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biorealm.obo
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format-version: 1.2
data-version: releases/2019-10-03
subsetdef: 1_STAR ""
subsetdef: 3_STAR ""
subsetdef: abnormal_slim ""
subsetdef: attribute_slim ""
subsetdef: disposition_slim ""
subsetdef: EnvO-Lite-GSC ""
subsetdef: gocheck_do_not_annotate ""
subsetdef: gocheck_do_not_manually_annotate ""
subsetdef: goslim_agr ""
subsetdef: goslim_aspergillus ""
subsetdef: goslim_candida ""
subsetdef: goslim_chembl ""
subsetdef: goslim_flybase_ribbon ""
subsetdef: goslim_generic ""
subsetdef: goslim_metagenomics ""
subsetdef: goslim_mouse ""
subsetdef: goslim_pir ""
subsetdef: goslim_plant ""
subsetdef: goslim_pombe ""
subsetdef: goslim_yeast ""
subsetdef: mpath_slim ""
subsetdef: reference ""
subsetdef: relational_slim ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: scalar_slim ""
subsetdef: TraitNet ""
subsetdef: upper_level ""
subsetdef: value_slim ""
ontology: biorealm
property_value: http://purl.org/dc/elements/1.1/description "None" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Biogeographic Area Ontology" xsd:string
property_value: http://purl.org/dc/terms/license "Unspecified" 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: 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:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000002
name: continuant
def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
relationship: part_of BFO:0000002 ! continuant
property_value: BFO:0000179 "continuant" xsd:string
property_value: BFO:0000180 "Continuant" xsd:string
property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string
property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"}
property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
relationship: part_of BFO:0000003 ! occurrent
property_value: BFO:0000179 "occurrent" xsd:string
property_value: BFO:0000180 "Occurrent" xsd:string
property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string
property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string
property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"}
property_value: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"}
property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"}
property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: part_of BFO:0000004 ! independent continuant
property_value: BFO:0000179 "ic" xsd:string
property_value: BFO:0000180 "IndependentContinuant" xsd:string
property_value: 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:0000006
name: spatial region
is_a: BFO:0000141 ! immaterial entity
disjoint_from: BFO:0000029 ! site
disjoint_from: BFO:0000029 ! site
disjoint_from: BFO:0000140 ! continuant fiat boundary
property_value: BFO:0000179 "s-region" xsd:string
property_value: BFO:0000180 "SpatialRegion" xsd:string
property_value: editor_note "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string
property_value: editor_note "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"}
property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"}
property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"}
property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"}
property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "process" xsd:string
property_value: BFO:0000180 "Process" xsd:string
property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string
property_value: 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: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: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 ! realizable entity
property_value: BFO:0000179 "realizable" xsd:string
property_value: BFO:0000180 "RealizableEntity" xsd:string
property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string
property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string
property_value: IAO:0000112 "the function of your reproductive organs" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string
property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: part_of BFO:0000019 ! quality
property_value: BFO:0000179 "quality" xsd:string
property_value: BFO:0000180 "Quality" xsd:string
property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string
property_value: IAO:0000112 "the color of a tomato" xsd:string
property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string
property_value: IAO:0000112 "the mass of this piece of gold." xsd:string
property_value: IAO:0000112 "the shape of your nose" xsd:string
property_value: IAO:0000112 "the shape of your nostril" xsd:string
property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"}
property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"}
property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
def: "b is a 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])" []
def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: part_of BFO:0000020 ! specifically dependent continuant
property_value: BFO:0000179 "sdc" xsd:string
property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
property_value: 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:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000023
name: role
def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." []
is_a: BFO:0000017 ! realizable entity
property_value: BFO:0000179 "role" xsd:string
property_value: BFO:0000180 "Role" xsd:string
property_value: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string
property_value: 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:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000024
name: fiat object
name: fiat object part
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "fiat-object-part" xsd:string
property_value: BFO:0000180 "FiatObjectPart" xsd:string
property_value: editor_note "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string
property_value: IAO:0000112 "or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29" xsd:string
property_value: IAO:0000112 "the division of the brain into regions" xsd:string
property_value: IAO:0000112 "the division of the planet into hemispheres" xsd:string
property_value: IAO:0000112 "the dorsal and ventral surfaces of the body" xsd:string
property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xsd:string
property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string
property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string
property_value: IAO:0000600 "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"}
property_value: IAO:0000602 "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000027
name: object aggregate
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "object-aggregate" xsd:string
property_value: BFO:0000180 "ObjectAggregate" xsd:string
property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"}
property_value: editor_note "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string
property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string
property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string
property_value: IAO:0000112 "a symphony orchestra" xsd:string
property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string
property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string
property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string
property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string
property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string
property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string
property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string
property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string
property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string
property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string
property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"}
property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000029
name: site
is_a: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "site" xsd:string
property_value: BFO:0000180 "Site" xsd:string
property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string
property_value: IAO:0000112 "a rabbit hole" xsd:string
property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string
property_value: IAO:0000112 "Manhattan Canyon)" xsd:string
property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string
property_value: IAO:0000112 "the Grand Canyon" xsd:string
property_value: IAO:0000112 "the hold of a ship" xsd:string
property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string
property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string
property_value: IAO:0000112 "the interior of your bedroom" xsd:string
property_value: IAO:0000112 "the interior of your office" xsd:string
property_value: IAO:0000112 "the interior of your refrigerator" xsd:string
property_value: IAO:0000112 "the lumen of your gut" xsd:string
property_value: IAO:0000112 "the Piazza San Marco" xsd:string
property_value: IAO:0000112 "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:0000030
name: object
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "object" xsd:string
property_value: BFO:0000180 "Object" xsd:string
property_value: editor_note "BFO 2 Reference: an object is a maximal causally unified material entity" xsd:string
property_value: editor_note "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting." xsd:string
property_value: editor_note "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)." xsd:string
property_value: editor_note "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47" xsd:string
property_value: editor_note "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string
property_value: IAO:0000112 "atom" xsd:string
property_value: IAO:0000112 "cell" xsd:string
property_value: IAO:0000112 "cells and organisms" xsd:string
property_value: IAO:0000112 "engineered artifacts" xsd:string
property_value: IAO:0000112 "grain of sand" xsd:string
property_value: IAO:0000112 "molecule" xsd:string
property_value: IAO:0000112 "organelle" xsd:string
property_value: IAO:0000112 "organism" xsd:string
property_value: IAO:0000112 "planet" xsd:string
property_value: IAO:0000112 "solid portions of matter" xsd:string
property_value: IAO:0000112 "star" xsd:string
property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"}
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
relationship: part_of BFO:0000031 ! generically dependent 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: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: 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: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:0000140
name: continuant fiat boundary
def: "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"}
is_a: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "cf-boundary" xsd:string
property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string
property_value: editor_note "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" xsd:string
property_value: editor_note "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions." xsd:string
property_value: editor_note "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"}
property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string
property_value: IAO:0000602 "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"}
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: BIOREALM:00000000
name: root node
[Term]
id: CARO:0000000
name: anatomical entity
is_a: CARO:0030000 ! biological entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl
[Term]
id: CARO:0000003
name: anatomical structure
name: connected anatomical structure
is_a: CARO:0000006 ! material anatomical entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl
[Term]
id: CARO:0000006
name: material anatomical entity
is_a: BFO:0000040 ! material entity
is_a: CARO:0000000 ! anatomical entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl
[Term]
id: CARO:0001010
name: organism or virus or viroid
def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." []
is_a: PCO:0000031 ! organismal entity
property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string
property_value: IAO:0000589 "organism or virus" xsd:string
[Term]
id: CARO:0030000
name: biological entity
is_a: BFO:0000004 ! independent continuant
[Term]
id: CHEBI:10545
name: electron
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 "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:138103
name: inorganic acid
namespace: chebi_ontology
def: "A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water." []
subset: 3_STAR
synonym: "inorganic acids" RELATED [ChEBI]
synonym: "mineral acid" RELATED [ChEBI]
synonym: "mineral acids" RELATED [ChEBI]
xref: Wikipedia:Mineral_acid
is_a: CHEBI:39141 ! Bronsted acid
[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:15022
name: electron donor
namespace: chebi_ontology
def: "A molecular entity that can transfer an electron to another molecular entity." []
subset: 3_STAR
synonym: "donneur d'electron" RELATED [IUPAC]
synonym: "electron donor" EXACT IUPAC_NAME [IUPAC]
synonym: "Elektronendonator" RELATED [ChEBI]
is_a: CHEBI:17891 ! donor
[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:15377
name: water
namespace: chebi_ontology
alt_id: CHEBI:10743
alt_id: CHEBI:13352
alt_id: CHEBI:27313
alt_id: CHEBI:42043
alt_id: CHEBI:42857
alt_id: CHEBI:43228
alt_id: CHEBI:44292
alt_id: CHEBI:44701
alt_id: CHEBI:44819
alt_id: CHEBI:5585
def: "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms." []
subset: 3_STAR
synonym: "[OH2]" RELATED [IUPAC]
synonym: "acqua" RELATED [ChEBI]
synonym: "agua" RELATED [ChEBI]
synonym: "aqua" RELATED [ChEBI]
synonym: "BOUND WATER" RELATED [PDBeChem]
synonym: "dihydridooxygen" RELATED [IUPAC]
synonym: "dihydrogen oxide" RELATED [IUPAC]
synonym: "eau" RELATED [ChEBI]
synonym: "H2O" RELATED [KEGG_COMPOUND]
synonym: "H2O" RELATED [UniProt]
synonym: "HOH" RELATED [ChEBI]
synonym: "hydrogen hydroxide" RELATED [ChEBI]
synonym: "oxidane" EXACT IUPAC_NAME [IUPAC]
synonym: "Wasser" RELATED [ChEBI]
synonym: "WATER" EXACT [PDBeChem]
synonym: "Water" EXACT [KEGG_COMPOUND]
synonym: "water" EXACT IUPAC_NAME [IUPAC]
xref: Beilstein:3587155 "Beilstein"
xref: CAS:7732-18-5 "KEGG COMPOUND"
xref: Gmelin:117 "Gmelin"
xref: HMDB:HMDB0002111
xref: KEGG:C00001
xref: KEGG:D00001
xref: MetaCyc:WATER
xref: MolBase:1
xref: PDBeChem:HOH
xref: PDBeChem:MTO
xref: Reaxys:3587155 "Reaxys"
xref: Wikipedia:Water
is_a: CHEBI:33693 ! oxygen hydride
is_a: CHEBI:37176 ! mononuclear parent hydride
is_a: CHEBI:52625 ! inorganic hydroxy compound
relationship: has_role CHEBI:48360 ! amphiprotic solvent
relationship: has_role CHEBI:75771 ! mouse metabolite
relationship: has_role CHEBI:75772 ! Saccharomyces cerevisiae metabolite
relationship: has_role CHEBI:76413 ! greenhouse gas
relationship: has_role CHEBI:76971 ! Escherichia coli metabolite
relationship: has_role CHEBI:77746 ! human metabolite
relationship: is_conjugate_acid_of CHEBI:16234 ! hydroxide
relationship: is_conjugate_base_of CHEBI:29412 ! oxonium
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "H2O" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/H2O/h1H2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "XLYOFNOQVPJJNP-UHFFFAOYSA-N" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "18.01530" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "18.01056" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "18.011" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[H]O[H]" xsd:string
[Term]
id: CHEBI:15379
name: dioxygen
namespace: chebi_ontology
alt_id: CHEBI:10745
alt_id: CHEBI:13416
alt_id: CHEBI:23833
alt_id: CHEBI:25366
alt_id: CHEBI:30491
alt_id: CHEBI:44742
alt_id: CHEBI:7860
subset: 3_STAR
synonym: "[OO]" RELATED [MolBase]
synonym: "dioxygen" EXACT IUPAC_NAME [IUPAC]
synonym: "dioxygene" RELATED [ChEBI]
synonym: "Disauerstoff" RELATED [ChEBI]
synonym: "E 948" RELATED [ChEBI]
synonym: "E-948" RELATED [ChEBI]
synonym: "E948" RELATED [ChEBI]
synonym: "molecular oxygen" RELATED [ChEBI]
synonym: "O2" RELATED [UniProt]
synonym: "O2" RELATED [IUPAC]
synonym: "O2" RELATED [KEGG_COMPOUND]
synonym: "Oxygen" RELATED [KEGG_COMPOUND]
synonym: "OXYGEN MOLECULE" RELATED [PDBeChem]
xref: CAS:7782-44-7 "KEGG COMPOUND"
xref: Gmelin:485 "Gmelin"
xref: HMDB:HMDB0001377
xref: KEGG:C00007
xref: KEGG:D00003
xref: MetaCyc:OXYGEN-MOLECULE
xref: MolBase:750
xref: PDBeChem:OXY
xref: PMID:10906528 "Europe PMC"
xref: PMID:16977326 "Europe PMC"
xref: PMID:18210929 "Europe PMC"
xref: PMID:18638417 "Europe PMC"
xref: PMID:19840863 "Europe PMC"
xref: PMID:7710549 "Europe PMC"
xref: PMID:9463773 "Europe PMC"
xref: Wikipedia:Oxygen
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:25362 ! elemental molecule
is_a: CHEBI:33263 ! diatomic oxygen
relationship: has_role CHEBI:27027 ! micronutrient
relationship: has_role CHEBI:33893 ! reagent
relationship: has_role CHEBI:35472 ! anti-inflammatory drug
relationship: has_role CHEBI:63248 ! oxidising agent
relationship: has_role CHEBI:75772 ! Saccharomyces cerevisiae metabolite
relationship: has_role CHEBI:77746 ! human metabolite
relationship: has_role CHEBI:77974 ! food packaging gas
relationship: is_conjugate_base_of CHEBI:29793 ! hydridodioxygen(1+)
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "O2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/O2/c1-2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "MYMOFIZGZYHOMD-UHFFFAOYSA-N" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "31.99880" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "31.98983" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "O=O" xsd:string
[Term]
id: CHEBI:16042
name: halide anion
namespace: chebi_ontology
alt_id: CHEBI:14384
alt_id: CHEBI:5605
def: "A monoatomic monoanion resulting from the addition of an electron to any halogen atom." []
subset: 3_STAR
synonym: "a halide anion" RELATED [UniProt]
synonym: "Halide" RELATED [KEGG_COMPOUND]
synonym: "halide anions" RELATED [ChEBI]
synonym: "halide ions" EXACT IUPAC_NAME [IUPAC]
synonym: "halide(1-)" RELATED [ChEBI]
synonym: "halides" RELATED [ChEBI]
synonym: "halogen anion" RELATED [ChEBI]
synonym: "HX" RELATED [KEGG_COMPOUND]
xref: KEGG:C00462
is_a: CHEBI:33429 ! monoatomic monoanion
is_a: CHEBI:79389 ! monovalent inorganic anion
property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "X" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "0.0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "0.0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[*-]" xsd:string
[Term]
id: CHEBI:16234
name: hydroxide
namespace: chebi_ontology
alt_id: CHEBI:13365
alt_id: CHEBI:13419
alt_id: CHEBI:44641
alt_id: CHEBI:5594
subset: 3_STAR
synonym: "HO-" RELATED [KEGG_COMPOUND]
synonym: "hydridooxygenate(1-)" EXACT IUPAC_NAME [IUPAC]
synonym: "hydroxide" EXACT IUPAC_NAME [IUPAC]
synonym: "HYDROXIDE ION" RELATED [PDBeChem]
synonym: "Hydroxide ion" RELATED [KEGG_COMPOUND]
synonym: "OH(-)" RELATED [IUPAC]
synonym: "OH-" RELATED [KEGG_COMPOUND]
synonym: "oxidanide" EXACT IUPAC_NAME [IUPAC]
xref: CAS:14280-30-9 "NIST Chemistry WebBook"
xref: Gmelin:24714 "Gmelin"
xref: KEGG:C01328
xref: PDBeChem:OH
is_a: CHEBI:33693 ! oxygen hydride
relationship: has_role CHEBI:75771 ! mouse metabolite
relationship: is_conjugate_base_of CHEBI:15377 ! water
property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "HO" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/H2O/h1H2/p-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "XLYOFNOQVPJJNP-UHFFFAOYSA-M" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "17.00734" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "17.003" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "17.00329" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[O-][H]" xsd:string
[Term]
id: CHEBI:16526
name: carbon dioxide
namespace: chebi_ontology
alt_id: CHEBI:13282
alt_id: CHEBI:13283
alt_id: CHEBI:13284
alt_id: CHEBI:13285
alt_id: CHEBI:23011
alt_id: CHEBI:3283
alt_id: CHEBI:48829
def: "A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food." []
subset: 3_STAR
synonym: "[CO2]" RELATED [MolBase]
synonym: "CARBON DIOXIDE" EXACT [PDBeChem]
synonym: "Carbon dioxide" EXACT [KEGG_COMPOUND]
synonym: "carbon dioxide" EXACT IUPAC_NAME [IUPAC]
synonym: "carbonic anhydride" RELATED [UM-BBD]
synonym: "CO2" RELATED [UniProt]
synonym: "CO2" RELATED [KEGG_COMPOUND]
synonym: "dioxidocarbon" EXACT IUPAC_NAME [IUPAC]
synonym: "E 290" RELATED [ChEBI]
synonym: "E-290" RELATED [ChEBI]
synonym: "E290" RELATED [ChEBI]
synonym: "methanedione" EXACT IUPAC_NAME [IUPAC]
synonym: "R-744" RELATED [ChEBI]
xref: Beilstein:1900390 "Beilstein"
xref: CAS:124-38-9 "KEGG COMPOUND"
xref: Drug_Central:4256 "DrugCentral"
xref: Gmelin:989 "Gmelin"
xref: HMDB:HMDB0001967
xref: KEGG:C00011
xref: KEGG:D00004
xref: MetaCyc:CARBON-DIOXIDE
xref: MolBase:752
xref: PDBeChem:CO2
xref: PMID:10826146 "Europe PMC"
xref: PMID:11094503 "Europe PMC"
xref: PMID:11584085 "Europe PMC"
xref: PMID:11802652 "Europe PMC"
xref: PMID:14639145 "Europe PMC"
xref: PMID:15050588 "Europe PMC"
xref: PMID:16591971 "Europe PMC"
xref: PMID:16656478 "Europe PMC"
xref: PMID:16659660 "Europe PMC"
xref: PMID:17190796 "Europe PMC"
xref: PMID:17448243 "Europe PMC"
xref: PMID:17878298 "Europe PMC"
xref: PMID:17884085 "Europe PMC"
xref: PMID:19043767 "Europe PMC"
xref: PMID:19259576 "Europe PMC"
xref: PMID:19854893 "Europe PMC"
xref: PMID:23384758 "Europe PMC"
xref: PMID:23828359 "Europe PMC"
xref: PMID:24258718 "Europe PMC"
xref: PMID:8482095 "Europe PMC"
xref: PMID:8818713 "Europe PMC"
xref: PMID:8869828 "Europe PMC"
xref: PMID:9611769 "Europe PMC"
xref: PMID:9730350 "Europe PMC"
xref: PPDB:119
xref: Reaxys:1900390 "Reaxys"
xref: UM-BBD_compID:c0131 "UM-BBD"
xref: Wikipedia:Carbon_dioxide
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:23014 ! carbon oxide
is_a: CHEBI:64708 ! one-carbon compound
is_a: FOODON:03412972 ! food additive
relationship: has_role CHEBI:35620 ! vasodilator agent
relationship: has_role CHEBI:38867 ! anaesthetic
relationship: has_role CHEBI:46787 ! solvent
relationship: has_role CHEBI:48706 ! antagonist
relationship: has_role CHEBI:75771 ! mouse metabolite
relationship: has_role CHEBI:75772 ! Saccharomyces cerevisiae metabolite
relationship: has_role CHEBI:76413 ! greenhouse gas
relationship: has_role CHEBI:76971 ! Escherichia coli metabolite
relationship: has_role CHEBI:77746 ! human metabolite
relationship: has_role CHEBI:77974 ! food packaging gas
relationship: has_role CHEBI:78017 ! food propellant
relationship: has_role CHEBI:78433 ! refrigerant
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/CO2/c2-1-3" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "CURLTUGMZLYLDI-UHFFFAOYSA-N" 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:17883
name: hydrogen chloride
namespace: chebi_ontology
alt_id: CHEBI:13364
alt_id: CHEBI:24635
alt_id: CHEBI:5590
def: "A mononuclear parent hydride consisting of covalently bonded hydrogen and chlorine atoms." []
subset: 3_STAR
synonym: "[HCl]" RELATED [IUPAC]
synonym: "chlorane" EXACT IUPAC_NAME [IUPAC]
synonym: "chloridohydrogen" EXACT IUPAC_NAME [IUPAC]
synonym: "chlorure d'hydrogene" RELATED [ChEBI]
synonym: "Chlorwasserstoff" RELATED [ChEBI]
synonym: "cloruro de hidrogeno" RELATED [ChEBI]
synonym: "HCl" RELATED [KEGG_COMPOUND]
synonym: "hydrochloric acid" RELATED [ChemIDplus]
synonym: "Hydrochloride" RELATED [KEGG_COMPOUND]
synonym: "Hydrogen chloride" EXACT [KEGG_COMPOUND]
synonym: "hydrogen chloride" EXACT IUPAC_NAME [IUPAC]
synonym: "Hydrogenchlorid" RELATED [ChEBI]
synonym: "Wasserstoffchlorid" RELATED [ChEBI]
xref: CAS:7647-01-0 "KEGG COMPOUND"
xref: Drug_Central:4568 "DrugCentral"
xref: Gmelin:322 "Gmelin"
xref: HMDB:HMDB0002306
xref: KEGG:C01327
xref: KEGG:D02057
xref: MetaCyc:HCL
xref: PMID:15823700 "Europe PMC"
xref: PMID:17492841 "Europe PMC"
xref: PMID:22804993 "Europe PMC"
xref: Reaxys:1098214 "Reaxys"
xref: Wikipedia:HCl
xref: Wikipedia:Hydrochloric_acid
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:18140 ! hydrogen halide
is_a: CHEBI:23117 ! chlorine molecular entity
is_a: CHEBI:37176 ! mononuclear parent hydride
is_a: FOODON:03412972 ! food additive
relationship: has_role CHEBI:75771 ! mouse metabolite
relationship: is_conjugate_acid_of CHEBI:17996 ! chloride
relationship: is_conjugate_base_of CHEBI:50315 ! chloronium
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "ClH" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "HCl" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/ClH/h1H" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "VEXZGXHMUGYJMC-UHFFFAOYSA-N" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "36.46064" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "35.97668" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "Cl[H]" 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:17996
name: chloride
namespace: chebi_ontology
alt_id: CHEBI:13291
alt_id: CHEBI:13970
alt_id: CHEBI:3616
alt_id: CHEBI:3731
alt_id: CHEBI:48804
def: "A halide anion formed when chlorine picks up an electron to form an an anion." []
subset: 3_STAR
synonym: "Chloride" EXACT [KEGG_COMPOUND]
synonym: "chloride" EXACT [UniProt]
synonym: "chloride" EXACT IUPAC_NAME [IUPAC]
synonym: "CHLORIDE ION" RELATED [PDBeChem]
synonym: "Chloride ion" RELATED [KEGG_COMPOUND]
synonym: "Chloride(1-)" RELATED [ChemIDplus]
synonym: "chloride(1-)" EXACT IUPAC_NAME [IUPAC]
synonym: "Chlorine anion" RELATED [NIST_Chemistry_WebBook]
synonym: "Cl(-)" RELATED [IUPAC]
synonym: "Cl-" RELATED [KEGG_COMPOUND]
xref: Beilstein:3587171 "Beilstein"
xref: CAS:16887-00-6 "KEGG COMPOUND"
xref: Gmelin:14910 "Gmelin"
xref: KEGG:C00115
xref: KEGG:C00698
xref: PDBeChem:CL
xref: UM-BBD_compID:c0884 "UM-BBD"
is_a: CHEBI:16042 ! halide anion
is_a: CHEBI:33432 ! monoatomic chlorine
relationship: has_role CHEBI:76971 ! Escherichia coli metabolite
relationship: has_role CHEBI:77746 ! human metabolite
relationship: is_conjugate_base_of CHEBI:17883 ! hydrogen chloride
property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "Cl" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/ClH/h1H/p-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "VEXZGXHMUGYJMC-UHFFFAOYSA-M" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "35.45270" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "34.96940" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[Cl-]" xsd:string
[Term]
id: CHEBI:17997
name: dinitrogen
namespace: chebi_ontology
alt_id: CHEBI:13388
alt_id: CHEBI:14660
alt_id: CHEBI:25365
alt_id: CHEBI:43128
alt_id: CHEBI:7593
def: "An elemental molecule consisting of two trivalently-bonded nitrogen atoms." []
subset: 3_STAR
synonym: "dinitrogen" EXACT IUPAC_NAME [IUPAC]
synonym: "molecular nitrogen" RELATED [ChEBI]
synonym: "N#N" RELATED [ChEBI]
synonym: "N2" RELATED [IUPAC]
synonym: "N2" RELATED [KEGG_COMPOUND]
synonym: "N2" RELATED [UniProt]
synonym: "Nitrogen" RELATED [KEGG_COMPOUND]
xref: CAS:7727-37-9 "NIST Chemistry WebBook"
xref: Drug_Central:4251 "DrugCentral"
xref: Gmelin:150 "Gmelin"
xref: HMDB:HMDB0001371
xref: KEGG:C00697
xref: KEGG:D00083
xref: MetaCyc:NITROGEN-MOLECULE
xref: PDBeChem:HDZ
xref: PMID:18334638 "Europe PMC"
xref: PMID:22237545 "Europe PMC"
xref: Reaxys:15940095 "Reaxys"
xref: Wikipedia:Nitrogen
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:25362 ! elemental molecule
is_a: CHEBI:33266 ! diatomic nitrogen
relationship: has_role CHEBI:77974 ! food packaging gas
relationship: has_role CHEBI:78017 ! food propellant
relationship: is_conjugate_base_of CHEBI:30102 ! diazynium
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "N2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchi "InChI=1S/N2/c1-2" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/inchikey "IJGRMHOSHXDMSA-UHFFFAOYSA-N" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "28.01348" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "28.00615" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "N#N" xsd:string
[Term]
id: CHEBI:18140
name: hydrogen halide
namespace: chebi_ontology
alt_id: CHEBI:13368
alt_id: CHEBI:37140
alt_id: CHEBI:5599
subset: 3_STAR
synonym: "HX" RELATED [UniProt]
synonym: "hydrogen halide" EXACT [IUPAC]
synonym: "hydrogen halides" EXACT IUPAC_NAME [IUPAC]
synonym: "hydrogen halides" RELATED [ChEBI]
is_a: CHEBI:33405 ! hydracid
relationship: has_role CHEBI:138103 ! inorganic acid
property_value: http://purl.obolibrary.org/obo/chebi/charge "0" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "HX" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "1.008" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "1.00783" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/smiles "[F,Cl,Br,I]" xsd:string
[Term]
id: CHEBI:22314
name: alkali metal atom
namespace: chebi_ontology
subset: 3_STAR
synonym: "alkali metal" RELATED [ChEBI]
synonym: "alkali metals" EXACT IUPAC_NAME [IUPAC]
synonym: "Alkalimetall" RELATED [ChEBI]
synonym: "Alkalimetalle" RELATED [ChEBI]
synonym: "metal alcalin" RELATED [ChEBI]
synonym: "metal alcalino" RELATED [ChEBI]
synonym: "metales alcalinos" RELATED [ChEBI]
synonym: "metaux alcalins" RELATED [ChEBI]
is_a: CHEBI:33318 ! main group element atom
is_a: CHEBI:33521 ! metal atom
is_a: CHEBI:33559 ! s-block element atom
[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]