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digitrubber.obo
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digitrubber.obo
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format-version: 1.2
data-version: releases/2023-06-01
date: 01:06:2023 08:05
subsetdef: 1_STAR ""
subsetdef: 2_STAR ""
subsetdef: 3_STAR ""
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: ro-eco ""
subsetdef: RO:0002259 ""
synonymtypedef: IUPAC_NAME ""
ontology: digitrubber
property_value: http://purl.org/dc/terms/description "DigitRubber Ontology" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
property_value: http://purl.org/dc/terms/title "DigitRubber Ontology" xsd:string
property_value: owl:versionInfo "2023-06-01" xsd:string
[Term]
id: APOLLO_SV:00000008
name: software development
def: "A planned process that has specified output a software product and that involves the creation of source code." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Software_development" xsd:string
property_value: IAO:0000600 "A planned process resulting in a software product involving the creation of source code." xsd:string
[Term]
id: APOLLO_SV:00000796
name: dataset creating
def: "A planned process that has a data set as its specified output." []
is_a: OBI:0000011 ! planned process
intersection_of: OBI:0000011 ! planned process
intersection_of: OBI:0000299 IAO:0000100 ! has_specified_output data set
relationship: OBI:0000299 IAO:0000100 ! has_specified_output data set
property_value: IAO:0000111 "creating a data set" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "data set creation" xsd:string
property_value: IAO:0000118 "dataset creation" xsd:string
[Term]
id: BFO:0000001
name: entity
property_value: BFO:0000179 "entity" xsd:string
property_value: BFO:0000180 "Entity" xsd:string
property_value: IAO:0000112 "Julius Caesar" xsd:string
property_value: IAO:0000112 "the Second World War" xsd:string
property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
property_value: IAO:0000112 "your body mass index" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string
property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"}
property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000002
name: continuant
def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant
property_value: BFO:0000179 "continuant" xsd:string
property_value: BFO:0000180 "Continuant" xsd:string
property_value: IAO:0000111 "continuant" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string
property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"}
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl
property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent
property_value: BFO:0000179 "occurrent" xsd:string
property_value: BFO:0000180 "Occurrent" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string
property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"}
property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"}
property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"}
property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant
property_value: BFO:0000179 "ic" xsd:string
property_value: BFO:0000180 "IndependentContinuant" xsd:string
property_value: IAO:0000112 "a chair" xsd:string
property_value: IAO:0000112 "a heart" xsd:string
property_value: IAO:0000112 "a leg" xsd:string
property_value: IAO:0000112 "a molecule" xsd:string
property_value: IAO:0000112 "a spatial region" xsd:string
property_value: IAO:0000112 "an atom" xsd:string
property_value: IAO:0000112 "an orchestra." xsd:string
property_value: IAO:0000112 "an organism" xsd:string
property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string
property_value: IAO:0000112 "the interior of your mouth" xsd:string
property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "process" xsd:string
property_value: BFO:0000180 "Process" xsd:string
property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string
property_value: IAO:0000112 "a process of meiosis" xsd:string
property_value: IAO:0000112 "a process of sleeping" xsd:string
property_value: IAO:0000112 "the course of a disease" xsd:string
property_value: IAO:0000112 "the flight of a bird" xsd:string
property_value: IAO:0000112 "the life of an organism" xsd:string
property_value: IAO:0000112 "your process of aging." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string
property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role
property_value: BFO:0000179 "disposition" xsd:string
property_value: BFO:0000180 "Disposition" xsd:string
property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string
property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string
property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string
property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string
property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"}
property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"}
property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"}
property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000017
name: realizable entity
def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity
property_value: BFO:0000179 "realizable" xsd:string
property_value: BFO:0000180 "RealizableEntity" xsd:string
property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string
property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string
property_value: IAO:0000112 "the function of your reproductive organs" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string
property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality
property_value: BFO:0000179 "quality" xsd:string
property_value: BFO:0000180 "Quality" xsd:string
property_value: IAO:0000111 "quality" xsd:string
property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string
property_value: IAO:0000112 "the color of a tomato" xsd:string
property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string
property_value: IAO:0000112 "the mass of this piece of gold." xsd:string
property_value: IAO:0000112 "the shape of your nose" xsd:string
property_value: IAO:0000112 "the shape of your nostril" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl
property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"}
property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"}
property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant
property_value: BFO:0000179 "sdc" xsd:string
property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
property_value: IAO:0000111 "specifically dependent continuant" xsd:string
property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string
property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string
property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string
property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string
property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string
property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string
property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string
property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the shape of this hole." xsd:string
property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string
property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl
property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000023
name: role
def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." []
is_a: BFO:0000017 ! realizable entity
property_value: BFO:0000179 "role" xsd:string
property_value: BFO:0000180 "Role" xsd:string
property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string
property_value: IAO:0000112 "the priest role" xsd:string
property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string
property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string
property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string
property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string
property_value: IAO:0000112 "the student role" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string
property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000031
name: generically dependent continuant
def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." []
def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
is_a: BFO:0000002 ! continuant
property_value: BFO:0000179 "gdc" xsd:string
property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string
property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string
property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string
property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string
property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition
property_value: BFO:0000179 "function" xsd:string
property_value: BFO:0000180 "Function" xsd:string
property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string
property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string
property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string
property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"}
property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant
disjoint_from: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "material" xsd:string
property_value: BFO:0000180 "MaterialEntity" xsd:string
property_value: IAO:0000111 "material entity" xsd:string
property_value: IAO:0000112 "a flame" xsd:string
property_value: IAO:0000112 "a forest fire" xsd:string
property_value: IAO:0000112 "a human being" xsd:string
property_value: IAO:0000112 "a hurricane" xsd:string
property_value: IAO:0000112 "a photon" xsd:string
property_value: IAO:0000112 "a puff of smoke" xsd:string
property_value: IAO:0000112 "a sea wave" xsd:string
property_value: IAO:0000112 "a tornado" xsd:string
property_value: IAO:0000112 "an aggregate of human beings." xsd:string
property_value: IAO:0000112 "an energy wave" xsd:string
property_value: IAO:0000112 "an epidemic" xsd:string
property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000141
name: immaterial entity
is_a: BFO:0000004 ! independent continuant
property_value: BFO:0000179 "immaterial" xsd:string
property_value: BFO:0000180 "ImmaterialEntity" xsd:string
property_value: IAO:0000116 "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: CHEBI:133602
name: carbon black nanoparticle
namespace: chebi_ontology
def: "Any form of carbon black which has a particle size of less than 100 nm in each dimension." []
subset: 3_STAR
synonym: "carbon black nanoparticles" RELATED [ChEBI]
xref: PMCID:PMC3190904 {source="Europe PMC"}
xref: PMID:21525001 {source="Europe PMC"}
xref: PMID:22753103 {source="Europe PMC"}
xref: PMID:24078381 {source="Europe PMC"}
xref: PMID:24283474 {source="Europe PMC"}
xref: PMID:25056782 {source="Europe PMC"}
xref: PMID:25071917 {source="Europe PMC"}
xref: PMID:25184212 {source="Europe PMC"}
xref: PMID:25451823 {source="Europe PMC"}
xref: PMID:25833640 {source="Europe PMC"}
xref: PMID:25966413 {source="Europe PMC"}
xref: PMID:26066782 {source="Europe PMC"}
xref: PMID:26551751 {source="Europe PMC"}
xref: PMID:26914170 {source="Europe PMC"}
xref: PMID:27460290 {source="Europe PMC"}
xref: PMID:27534448 {source="Europe PMC"}
is_a: CHEBI:50803 ! nanoparticle
is_a: CHEBI:50812 ! carbon nanostructure
is_a: CHEBI:82297 ! carbon black
[Term]
id: CHEBI:17514
name: cyanide
namespace: chebi_ontology
alt_id: CHEBI:14038
alt_id: CHEBI:3969
alt_id: CHEBI:41780
def: "A pseudohalide anion that is the conjugate base of hydrogen cyanide." []
subset: 3_STAR
synonym: "CN(-)" RELATED [IUPAC]
synonym: "CN-" RELATED [KEGG_COMPOUND]
synonym: "Cyanide" EXACT [KEGG_COMPOUND]
synonym: "Cyanide" EXACT [ChEBI]
synonym: "cyanide" EXACT IUPAC_NAME [IUPAC]
synonym: "CYANIDE ION" RELATED [PDBeChem]
synonym: "nitridocarbonate(1-)" EXACT IUPAC_NAME [IUPAC]
synonym: "Prussiate" RELATED [KEGG_COMPOUND]
synonym: "Zyanid" RELATED [ChEBI]
xref: Beilstein:1900509 {source="Beilstein"}
xref: CAS:57-12-5 {source="ChemIDplus"}
xref: CAS:57-12-5 {source="NIST Chemistry WebBook"}
xref: CAS:57-12-5 {source="KEGG COMPOUND"}
xref: Gmelin:89 {source="Gmelin"}
xref: HMDB:HMDB0002084
xref: KEGG:C00177
xref: MetaCyc:CPD-13584
xref: PDBeChem:CYN
xref: PMID:11386635 {source="Europe PMC"}
xref: PMID:14871577 {source="Europe PMC"}
xref: PMID:17554165 {source="Europe PMC"}
xref: PMID:7839575 {source="Europe PMC"}
xref: Reaxys:1900509 {source="Reaxys"}
xref: Wikipedia:Cyanide
is_a: CHEBI:36828 ! pseudohalide anion
property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "CN" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/CN/c1-2/q-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "XFXPMWWXUTWYJX-UHFFFAOYSA-N" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "26.01740" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "26.00362" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[C-]#N" xsd:string
[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: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." []
subset: 3_STAR
synonym: "entidad molecular" RELATED [IUPAC]
synonym: "entidades moleculares" RELATED [IUPAC]
synonym: "entite moleculaire" RELATED [IUPAC]
synonym: "molecular entities" RELATED [IUPAC]
synonym: "molecular entity" EXACT IUPAC_NAME [IUPAC]
synonym: "molekulare Entitaet" RELATED [ChEBI]
is_a: CHEBI:24431 ! chemical entity
[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." []
subset: 3_STAR
synonym: "chemical entity" EXACT [UniProt]
[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
[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." []
subset: 3_STAR
synonym: "organic heterocycle" 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:24870
name: ion
namespace: chebi_ontology
def: "A molecular entity having a net electric charge." []
subset: 3_STAR
synonym: "Ion" EXACT [ChEBI]
synonym: "ion" EXACT IUPAC_NAME [IUPAC]
synonym: "ion" EXACT [ChEBI]
synonym: "Ionen" RELATED [ChEBI]
synonym: "iones" RELATED [ChEBI]
synonym: "ions" RELATED [ChEBI]
is_a: CHEBI:23367 ! molecular entity
[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: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: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:26835
name: sulfur molecular entity
namespace: chebi_ontology
subset: 3_STAR
synonym: "sulfur molecular entities" RELATED [ChEBI]
synonym: "sulfur molecular entity" EXACT [ChEBI]
is_a: CHEBI:33304 ! chalcogen molecular entity
[Term]
id: CHEBI:28798
name: rubber particle
namespace: chebi_ontology
alt_id: CHEBI:26584
alt_id: CHEBI:8905
def: "A polymer consisting of cis-linked prenyl units." []
subset: 3_STAR
synonym: "Rubber" RELATED [KEGG_COMPOUND]
synonym: "Rubber (all-cis)" RELATED [KEGG_COMPOUND]
synonym: "Rubber particle" EXACT [KEGG_COMPOUND]
xref: KEGG:C02321
is_a: CHEBI:60027 ! polymer
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "(C5H8)n.H2" xsd:string
[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
[Term]
id: CHEBI:33259
name: elemental molecular entity
namespace: chebi_ontology
def: "A molecular entity all atoms of which have the same atomic number." []
subset: 3_STAR
synonym: "homoatomic entity" RELATED [ChEBI]
synonym: "homoatomic molecular entities" RELATED [ChEBI]
synonym: "homoatomic molecular entity" RELATED [ChEBI]
is_a: CHEBI:23367 ! molecular entity
[Term]
id: CHEBI:33261
name: organosulfur compound
namespace: chebi_ontology
alt_id: CHEBI:23010
alt_id: CHEBI:25714
def: "An organosulfur compound is a compound containing at least one carbon-sulfur bond." []
subset: 3_STAR
synonym: "organosulfur compound" EXACT [ChEBI]
synonym: "organosulfur compounds" RELATED [ChEBI]
xref: Wikipedia:Organosulfur_compounds
is_a: CHEBI:26835 ! sulfur molecular entity
is_a: CHEBI:36962 ! organochalcogen compound
[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: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." []
subset: 3_STAR
synonym: "heteroorganic entities" RELATED [ChEBI]
synonym: "organoelement compounds" RELATED [ChEBI]
is_a: CHEBI:50860 ! organic molecular entity
[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 entity" EXACT [ChEBI]
is_a: CHEBI:33675 ! p-block molecular entity
[Term]
id: CHEBI:33304
name: chalcogen molecular entity
namespace: chebi_ontology
def: "Any p-block molecular entity containing a chalcogen." []
subset: 3_STAR
synonym: "chalcogen compounds" RELATED [ChEBI]
synonym: "chalcogen molecular entities" RELATED [ChEBI]
synonym: "chalcogen molecular entity" EXACT [ChEBI]
is_a: CHEBI:33675 ! p-block molecular entity
[Term]
id: CHEBI:33415
name: elemental carbon
namespace: chebi_ontology
subset: 3_STAR
synonym: "carbon" RELATED [ChemIDplus]
xref: CAS:7440-44-0 {source="ChemIDplus"}
xref: CAS:7440-44-0 {source="NIST Chemistry WebBook"}
xref: CAS:82600-58-6 {source="NIST Chemistry WebBook"}
xref: Gmelin:8868 {source="Gmelin"}
is_a: CHEBI:33259 ! elemental molecular entity
is_a: CHEBI:50860 ! organic molecular entity
[Term]
id: CHEBI:33471
name: hydrocarbylene group
namespace: chebi_ontology
def: "A bivalent group formed by removing two hydrogen atoms from a hydrocarbon, the free valencies of which are not engaged in a double bond." []
subset: 3_STAR
synonym: "groupe hydrocarbylene" RELATED [IUPAC]
synonym: "grupo hidrocarbileno" RELATED [IUPAC]
synonym: "grupos hidrocarbileno" RELATED [IUPAC]
synonym: "hydrocarbylene group" EXACT IUPAC_NAME [IUPAC]
synonym: "hydrocarbylene groups" EXACT IUPAC_NAME [IUPAC]
is_a: CHEBI:51422 ! organodiyl group
[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." []
subset: 3_STAR
synonym: "main group compounds" RELATED [ChEBI]
synonym: "main group molecular entities" RELATED [ChEBI]
is_a: CHEBI:23367 ! molecular entity
[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 entity" EXACT [ChEBI]
is_a: CHEBI:33675 ! p-block molecular entity
[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]
xref: Wikipedia:Cyclic_compound
is_a: CHEBI:25367 ! molecule
[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." []
subset: 3_STAR
synonym: "aromatic compounds" EXACT IUPAC_NAME [IUPAC]
synonym: "aromatic molecular entity" EXACT IUPAC_NAME [IUPAC]
synonym: "aromatics" 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]
is_a: CHEBI:33655 ! aromatic compound
is_a: CHEBI:33832 ! organic cyclic compound
[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." []
subset: 3_STAR
synonym: "p-block compounds" RELATED [ChEBI]
synonym: "p-block molecular entities" RELATED [ChEBI]
synonym: "p-block molecular entitiy" RELATED [ChEBI]
is_a: CHEBI:33579 ! main group 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]
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)." []
subset: 3_STAR
synonym: "hetarenes" RELATED [IUPAC]
synonym: "heteroarenes" EXACT IUPAC_NAME [IUPAC]
is_a: CHEBI:24532 ! organic heterocyclic compound
is_a: CHEBI:33659 ! organic aromatic compound
[Term]
id: CHEBI:35352
name: organonitrogen compound
namespace: chebi_ontology
def: "Any heteroorganic entity containing at least one carbon-nitrogen bond." []
subset: 3_STAR
synonym: "organonitrogen compounds" EXACT IUPAC_NAME [IUPAC]
synonym: "organonitrogens" RELATED [ChEBI]
is_a: CHEBI:33285 ! heteroorganic entity
is_a: CHEBI:51143 ! nitrogen molecular entity
[Term]
id: CHEBI:35489
name: organic disulfide
namespace: chebi_ontology
def: "Compounds of structure RSSR in which R and R' are organic groups." []
subset: 3_STAR
synonym: "an organic disulfide" RELATED [UniProt]
synonym: "disulfides" EXACT IUPAC_NAME [IUPAC]
synonym: "organic disulfides" RELATED [ChEBI]
is_a: CHEBI:33261 ! organosulfur compound
is_a: CHEBI:48343 ! disulfide
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "S2R2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "64.13000" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "63.94414" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[*]SS[*]" xsd:string
[Term]
id: CHEBI:36357
name: polyatomic entity
namespace: chebi_ontology
def: "Any molecular entity consisting of more than one atom." []
subset: 3_STAR
synonym: "polyatomic entities" RELATED [ChEBI]
is_a: CHEBI:23367 ! molecular entity
[Term]
id: CHEBI:36358
name: polyatomic ion
namespace: chebi_ontology
def: "An ion consisting of more than one atom." []
subset: 3_STAR
synonym: "polyatomic ions" RELATED [ChEBI]
is_a: CHEBI:24870 ! ion
is_a: CHEBI:36357 ! polyatomic entity
[Term]
id: CHEBI:36828
name: pseudohalide anion
namespace: chebi_ontology
subset: 3_STAR
synonym: "pseudohalide anions" RELATED [ChEBI]
synonym: "pseudohalide ions" EXACT IUPAC_NAME [IUPAC]
synonym: "pseudohalides" RELATED [ChEBI]
synonym: "pseudohalogen anion" RELATED [ChEBI]
synonym: "pseudohalogen ion" RELATED [ChEBI]
is_a: CHEBI:36829 ! polyatomic monoanion
[Term]
id: CHEBI:36829
name: polyatomic monoanion
namespace: chebi_ontology
subset: 3_STAR
synonym: "polyatomic monoanions" RELATED [ChEBI]
is_a: CHEBI:33273 ! polyatomic anion
is_a: CHEBI:36830 ! monoanion
[Term]
id: CHEBI:36830
name: monoanion
namespace: chebi_ontology
subset: 3_STAR
synonym: "monoanions" RELATED [ChEBI]
is_a: CHEBI:22563 ! anion
property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string
[Term]
id: CHEBI:36962
name: organochalcogen compound
namespace: chebi_ontology
def: "An organochalcogen compound is a compound containing at least one carbon-chalcogen bond." []
subset: 3_STAR
synonym: "organochalcogen compound" EXACT [ChEBI]
synonym: "organochalcogen compounds" RELATED [ChEBI]
is_a: CHEBI:33285 ! heteroorganic entity
is_a: CHEBI:33304 ! chalcogen molecular entity
[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." []
subset: 3_STAR
synonym: "heterocyclic organonitrogen 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:38106
name: organosulfur heterocyclic compound
namespace: chebi_ontology
subset: 3_STAR
synonym: "heterocyclic organosulfur compounds" RELATED [ChEBI]
synonym: "organosulfur heterocyclic compounds" RELATED [ChEBI]
is_a: CHEBI:24532 ! organic heterocyclic compound
is_a: CHEBI:33261 ! organosulfur 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:38418
name: 1,3-thiazoles
namespace: chebi_ontology
alt_id: CHEBI:26949
alt_id: CHEBI:38417
subset: 3_STAR
synonym: "1,3-thiazoles" EXACT [ChEBI]
is_a: CHEBI:48901 ! thiazoles
[Term]
id: CHEBI:48343
name: disulfide
namespace: chebi_ontology
def: "Compounds of structure RSSR'." []
subset: 3_STAR
synonym: "disulfides" RELATED [ChEBI]
is_a: CHEBI:26835 ! sulfur molecular entity
[Term]
id: CHEBI:48901
name: thiazoles
namespace: chebi_ontology
def: "An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom." []
subset: 3_STAR
synonym: "thiazole" RELATED [ChEBI]
is_a: CHEBI:38106 ! organosulfur heterocyclic compound
is_a: CHEBI:68452 ! azole
[Term]
id: CHEBI:50795
name: nanostructure
namespace: chebi_ontology
def: "A nanometre sized object." []
subset: 3_STAR
synonym: "nanoestructura" RELATED [ChEBI]
is_a: CHEBI:36357 ! polyatomic entity
[Term]
id: CHEBI:50803
name: nanoparticle
namespace: chebi_ontology
def: "A nanosized spherical or capsule-shaped structure." []
subset: 3_STAR
synonym: "nanoparticles" RELATED [ChEBI]
synonym: "nanoparticula" RELATED [ChEBI]
synonym: "nanoparticule" RELATED [ChEBI]
synonym: "Nanoteilchen" RELATED [ChEBI]
synonym: "NP" RELATED [ChEBI]
is_a: CHEBI:50795 ! nanostructure
[Term]
id: CHEBI:50812
name: carbon nanostructure
namespace: chebi_ontology
subset: 3_STAR
synonym: "carbon nanostructures" RELATED [ChEBI]
is_a: CHEBI:33415 ! elemental carbon
is_a: CHEBI:50795 ! nanostructure
[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." []
subset: 3_STAR
synonym: "organic compounds" RELATED [ChEBI]
synonym: "organic entity" RELATED [ChEBI]
synonym: "organic molecular entities" RELATED [ChEBI]
is_a: CHEBI:33582 ! carbon group molecular entity
[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 molecular entities" RELATED [ChEBI]
synonym: "Nitrogenous compounds" RELATED [KEGG_COMPOUND]
xref: KEGG:C06061
is_a: CHEBI:33302 ! pnictogen molecular entity
[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:5686
name: heterocyclic compound
namespace: chebi_ontology
def: "A cyclic compound having as ring members atoms of at least two different elements." []
subset: 3_STAR
synonym: "compuesto heterociclico" RELATED [IUPAC]
synonym: "compuestos heterociclicos" RELATED [IUPAC]
synonym: "heterocycle" RELATED [ChEBI]
synonym: "Heterocyclic compound" EXACT [KEGG_COMPOUND]
synonym: "heterocyclic compounds" RELATED [ChEBI]
is_a: CHEBI:33595 ! cyclic compound
[Term]
id: CHEBI:59999
name: chemical substance
namespace: chebi_ontology
def: "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types." []
subset: 3_STAR
synonym: "Chemische Substanz" RELATED [ChEBI]
is_a: CHEBI:24431 ! chemical entity
[Term]
id: CHEBI:60004
name: mixture
namespace: chebi_ontology
def: "A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind." []
subset: 3_STAR
synonym: "Mischung" RELATED [ChEBI]
is_a: CHEBI:59999 ! chemical substance
[Term]
id: CHEBI:60027
name: polymer
namespace: chebi_ontology
def: "A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc.." []
subset: 3_STAR
synonym: "Kunststoff" RELATED [ChEBI]
synonym: "Polymer" EXACT [ChEBI]
xref: Wikipedia:Polymer
is_a: CHEBI:60004 ! mixture
[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: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:82297
name: carbon black
namespace: chebi_ontology
def: "An elemental carbon in the form of virtually pure colloidal particles that are produced by incomplete combustion or thermal decomposition of gaseous or liquid hydrocarbons under controlled conditions. A black, finely divided pellet or powder, its properties of specific surface area, particle size and structure, conductivity and colour can be varied by varying the exact conditions for its production. It is used in tyres, rubber and plastic products, printing inks and coatings." []
subset: 3_STAR