_comment: Created with OWL2VOWL (version 0.3.7), http://vowl.visualdataweb.org

languages: en undefined

identifier: hasDbXref

type: label

value: A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ).

identifier: hasExactSynonym

value: shrunken

type: iri

identifier: hasOBONamespace

value: quality

identifier: id

identifier: inSubset

identifier: hasAlternativeId

undefined: hypotrophic

attributes: anonymous union

value: heavy

value: high weight

value: A weight which is relatively high.

undefined: increased weight

attributes: intersection external

undefined: Thing

value: low weight

value: light weight

value: A weight which is relatively low.

undefined: decreased weight

value: An abnormally early start time of 'biological process'.

identifier: title

value: abnormallyPrematureBiologicalProcess

undefined: premature 'biological process'

value: decreased 'biological_process'.

undefined: decreased 'biological_process'

value: An abnormal level of 'chemical entity'.

value: abnormalLevelOfChemicalEntity

undefined: abnormal 'chemical entity' level

value: Decreased distance between 'anatomical entity1' and 'anatomical entity2'.

value: distance decreased between 'anatomical entity1' and 'anatomical entity2'

undefined: decreased distance between 'anatomical entity1' and 'anatomical entity2'

value: An abnormal amount of role in the 'independent continuant'.

undefined: abnormal role 'independent continuant' level

value: A size quality which is relatively high.

identifier: hasRelatedSynonym

value: enlarged

value: A structural quality inhering in a bearer by virtue of whether the bearer includes all its components.

value: The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.

undefined: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.

value: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.

value: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.

value: A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311).

value: Any abnormal duplication of the 'anatomical entity' in 'independent continuant'.

value: abnormally duplicated 'anatomical entity' in 'independent continuant'

undefined: abnormal duplication of 'anatomical entity' in 'independent continuant'

value: An anatomical structure that has more than one cell as a part.

value: A broken quality inhering in a bearer by virtue of the bearer's being broken open.

value: A resistance to a stimulus which is relatively low.

value: A resistance to a stimulus which is relatively high.

value: 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.

value: 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])

value: 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])

value: 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])

value: 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])

value: 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

value: 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

value: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

value: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]

value: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]

value: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]

value: An entity that has temporal parts and that happens, unfolds or develops through time.

value: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])

value: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])

value: 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.

value: 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.

value: 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.

value: 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

value: 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])

value: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

value: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]

value: 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

value: 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

value: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

value: An anatomical structure consisting of one or more cells.

value: Any structural anomaly that causes there to be an abnormal number 'anatomical entity' in 'independent continuant'.

value: abnormal number of 'anatomical entity's in 'independent continuant'

value: altered number of 'anatomical entity's in 'independent continuant'

undefined: abnormal number of anatomical entities of type 'anatomical entity' in 'independent continuant'

value: the bottom right portion of a human torso

value: 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])

value: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

value: 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])

value: 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])

value: (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]

value: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

value: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]

value: A length quality which is relatively large.

value: A length quality which is relatively small.

value: down regulation of phosphate metabolic process

value: down-regulation of phosphate metabolic process

value: negative regulation of phosphate metabolism

value: downregulation of phosphate metabolic process

value: Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.

value: inhibition of phosphate metabolic process

undefined: negative regulation of phosphate metabolic process

value: positive regulation of phosphate metabolism

value: up-regulation of phosphate metabolic process

value: up regulation of phosphate metabolic process

value: upregulation of phosphate metabolic process

value: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.

value: stimulation of phosphate metabolic process

value: activation of phosphate metabolic process

undefined: positive regulation of phosphate metabolic process

value: An abnormally blistered 'anatomical entity' in 'independent continuant'.

value: 'independent continuant' 'anatomical entity' with blister

undefined: abnormally blistered 'anatomical entity' in 'independent continuant'

value: A temporal distribution pattern of process occurrences within a regulation/reference process.

value: A quality inhering in a bearer by virtue of the bearer's being present in two copies.

value: Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

value: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.

value: A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.

value: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

undefined: regulation of cellular metabolic process

value: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.

undefined: regulation of phosphorus metabolic process

value: down-regulation of cellular metabolic process

value: negative regulation of cellular metabolism

value: down regulation of cellular metabolic process

value: downregulation of cellular metabolic process

value: Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

value: inhibition of cellular metabolic process

undefined: negative regulation of cellular metabolic process

value: positive regulation of cellular metabolism

value: up-regulation of cellular metabolic process

value: upregulation of cellular metabolic process

value: up regulation of cellular metabolic process

value: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

value: stimulation of cellular metabolic process

value: activation of cellular metabolic process

undefined: positive regulation of cellular metabolic process

value: The temporal relation between the end of the process with respect to a reference process.

value: The presence of a reduced number of 'anatomical entity' in the 'independent continuant'.

value: Reduced number of 'anatomical entity' in the 'independent continuant'

undefined: Decreased number of 'anatomical entity' in the 'independent continuant'

undefined: See comments of relational quality of a physical entity.

value: The temporal relation between the start of the process with respect to a reference process.

value: multiply inhering quality of a physical entity

value: A quality which inheres in a continuant.

undefined: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

value: A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.

value: The presence of an abscess of the 'anatomical entity'.

value: Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.

value: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

value: positive regulation of organismal metabolism

value: positive regulation of multicellular organismal metabolic process

value: stimulation of organismal metabolic process

value: up-regulation of organismal metabolic process

undefined: positive regulation of metabolic process

value: A 1-D extent quality which is equal to the distance between two points.

value: A quality that has a value that is increased compared to normal or average.

value: A quality that has a value that is decreased compared to normal or average.

value: Partial or complete wasting (loss) of 'anatomical entity' tissue that was once present.

value: negative regulation of organismal metabolism

value: Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

value: inhibition of organismal metabolic process

value: negative regulation of multicellular organismal metabolic process

undefined: negative regulation of metabolic process

value: Partial or complete degeneration of 'anatomical entity' tissue that was once present.

value: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.

value: Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

undefined: negative regulation of cell communication

value: A physical quality inhering in a bearer that has mass near a gravitational body.

value: A quality of a process that has a value that is increased compared to normal or average.

value: A quality of an object that has a value that is increased compared to normal or average.

value: A quality of a process that has a value that is decreased compared to normal or average.

value: Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

value: A quality of an object that has a value that is decreased compared to normal or average.

value: Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

undefined: positive regulation of cell communication

value: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.

value: A distance which is lesser relative to the normal or average.

value: A distance which is greater relative to the normal or average.

value: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.

undefined: regulation of phosphate metabolic process

value: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

value: regulation of organismal metabolic process

value: regulation of multicellular organismal metabolic process

value: An abnormal increase in weight or an increased distribution of mass in the 'anatomical entity'.

value: A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent.

value: Impaired or decreased 'behavior process'.

value: An abnormally formed/malformed 'anatomical entity'.

value: Any functional anomaly of the 'cellular component'.

undefined: abnormality of 'cellular component' function

value: Any abnormal bending of the 'anatomical entity'.

value: abnormal degree of pigmentation of the 'anatomical entity'.

value: abnormal pigmentation of the 'anatomical entity'

undefined: abnormal degree of pigmentation of the 'anatomical entity'

value: A quality of a process which starts later than the natural start time or the reference process.

value: An abnormally blistered 'anatomical entity'.

undefined: abnormally blistered 'anatomical entity'

value: Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.

undefined:
MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history.

MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.

value: Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.

undefined: This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class.

value: An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.

undefined: deprecate and replace with CL or GO term?

value: Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid.  This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle.

value: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome.

undefined: Note - CARO explicitly declares organisms substances to be part of (some) organism.

value: An abnormally formed/malformed 'anatomical entity' in 'independent continuant'.

value: malformed 'anatomical entity' in 'independent continuant'

undefined: abnormally formed 'anatomical entity' in 'independent continuant'

value: 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.

undefined: 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.

value: A decreased occurrence of 'biological process' in 'independent continuant'.

undefined: decreased occurrence of 'biological process' in 'independent continuant'

value: An anatomical structure that has no cells or cell parts as a part.

undefined: Example.  Insect cuticle, eggshell, hair.

value: A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.

undefined: MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures.  Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.".  One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?

value: A morphological quality inhering in a bearer by virtue of the bearer's absence or closure of a normal body orifice or tubular passage.

value: An increased occurrence of 'biological process' in 'independent continuant'.

undefined: increased occurrence of 'biological process' in 'independent continuant'

value: Abnormal cell proliferation in 'anatomical_entity'.

undefined: abnormal cell proliferation in 'anatomical_entity'

value: Abnormal proliferation of 'cell' in 'anatomical entity'.

undefined: abnormal 'cell' proliferation in 'anatomical entity'

value: Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.

value: Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism.

value: abnormally incompletely closed 'anatomical entity'

value: Abnormally incompletely closed 'anatomical entity'.

undefined: abnormal incomplete closing of the 'anatomical entity'

value: of one-sided specifically dependent continuants: the mass of this tomato

value: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction

value: the function of this heart: to pump blood

value: the pink color of a medium rare piece of grilled filet mignon at its center

value: the mutual dependence of proton donors and acceptors in chemical reactions [79

value: 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

value: 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.

value: 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])

value: 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.

value: 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])

value: 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.

value: (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]

value: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]

value: 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.

value: the role of a boundary to demarcate two neighboring administrative territories

value: the role of a stone in marking a property boundary

value: the role of a building in serving as a military target

value: 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.

value: 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.

value: 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])

value: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

value: An abnormality of the 'biological process' in 'independent continuant'.

undefined: abnormal 'biological process' in 'independent continuant'

value: A decreased amount in the level of 'chemical entity'.

value: A role is particular behaviour which a material entity may exhibit.

value: The chemical reactions and pathways by which individual cells transform chemical substances.

value: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

value: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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.

undefined: 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. Note that 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 ND, no data, is used to indicate this.

value: Absent or undetectable 'biological process' in 'independent continuant'.

undefined: absent 'biological process' in 'independent continuant'

value: The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

value: metabolic process resulting in cell growth

value: multicellular organism metabolic process

undefined: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.

value: An abnormal increase in length in 'anatomical entity' in location 'independent continuant'.

undefined: increased 'anatomical entity' length in 'independent continuant'

value: Any constituent part of a cell, the basic structural and functional unit of all organisms.

undefined: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

value: skinny or decreased width of the 'anatomical entity' in 'independent continuant'.

value: skinny 'anatomical entity' in 'independent continuant'

undefined: decreased width of the 'anatomical entity' in 'independent continuant'

value: the role of this boundary to delineate where Utah and Colorado meet

value: the disposition of your blood to coagulate

value: the function of your reproductive organs

value: the disposition of this piece of metal to conduct electricity.

value: 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.

value: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])

value: 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])

value: (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]

value: (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]

value: a process of cell-division, \ a beating of the heart

value: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

value: 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])

value: 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)

value: (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]

value: A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary and outwards in relation to the physical space occupied by another entity.

value: Partial or complete degeneration of 'cellular component'.

value: degeneration of the 'cellular component'

value: An individual member of a clade of cellular organisms.

undefined: A general term for organism that is agnostic about single cell vs multi-cellular.  Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.

value: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

value: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])

value: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])

value: 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

value: 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.

value: 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.

value: 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])

value: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]

value: (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]

value: (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]

value: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex.  Or, a substance produced by a cellular organism with granularity above the level of a protein complex.

undefined: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach).  The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.

value: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.

undefined: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.

value: An abnormal level of 'chemical entity' in the 'independent continuant'.

undefined: abnormal 'independent continuant' 'chemical entity' level

value: Any structural anomaly that causes there to be an abnormal number 'anatomical entity'.

undefined: abnormal number of anatomical enitites of type 'anatomical entity'

value: A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form.

value: An abnormally apoptotic 'anatomical entity'.

undefined: abnormally apoptotic 'anatomical entity'

value: Any structural anomaly in the shape of the 'entity'.

value: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop

value: 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.

value: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.

value: 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.

value: 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])

value: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

value: Calcification of the 'anatomical entity'.

value: An increase in the thickness of the 'anatomical entity'.

undefined: increased thickness of the 'anatomical entity'

value: loss of pigment in the 'anatomical entity'

value: Decreased or loss of pigmentation of 'anatomical entity'.

undefined: decreased pigmentation in the 'anatomical entity'

value: Any process that modulates the frequency, rate or extent of protein binding.

value: A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s).

value: A functional quality held by the bearer when the latter exhibits increased ability to perform a regular function(s).

value: A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting.

value: negative regulation of physiological process

value: Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

undefined: negative regulation of biological process

value: positive regulation of physiological process

value: Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

undefined: positive regulation of biological process

value: loss of 'anatomical entity' due to degeneration

value: Complete wasting (loss) of 'anatomical entity' tissue that was once present.

undefined: missing 'anatomical entity' due to degeneration

value: longer, increased length of, 'anatomical entity'

undefined: increased length of the 'anatomical entity'

value: A morphological abnormality of the 'anatomical entity' in the 'independent continuant'.

value: Abnormal morphology of the 'anatomical entity' in the 'independent continuant'

undefined: abnormal 'anatomical entity' morphology in the 'independent continuant'

value: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.

value: A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width.

value: A decrease in the level of 'chemical entity' in 'independent continuant'.

undefined: decreased level of 'chemical entity' in 'independent continuant'

value: An increase in the size of the 'anatomical entity'.

undefined: increased size of the 'anatomical entity'

value: Any process that activates or increases the activity of an enzyme.

value: positive regulation of metalloenzyme activity

undefined: positive regulation of catalytic activity

value: down-regulation of metalloenzyme activity

value: Any process that stops or reduces the activity of an enzyme.

value: negative regulation of metalloenzyme activity

value: downregulation of metalloenzyme activity

value: down regulation of metalloenzyme activity

undefined: negative regulation of catalytic activity

value: Any structural anomaly of the 'cellular component'.

undefined: abnormal morphology of 'cellular component'

value: Any unspecified morphological anomaly of part of the 'anatomical entity', such as, for example, abnormal shape or colour.

value: abnormal morphology of 'anatomical entity'

value: Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

value: positive regulation of cellular physiological process

value: Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

value: negative regulation of cellular physiological process

value: Absent or undetectable level of 'chemical entity'.

value: An abnormally localised 'anatomical entity'.

value: abnormal position of 'anatomical entity'

undefined: Abnormally localised 'anatomical entity'

value: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.

value: decreased sensitivity of organism to 'chemical entity'

value: Increased resistance of organism to 'chemical entity'.

undefined: increased resistance of organism to 'chemical entity'

value: 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.

undefined: GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA

value: A developmental defect resulting in complete obliteration of the lumen of the 'anatomical entity'.

value: A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.

value: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.

value: The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

value: Increased distance between 'entity1' and 'entity2'.

value: distance increased between 'entity1' and 'entity2'

undefined: increased distance between 'entity1' and 'entity2'

undefined: TODO: define this or obsolete it and move children somewhere else.

value: The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly.

undefined: Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type.

value: The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part.

undefined: In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger.

value: A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity.

undefined: Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2.

value: Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.

value: negative regulation of signalling process

value: negative regulation of signaling process

value: Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.

value: positive regulation of signalling process

value: positive regulation of signaling process

value: Any structural anomaly of 'anatomical entity' that causes there to be fewer parts of type 'anatomical entity'.

value: fewer 'anatomical entity's in 'anatomical entity'

undefined: 'anatomical entity' that has fewer parts of type 'anatomical entity'

value: A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.

value: A degree of pigmentation quality inhering in a bearer by virtue of the bearer's lacking substances produced by living organisms that have a color resulting from selective color absorption.

value: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.

value: A quality inhering in a bearer by virtue of the bearer's having or lacking of substances produced by living organisms that have a color resulting from selective color absorption.

value: The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.

undefined: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.

value: A degree of pigmentation quality inhering in a bearer by virtue of the bearer's having substances produced by living organisms that have a color resulting from selective color absorption.

value: Any process that modulates the frequency, rate or extent of a signaling process.

value: Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.

undefined: Important for alignment with Darwin Core class "Organism".

value: A degree of pigmentation quality that is relatively high.

value: A degree of pigmentation quality that is relative low.

value: The number of entities of this type that are part of the whole organism.

undefined: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.

value: Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).

undefined: transferase activity, transferring phosphorus-containing groups

undefined: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.

value: Decreased resistance of organism to 'chemical entity'.

value: increased sensitivity of organism to 'chemical entity'

undefined: decreased resistance of organism to 'chemical entity'

value: Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

undefined: positive regulation of response to stimulus

value: Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

undefined: negative regulation of response to stimulus

value: Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

value: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

undefined: 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.

value: A quality that is the extent of space between two entities.

value: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence.

value: A quality of a process which ends earlier than the natural end time or reference process.

undefined: TODO: the definition is incorrect. See absent.

value: A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).

undefined: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.

value: An abnormal reduction in the volume of the 'anatomical entity'.

undefined: decreased volume of the 'anatomical entity'

value: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.

value: The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

value: Any process that modulates the frequency, rate or extent of transferase activity, the 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.

undefined: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.

value: An abnormal position of the 'anatomical entity' in the 'independent continuant'.

undefined: abnormal 'anatomical entity' topology in 'independent continuant'

value: skinny or decreased width of the 'anatomical entity'.

undefined: decreased width of the 'anatomical entity'

value: Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.

value: An abnormal concentration of chemical in 'independent continuant'.

undefined: abnormal chemical concentration in 'independent continuant'

value: Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.

undefined: negative regulation of transferase activity

value: Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.

undefined: positive regulation of transferase activity

value: A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus.

value: An increase in the thickness of the 'anatomical entity' in the 'independent continuant'.

value: thickened 'anatomical entity' in 'independent continuant'

undefined: increased thickness of the 'anatomical entity' in 'independent continuant'

value: A structural quality inhering in a bearer by virtue of the bearer exhibiting deterioration of its structure.

value: The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).

value: The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.

undefined: phosphate-containing compound metabolic process

value: A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.

value: Any unspecified morphological anomaly of the 'anatomical entity', such as, for example, abnormal shape or colour.

value: Any structural anomaly that causes 'anatomical entity' to be 'shape' shaped.

value: abnormal 'shape' shape of 'anatomical entity'

value: A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.

value: A quality denoting the lack of an entity.

undefined: See documentation here: http://code.google.com/p/phenotype-ontologies/wiki/ModelingOfAbsence

value: A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.

value: A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity.

value: A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s).

value: A quality inhering in a bearer by virtue of the bearer's existence.

value: extra or missing physical or functional parts

value: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.

value: A quality of a process inhering in a bearer by virtue of the bearer's processual parts.

value: Any process that activates or increases the frequency, rate or extent of signal transduction.

value: positive regulation of signalling pathway

value: positive regulation of signaling pathway

undefined: positive regulation of signal transduction

value: Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.

value: negative regulation of signaling pathway

value: negative regulation of signalling pathway

undefined: negative regulation of signal transduction

value: Any process that modulates the frequency, rate or extent of signal transduction.

value: A deviation from the normal size of the 'anatomical entity'.

value: abnormal size of the 'anatomical entity'

value: The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.

value: The presence of an increased number of 'anatomical entity'.

value: The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.

value: An increase in the size of the 'anatomical entity' in the 'independent continuant'.

value: enlarged 'anatomical entity' in 'independent continuant'

undefined: increased size of the 'anatomical entity' in 'independent continuant'

value: A quality of a process which starts earlier than the natural start time or the reference process.

value: decreased sensitivity of organism to 'entity'

value: Increased resistance of organism to 'entity'.

undefined: increased resistance of organism to 'entity'

value: A branched quality inhering in a bearer by virtue of the bearer's being divided into two branches.

value: An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.

value: An increase in the level of 'chemical entity' in 'independent continuant'.

value: increased level of 'chemical entity' in 'independent continuant'

undefined: increased level of 'chemical entity' in 'independent continuant'

value: 'independent continuant' 'anatomical entity' with apoptosis

value: An abnormally apoptotic 'anatomical entity' in 'independent continuant'.

undefined: abnormally apoptotic 'anatomical entity' in 'independent continuant'

value: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

value: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.

value: A shape quality inhering in a bearer by virtue of the bearer's being divided or broken up into parts or divisions.

value: A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.

value: A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.

undefined: For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).

value: A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary.

value: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

value: Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.

value: Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.

value: Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.

value: Enhanced or improved 'behavior process'.

value: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.

value: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities

value: abnormally changed resistance of organism to 'entity'.

value: abnormally changed  sensitivity of organism to 'entity'

undefined: abnormally changed resistance of organism to 'entity'

value: An abnormal development of the 'anatomical entity'.

undefined: abnormal development of 'anatomical entity'

value: Defective development of the 'anatomical entity'.

value: An abnormal location of 'anatomical entity'.

undefined: abnormal location of 'anatomical entity'

value: Any functional anomaly of the 'anatomical entity'.

undefined: abnormality of 'anatomical entity' physiology

value: An abnormally decreased level of role in the 'independent continuant'.

undefined: decreased role 'independent continuant' level

value: A composite chromatic quality composed of hue, saturation and intensity parts.

value: Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

value: down regulation of developmental process

value: down-regulation of developmental process

undefined: negative regulation of developmental process

value: Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.

value: Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.

value: Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

undefined: positive regulation of developmental process

value: Missing 'anatomical entity' in the 'independent continuant'

value: Absence of the 'anatomical entity' in the 'independent continuant'.

undefined: Absent 'anatomical entity' in the 'independent continuant'

value: A decreased occurrence of 'biological_process'.

undefined: decreased occurrence of 'biological_process'

value: A positional quality inhering in a bearer by virtue the bearer's being changed in abnormal position.

value: Arrested 'biological_process' in 'independent continuant'.

undefined: arrested 'biological_process' in 'independent continuant'

value: A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.

value: Any process that modulates the frequency, rate or extent of cell proliferation.

undefined: regulation of cell population proliferation

value: An increased amount in the level of 'chemical entity'.

value: An abnormal 'anatomical entity' with one or more lesions.

value: A structural quality inhering in a bearer by virtue of the bearer's consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis.

value: A structural quality inhering in a bearer whose structure deteriorates or is lost over time due to an active pathological process.

value: Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.

undefined: negative regulation of phosphorus metabolic process

value: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

value: Absent or undetectable level of 'chemical entity' in 'independent continuant'.

undefined: absent 'chemical entity' in 'independent continuant'

value: Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.

undefined: positive regulation of phosphorus metabolic process

value: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.

value: decreased 'biological_process' in 'independent continuant'.

undefined: decreased 'biological_process' in 'independent continuant'

value: Partial or complete degeneration of 'cellular component' tissue in the 'independent continuant' that was once present.

value: degeneration of the 'cellular component' in 'independent continuant'

undefined: 'cellular component' degeneration in 'independent continuant'

value: A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view.

value: Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell.  Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.

value: A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view.

value: An abnormal increase or decrease of weight or an abnormal distribution of mass in the 'anatomical entity'.

undefined: abnormality of 'anatomical entity' weight

value: Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

value: The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

undefined: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.

value: Any process that modulates a measurable attribute of any biological process, quality or function.

value: Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

value: Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.

value: The presence of a reduced number of 'anatomical entity'.

value: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.

undefined: Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain.

value: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.

value: A shape quality inhering in a bearer by virtue of the bearer's having one or more angle(s) in its length.

value: A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view.

value: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

value: The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type.

value: A functionality quality held by the bearer when the latter is able to perform a regular function(s).

value: A quality that inheres in an entire organism or part of an organism.

value: absence of pigment in the 'anatomical entity'

value: complete loss of pigmentation in the 'anatomical entity'

value: complete loss of pigmenation of the 'anatomical entity'.

value: Any process that activates or increases the rate or extent of cell proliferation.

value: positive regulation of cell proliferation

undefined: positive regulation of cell population proliferation

value: The multiplication or reproduction of cells, resulting in the expansion of a cell population.

undefined: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.

value: A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells.

value: Any process that stops, prevents or reduces the rate or extent of cell proliferation.

value: negative regulation of cell proliferation

undefined: negative regulation of cell population proliferation

value: short 'anatomical entity' in 'independent continuant'

value: Decreased length or shortening of the 'anatomical entity' in the 'independent continuant'.

undefined: decreased length of 'anatomical entity' in 'independent continuant'

value: An abnormally decreased functionality of the 'anatomical entity'.

undefined: abnormally decreased functionality of the 'anatomical entity'

value: Any abnormal duplication of the 'anatomical entity'.

value: abnormally duplicated 'anatomical entity'

value: abnormal duplication of 'anatomical entity'

undefined: abnormal duplication of 'anatomical entity'

value: A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.

value: A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend.

value: A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation.

value: A branchiness quality inhering in a bearer by virtue of the bearer's having branches.

value: The presence of an increased number of 'cellular component'.

undefined: Increased number of 'cellular component'

value: A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s).

value: Decreased qualitatively 'biological process'.

undefined: decreased qualitatively 'biological process'

value: abnormal distance between 'anatomical_entity1' and 'anatomical_entity2'.

value: abnormal distance between 'anatomical_entity1' and 'anatomical_entity2'

value: distance abnormal between 'anatomical_entity1' and 'anatomical_entity2'

undefined: abnormal distance between 'anatomical_entity1' and 'anatomical_entity2'

value: The presence of a reduced number of 'cellular component'.

undefined: Decreased number of 'cellular component'

value: A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.

value: An abnormality in the cell differentiation of the 'cell type'.

undefined: abnormal 'cell type' cell differentiation

value: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.

value: A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.

value: A positional quality inhering in a bearer by virtue the bearer's being changed in position.

value: 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.

value: Absent or undetectable level of 'molecular function'.

value: An increased occurrence of 'biological_process'.

undefined: increased occurrence of 'biological_process'

value: Any process that activates or increases the frequency, rate or extent of protein binding.

value: An abnormal reduction in the size of the 'anatomical entity'.

undefined: decreased size of the 'anatomical entity'

value: Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.

value: An abnormally increased level of role in the 'independent continuant'.

undefined: increased 'independent continuant' role level

value: An increase in the height of the 'anatomical entity' in the 'independent continuant'.

value: higher 'anatomical entity' in 'independent continuant'

undefined: increased height of 'anatomical entity' in 'independent continuant'

value: A texture quality inhering in a bearer by virtue of a local accumulation of fluid underneath the surface of the bearer.

value: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.

undefined: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

value: Decreased length or shortening of the 'anatomical entity'.

value: A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).

undefined: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).

value: An abnormal decrease in weight or a decreased distribution of mass in the 'anatomical entity'.

value: Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.

undefined: negative regulation of molecular function

value: Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.

undefined: positive regulation of molecular function

value: Any structural anomaly that causes there to be extra parts of type 'anatomical entity' in 'independent continuant'.

value: extra 'anatomical entity's in 'independent continuant'

undefined: has extra parts of type 'anatomical entity' in 'independent continuant'

value: Abnormally reduced functionality of 'molecular function'.

value: The presence of excessive fibrous connective tissue in the 'anatomical entity'.

value: Decreased resistance of organism to 'entity'.

value: increased sensitivity of organism to 'entity'

undefined: decreased resistance of organism to 'entity'

value: A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.

value: degeneration of the 'anatomical entity' in 'independent continuant'

value: Partial or complete degeneration of 'anatomical entity' tissue in the 'independent continuant' that was once present.

undefined: 'anatomical entity' degeneration in 'independent continuant'

value: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

value: increasing of pigment in the 'anatomical entity'

value: Increased or increasing of pigmentation of 'anatomical entity'.

undefined: increased pigmentation in the 'anatomical entity'

value: A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus.

value: Any structural anomaly that causes there to be extra parts of type 'anatomical entity'.

undefined: has extra parts of type 'anatomical entity'

value: fewer 'anatomical entity's in 'anatomical entity', located in 'independent continuant'

value: Any structural anomaly that causes there to be fewer parts of type 'anatomical entity' in the 'anatomical entity'.

undefined: has fewer parts of type 'anatomical entity' in 'anatomical entity', which is located in 'independent continuant'

value: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.

value: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

value: A partial or complete breakage of the 'anatomical entity'.

value: The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).

undefined: Definition discussed in https://github.com/geneontology/go-ontology/issues/14220

value: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.

value: Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.

value: Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.

value: down regulation of receptor-associated protein activity

value: Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.

value: Any anomaly that causes there to be an abnormal number 'cellular component'.

value: abnormal number of 'cellular component's

value: Any process that modulates the activity of an enzyme.

value: Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

value: A molecular function that modulates the activity of a gene product or complex.  Examples include enzyme regulators and channel regulators.

undefined: abnormal closing of the 'anatomical entity'

value: Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

value: regulation of cellular physiological process

value: The presence of an increased number of 'anatomical entity' in the 'independent continuant'.

value: Extra 'anatomical entity' in the 'independent continuant'

undefined: Increased number of 'anatomical entity' in the 'independent continuant'

value: A functional abnormality of the 'anatomical entity' in 'independent continuant'.

undefined: 'anatomical entity' dysfunction in 'independent continuant'

value: An increase in the height of the 'anatomical entity'.

undefined: increased height of the 'anatomical entity'

value: The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

value: A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).

undefined: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.

value: A hyperactivity of the 'anatomical entity' in the 'independent continuant'.

undefined: 'anatomical entity' hyperactivity in 'independent continuant'

value: A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.

value: protruding 'anatomical entity' in 'independent continuant'

value: hernial protrusion of the 'anatomical entity' through an opening or defect in the 'independent continuant'.

undefined: abnormal protrusion of 'anatomical entity' through 'independent continuant'

value: Decreased qualitatively 'biological process' in 'independent continuant'.

undefined: decreased qualitatively 'biological process' in 'independent continuant'

value: Any abnormal 'anatomical entity' that is 'curved'ly.

value: Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

undefined: Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.

value: abnormally small 'anatomical entity' in 'independent continuant'

value: An abnormal reduction in the size of the 'anatomical entity' in the 'independent continuant'.

undefined: decreased size of the 'anatomical entity' in the 'independent continuant'

value: Increased 'biological process' in 'independent continuant'.

undefined: increased 'biological process' in 'independent continuant'

value: Regulation precludes parthood; the regulatory process may not be within the regulated process.

value: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.

value: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit

value: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.

value: this investigator participates in this investigation

value: this blood clot participates in this blood coagulation

value: this input material (or this output material) participates in this process

value: a relation between a continuant and a process, in which the continuant is somehow involved in the process

value: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence

value: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.

value: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence

value: A dependent inheres in its bearer at all times for which the dependent exists.

value: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.

value: positively regulates (process to process)

value: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.

value: negatively regulates (process to process)

value: x actively participates in y if and only if x participates in y and x realizes some active role

value: 'heart development' has active participant some Shh protein

value: x has participant y if and only if x realizes some active role that inheres in y

value: This may be obsoleted and replaced by the original 'has agent' relation

value: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".

value: osteoclast SubClassOf 'capable of' some 'bone resorption'

value: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)

value: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.

value: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.

value: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.

undefined: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

value: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

undefined: helper property (not for use in curation)

value: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.

value: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.

undefined: has negative regulatory component activity

undefined: By convention GO molecular functions are classified by their effector function.  Internal regulatory functions are treated as components.  For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

value: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.

value: this investigation has participant this investigator

value: this process has participant this input material (or this output material)

value: this blood coagulation has participant this blood clot

value: a relation between a process and a continuant, in which the continuant is somehow involved in the process

value: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.

value: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

value: A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.

undefined: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

value: w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.

value: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.

undefined: has positive regulatory component activity

undefined: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components.  So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

value: this investigator role is a role of this person

value: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence

value: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.

value: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.

value: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674),  A 'has component activity' B and B is the effector (output function) of B.  Each compound function has only one effector activity.

undefined: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

value: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.

value: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.

undefined: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

value: this person has role this investigator role (more colloquially: this person has this role of investigator)

value: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence

value: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.

value: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.

value: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.

value: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.

value: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

undefined: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.

value: p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).

value: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.

value: X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)

value: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

value: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.

value: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

undefined: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

value: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t

undefined: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

value: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.

value: directly positively regulates (process to process)

value: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.

value: directly negatively regulates (process to process)

value: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.

undefined: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

value: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)

value: my brain is part of my body (continuant parthood, two material entities)

value: this day is part of this year (occurrent parthood)

value: a core relation that holds between a part and its whole

value:
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)

A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.

value: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime

value: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.

value: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

value: This relation groups causal relations between material entities and causal relations between processes

value:
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.

To define causal relations in an activity-flow type network, we make use of 3 primitives:

 * Temporal: how do the intervals of the two occurrents relate?
 * Is the causal relation regulatory?
 * Is the influence positive or negative

The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.

For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.

For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.

Each of these 3 primitives can be composed to yield a cross-product of different relation types.

value: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

undefined: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.

value: c involved in regulation of p if c is involved in some p' and p' positively regulates some p

value: c involved in regulation of p if c is involved in some p' and p' regulates some p

value: inverse of causally upstream of or within

value: A protein that enables activity in a cytosol.

value: c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.

value: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p

value: OWL does not allow defining object properties via a Union

undefined: involved in or involved in regulation of

value: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p

value: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.

value: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2

value: this year has part this day (occurrent parthood)

value: my body has part my brain (continuant parthood, two material entities)

value: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)

value: a core relation that holds between a whole and its part

value: Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.

value: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.

value:
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)

A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.

undefined: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.

value: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p  must be an input of q.

value: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain

value: Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of.  For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.

undefined: activity directly negatively regulates activity of

value: Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of.  For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.

value: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

value: Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of.  For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.

undefined: activity directly positively regulates activity of

value: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.

value: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.

value: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.

value: Considering relabeling as 'pairwise interacts with'

value: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.

en: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

value: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative

value: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive

undefined: acts upstream of or within, negative effect

undefined: acts upstream of or within, positive effect

value: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.

en: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

value: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

value: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].

en: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

undefined: causally upstream of or within, positive effect

undefined: causally upstream of or within, negative effect

value: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.

value: Holds between c and p if and only if c is capable of some activity a, and a regulates p.

value: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.

undefined: causal relation between material entity and a process

value: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

value: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'

value: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p

value: x overlaps y if and only if there exists some z such that x has part z and z part of y

value: A overlaps B if they share some part in common.

value: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)

value: renin -> arteriolar smooth muscle contraction

value: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.

value: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch

undefined: causal relation between material entities

value: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2

value: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.

value: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.

value: A relationship between a material entity and a process where the material entity has some causal role that influences the process

undefined: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

undefined: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

value: this relation holds between c and p when c is part of some c', and c' is capable of p.

value: This is a grouping relation that collects relations used for the purpose of connecting structure and function

value: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.

value: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.

value: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.

value: a particular instances of akt-2 enables some instance of protein kinase activity

value: Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b

value: causally influences (material entity to material entity)

value: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

value: A relationship that holds between entities participating in some developmental process (GO:0032502)

value: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships

value: A mereological relationship or a topological relationship

value: c involved_in p if and only if c enables some process p', and p' is part of p

value: This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.

value: A relation that holds between an attribute or a qualifier and another attribute.

value: causally influenced by (material entity to material entity)

value: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.

value: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity

value: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.

value: Because part_of is transitive, inheres in is a sub-relation of inheres in part of

undefined: molecular interaction relation helper property

value: p has anatomical participant c iff p has participant c, and c is an anatomical entity

value: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.

value: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.

value: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.

en: For use in recording has_part with a cardinality constraint.