkylamine biosynthesis" EXACT [] synonym: "indolalkylamine formation" EXACT [] synonym: "indolalkylamine synthesis" EXACT [] is_a: GO:0006586 ! indolalkylamine metabolic process is_a: GO:0042401 ! biogenic amine biosynthetic process is_a: GO:0042435 ! indole-containing compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:38631 ! aminoalkylindole relationship: has_primary_output CHEBI:38631 ! aminoalkylindole [Term] id: GO:0046333 name: octopamine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving octopamine, 1-(p-hydroxyphenyl)-2-aminoethanol. The D enantiomer is about one-tenth as active as norepinephrine and is found in the salivary glands of Octopus and Eledone species." [ISBN:0198506732] synonym: "octopamine metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0042133 ! neurotransmitter metabolic process is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:58025 ! octopaminium relationship: has_primary_input_or_output CHEBI:58025 ! octopaminium [Term] id: GO:0046358 name: butyrate biosynthetic process namespace: biological_process alt_id: GO:0043439 def: "The chemical reactions and pathways resulting in the formation of butyrate, the anion of butyric acid." [ISBN:0198506732] synonym: "butanoic acid anabolism" EXACT [] synonym: "butanoic acid biosynthesis" EXACT [] synonym: "butanoic acid biosynthetic process" EXACT [] synonym: "butanoic acid formation" EXACT [] synonym: "butanoic acid synthesis" EXACT [] synonym: "butyrate anabolism" EXACT [] synonym: "butyrate biosynthesis" EXACT [] synonym: "butyrate formation" EXACT [] synonym: "butyrate synthesis" EXACT [] is_a: GO:0019605 ! butyrate metabolic process is_a: GO:0051790 ! short-chain fatty acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17968 ! butyrate relationship: has_primary_output CHEBI:17968 ! butyrate [Term] id: GO:0046394 name: carboxylic acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732] synonym: "carboxylic acid anabolism" EXACT [] synonym: "carboxylic acid biosynthesis" EXACT [] synonym: "carboxylic acid formation" EXACT [] synonym: "carboxylic acid synthesis" EXACT [] is_a: GO:0016053 ! organic acid biosynthetic process is_a: GO:0019752 ! carboxylic acid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:29067 ! carboxylic acid anion relationship: has_primary_output CHEBI:29067 ! carboxylic acid anion [Term] id: GO:0046459 name: short-chain fatty acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a fatty acid with an aliphatic tail of less than 6 carbons." [Wikipedia:Fatty_acid_metabolism] synonym: "short-chain fatty acid metabolism" EXACT [] is_a: GO:0006631 ! fatty acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:58951 ! short-chain fatty acid anion relationship: has_primary_input_or_output CHEBI:58951 ! short-chain fatty acid anion [Term] id: GO:0046483 name: heterocycle metabolic process namespace: biological_process def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198506732] subset: goslim_pir synonym: "heterocycle metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:5686 ! heterocyclic compound relationship: has_primary_input_or_output CHEBI:5686 ! heterocyclic compound [Term] id: GO:0050997 name: quaternary ammonium group binding namespace: molecular_function def: "Binding to a quaternary ammonium group, including glycine betaine, choline, carnitine and proline. A quaternary ammonium group is any compound that can be regarded as derived from ammonium hydroxide or an ammonium salt by replacement of all four hydrogen atoms of the NH4+ ion by organic groups." [GOC:ai] synonym: "quaternary amine binding" EXACT [] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:26469 ! quaternary nitrogen compound relationship: has_input CHEBI:26469 ! quaternary nitrogen compound [Term] id: GO:0051081 name: nuclear membrane disassembly namespace: biological_process def: "The controlled breakdown of the nuclear membranes, for example during cellular division." [GOC:ai] synonym: "nuclear envelope breakdown" RELATED [] synonym: "nuclear envelope catabolism" RELATED [] synonym: "nuclear envelope degradation" RELATED [] synonym: "nuclear envelope disassembly" RELATED [] is_a: GO:0030397 ! membrane disassembly is_a: GO:0071763 ! nuclear membrane organization intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0031965 ! nuclear membrane relationship: results_in_disassembly_of GO:0031965 ! nuclear membrane [Term] id: GO:0051378 name: serotonin binding namespace: molecular_function def: "Binding to serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:ai] synonym: "5-hydroxytryptamine binding" EXACT [] is_a: GO:0043169 ! cation binding is_a: GO:0043176 ! amine binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:350546 ! serotonin(1+) relationship: has_input CHEBI:350546 ! serotonin(1+) [Term] id: GO:0051381 name: histamine binding namespace: molecular_function def: "Binding to histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:ai] is_a: GO:0043169 ! cation binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:58432 ! histaminium relationship: has_input CHEBI:58432 ! histaminium [Term] id: GO:0051790 name: short-chain fatty acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a fatty acid with an aliphatic tail of less than 6 carbons." [Wikipedia:Fatty_acid_metabolism] synonym: "short chain fatty acid biosynthesis" EXACT [] synonym: "short chain fatty acid biosynthetic process" EXACT [] synonym: "short-chain fatty acid anabolism" EXACT [] synonym: "short-chain fatty acid biosynthesis" EXACT [] synonym: "short-chain fatty acid formation" EXACT [] synonym: "short-chain fatty acid synthesis" EXACT [] is_a: GO:0006633 ! fatty acid biosynthetic process is_a: GO:0046459 ! short-chain fatty acid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:58951 ! short-chain fatty acid anion relationship: has_primary_output CHEBI:58951 ! short-chain fatty acid anion [Term] id: GO:0052803 name: imidazole-containing compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." [GOC:curators] synonym: "imidazole metabolism" EXACT [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24780 ! imidazoles relationship: has_primary_input_or_output CHEBI:24780 ! imidazoles [Term] id: GO:0055086 name: nucleobase-containing small molecule metabolic process namespace: biological_process def: "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide." [GOC:vw] subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe subset: goslim_yeast subset: prokaryote_subset synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside and nucleotide metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0044281 ! small molecule metabolic process [Term] id: GO:0061024 name: membrane organization namespace: biological_process alt_id: GO:0016044 alt_id: GO:0044802 def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: prokaryote_subset synonym: "cellular membrane organisation" EXACT [] synonym: "cellular membrane organization" EXACT [] synonym: "membrane organisation" EXACT [GOC:mah] synonym: "membrane organization and biogenesis" RELATED [GOC:mah] synonym: "single-organism membrane organization" RELATED [] is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0016020 ! membrane relationship: results_in_organization_of GO:0016020 ! membrane created_by: jl creation_date: 2010-02-08T02:43:11Z [Term] id: GO:0061695 name: transferase complex, transferring phosphorus-containing groups namespace: cellular_component def: "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:bhm, GOC:dph] is_a: GO:1990234 ! transferase complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0016772 ! transferase activity, transferring phosphorus-containing groups relationship: capable_of GO:0016772 ! transferase activity, transferring phosphorus-containing groups created_by: dph creation_date: 2015-05-06T11:22:38Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process alt_id: GO:0006461 alt_id: GO:0034622 alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_pombe subset: prokaryote_subset synonym: "cellular macromolecule complex assembly" RELATED [] synonym: "cellular protein complex assembly" EXACT [] synonym: "cellular protein-containing complex assembly" RELATED [] synonym: "chaperone activity" RELATED [] synonym: "macromolecular complex assembly" RELATED [] synonym: "macromolecule complex assembly" RELATED [] synonym: "protein complex assembly" RELATED [] synonym: "protein complex formation" RELATED [] is_a: GO:0022607 ! cellular component assembly is_a: GO:0043933 ! protein-containing complex organization intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0032991 ! protein-containing complex relationship: results_in_assembly_of GO:0032991 ! protein-containing complex property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI [Term] id: GO:0070405 name: ammonium ion binding namespace: molecular_function def: "Binding to ammonium ions (NH4+)." [CHEBI:28938, GOC:ecd] synonym: "ammonium binding" RELATED [] is_a: GO:0043169 ! cation binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:28938 ! ammonium relationship: has_input CHEBI:28938 ! ammonium [Term] id: GO:0070925 name: organelle assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] subset: goslim_yeast is_a: GO:0006996 ! organelle organization is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] id: GO:0071704 name: organic substance metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] synonym: "organic molecular entity metabolic process" EXACT [] synonym: "organic molecular entity metabolism" EXACT [] synonym: "organic substance metabolism" EXACT [] is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:50860 ! organic molecular entity relationship: has_primary_input_or_output CHEBI:50860 ! organic molecular entity created_by: mah creation_date: 2010-03-08T03:32:18Z [Term] id: GO:0071709 name: membrane assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a membrane." [GOC:mah] is_a: GO:0022607 ! cellular component assembly is_a: GO:0061024 ! membrane organization intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0016020 ! membrane relationship: part_of GO:0044091 ! membrane biogenesis relationship: results_in_assembly_of GO:0016020 ! membrane created_by: mah creation_date: 2010-03-10T11:19:17Z [Term] id: GO:0071763 name: nuclear membrane organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane." [GOC:mah] synonym: "nuclear membrane organisation" EXACT [GOC:mah] synonym: "nuclear membrane organization and biogenesis" RELATED [GOC:mah] is_a: GO:0061024 ! membrane organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0031965 ! nuclear membrane relationship: part_of GO:0006998 ! nuclear envelope organization relationship: results_in_organization_of GO:0031965 ! nuclear membrane created_by: mah creation_date: 2010-03-29T03:59:35Z [Term] id: GO:0071826 name: ribonucleoprotein complex subunit organization namespace: biological_process def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex." [GOC:mah] synonym: "protein-RNA complex subunit organization" EXACT [GOC:mah] synonym: "ribonucleoprotein complex subunit organisation" EXACT [GOC:mah] synonym: "RNA-protein complex subunit organization" EXACT [GOC:mah] is_a: GO:0043933 ! protein-containing complex organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] subset: goslim_flybase_ribbon subset: goslim_metagenomics synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah] synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah] synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] id: GO:0071944 name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon is_a: GO:0110165 ! cellular anatomical entity created_by: mah creation_date: 2010-10-04T01:51:47Z [Term] id: GO:0072330 name: monocarboxylic acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group." [GOC:mah] synonym: "monocarboxylic acid anabolism" EXACT [GOC:mah] synonym: "monocarboxylic acid biosynthesis" EXACT [GOC:mah] synonym: "monocarboxylic acid formation" EXACT [GOC:mah] synonym: "monocarboxylic acid synthesis" EXACT [GOC:mah] is_a: GO:0032787 ! monocarboxylic acid metabolic process is_a: GO:0046394 ! carboxylic acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:35757 ! monocarboxylic acid anion relationship: has_primary_output CHEBI:35757 ! monocarboxylic acid anion created_by: mah creation_date: 2010-11-02T04:51:32Z [Term] id: GO:0090304 name: nucleic acid metabolic process namespace: biological_process def: "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0043170 ! macromolecule metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33696 ! nucleic acid relationship: has_primary_input_or_output CHEBI:33696 ! nucleic acid created_by: tb creation_date: 2010-04-07T10:18:47Z [Term] id: GO:0097159 name: organic cyclic compound binding namespace: molecular_function def: "Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [GOC:sjw, PMID:7583672] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:33832 ! organic cyclic compound relationship: has_input CHEBI:33832 ! organic cyclic compound created_by: pr creation_date: 2011-09-23T02:31:01Z [Term] id: GO:0097164 name: ammonium ion metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the ammonium ion." [GOC:dhl, GOC:tb, PMID:14671018] synonym: "ammonium ion metabolism" EXACT [] synonym: "ammonium metabolic process" RELATED [] is_a: GO:0006807 ! nitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:28938 ! ammonium relationship: has_primary_input_or_output CHEBI:28938 ! ammonium created_by: pr creation_date: 2011-09-28T04:21:30Z [Term] id: GO:0098590 name: plasma membrane region namespace: cellular_component def: "A membrane that is a (regional) part of the plasma membrane." [GOC:dos] comment: Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. subset: gocheck_do_not_manually_annotate synonym: "region of plasma membrane" EXACT [] is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] id: GO:0098772 name: molecular function regulator activity namespace: molecular_function def: "A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition." [GOC:dos, GOC:pt] subset: gocheck_do_not_annotate subset: goslim_flybase_ribbon subset: goslim_generic subset: prokaryote_subset synonym: "molecular function regulator" EXACT [] is_a: GO:0003674 ! molecular_function intersection_of: GO:0003674 ! molecular_function intersection_of: directly_regulates GO:0003674 ! molecular_function relationship: directly_regulates GO:0003674 ! molecular_function relationship: has_part GO:0005515 ! protein binding property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20854" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20862" xsd:anyURI [Term] id: GO:0098796 name: membrane protein complex namespace: cellular_component def: "Any protein complex that is part of a membrane." [GOC:dos] subset: goslim_metagenomics is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0016020 ! membrane relationship: part_of GO:0016020 ! membrane [Term] id: GO:0098797 name: plasma membrane protein complex namespace: cellular_component def: "Any protein complex that is part of the plasma membrane." [GOC:dos] is_a: GO:0098796 ! membrane protein complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane [Term] id: GO:0099568 name: cytoplasmic region namespace: cellular_component def: "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm." [GOC:dos] subset: gocheck_do_not_annotate is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0099738 name: cell cortex region namespace: cellular_component def: "The complete extent of cell cortex that underlies some some region of the plasma membrane." [GOC:dos] subset: gocheck_do_not_annotate synonym: "perimembrane region" EXACT [] is_a: GO:0005938 ! cell cortex is_a: GO:0099568 ! cytoplasmic region intersection_of: GO:0005938 ! cell cortex intersection_of: part_of GO:0005938 ! cell cortex relationship: part_of GO:0005938 ! cell cortex [Term] id: GO:0101025 name: nuclear membrane biogenesis namespace: biological_process def: "The process in which a nuclear membrane is synthesized, aggregates, and bonds together." [GOC:vw] is_a: GO:0044091 ! membrane biogenesis intersection_of: GO:0044085 ! cellular component biogenesis intersection_of: has_output GO:0031965 ! nuclear membrane relationship: has_output GO:0031965 ! nuclear membrane relationship: part_of GO:0071763 ! nuclear membrane organization [Term] id: GO:0110165 name: cellular anatomical entity namespace: cellular_component def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] is_a: GO:0005575 ! cellular_component created_by: kmv creation_date: 2019-08-12T18:01:37Z [Term] id: GO:0140096 name: catalytic activity, acting on a protein namespace: molecular_function def: "Catalytic activity that acts to modify a protein." [GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_generic subset: prokaryote_subset is_a: GO:0003824 ! catalytic activity intersection_of: GO:0003824 ! catalytic activity intersection_of: has_input PR:000000001 ! protein relationship: has_input PR:000000001 ! protein property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI created_by: pg creation_date: 2017-09-14T10:32:59Z [Term] id: GO:0140098 name: catalytic activity, acting on RNA namespace: molecular_function def: "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." [GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_generic subset: prokaryote_subset is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid intersection_of: GO:0003824 ! catalytic activity intersection_of: has_input CHEBI:33697 ! ribonucleic acid relationship: has_input CHEBI:33697 ! ribonucleic acid property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI created_by: pg creation_date: 2017-09-14T12:05:21Z [Term] id: GO:0140513 name: nuclear protein-containing complex namespace: cellular_component def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus." [GOC:pg] subset: gocheck_do_not_annotate synonym: "nuclear complex" EXACT [] is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus created_by: pg creation_date: 2020-09-09T05:12:38Z [Term] id: GO:0140640 name: catalytic activity, acting on a nucleic acid namespace: molecular_function def: "Catalytic activity that acts to modify a nucleic acid." [GOC:pg] is_a: GO:0003824 ! catalytic activity intersection_of: GO:0003824 ! catalytic activity intersection_of: has_input CHEBI:33696 ! nucleic acid relationship: has_input CHEBI:33696 ! nucleic acid property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21402" xsd:anyURI created_by: pg creation_date: 2021-05-11T06:31:07Z [Term] id: GO:0140677 name: molecular function activator activity namespace: molecular_function def: "A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators] is_a: GO:0098772 ! molecular function regulator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_positively_regulates GO:0003674 ! molecular_function relationship: directly_positively_regulates GO:0003674 ! molecular_function property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21782" xsd:anyURI created_by: pg creation_date: 2021-07-07T07:24:16Z [Term] id: GO:0140678 name: molecular function inhibitor activity namespace: molecular_function def: "A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators] is_a: GO:0098772 ! molecular function regulator activity intersection_of: GO:0098772 ! molecular function regulator activity intersection_of: directly_negatively_regulates GO:0003674 ! molecular_function relationship: directly_negatively_regulates GO:0003674 ! molecular_function property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21782" xsd:anyURI created_by: pg creation_date: 2021-07-07T07:24:32Z [Term] id: GO:0150005 name: enzyme activator complex namespace: cellular_component def: "A protein complex capable of activating an enzyme. Activating subunits may dissociate from the catalytic unit before the enzyme is active." [GOC:bhm, PMID:16244137, PMID:28710280] is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0008047 ! enzyme activator activity relationship: capable_of GO:0008047 ! enzyme activator activity [Term] id: GO:1900619 name: acetate ester metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid." [GOC:TermGenie] synonym: "acetate ester metabolism" EXACT [GOC:TermGenie] synonym: "acetyl ester metabolic process" EXACT [CHEBI:47622] synonym: "acetyl ester metabolism" EXACT [CHEBI:47622] is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:47622 ! acetate ester relationship: has_primary_input_or_output CHEBI:47622 ! acetate ester created_by: bf creation_date: 2012-05-16T12:29:51Z [Term] id: GO:1900620 name: acetate ester biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an acetate esteran acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid." [GOC:TermGenie, PMID:15042596] synonym: "acetate ester anabolism" EXACT [GOC:TermGenie] synonym: "acetate ester biosynthesis" EXACT [GOC:TermGenie] synonym: "acetate ester formation" EXACT [GOC:TermGenie] synonym: "acetate ester synthesis" EXACT [GOC:TermGenie] synonym: "acetyl ester biosynthesis" EXACT [CHEBI:47622] synonym: "acetyl ester biosynthetic process" EXACT [CHEBI:47622] is_a: GO:1900619 ! acetate ester metabolic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:47622 ! acetate ester relationship: has_primary_output CHEBI:47622 ! acetate ester created_by: bf creation_date: 2012-05-16T12:30:12Z [Term] id: GO:1901160 name: primary amino compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving primary amino compound." [GOC:TermGenie] synonym: "primary amino compound metabolism" EXACT [GOC:TermGenie] is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:50994 ! primary amino compound relationship: has_primary_input_or_output CHEBI:50994 ! primary amino compound created_by: bf creation_date: 2012-07-18T04:44:39Z [Term] id: GO:1901162 name: primary amino compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of primary amino compound." [GOC:TermGenie] synonym: "primary amino compound anabolism" EXACT [GOC:TermGenie] synonym: "primary amino compound biosynthesis" EXACT [GOC:TermGenie] synonym: "primary amino compound formation" EXACT [GOC:TermGenie] synonym: "primary amino compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901160 ! primary amino compound metabolic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:50994 ! primary amino compound relationship: has_primary_output CHEBI:50994 ! primary amino compound created_by: bf creation_date: 2012-07-18T04:45:14Z [Term] id: GO:1901338 name: catecholamine binding namespace: molecular_function def: "Binding to catecholamine." [GOC:TermGenie] is_a: GO:0097159 ! organic cyclic compound binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:33567 ! catecholamine relationship: has_input CHEBI:33567 ! catecholamine created_by: bf creation_date: 2012-09-03T14:08:44Z [Term] id: GO:1901360 name: organic cyclic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33832 ! organic cyclic compound relationship: has_primary_input_or_output CHEBI:33832 ! organic cyclic compound created_by: bf creation_date: 2012-09-14T09:03:51Z [Term] id: GO:1901362 name: organic cyclic compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound anabolism" EXACT [GOC:TermGenie] synonym: "organic cyclic compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organic cyclic compound formation" EXACT [GOC:TermGenie] synonym: "organic cyclic compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33832 ! organic cyclic compound relationship: has_primary_output CHEBI:33832 ! organic cyclic compound created_by: bf creation_date: 2012-09-14T09:05:22Z [Term] id: GO:1901363 name: heterocyclic compound binding namespace: molecular_function def: "Binding to heterocyclic compound." [GOC:TermGenie] is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:5686 ! heterocyclic compound relationship: has_input CHEBI:5686 ! heterocyclic compound created_by: bf creation_date: 2012-09-14T13:53:50Z [Term] id: GO:1901564 name: organonitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] synonym: "organonitrogen compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:35352 ! organonitrogen compound relationship: has_primary_input_or_output CHEBI:35352 ! organonitrogen compound created_by: pr creation_date: 2012-11-04T15:17:52Z [Term] id: GO:1901566 name: organonitrogen compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organonitrogen compound." [GOC:pr, GOC:TermGenie] synonym: "organonitrogen compound anabolism" EXACT [GOC:TermGenie] synonym: "organonitrogen compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organonitrogen compound formation" EXACT [GOC:TermGenie] synonym: "organonitrogen compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901564 ! organonitrogen compound metabolic process is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:35352 ! organonitrogen compound relationship: has_primary_output CHEBI:35352 ! organonitrogen compound created_by: pr creation_date: 2012-11-04T15:18:00Z [Term] id: GO:1901576 name: organic substance biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] synonym: "organic molecular entity biosynthetic process" EXACT [] synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] synonym: "organic substance anabolism" EXACT [] synonym: "organic substance biosynthesis" EXACT [] synonym: "organic substance formation" EXACT [] synonym: "organic substance synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:50860 ! organic molecular entity relationship: has_primary_output CHEBI:50860 ! organic molecular entity created_by: pr creation_date: 2012-11-05T11:04:40Z [Term] id: GO:1901605 name: alpha-amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an alpha-amino acid." [GOC:TermGenie] synonym: "alpha-amino acid metabolism" EXACT [GOC:TermGenie] is_a: GO:0006520 ! amino acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:78608 ! alpha-amino acid zwitterion relationship: has_primary_input_or_output CHEBI:78608 ! alpha-amino acid zwitterion created_by: tb creation_date: 2012-11-08T17:39:50Z [Term] id: GO:1901607 name: alpha-amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an alpha-amino acid." [GOC:TermGenie] synonym: "alpha-amino acid anabolism" EXACT [GOC:TermGenie] synonym: "alpha-amino acid biosynthesis" EXACT [GOC:TermGenie] synonym: "alpha-amino acid formation" EXACT [GOC:TermGenie] synonym: "alpha-amino acid synthesis" EXACT [GOC:TermGenie] is_a: GO:0008652 ! amino acid biosynthetic process is_a: GO:1901605 ! alpha-amino acid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:78608 ! alpha-amino acid zwitterion relationship: has_primary_output CHEBI:78608 ! alpha-amino acid zwitterion created_by: tb creation_date: 2012-11-08T17:39:58Z [Term] id: GO:1901615 name: organic hydroxy compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic hydroxy compound." [GOC:pr, GOC:TermGenie] synonym: "organic hydroxy compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33822 ! organic hydroxy compound relationship: has_primary_input_or_output CHEBI:33822 ! organic hydroxy compound created_by: pr creation_date: 2012-11-13T12:54:27Z [Term] id: GO:1901617 name: organic hydroxy compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic hydroxy compound." [GOC:pr, GOC:TermGenie] synonym: "organic hydroxy compound anabolism" EXACT [GOC:TermGenie] synonym: "organic hydroxy compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organic hydroxy compound formation" EXACT [GOC:TermGenie] synonym: "organic hydroxy compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901576 ! organic substance biosynthetic process is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33822 ! organic hydroxy compound relationship: has_primary_output CHEBI:33822 ! organic hydroxy compound created_by: pr creation_date: 2012-11-13T12:54:36Z [Term] id: GO:1902494 name: catalytic complex namespace: cellular_component def: "A protein complex which is capable of catalytic activity." [GOC:bhm, GOC:TermGenie, PMID:8077207] subset: goslim_metagenomics synonym: "enzyme complex" EXACT [GOC:bhm, GOC:jl] is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0003824 ! catalytic activity relationship: capable_of GO:0003824 ! catalytic activity property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/19980" xsd:anyURI created_by: bhm creation_date: 2013-11-13T16:18:47Z [Term] id: GO:1903008 name: organelle disassembly namespace: biological_process def: "The disaggregation of an organelle into its constituent components." [GO_REF:0000079, GOC:TermGenie] synonym: "organelle degradation" EXACT [] is_a: GO:0006996 ! organelle organization is_a: GO:0022411 ! cellular component disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0043226 ! organelle relationship: results_in_disassembly_of GO:0043226 ! organelle created_by: jl creation_date: 2014-05-13T12:36:03Z [Term] id: GO:1905690 name: nucleus disassembly namespace: biological_process def: "The disaggregation of a nucleus into its constituent components." [GO_REF:0000079, GOC:autophagy, GOC:pr, GOC:TermGenie] synonym: "cell nucleus disassembly" EXACT [GOC:TermGenie] is_a: GO:0006997 ! nucleus organization is_a: GO:1903008 ! organelle disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0005634 ! nucleus relationship: results_in_disassembly_of GO:0005634 ! nucleus created_by: pr creation_date: 2016-11-14T13:38:57Z [Term] id: GO:1990234 name: transferase complex namespace: cellular_component def: "A protein complex capable of catalyzing 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)." [GOC:bhm, PMID:16540464] is_a: GO:1902494 ! catalytic complex intersection_of: GO:1902494 ! catalytic complex intersection_of: capable_of GO:0016740 ! transferase activity relationship: capable_of GO:0016740 ! transferase activity created_by: bhm creation_date: 2013-11-12T13:20:12Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component alt_id: GO:0030529 alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] synonym: "intracellular ribonucleoprotein complex" NARROW [] synonym: "protein-RNA complex" EXACT [] synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex relationship: has_part CHEBI:33697 ! ribonucleic acid created_by: pr creation_date: 2015-11-19T12:26:37Z [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] def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities." [PATOC:GVG] synonym: "trait" EXACT [] is_a: BFO:0000020 ! specifically dependent continuant [Term] id: PATO:0000051 name: morphology namespace: quality def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0000052 name: shape namespace: quality alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim synonym: "relational shape quality" EXACT [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000125 name: mass namespace: quality def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [PATOC:GVG] comment: For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. subset: attribute_slim subset: relational_slim subset: scalar_slim 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: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: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: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: "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:0001396 name: cellular quality namespace: quality def: "A monadic quality of continuant that exists at the cellular level of organisation." [PATOC:GVG] is_a: PATO:0070044 ! anatomical structure quality [Term] id: PATO:0001404 name: nucleate quality namespace: quality def: "A cellular quality inhering in a bearer by virtue of bearer's number of nuclei." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001396 ! cellular quality [Term] id: PATO:0001405 name: anucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality [Term] id: PATO:0001406 name: binucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001908 ! multinucleate [Term] id: PATO:0001407 name: mononucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0002505 ! nucleated [Term] id: PATO:0001861 name: fasciculated namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's forming a bundle of aligned anatomical fibers, as of muscle or nerve." [answers.com:answers.com] subset: mpath_slim subset: value_slim synonym: "fascicled" EXACT [] is_a: PATO:0002013 ! fasciculation property_value: RO:0002604 PATO:0001959 [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 [Term] id: PATO:0001908 name: multinucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0002505 ! nucleated [Term] id: PATO:0001987 name: saccular namespace: quality def: "A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance." [PATOC:MAH] subset: value_slim synonym: "sacular" EXACT [] is_a: PATO:0002014 ! structure, cavities property_value: IAO:0000118 "sacular" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="EXACT"} [Term] id: PATO:0001992 name: cellularity namespace: quality def: "An organismal quality inhering in a bearer by virtue of the bearer's consisting cells." [PATOC:GVG] subset: attribute_slim subset: scalar_slim is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0001993 name: multicellular namespace: quality def: "A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell." [PATOC:GVG] subset: value_slim is_a: PATO:0001992 ! cellularity [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: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:0002013 name: fasciculation namespace: quality def: "A structural quality inhering in a bearer by virtue of whether the bearer forms a bundle of anatomical fibers, as of muscle or nerve." [answers.com:http\://www.answers.com/] subset: attribute_slim is_a: PATO:0000141 ! structure [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: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: PATO:0002014 ! structure, cavities property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] id: PATO:0002124 name: laminar namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [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: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:0002309 name: fiber shaped namespace: quality def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter." [PATOC:DC] comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [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:0002505 name: nucleated namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] id: PATO:0010000 name: maximally connected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of a single, maximally connected structure." [GOC:dos] comment: What counts as maximally connected may be relative to some specification of granularity. is_a: PATO:0000141 ! structure property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:41:11Z [Term] id: PATO:0010001 name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] id: PATO:0070044 name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: CHEBI:36080 ! protein intersection_of: PR:000018263 ! amino acid chain intersection_of: has_gene_template SO:0000704 intersection_of: output_of GO:0006412 ! translation [Term] id: PR:000018263 name: amino acid chain namespace: protein def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] comment: Category=polymer. synonym: "peptide" NARROW [PRO:DAN] synonym: "polypeptide" NARROW [PRO:DAN] is_a: CHEBI:50047 ! organic amino compound relationship: has_constituent_monomer CHEBI:33708 {minCardinality="2"} ! amino-acid residue [Term] id: PR:000036194 name: eukaryotic protein namespace: protein def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: CHEBI:36080 ! protein is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein intersection_of: only_in_taxon NCBITaxon:2759 relationship: only_in_taxon NCBITaxon:2759 [Term] id: PR:000050567 name: protein-containing material entity namespace: protein def: "A material entity that minimally consists of a protein." [PRO:DAN] comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] synonym: "protein-containing complex" NARROW [PRO:DAN] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: has_part PR:000000001 ! protein relationship: has_part PR:000000001 ! protein [Term] id: RO:0002577 name: system def: "A material entity consisting of multiple components that are causally integrated." [] is_a: BFO:0000040 ! material entity property_value: editor_note "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string [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: example_of_usage "this fragility is a characteristic of this vase" xsd:string property_value: example_of_usage "this red color is a characteristic of this apple" xsd:string property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! 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: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: example_of_usage "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! 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: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: example_of_usage "this red color is a quality of this apple" xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: has_quality ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: example_of_usage "this investigator role is a role of this person" xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! 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: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: example_of_usage "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: bearer_of ! bearer of [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: example_of_usage "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: bearer_of ! bearer of [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition is_a: bearer_of ! bearer of inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 is_a: RO:0000052 ! characteristic of [Typedef] id: RO:0002000 name: 2D boundary of name: boundary_of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: example_of_usage "the surface of my skin is a 2D boundary of my body" xsd:string property_value: IAO:0000118 "2D_boundary_of" xsd:string property_value: IAO:0000118 "boundary of" xsd:string property_value: IAO:0000118 "is 2D boundary of" xsd:string property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002323 ! mereotopologically related to inverse_of: has_boundary ! has_boundary [Typedef] id: RO:0002006 name: has synaptic terminal of property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in [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: dos creation_date: 2017-05-24T09:31:17Z [Typedef] id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process created_by: dos creation_date: 2017-05-24T09:44:33Z [Typedef] id: RO:0002018 name: has component process def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: has_component ! has component created_by: dos creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates created_by: dos creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] is_a: RO:0002022 ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates created_by: dos creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] is_a: RO:0002022 ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates created_by: dos creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity created_by: dos creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002100 name: has soma location namespace: fly_anatomy.ontology def: "Relation between a neuron and an anatomical structure that its soma is part of." [] def: "Relation between a neuron and an anatomical structure that its soma is part of." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: overlaps ! overlaps transitive_over: part_of ! part_of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] expand_expression_to: "BFO_0000051 some (GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with namespace: fly_anatomy.ontology def: "Relation between a neuron and the neuron projection bundle it fasciculates with. FOL: x fasciculates_with y iff: exists some 'neuron ; CL_0000540'(x), some 'neuron projection bundle ; CARO_0001001'(y), some 'neuron projection ; GO_0043005'(np), np part_of x AND np overlaps y AND np aligned_with y" [https://orcid.org/0000-0002-7073-9172] def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] xref: RO:0002101 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection [Typedef] id: RO:0002103 name: synapsed by namespace: fly_anatomy.ontology def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] def: "Relation between an anatomical structure and a neuron that chemically synapses to it." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002103 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002485 ! receives input from inverse_of: RO:0002120 ! synapsed to expand_expression_to: "BFO_0000051 some (GO_0045211 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0042734 that BFO_0000050 some ?Y)))" [] expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] [Typedef] id: RO:0002110 name: has postsynaptic terminal in namespace: fly_anatomy.ontology def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] comment: Relation between a neuron and the structure in which its dendrite receives synapses. xref: RO:0002110 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in transitive_over: part_of ! part_of expand_expression_to: "BFO_0000051 some (GO_0045211 and BFO_0000050 some (GO_0045202 and BFO_0000050 some ?Y))" [] expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in namespace: fly_anatomy.ontology def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] xref: RO:0002113 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "synapses in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part_of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some ?Y))" [] expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002120 name: synapsed to namespace: fly_anatomy.ontology def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] def: "Relation between a neuron and an anatomical structure that it chemically synapses to." [https://orcid.org/0000-0002-7073-9172] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) xref: RO:0002120 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some ?Y)))" [] expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] [Typedef] id: RO:0002130 name: has synaptic terminal in namespace: fly_anatomy.ontology def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] def: "A relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [https://orcid.org/0000-0002-7073-9172] comment: expands to - X overlaps some ('synapse ; GO_0045202' that part_of some ?Y) xref: RO:0002130 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 is_a: overlaps ! overlaps transitive_over: part_of ! part_of expand_expression_to: "RO_0002131 some (GO_0045202 and BFO_0000050 some ?Y)" [] expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps [Typedef] id: RO:0002151 name: partially overlaps namespace: fly_anatomy.ontology def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" [] subset: ro-eco xref: RO:0002151 property_value: editor_note "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "proper overlaps" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (proper_overlaps ?x ?y)\n (and \n (overlaps ?x ?y)\n (not (part_of ?x ?y)) \n (not (part_of ?y ?x)))))" xsd:string property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps [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:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: example_of_usage "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: 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: example_of_usage "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process [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: editor_note "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 {http://purl.obolibrary.org/obo/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" [] 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 the process of evolution." 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)" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: example_of_usage "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 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: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 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: functionally_related_to ! 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 Involved:in holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of transitive_over: part_of ! part_of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant [Typedef] id: RO:0002354 name: formed as result of property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 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 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: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO: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: editor_note "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: functionally_related_to ! functionally related to is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] property_value: example_of_usage "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps [Typedef] id: RO:0002434 name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: 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:0002447 name: phosphorylates property_value: editor_note "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: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:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: has_part occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"} [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:0002485 name: receives input from property_value: editor_note "See notes for inverse relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: connected_to ! connected to [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: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string property_value: IAO:0000117 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:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of is_a: functionally_related_to ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] id: RO:0002586 name: results in breakdown of def: "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" [] is_a: has_input ! has input [Typedef] id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 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: example_of_usage "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: example_of_usage "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: functionally_related_to ! 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 http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect holds_over_chain: RO:0002327 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 http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect 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 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 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: pg creation_date: 2022-09-26T06:07:17Z [Typedef] id: RO:0012012 name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: regulates ! regulates is_a: RO:0012011 ! indirectly causally upstream of created_by: pg creation_date: 2022-09-26T06:08:01Z [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: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: example_of_usage "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: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string property_value: example_of_usage "this apple is bearer of this red color" xsd:string property_value: example_of_usage "this vase is bearer of this fragility" xsd:string property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true [Typedef] id: capable_of name: capable of namespace: external namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 property_value: example_of_usage "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: example_of_usage "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string property_value: IAO:0000117 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 namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 property_value: IAO:0000117 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 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: functionally_related_to ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: 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 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 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: editor_note "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: connected_to name: connected to namespace: uberon def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] xref: RO:0002170 property_value: example_of_usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] id: contains_process name: contains process namespace: uberon def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant xref: BFO:0000067 property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Typedef] id: dc-creator name: creator namespace: uberon xref: http://purl.org/dc/elements/1.1/creator is_metadata_tag: true [Typedef] id: dc-description name: description namespace: uberon xref: http://purl.org/dc/elements/1.1/description is_metadata_tag: true [Typedef] id: dc-title name: title namespace: uberon xref: http://purl.org/dc/elements/1.1/title is_metadata_tag: true [Typedef] id: dcterms-license name: license namespace: uberon xref: http://purl.org/dc/terms/license is_metadata_tag: true [Typedef] id: 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 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 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: editor_note name: editor note namespace: uberon xref: IAO:0000116 is_metadata_tag: true [Typedef] id: ends name: ends namespace: uberon def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: part_of ! part_of is_a: RO:0002222 ! temporally related to inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to [Typedef] id: example_of_usage name: example of usage namespace: uberon xref: IAO:0000112 is_metadata_tag: true [Typedef] id: functionally_related_to name: functionally related to namespace: uberon def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 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: has_boundary name: has 2D boundary name: has_boundary namespace: uberon def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: example_of_usage "my body has 2D boundary the surface of my skin" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has boundary" xsd:string property_value: IAO:0000118 "has_2D_boundary" xsd:string property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity domain: CARO:0000003 ! connected anatomical structure range: BFO:0000141 ! immaterial entity range: CARO:0000010 ! anatomical boundary is_a: RO:0002323 ! mereotopologically related to [Typedef] id: has_component name: has component namespace: external namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part [Typedef] id: has_end_location name: has end location namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in is_a: RO:0002479 ! has part that occurs in [Typedef] id: 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 domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant inverse_of: input_of ! 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: dos creation_date: 2017-05-24T09:31:01Z [Typedef] id: has_output name: has output namespace: external def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string holds_over_chain: ends_with has_output is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] id: has_part name: has part name: has_part namespace: external namespace: quality namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000111 "has part" 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 namespace: external def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: example_of_usage "this blood coagulation has participant this blood clot" xsd:string property_value: example_of_usage "this investigation has participant this investigator" xsd:string property_value: example_of_usage "this process has participant this input material (or this output material)" xsd:string property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: has_part has_participant [Typedef] id: has_primary_input_or_output name: has primary input or output namespace: external def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output namespace: external def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] id: has_quality name: has quality namespace: uberon def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] xref: RO:0000086 property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: example_of_usage "this apple has quality this red color" xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: bearer_of ! bearer of [Typedef] id: has_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: dos creation_date: 2017-05-24T09:30:46Z [Typedef] id: has_start_location name: has start location namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in is_a: RO:0002479 ! has part that occurs in [Typedef] id: 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 namespace: uberon 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 holds_over_chain: starts_with ends_with 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 holds_over_chain: ends_with starts_with is_a: precedes ! precedes [Typedef] id: in_taxon name: in taxon namespace: uberon def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] comment: Connects a biological entity to its taxon of origin. subset: ro-eco xref: RO:0002162 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints holds_over_chain: capable_of in_taxon holds_over_chain: connected_to in_taxon holds_over_chain: has_part in_taxon holds_over_chain: innervated_by in_taxon holds_over_chain: overlaps in_taxon holds_over_chain: part_of in_taxon holds_over_chain: produced_by in_taxon holds_over_chain: produces in_taxon holds_over_chain: results_in_developmental_progression_of in_taxon is_a: RO:0002320 ! evolutionarily related to [Typedef] id: innervated_by name: innervated_by namespace: uberon xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 inverse_of: innervates ! innervates [Typedef] id: innervates name: innervates namespace: fly_anatomy.ontology namespace: uberon def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002134 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 transitive_over: part_of ! part_of expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some ?Y)))" [] expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] [Typedef] id: input_of name: input of namespace: uberon def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in [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 namespace: gene_ontology 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 holds_over_chain: ends_with negatively_regulates 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: occurs_in name: occurs in namespace: external namespace: gene_ontology def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in inverse_of: contains_process ! contains process transitive_over: part_of ! part_of [Typedef] id: only_in_taxon name: only in taxon namespace: uberon def: "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 property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string property_value: example_of_usage "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints is_a: in_taxon ! in taxon [Typedef] id: output_of name: output of namespace: external namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in [Typedef] id: overlaps name: overlaps namespace: external namespace: uberon 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 {http://purl.obolibrary.org/obo/RO_0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] id: part_of name: part of name: part_of namespace: external namespace: quality namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 property_value: RO:0040042 BFO:0000017 property_value: RO:0040042 BFO:0000019 property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part [Typedef] id: participates_in name: participates in namespace: external namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 property_value: example_of_usage "this blood clot participates in this blood coagulation" xsd:string property_value: example_of_usage "this input material (or this output material) participates in this process" xsd:string property_value: example_of_usage "this investigator participates in this investigation" xsd:string property_value: IAO:0000111 "participates in" xsd:string property_value: IAO:0000118 "participates_in" xsd:string 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 namespace: gene_ontology 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: ends_with positively_regulates 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 namespace: external namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by is_transitive: true is_a: RO:0002086 ! ends after inverse_of: precedes ! precedes [Typedef] id: precedes name: precedes namespace: external namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to [Typedef] id: 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: produced_by name: produced by namespace: external namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: produces name: produces namespace: external namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by [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 namespace: gene_ontology 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 holds_over_chain: ends_with 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 [Typedef] id: results_in_assembly_of name: results in assembly of namespace: external 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:0002588 is_a: results_in_formation_of ! results in formation of is_a: results_in_organization_of ! results in organization of [Typedef] id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] id: results_in_developmental_progression_of name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process is_a: RO:0002324 ! developmentally related to [Typedef] id: results_in_disassembly_of name: results in disassembly of namespace: external xref: RO:0002590 is_a: results_in_organization_of ! results in organization of is_a: RO:0002586 ! results in breakdown of [Typedef] id: results_in_formation_of name: results in formation of namespace: external 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:0002297 property_value: example_of_usage "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: example_of_usage "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of [Typedef] id: results_in_organization_of name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] id: starts name: starts namespace: uberon def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Allen" xsd:string is_a: part_of ! part_of is_a: RO:0002222 ! temporally related to inverse_of: starts_with ! starts with [Typedef] id: starts_with name: starts with namespace: external namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 property_value: example_of_usage "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to