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pko.obo
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format-version: 1.2
data-version: http://si.eu-parc.eu//pko/releases/2023-11-13/pko.owl
subsetdef: 3_STAR ""
subsetdef: goslim_agr ""
subsetdef: goslim_candida ""
subsetdef: goslim_chembl ""
subsetdef: goslim_drosophila ""
subsetdef: goslim_flybase_ribbon ""
subsetdef: goslim_generic ""
subsetdef: goslim_metagenomics ""
subsetdef: goslim_mouse ""
subsetdef: goslim_pir ""
subsetdef: goslim_plant ""
subsetdef: goslim_pombe ""
subsetdef: goslim_yeast ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: prokaryote_subset ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
ontology: http://si.eu-parc.eu//pko.owl
property_value: dcterms-license https://creativecommons.org/licenses/unspecified
property_value: http://purl.org/dc/terms/description "None" xsd:string
property_value: http://purl.org/dc/terms/title "pharmokinetic-ontology" xsd:string
property_value: owl:versionInfo "2023-11-13" xsd:string
[Term]
id: BFO:0000001
name: entity
property_value: BFO:0000179 "entity" xsd:string
property_value: BFO:0000180 "Entity" xsd:string
property_value: IAO:0000112 "Julius Caesar" xsd:string
property_value: IAO:0000112 "the Second World War" xsd:string
property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
property_value: IAO:0000112 "your body mass index" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string
property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"}
property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000002
name: continuant
def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
relationship: part_of BFO:0000002 {all_only="true"} ! continuant
property_value: BFO:0000179 "continuant" xsd:string
property_value: BFO:0000180 "Continuant" xsd:string
property_value: 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 {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 {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 {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 {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 {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 {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 {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 {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 {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." []
relationship: part_of BFO:0000003 {all_only="true"} ! occurrent
[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])" [] {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:0000031 ! generically dependent continuant
relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant
property_value: BFO:0000179 "ic" xsd:string
property_value: BFO:0000180 "IndependentContinuant" xsd:string
property_value: 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 {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 {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 {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 {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 {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." []
is_a: BFO:0000003 ! occurrent
[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role
property_value: BFO:0000179 "disposition" xsd:string
property_value: BFO:0000180 "Disposition" xsd:string
property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string
property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string
property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string
property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string
property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"}
property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"}
property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"}
property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000017
name: realizable entity
def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity
property_value: BFO:0000179 "realizable" xsd:string
property_value: BFO:0000180 "RealizableEntity" xsd:string
property_value: 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 {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 {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 {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 {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 {all_only="true"} ! 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 {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 {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 {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 {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {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 {all_only="true"} ! 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 {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
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 {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000023
name: role
def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." []
is_a: CHEBI:50906 ! role
equivalent_to: CHEBI:50906 ! role
property_value: BFO:0000179 "role" xsd:string
property_value: BFO:0000180 "Role" xsd:string
property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string
property_value: IAO:0000112 "the priest role" xsd:string
property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string
property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string
property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string
property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string
property_value: IAO:0000112 "the student role" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string
property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {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 {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000031
name: generically dependent continuant
def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
is_a: BFO:0000002 ! continuant
property_value: BFO:0000179 "gdc" xsd:string
property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string
property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string
property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string
property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string
property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition
property_value: BFO:0000179 "function" xsd:string
property_value: BFO:0000180 "Function" xsd:string
property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string
property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string
property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string
property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"}
property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant
[Term]
id: CHEBI:50906
name: role
namespace: chebi_ontology
def: "A role is particular behaviour which a material entity may exhibit." []
subset: 3_STAR
is_a: BFO:0000023 ! role
[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
alt_id: GO:0005554
def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "molecular function" EXACT []
is_a: BFO:0000015 ! process
disjoint_from: GO:0008150 ! biological_process
[Term]
id: GO:0003824
name: catalytic activity
namespace: molecular_function
def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Enzyme
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
created_by: jl
creation_date: 2012-09-19T15:05:24Z
[Term]
id: GO:0016301
name: kinase activity
namespace: molecular_function
def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732]
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_yeast
synonym: "phosphokinase activity" EXACT []
xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm"
xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines"
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
[Term]
id: GO:0016740
name: transferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: prokaryote_subset
xref: EC:2.-.-.-
xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2"
xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1"
xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK"
xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248"
is_a: GO:0003824 ! catalytic activity
[Term]
id: GO:0016772
name: transferase activity, transferring phosphorus-containing groups
namespace: molecular_function
def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732]
comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
subset: goslim_chembl
xref: EC:2.7.-.-
is_a: GO:0016740 ! transferase activity
[Term]
id: IAO:0000027
name: data item
def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "data item" xsd:string
property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string
property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string
property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string
property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string
property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
property_value: IAO:0000118 "data" xsd:string
[Term]
id: IAO:0000030
name: information content entity
def: "A generically dependent continuant that is about some thing." []
is_a: BFO:0000031 ! generically dependent continuant
relationship: IAO:0000136 BFO:0000001 ! is about entity
property_value: IAO:0000111 "information content entity" xsd:string
property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string
property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000119 "OBI_0000142" xsd:string
[Term]
id: IAO:0000078
name: curation status specification
def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>" xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string
[Term]
id: IAO:0000102
name: data about an ontology part
def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "data about an ontology part" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
[Term]
id: IAO:0000225
name: obsolescence reason specification
def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "obsolescence reason specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
[Term]
id: IAO:0000300
name: textual entity
def: "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "textual entity" xsd:string
property_value: IAO:0000112 "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc." xsd:string
property_value: IAO:0000116 "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities." xsd:string
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "text" xsd:string
[Term]
id: IAO:0000409
name: denotator type
def: "A denotator type indicates how a term should be interpreted from an ontological perspective." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "denotator type" xsd:string
property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string
[Term]
id: IAO:0000605
name: abbreviation textual entity
def: "A textual entity listing abbreviations and their expansions that are used in a document." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "abbreviation textual entity" xsd:string
property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nBAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
[Term]
id: PATO:0000001
name: quality
namespace: quality
alt_id: PATO:0000072
def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG]
is_a: BFO:0000020 ! specifically dependent continuant
[Term]
id: PKO:0000000
name: root node
[Term]
id: PKO:0000004
name: Physiologically Based Pharmacokinetic Modeling
def: "Physiologically based pharmacokinetic (PBPK) modeling is a mathematical modeling technique that predicts the absorption, distribution, metabolism, and excretion (ADME) of synthetic or natural chemical substances in humans and other animal species" [] {IAO:0000119="10.1038/psp.2013.41"}
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "PBPK" xsd:string
[Term]
id: PKO:0000005
name: Whole body PBPK Model
def: "A whole-body PBPK model contains an explicit representation of the organs that are most relevant to the absorption, distribution, excretion, and metabolization of the drug/chemicals due to their physiological/pharmacological function or their volume" [] {IAO:0000119="10.1002/psp4.12134"}
is_a: PKO:0000004 ! Physiologically Based Pharmacokinetic Modeling
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "All organs PBPK" xsd:string
[Term]
id: PKO:0000006
name: Perfusion Limited Model
def: "Perfusion-limited models are a type of physiologically based pharmacokinetic (PBPK) model that assumes that the concentration of a substance in tissues reaches equilibrium with the substance in the circulation rapidly. In perfusion-limited models, the rate of drug uptake by tissues is limited by blood flow, and the rate of drug elimination is limited by the rate of diffusion from the tissue to the blood" [] {IAO:0000119="https://doi.org/10.3390/nano10071267"}
is_a: PKO:0000004 ! Physiologically Based Pharmacokinetic Modeling
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000007
name: Physiological Parameters
def: "Physiological parameters in PBPK modeling provide the structural framework of the model and are used to simulate the absorption, distribution, metabolism, and excretion (ADME) of a substance throughout the body. These parameters include body weight, height, organ volume, cardiac output, organ blood flow, and tissue composition." [] {IAO:0000119="10.3390/ijerph20043473"}
is_a: PKO:0000006 ! Perfusion Limited Model
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000008
name: Body Mass Index
def: "An individual's weight in kilograms divided by the square of the height in meters." [] {IAO:0000119="http://purl.obolibrary.org/obo/NCIT_C16358"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "BMI" xsd:string
[Term]
id: PKO:0000009
name: BW (Kg)
def: " Mass or quantity of heaviness of an individual. " [] {IAO:0000119="http://purl.bioontology.org/ontology/MESH/D001835"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "BW" xsd:string
[Term]
id: PKO:0000010
name: HT
def: "Height is a term used to describe the distance from the bottom to the top of someone or something standing upright" [] {IAO:0000119="Height Definition & Meaning - Merriam-Webster"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "HT" xsd:string
[Term]
id: PKO:0000011
name: Surface area
def: " A measure of total area i.e., surface of object occupies. or\n \nThe two dimensional measure of the outer layer of the body." [] {IAO:0000119="http://semanticscience.org/resource/SIO_001407\n\nhttp://purl.bioontology.org/ontology/MESH/D001830"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "BSA/SA" xsd:string
[Term]
id: PKO:0000012
name: Race
def: "A geographic ancestral origin category assigned to a population group ." [] {IAO:0000119="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17049"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000013
name: Blood flow
def: "Blood flow in PBPK modeling refers to the rate of blood flow to a particular organ or tissue, which is used to calculate the rate of drug delivery to that organ or tissue/chemical" [] {IAO:0000119="10.1002/psp4.12134"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "Q" xsd:string
[Term]
id: PKO:0000014
name: Cardiac Output
def: "Cardiac output in PBPK modeling refers to the volume of blood pumped by the heart per unit of time, which is used to calculate the rate of blood flow to different organs and tissues in the body" [] {IAO:0000119="10.3390/ijerph20043473"}
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "CO" xsd:string
[Term]
id: PKO:0000015
name: Qstomach
def: "Qstomach is a parameter used in PBPK modeling to describe the blood flow rate to the stomach, which is used to calculate the rate of drug/chemical delivery to the stomach. The value of Qstomach depends on the species of interest and is defined by the stomach weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000016
name: FQstomach
def: "Fraction of blood flow to stomach" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000015 ! Qstomach
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000017
name: Qintestine
def: "Qintestine is a parameter used in PBPK modeling to describe the blood flow rate to the intestine, which is used to calculate the rate of drug/chemical delivery to the intestine. The value of Qintestine depends on the species of interest and is defined by the intestine weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000018
name: FQintestine
def: "Fraction of blood flow to intestine" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000017 ! Qintestine
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000019
name: Qsmall intestine
def: "Qsmall intestine is a parameter used in PBPK modeling to describe the blood flow rate to the small intestine, which is used to calculate the rate of drug/chemical delivery to the small intestine. The value of Qsmall intestine depends on the species of interest and is defined by the small intestine weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000020
name: FQsmall intestine
def: "Fraction of blood flow to small intestine" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000019 ! Qsmall intestine
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000021
name: Qlarge intestine
def: "Qlarge intestine is a parameter used in PBPK modeling to describe the blood flow rate to the large intestine, which is used to calculate the rate of drug/chemical delivery to the large intestine. The value of Qlarge intestine depends on the species of interest and is defined by the large intestine weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000022
name: FQlarge intestine
def: "Fraction of blood flow to large intestine" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000021 ! Qlarge intestine
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000023
name: Qpancreas
def: "Qpancreas is a parameter used in PBPK modeling to describe the blood flow rate to the pancreas, which is used to calculate the rate of drug/chemical delivery to the pancreas. The value of Qpancreas depends on the species of interest and is defined by the pancreas weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000024
name: FQpancreas
def: "Fraction of blood flow to pancreas" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000023 ! Qpancreas
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000025
name: Qliver
def: "Qliver is a parameter used in PBPK modeling to describe the blood flow rate to the liver, which is used to calculate the rate of drug/chemical delivery to the liver. The value of Qliver depends on the species of interest and is defined by the liver weight/volume and cardiac output" [] {IAO:0000119="10.1002/psp4.12134\nhttps://www.ema.europa.eu/en/documents/scientific-guideline/guideline-reporting-physiologically-based-pharmacokinetic-pbpk-modelling-simulation_en.pdf"}
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000026
name: FQliver
def: "Fraction of blood flow to liver" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000025 ! Qliver
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000027
name: Qkidney
def: "Qkidney is a parameter used in PBPK modeling to describe the blood flow rate to the kidney, which is used to calculate the rate of drug/chemical delivery to the kidney. The value of Qkidney depends on the species of interest and is defined by the kidney weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000028
name: FQkidney
def: "Fraction of blood flow to kidney" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000027 ! Qkidney
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000029
name: Qmuscle
def: "Qmuscle is a parameter used in PBPK modeling to describe the blood flow rate to the muscle, which is used to calculate the rate of drug/chemical delivery to the muscle. The value of Qmuscle depends on the species of interest and is defined by the muscle weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000030
name: FQmuscle
def: "Fraction of blood flow to muscle" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000029 ! Qmuscle
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000031
name: Qheart
def: "Qheart is a parameter used in PBPK modeling to describe the blood flow rate to the heart, which is used to calculate the rate of drug/chemical delivery to the heart. The value of Qheart depends on the species of interest and is defined by the heart weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000032
name: FQheart
def: "Fraction of blood flow to heart" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000031 ! Qheart
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000033
name: Qfat
def: "Qfat is a parameter used in PBPK modeling to describe the blood flow rate to the fat, which is used to calculate the rate of drug/chemical delivery to the fat. The value of Qfat depends on the species of interest and is defined by the fat weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "Qadipose tissue" xsd:string
[Term]
id: PKO:0000034
name: FQfat
def: "Fraction of blood flow to fat" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000033 ! Qfat
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000035
name: Qgonads
def: "Qgonads is a parameter used in PBPK modeling to describe the blood flow rate to the gonads, which is used to calculate the rate of drug/chemical delivery to the gonads. The value of Qgonads depends on the species of interest and is defined by the gonads weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000036
name: FQgonads
def: "Fraction of blood flow to gonads" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000035 ! Qgonads
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000037
name: Qskin
def: "Qskin is a parameter used in PBPK modeling to describe the blood flow rate to the skin, which is used to calculate the rate of drug/chemical delivery to the skin. The value of Qskin depends on the species of interest and is defined by the skin weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000038
name: FQskin
def: "Fraction of blood flow to skin" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000037 ! Qskin
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000039
name: Qbone
def: "Qbone is a parameter used in PBPK modeling to describe the blood flow rate to the bone, which is used to calculate the rate of drug/chemical delivery to the bone. The value of Qbone depends on the species of interest and is defined by the bone weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000040
name: FQbone
def: "Fraction of blood flow to bone" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000039 ! Qbone
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000041
name: Qbrain
def: "Qbrain is a parameter used in PBPK modeling to describe the blood flow rate to the brain, which is used to calculate the rate of drug/chemical delivery to the brain. The value of Qbrain depends on the species of interest and is defined by the brain weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000042
name: FQbrain
def: "Fraction of blood flow to brain" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000041 ! Qbrain
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000043
name: Qspleen
def: "Qspleen is a parameter used in PBPK modeling to describe the blood flow rate to the spleen, which is used to calculate the rate of drug/chemical delivery to the spleen. The value of Qspleen depends on the species of interest and is defined by the spleen weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000044
name: FQspleen
def: "Fraction of blood flow to spleen" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000043 ! Qspleen
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000045
name: Qlung
def: "Qlung is a parameter used in PBPK modeling to describe the blood flow rate to the lung, which is used to calculate the rate of drug/chemical delivery to the lung. The value of Qlung depends on the species of interest and is defined by the lung weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000046
name: FQlung
def: "Fraction of blood flow to lung" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000045 ! Qlung
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000047
name: Qpoorly perfused
def: "Qpoorly perfused is a parameter used in PBPK modeling to describe the blood flow rate to the poorly perfused organ/tissue, which is used to calculate the rate of drug/chemical delivery to the poorly perfused organ/tissue. The value of Qpoorly perfused depends on the species of interest and is defined by the poorly perfused organ/tissue weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000048
name: FQpoorly perfused
def: "Fraction of blood flow to poorly perfused tissues/organ" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000047 ! Qpoorly perfused
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000049
name: Qrichly perfused
def: "Qrichly perfused is a parameter used in PBPK modeling to describe the blood flow rate to the richly perfused organ/tissue, which is used to calculate the rate of drug/chemical delivery to the richly perfused organ/tissue. The value of Qrichly perfused depends on the species of interest and is defined by the richly perfused organ/tissue weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000050
name: FQrichly perfused
def: "Fraction of blood flow to richly perfused tissues/organs" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000049 ! Qrichly perfused
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000051
name: Qrestbody
def: "Qrestbody is a parameter used in PBPK modeling to describe the blood flow rate to the remaining organ/tissue, which is used to calculate the rate of drug/chemical delivery to the remaining organ/tissue. The value of Qrestbody can be obtained by subtracting the total body blood flow with the blood flow of each organs/tissue present in the model." []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000052
name: FQrestbody
is_a: PKO:0000051 ! Qrestbody
[Term]
id: PKO:0000053
name: Qgallballder
def: "Qgall bladder is a parameter used in PBPK modeling to describe the blood flow rate to the gall bladder, which is used to calculate the rate of drug/chemical delivery to the gall bladder. The value of Qgall bladder depends on the species of interest and is defined by the gall bladder weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000054
name: FQgallballder
is_a: PKO:0000053 ! Qgallballder
[Term]
id: PKO:0000055
name: Qportal vein
def: "Qportal vein is a parameter used in PBPK modeling to describe the blood flow rate to the portal vein, which is used to calculate the rate of drug/chemical delivery to the stomach. The value of Qportal vein depends on the species of interest and is defined by the portal vein weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000056
name: FQportal vein
is_a: PKO:0000055 ! Qportal vein
[Term]
id: PKO:0000057
name: Qlymph
def: "Qlymph is a parameter used in PBPK modeling to describe the blood flow rate to the lymph, which is used to calculate the rate of drug/chemical delivery to the lymph. The value of Qlymph depends on the species of interest and is defined by the lymph weight/volume and cardiac output" []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000058
name: FQlymph
is_a: PKO:0000057 ! Qlymph
[Term]
id: PKO:0000059
name: Arterial blood flow
def: "Arterial blood flow in PBPK modeling represents the rate of blood flow to the tissues and organs through the arterial system. This parameter is essential for estimating the distribution of drugs and other substances in the body" [] {IAO:0000119="10.1007/s40268-020-00325-0\n10.1186/1472-6904-4-2"}
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000060
name: Venous blood flow
def: "Venous blood flow in PBPK modeling represents the rate of blood flow returning from the tissues and organs through the venous system. This parameter is essential for estimating the distribution of drugs/chemicals and other substances in the body." []
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000061
name: Glomerular filtration rate
def: "Glomerular filtration rate (GFR) is a measure of kidney function that describes the flow rate of filtered fluid through the kidney" [] {IAO:0000119="Glomerular filtration rate - Wikipedia"}
is_a: PKO:0000013 ! Blood flow
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "GFR" xsd:string
[Term]
id: PKO:0000062
name: Volume of organ
def: "Organ volume in PBPK modeling refers to the volume of a specific organ or tissue in the body. " [] {IAO:0000119="10.1002/psp4.12205"}
is_a: PKO:0000007 ! Physiological Parameters
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
property_value: IAO:0000605 "Vorgan" xsd:string
[Term]
id: PKO:0000063
name: Vstomach
def: "Volume of stomach" [] {IAO:0000119="https://doi.org/10.1016/j.envres.2022.114074"}
is_a: PKO:0000062 ! Volume of organ
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000064
name: Fstomach
def: "stomach volume as total body weight fraction" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000063 ! Vstomach
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000065
name: Vintestine
def: "Volume of intestine" [] {IAO:0000119="https://doi.org/10.1016/j.envres.2022.114074"}
is_a: PKO:0000062 ! Volume of organ
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000066
name: Fintestine
def: "intestine volume as total body weight fraction" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000065 ! Vintestine
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000067
name: Vsmall intestine
def: "Volume of small intestine" [] {IAO:0000119="https://doi.org/10.1016/j.envres.2022.114074"}
is_a: PKO:0000062 ! Volume of organ
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000068
name: Fsmall intestine
def: "small intestine volume as total body weight fraction" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000067 ! Vsmall intestine
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000069
name: Vlarge intestine
def: "Volume of large intestine" [] {IAO:0000119="https://doi.org/10.1016/j.envres.2022.114074"}
is_a: PKO:0000062 ! Volume of organ
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000070
name: Flarge intestine
def: "large intestine volume as total body weight fraction" [] {IAO:0000119="https://doi.org/10.1016/j.toxlet.2023.06.006"}
is_a: PKO:0000069 ! Vlarge intestine
property_value: IAO:0000117 "0000-0001-8345-1349" xsd:string
property_value: IAO:0000117 "0000-0002-9795-5967" xsd:string
[Term]
id: PKO:0000071
name: Vpancreas
def: "Volume of pancreas" [] {IAO:0000119="https://doi.org/10.1016/j.envres.2022.114074"}
is_a: PKO:0000062 ! Volume of organ