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seont.obo
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format-version: 1.2
data-version: releases/2020-06-10
subsetdef: EnvO-Lite-GSC ""
subsetdef: goslim_aspergillus ""
subsetdef: goslim_candida ""
subsetdef: goslim_chembl ""
subsetdef: goslim_generic ""
subsetdef: goslim_metagenomics ""
subsetdef: goslim_pir ""
subsetdef: goslim_plant ""
subsetdef: goslim_pombe ""
subsetdef: goslim_yeast ""
subsetdef: reference ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: TraitNet ""
ontology: seont
property_value: http://purl.org/dc/elements/1.1/description "None" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "SEOnt" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
[Term]
id: AGRO:00000006
name: irrigation process
def: "A planned process in which water is artificially supplied to plant or soil to sustain plants. " [https://en.wikipedia.org/wiki/Irrigation\n, www.dictionary.com/browse/irrigation]
synonym: "irrigation" EXACT []
is_a: AGRO:00002071 ! agricultural process
is_a: ENVO:02500031 ! hydrological process
relationship: RO:0000057 AGRO:00000241 ! has participant irrigation equipment
relationship: RO:0000057 ENVO:00002006 ! has participant liquid water
[Term]
id: AGRO:00000008
name: irrigation water source role
def: "A role that inheres in a water body that is realised in an irrigation process where water is transported from that water body to the target of the irrigation process." []
is_a: BFO:0000023 ! role
relationship: BFO:0000054 AGRO:00000006 ! irrigation process
relationship: RO:0000052 ENVO:00000063 ! inheres in water body
[Term]
id: AGRO:00000009
name: irrigation source
def: "A water body from which water is taken during an irrigation process and transported to the target of the irrigation process." []
is_a: ENVO:00000063 ! water body
intersection_of: BFO:0000040 ! material entity
intersection_of: RO:0000087 AGRO:00000008 ! has role irrigation water source role
relationship: RO:0000087 AGRO:00000008 ! has role irrigation water source role
[Term]
id: AGRO:00000032
name: plant reproductive material
def: "A plant anatomical entity that is defined to mean plants or parts of plant capable of and intended for producing or reproducing entire plants." [http://ec.europa.eu/dgs/health_food-safety/pressroom/docs/proposal_aphp_en.pdf]
is_a: PO:0025131 ! plant anatomical entity
[Term]
id: AGRO:00000054
name: irrigation method
def: "A plan specification which describes how water is applied to plants or soil." []
is_a: IAO:0000104 ! plan specification
[Term]
id: AGRO:00000116
name: draft animal
def: "Organism used to pull agricultural implements." []
synonym: "draught animal" EXACT []
synonym: "working animal" EXACT []
is_a: OBI:0100026 ! organism
intersection_of: OBI:0100026 ! organism
intersection_of: RO:0000087 AGRO:00002004 ! has role draft animal role
relationship: RO:0000087 AGRO:00002004 ! has role draft animal role
[Term]
id: AGRO:00000124
name: tractor
def: "A mobile machine specifically designed to deliver a high tractive effort at slow speeds, and mainly used for the purposes of hauling a trailer or machinery used in agriculture or construction." [https://en.wikipedia.org/wiki/Tractor]
is_a: AGRO:00000416 ! agricultural implement
[Term]
id: AGRO:00000154
name: crop residue
is_a: PO:0025131 ! plant anatomical entity
relationship: RO:0001000 PO:0009011 ! derives from plant structure
property_value: IAO:0000232 "Plant material remaining on the field ground after harvesting, including leaves, stalks, roots." xsd:string {xref="https://stats.oecd.org/glossary/detail.asp?ID=480"}
[Term]
id: AGRO:00000155
name: row
def: "two or more crop plants planted in a line." []
is_a: ENVO:01000408 ! environmental zone
relationship: part_of ENVO:00000114 ! agricultural field
[Term]
id: AGRO:00000156
name: interrow
def: "A site which is located between two rows of crop plants." []
is_a: ENVO:01000408 ! environmental zone
relationship: part_of ENVO:00000114 ! agricultural field
relationship: RO:0002609 AGRO:00000155 ! related via dependence to row
[Term]
id: AGRO:00000241
name: irrigation equipment
def: "An equipment that is used during an irrigation process." []
is_a: AGRO:00000416 ! agricultural implement
intersection_of: AGRO:00000416 ! agricultural implement
intersection_of: RO:0000056 AGRO:00000006 ! participates in irrigation process
relationship: RO:0000056 AGRO:00000006 ! participates in irrigation process
[Term]
id: AGRO:00000301
name: agricultural experimental plot
def: "A site within which an agricultural experimental process is conducted" [http://www.fao.org/wairdocs/ilri/x5546e/x5546e0a.htm]
synonym: "plot" EXACT []
is_a: ENVO:01000408 ! environmental zone
relationship: BFO:0000067 AGRO:00000370 ! contains process agricultural experiment
property_value: IAO:0000116 "This should be harmonized with statistical plot designs, perhaps with STATO" xsd:string
[Term]
id: AGRO:00000315
name: plot spacing
def: "Distance quality that represents the distance between two plots." []
is_a: PATO:0000040 ! distance
intersection_of: PATO:0000040 ! distance
intersection_of: RO:0000052 AGRO:00000301 ! inheres in agricultural experimental plot
relationship: RO:0000052 AGRO:00000301 ! inheres in agricultural experimental plot
[Term]
id: AGRO:00000316
name: distance between plants
def: "Distance between two rows." []
def: "The distance of a whole plant" []
synonym: "distance between rows" EXACT []
synonym: "interrow" EXACT []
synonym: "row spacing" EXACT []
synonym: "space between rows" EXACT []
is_a: PATO:0000040 ! distance
intersection_of: PATO:0000040 ! distance
intersection_of: PATO:0000040 ! distance
intersection_of: RO:0000052 AGRO:00000155 ! inheres in row
intersection_of: RO:0000052 PO:0000003 ! inheres in whole plant
relationship: RO:0000052 AGRO:00000155 ! inheres in row
relationship: RO:0000052 PO:0000003 ! inheres in whole plant
[Term]
id: AGRO:00000318
name: distance between rows
def: "Average distance between plants in a same row." []
def: "The distance of a row" []
synonym: "space between plants in row" EXACT []
is_a: PATO:0000040 ! distance
intersection_of: PATO:0000040 ! distance
intersection_of: RO:0000052 AGRO:00000155 ! inheres in row
relationship: RO:0000052 AGRO:00000155 ! inheres in row
relationship: RO:0000052 PO:0000003 ! inheres in whole plant
[Term]
id: AGRO:00000322
name: treatment
def: "A process during which some material is applied to a subject" [http://www.fao.org/wairdocs/ilri/x5546e/x5546e0a.htm]
is_a: AGRO:00002071 ! agricultural process
relationship: part_of PECO:0001001 ! plant exposure
relationship: RO:0002609 AGRO:00000341 ! related via dependence to experimental factor
[Term]
id: AGRO:00000325
name: crop
def: "A crop is any cultivated plant, fungus, or alga that is harvested for food, clothing, livestock,fodder, biofuel, medicine, or other uses" [https://en.wikipedia.org/wiki/Crop]
is_a: OBI:0100026 ! organism
intersection_of: OBI:0100026 ! organism
intersection_of: RO:0000056 AGRO:00000370 ! participates in agricultural experiment
relationship: RO:0000056 AGRO:00000370 ! participates in agricultural experiment
[Term]
id: AGRO:00000338
name: higher-level landform
def: "The landform refers to the shape of the land surface in the area in which the agronomic trial site is located." [http://www.fao.org/docrep/019/a0541e/a0541e.pdf]
is_a: ENVO:00000191 ! solid astronomical body part
[Term]
id: AGRO:00000339
name: agronomic land element
def: "Description of the geomorphology of the immediate surroundings of the experimental site." [http://www.fao.org/docrep/019/a0541e/a0541e.pdf]
is_a: ENVO:00000191 ! solid astronomical body part
[Term]
id: AGRO:00000341
name: experimental factor
def: "A factor of an experiment is a controlled independent variable; a variable whose levels are set by the experimenter. A factor is a general type or category of treatments. Different treatments constitute different levels of a factor." [http://www.stat.yale.edu/Courses/1997-98/101/expdes.htm]
is_a: XCO:0000000 ! experimental condition
[Term]
id: AGRO:00000343
name: agronomic experimental design
def: "A plan specification that states how treatments are allocated to the experimental units during an agronomic trial. It refers to the conceptual framework within which the experiment is conducted." [http://www.simplypsychology.org/experimental-designs.html, https://en.wikipedia.org/wiki/Design_of_experiments, https://www.okstate.edu/ag/agedcm4h/academic/aged5980a/5980/newpage2.htm]
is_a: OBI:0500000 ! study design
[Term]
id: AGRO:00000355
name: slope shape
def: "Shape quality that refers to the general shape of a slope in both vertical and horizontal directions." [FAO\, 1990]
synonym: "slope form" EXACT []
is_a: PATO:0000052 ! shape
intersection_of: PATO:0000052 ! shape
intersection_of: RO:0000052 ENVO:00002000 ! inheres in slope
relationship: RO:0000052 ENVO:00002000 ! inheres in slope
[Term]
id: AGRO:00000369
name: experiment
def: "A planned process in which a procedure is carried out to support, refute, or validate a hypothesis." [https://en.wikipedia.org/wiki/Experiment]
synonym: "trial" EXACT []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000116 "This class is relevant to more than the agronomy domain. It should be replaced by a class in a more general ontology of experiments" xsd:string
[Term]
id: AGRO:00000370
name: agricultural experiment
def: "An experiment in which a scientific method is implemented for testing certain agricultural phenomena." []
synonym: "agronomic experiment" RELATED []
is_a: AGRO:00000369 ! experiment
is_a: AGRO:00002071 ! agricultural process
is_a: OBI:0000471 ! study design execution
relationship: has_part AGRO:00000322 ! treatment
[Term]
id: AGRO:00000416
name: agricultural implement
is_a: BFO:0000030 ! object
[Term]
id: AGRO:00000480
name: mono-cropping experiment {source="Richard Ostler"}
def: "An agricultural experiment involving the prolonged growing of a single crop." []
synonym: "continuous crop experiment" EXACT []
synonym: "continuous mono-cropping experiment" EXACT []
synonym: "monoculture experiment" EXACT []
is_a: AGRO:00000370 ! agricultural experiment
relationship: RO:0000057 AGRO:00000325 ! has participant crop
[Term]
id: AGRO:00002004
name: draft animal role
def: "A role that inheres in an animal that is kept by humans and trained to perform tasks." []
synonym: "draft animal" EXACT []
synonym: "draught animal" EXACT []
synonym: "working animal" EXACT []
is_a: BFO:0000023 ! role
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8461-9745
[Term]
id: AGRO:00002005
name: human power role
def: "A role that inheres in a human to power an implement." []
is_a: BFO:0000023 ! role
relationship: RO:0000081 NCBITaxon:9606 ! role of Homo sapiens
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8461-9745
[Term]
id: AGRO:00002071
name: agricultural process
def: "A planned process which occurs during an agricultural experiment." []
is_a: OBI:0000011 ! planned process
relationship: BFO:0000066 AGRO:00000301 ! occurs in agricultural experimental plot
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8461-9745
[Term]
id: AGRO:00020000
name: inter-cropping experiment
def: "An agricultural experiment during which at least two different crops are grown at the same time." []
is_a: AGRO:00000370 ! agricultural experiment
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8461-9745
[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:0000412 http://purl.obolibrary.org/obo/obi.owl
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: 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/obi.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl
property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
relationship: part_of BFO:0000003 ! occurrent
property_value: BFO:0000179 "occurrent" xsd:string
property_value: BFO:0000180 "Occurrent" xsd:string
property_value: 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:0000412 http://purl.obolibrary.org/obo/ro.owl
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:0000412 http://purl.obolibrary.org/obo/ro.owl
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:0000412 http://purl.obolibrary.org/obo/ro.owl
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:0000412 http://purl.obolibrary.org/obo/ro.owl
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
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"}
def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: part_of BFO:0000020 ! specifically dependent continuant
property_value: BFO:0000179 "sdc" xsd:string
property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
property_value: 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/ro.owl
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:0000412 http://purl.obolibrary.org/obo/ro.owl
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: 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:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" 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: 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:0000116 "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: IAO:0000116 "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: IAO:0000116 "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:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"}
property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000029
name: site
is_a: BFO:0000141 ! immaterial entity
[Term]
id: BFO:0000030
name: object
is_a: BFO:0000040 ! material entity
[Term]
id: BFO:0000031
name: generically dependent continuant
def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." []
def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
is_a: BFO:0000002 ! continuant
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:0000412 http://purl.obolibrary.org/obo/obi.owl
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: 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/ro.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
[Term]
id: CARO:0000003
name: 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
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: CHEBI:10545
name: electron
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." []
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]
is_a: CHEBI:36338 ! lepton
[Term]
id: CHEBI:138103
name: inorganic acid
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." []
synonym: "inorganic acids" RELATED [ChEBI]
synonym: "mineral acid" RELATED [ChEBI]
synonym: "mineral acids" RELATED [ChEBI]
is_a: CHEBI:39141 ! Bronsted acid
[Term]
id: CHEBI:138675
name: gas molecular entity
def: "Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa)." []
synonym: "gas molecular entities" RELATED [ChEBI]
synonym: "gaseous molecular entities" RELATED [ChEBI]
synonym: "gaseous molecular entity" RELATED [ChEBI]
is_a: CHEBI:33579 ! main group molecular entity
[Term]
id: CHEBI:15022
name: electron donor
is_a: CHEBI:17891 ! donor
[Term]
id: CHEBI:15339
name: acceptor
def: "A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity." []
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]
is_a: CHEBI:51086 ! chemical role
[Term]
id: CHEBI:15377
name: water
def: "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms." []
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]
is_a: CHEBI:33693 ! oxygen hydride
is_a: CHEBI:37176 ! mononuclear parent hydride
is_a: CHEBI:52625 ! inorganic hydroxy compound
relationship: is_conjugate_acid_of CHEBI:16234 ! hydroxide
relationship: is_conjugate_base_of CHEBI:29412 ! oxonium
relationship: RO:0000087 CHEBI:48360 ! has role amphiprotic solvent
relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite
relationship: RO:0000087 CHEBI:75772 ! has role Saccharomyces cerevisiae metabolite
relationship: RO:0000087 CHEBI:76413 ! has role greenhouse gas
relationship: RO:0000087 CHEBI:76971 ! has role Escherichia coli metabolite
relationship: RO:0000087 CHEBI:77746 ! has role human metabolite
[Term]
id: CHEBI:15379
name: dioxygen
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:25362 ! elemental molecule
is_a: CHEBI:33263 ! diatomic oxygen
[Term]
id: CHEBI:16042
name: halide anion
def: "A monoatomic monoanion resulting from the addition of an electron to any halogen atom." []
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]
is_a: CHEBI:33429 ! monoatomic monoanion
is_a: CHEBI:79389 ! monovalent inorganic anion
[Term]
id: CHEBI:16234
name: hydroxide
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]
is_a: CHEBI:33693 ! oxygen hydride
relationship: is_conjugate_base_of CHEBI:15377 ! water
relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite
[Term]
id: CHEBI:16526
name: carbon dioxide
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." []
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
[Term]
id: CHEBI:17883
name: hydrogen chloride
def: "A mononuclear parent hydride consisting of covalently bonded hydrogen and chlorine atoms." []
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]
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: is_conjugate_acid_of CHEBI:17996 ! chloride
relationship: is_conjugate_base_of CHEBI:50315 ! chloronium
relationship: RO:0000087 CHEBI:75771 ! has role mouse metabolite
[Term]
id: CHEBI:17891
name: donor
def: "A molecular entity that can transfer (\"donate\") an electron, a pair of electrons, an atom or a group to another molecular entity." []
synonym: "Donator" RELATED [ChEBI]
synonym: "donneur" RELATED [ChEBI]
synonym: "Donor" EXACT [KEGG_COMPOUND]
is_a: CHEBI:51086 ! chemical role
[Term]
id: CHEBI:17996
name: chloride
def: "A halide anion formed when chlorine picks up an electron to form an an anion." []
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]
is_a: CHEBI:16042 ! halide anion
is_a: CHEBI:33432 ! monoatomic chlorine
relationship: is_conjugate_base_of CHEBI:17883 ! hydrogen chloride
relationship: RO:0000087 CHEBI:23357 ! has role cofactor
relationship: RO:0000087 CHEBI:76971 ! has role Escherichia coli metabolite
relationship: RO:0000087 CHEBI:77746 ! has role human metabolite
[Term]
id: CHEBI:17997
name: dinitrogen
def: "An elemental molecule consisting of two trivalently-bonded nitrogen atoms." []
synonym: "dinitrogen" EXACT IUPAC_NAME [IUPAC]
synonym: "molecular nitrogen" RELATED [ChEBI]
synonym: "N#N" RELATED [ChEBI]
synonym: "N2" RELATED [KEGG_COMPOUND]
synonym: "N2" RELATED [UniProt]
synonym: "N2" RELATED [IUPAC]
synonym: "Nitrogen" RELATED [KEGG_COMPOUND]
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:25362 ! elemental molecule
is_a: CHEBI:33266 ! diatomic nitrogen
relationship: is_conjugate_base_of CHEBI:30102 ! diazynium
relationship: RO:0000087 CHEBI:77974 ! has role food packaging gas
relationship: RO:0000087 CHEBI:78017 ! has role food propellant
[Term]
id: CHEBI:18140
name: hydrogen halide
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: RO:0000087 CHEBI:138103 ! has role inorganic acid
[Term]
id: CHEBI:22314
name: alkali metal atom
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
def: "A monoatomic or polyatomic species having one or more elementary charges of the electron." []
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
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)." []
synonym: "Base" EXACT [ChEBI]
synonym: "base" EXACT [ChEBI]
synonym: "base" EXACT IUPAC_NAME [IUPAC]
synonym: "Base1" RELATED [KEGG_COMPOUND]
synonym: "Base2" RELATED [KEGG_COMPOUND]
synonym: "Basen" RELATED [ChEBI]
synonym: "bases" RELATED [ChEBI]
synonym: "Nucleobase" RELATED [KEGG_COMPOUND]
is_a: CHEBI:51086 ! chemical role
[Term]
id: CHEBI:23014
name: carbon oxide
is_a: CHEBI:25701 ! organic oxide
is_a: CHEBI:36963 ! organooxygen compound
[Term]
id: CHEBI:23114
name: chloride salt
synonym: "chloride salts" RELATED [ChEBI]
synonym: "chlorides" RELATED [ChEBI]
is_a: CHEBI:23117 ! chlorine molecular entity
is_a: CHEBI:33958 ! halide salt
relationship: has_part CHEBI:17996 ! chloride
[Term]
id: CHEBI:23116
name: chlorine atom
synonym: "17Cl" RELATED [IUPAC]
synonym: "Chlor" RELATED [ChEBI]
synonym: "chlore" RELATED [ChEBI]
synonym: "chlorine" EXACT IUPAC_NAME [IUPAC]
synonym: "chlorine" RELATED [ChEBI]
synonym: "chlorum" RELATED [ChEBI]
synonym: "Cl" RELATED [IUPAC]
synonym: "cloro" RELATED [ChEBI]
is_a: CHEBI:24473 ! halogen
relationship: RO:0000087 CHEBI:27027 ! has role micronutrient
[Term]
id: CHEBI:23117
name: chlorine molecular entity
def: "A halogen molecular entity containing one or more atoms of chlorine." []
is_a: CHEBI:24471 ! halogen molecular entity
relationship: has_part CHEBI:23116 ! chlorine atom
[Term]
id: CHEBI:23357
name: cofactor
def: "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group)." []
synonym: "cofactor" EXACT [IUPAC]
synonym: "cofactors" EXACT IUPAC_NAME [IUPAC]
is_a: CHEBI:52206 ! biochemical role
[Term]
id: CHEBI:23367
name: molecular entity
def: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." []
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:23905
name: monoatomic anion
synonym: "monoatomic anions" RELATED [ChEBI]
is_a: CHEBI:22563 ! anion
is_a: CHEBI:24867 ! monoatomic ion
[Term]
id: CHEBI:23906
name: monoatomic cation
synonym: "monoatomic cations" RELATED [ChEBI]
is_a: CHEBI:24867 ! monoatomic ion
is_a: CHEBI:36916 ! cation
[Term]
id: CHEBI:24431
name: chemical entity
def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." []
synonym: "chemical entity" EXACT [UniProt]
is_a: BFO:0000040 ! material entity
[Term]
id: CHEBI:24432
name: biological role
def: "A role played by the molecular entity or part thereof within a biological context." []
synonym: "biological function" RELATED [ChEBI]
is_a: CHEBI:50906 ! role
property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl
[Term]
id: CHEBI:24433
name: group
def: "A defined linked collection of atoms or a single atom within a molecular entity." []
synonym: "group" EXACT IUPAC_NAME [IUPAC]
synonym: "groupe" RELATED [IUPAC]
synonym: "grupo" RELATED [IUPAC]
synonym: "grupos" RELATED [IUPAC]
synonym: "Gruppe" RELATED [ChEBI]
synonym: "Rest" RELATED [ChEBI]
is_a: CHEBI:24431 ! chemical entity
relationship: has_part CHEBI:33250 ! atom
[Term]
id: CHEBI:24471
name: halogen molecular entity
synonym: "halogen compounds" RELATED [ChEBI]
synonym: "halogen molecular entities" RELATED [ChEBI]
synonym: "halogen molecular entity" EXACT [ChEBI]
is_a: CHEBI:33675 ! p-block molecular entity
relationship: has_part CHEBI:24473 ! halogen
[Term]
id: CHEBI:24473
name: halogen
synonym: "group 17 elements" RELATED [ChEBI]
synonym: "group VII elements" RELATED [ChEBI]
synonym: "halogen" EXACT IUPAC_NAME [IUPAC]
synonym: "Halogene" RELATED [ChEBI]
synonym: "halogene" RELATED [ChEBI]
synonym: "halogenes" RELATED [ChEBI]
synonym: "halogeno" RELATED [ChEBI]
synonym: "halogenos" RELATED [ChEBI]
synonym: "halogens" EXACT IUPAC_NAME [IUPAC]
is_a: CHEBI:25585 ! nonmetal atom
is_a: CHEBI:33560 ! p-block element atom
[Term]
id: CHEBI:24651
name: hydroxides
def: "Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-))." []
is_a: CHEBI:25806 ! oxygen molecular entity
is_a: CHEBI:33608 ! hydrogen molecular entity
is_a: CHEBI:37577 ! heteroatomic molecular entity
relationship: has_part CHEBI:43176 ! hydroxy group
[Term]
id: CHEBI:24834
name: inorganic anion
synonym: "inorganic anions" RELATED [ChEBI]
is_a: CHEBI:22563 ! anion
is_a: CHEBI:36914 ! inorganic ion
[Term]
id: CHEBI:24835
name: inorganic molecular entity
def: "A molecular entity that contains no carbon." []
synonym: "anorganische Verbindungen" RELATED [ChEBI]
synonym: "inorganic compounds" RELATED [ChEBI]
synonym: "inorganic entity" RELATED [ChEBI]
synonym: "inorganic molecular entities" RELATED [ChEBI]
synonym: "inorganics" RELATED [ChEBI]
is_a: CHEBI:23367 ! molecular entity
[Term]
id: CHEBI:24839
name: inorganic salt
synonym: "anorganisches Salz" RELATED [ChEBI]
synonym: "inorganic salts" RELATED [ChEBI]
is_a: CHEBI:24835 ! inorganic molecular entity
is_a: CHEBI:24866 ! salt
[Term]
id: CHEBI:24866
name: salt