OBO Relations Ontology
type: Ontology
version IRI: ro.owl
imports: annotations.owl
imports: pato import.owl
imports: temporal-intervals.owl
imports: go cc import.owl
imports: chemical.owl
imports: go mf import.owl
imports: core.owl
imports: rohom.owl
imports: other import.owl
imports: go-biotic.owl
imports: el-constraints.owl
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
source: ro

IAO_0000426
IAO_0000115: An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
sub property of: logical macro assertion on an object property

RO_0001900
IAO_0000115: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

never in taxon
type: AnnotationProperty
IAO_0000112: tooth SubClassOf 'never in taxon' value 'Aves'
IAO_0000115: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
IAO_0000425: ?X DisjointWith RO_0002162 some ?Y
sub property of: taxonomic class assertion

mutually spatially disjoint with
type: AnnotationProperty
IAO_0000115: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
IAO_0000118: non-overlapping with
IAO_0000118: shares no parts with
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
IAO_0000115: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
sub property of: logical macro assertion on a class

ambiguous for taxon
type: AnnotationProperty
IAO_0000115: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
sub property of: taxonomic class assertion

dubious for taxon
type: AnnotationProperty
IAO_0000115: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
comment: This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
sub property of: taxonomic class assertion

present in taxon
type: AnnotationProperty
IAO_0000115: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
sub property of: taxonomic class assertion

defined by inverse
type: AnnotationProperty
sub property of: subset_property

logical macro assertion
type: AnnotationProperty
IAO_0000115: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

annotation property cardinality
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
sub property of: logical macro assertion on an annotation property
range: nonNegativeInteger

logical macro assertion on a class
type: AnnotationProperty
IAO_0000115: A logical macro assertion whose domain is an IRI for a class
IAO_0000116: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
sub property of: logical macro assertion

logical macro assertion on a property
type: AnnotationProperty
IAO_0000115: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
IAO_0000115: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty
sub property of: logical macro assertion on a property

dispositional interpretation
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
sub property of: logical macro assertion on an object property

has no connections with
type: AnnotationProperty
IAO_0000112: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
IAO_0000115: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
IAO_0000118: shares no connection with
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
IAO_0000115: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
sub property of: inherited annotation property

always present in taxon
type: AnnotationProperty
IAO_0000112: brain always_present_in_taxon 'Vertebrata'
IAO_0000112: forelimb always_present_in_taxon Euarchontoglires
IAO_0000115: S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
IAO_0000116: This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
IAO_0000118: never lost in
sub property of: present in taxon

temporal logical macro assertion on a class
type: AnnotationProperty
IAO_0000232: This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
sub property of: logical macro assertion on a class

measurement property has unit
type: AnnotationProperty
sub property of: logical macro assertion on an annotation property

has start time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

has end time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

start, days post fertilization
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
sub property of: has start time value

end, days post fertilization
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
sub property of: has end time value

start, years post birth
type: AnnotationProperty
IAO_0000115: Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
sub property of: has start time value

end, years post birth
type: AnnotationProperty
IAO_0000115: Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
sub property of: has end time value

start, months post birth
type: AnnotationProperty
IAO_0000115: Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
sub property of: has start time value

end, months post birth
type: AnnotationProperty
IAO_0000115: Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
sub property of: has end time value

month of gestation
type: AnnotationProperty
IAO_0000115: Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
sub property of: temporal logical macro assertion on a class

has developmental stage marker
type: AnnotationProperty
IAO_0000115: A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
sub property of: temporal logical macro assertion on a class

start, days post coitum
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the start of the stage and the time of coitum.
IAO_0000232: For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
sub property of: has start time value

end, days post coitum
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the end of the stage and the time of coitum.
sub property of: has end time value

start, weeks post birth
type: AnnotationProperty
sub property of: has start time value

end, weeks post birth
type: AnnotationProperty
sub property of: has end time value

is asymmetric relational form of process class
type: AnnotationProperty
IAO_0000115: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
sub property of: is relational form of process class

is symmetric relational form of process class
type: AnnotationProperty
IAO_0000115: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
sub property of: is relational form of process class

is relational form of process class
type: AnnotationProperty
IAO_0000115: R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
sub property of: is relational form of a class

is direct form of
type: AnnotationProperty
IAO_0000115: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
IAO_0000116: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
IAO_0000115: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion

is a defining property chain axiom
type: AnnotationProperty
IAO_0000115: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
sub property of: logical macro assertion on an axiom

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
IAO_0000115: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
sub property of: is a defining property chain axiom

is relational form of a class
type: AnnotationProperty
IAO_0000115: An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
sub property of: logical macro assertion on an object property

logical macro assertion involving identity
type: AnnotationProperty
IAO_0000115: A shortcut relationship that holds between two entities based on their identity criteria
sub property of: logical macro assertion

in approximate one to one relationship with
type: AnnotationProperty
IAO_0000115: A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
sub property of: logical macro assertion involving identity

is approximately equivalent to
type: AnnotationProperty
IAO_0000115: x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
IAO_0000232: The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
sub property of: in approximate one to one relationship with

is opposite of
type: AnnotationProperty
IAO_0000112: 'anterior end of organism' is-opposite-of 'posterior end of organism'
IAO_0000112: 'increase in temperature' is-opposite-of 'decrease in temperature'
IAO_0000115: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: in approximate one to one relationship with

is indistinguishable from
type: AnnotationProperty
IAO_0000115: x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: is approximately equivalent to

evidential logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion on an axiom

axiom has evidence
type: AnnotationProperty
IAO_0000115: A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
IAO_0000232: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

axiom contradicted by evidence
type: AnnotationProperty
IAO_0000115: A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
IAO_0000232: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

is representative IRI for equivalence set
type: AnnotationProperty
IAO_0000112: In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
IAO_0000115: this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
IAO_0000232: If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
see also: OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
sub property of: logical macro assertion involving identity

is directional form of
type: AnnotationProperty
IAO_0000115: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created by: cjm
creation date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

eco subset
type: AnnotationProperty
sub property of: subset_property

subset_property
type: AnnotationProperty

in_subset
type: AnnotationProperty

has consumer
type: ObjectProperty
IAO_0000112: sardine has consumer some homo sapiens
IAO_0000114: IAO_0000428
IAO_0000115: 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
IAO_0000117: Damion Dooley

in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
IAO_0000117: David Osumi-Sutherland
IAO_0000426: (forall (?x ?y) (iff (neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (or (synapsed_by ?x ?y) (synapsed_to ?x ?y))))) (forall (...s ?x ?y ?z) (iff (neural_circuit_path ...s ?x ?y ?z) (and (neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (or (synapsed_by ?y ?z) (synapsed_to ?y ?z))))) (forall (?x ?y) (iff (in_neural_circuit_with ?x ?y) (exists (...s) (neural_circuit_path ?x ...s ?y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

upstream in neural circuit with
type: ObjectProperty
sub property of: in neural circuit with
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
IAO_0000117: David Osumi-Sutherland
IAO_0000426: (forall (?x ?y) (iff (upstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_to ?x ?y)))) (forall (...s ?x ?y ?z) (iff (upstream_neural_circuit_path ...s ?x ?y ?z ) (and (upstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_to ?y ?z)))) (forall (?x ?y) (iff (upstream_in_neural_circuit_with ?x ?y) (exists (...s) (upstream_neural_circuit_path ?x ...s ?y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

downstream in neural circuit with
type: ObjectProperty
sub property of: in neural circuit with
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
IAO_0000117: David Osumi-Sutherland
IAO_0000426: (forall (?x ?y) (iff (downstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_by ?x ?y)))) (forall (...s ?x ?y ?z) (iff (downstream_neural_circuit_path ...s ?x ?y ?z ) (and (downstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_by ?y ?z)))) (forall (?x ?y) (iff (downstream_in_neural_circuit_with ?x ?y) (exists (...s) (downstream_neural_circuit_path ?x ...s ?y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

contained in
type: ObjectProperty
inverse of: contains
domain: BFO_0000040
range: BFO_0000004
property chain axiom: RO_0001025
property chain axiom: BFO_0000050
IAO_0000111: contained in
IAO_0000116: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
IAO_0000116: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
IAO_0000116: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
IAO_0000118: contained_in
RO_0001900: RO_0001901
in_subset: eco subset

contains
type: ObjectProperty
IAO_0000111: contains
RO_0001900: RO_0001901
in_subset: eco subset

is allergic trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has allergic trigger
domain: BFO_0000040
IAO_0000112: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
IAO_0000115: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

is autoimmune trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has autoimmune trigger
domain: BFO_0000040
IAO_0000115: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has allergic trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: BFO_0000040
IAO_0000112: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
IAO_0000115: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has autoimmune trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: BFO_0000040
IAO_0000115: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

aligned with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000116: May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
IAO_0000117: David Osumi-Sutherland
RO_0001900: RO_0001901

RO_0002002
sub property of: mereotopologically related to
IAO_0000117: David Osumi-Sutherland

electrically_synapsed_to
type: ObjectProperty
sub property of: in neural circuit with
IAO_0000115: A relation that holds between two neurons that are electrically coupled via gap junctions.
IAO_0000117: David Osumi-Sutherland
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

tracheates
type: ObjectProperty
sub property of: contained in
domain: CARO_0000003
range: CARO_0000003
IAO_0000115: The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
IAO_0000117: David Osumi-Sutherland

innervated_by
type: ObjectProperty
inverse of: innervates
IAO_0000117: David Osumi-Sutherland
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in
IAO_0000117: David Osumi-Sutherland

bounding layer of
type: ObjectProperty
sub property of: BFO_0000050
domain: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002124
range: BFO_0000040
IAO_0000115: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
domain: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001199
range: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001199
IAO_0000115: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

cell expresses
type: ObjectProperty
sub property of: expresses
domain: CL_0000000
IAO_0000115: A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
IAO_0000117: David Osumi-Sutherland
description: x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y

regulates in other organism
type: ObjectProperty
sub property of: causally upstream of or within
domain: BFO_0000015
range: BFO_0000015
IAO_0000115: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
IAO_0000117: David Osumi-Sutherland

regulates transport of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: transports or maintains localization of
IAO_0000115: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset

occurent part of
type: ObjectProperty
sub property of: BFO_0000050
sub property of: causally upstream of or within
domain: BFO_0000003
range: BFO_0000003
IAO_0000115: A part of relation that applies only between occurents.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
IAO_0000115: 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.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
IAO_0000115: 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.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: 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'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
IAO_0000115: 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.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: 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'.

has necessary component activity
type: ObjectProperty
sub property of: has component activity
sub property of: positively regulated by
created by: dos
creation date: 2017-05-24T09:36:08Z
comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
IAO_0000115: 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.
created by: dos
creation date: 2017-05-24T09:49:21Z

has ligand
type: ObjectProperty
sub property of: has input
domain: GO_0004872
IAO_0000115: 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.
created by: dos
creation date: 2017-07-19T17:30:36Z

transports
type: ObjectProperty
sub property of: transports or maintains localization of
IAO_0000115: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
created by: dos
creation date: 2017-07-20T17:11:08Z

occurs across
type: ObjectProperty
sub property of: has part that occurs in
IAO_0000115: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
created by: dos
creation date: 2017-07-20T17:19:37Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: 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.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: 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.
has db xref: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
IAO_0000115: 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.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: IAO_0000115
annotated target: 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.
has db xref: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
IAO_0000115: 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.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: IAO_0000115
annotated target: 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.
has db xref: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulates
type: FunctionalProperty
IAO_0000115: 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.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: IAO_0000115
annotated target: 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.
has db xref: GOC:dos

in register with
type: ObjectProperty
sub property of: mereotopologically related to
domain: image
range: image
IAO_0000115: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
creation date: 2017-12-07T12:58:06Z
created by: dos

Axiom
annotated source: in register with
annotated property: IAO_0000115
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
has db xref: GOC:dos

RO_0002082
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset

encompasses
type: ObjectProperty
sub property of: RO_0002088
inverse of: RO_0002092
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000118: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

RO_0002090
property chain axiom: RO_0002230
property chain axiom: RO_0002224
IAO_0000117: David Osumi-Sutherland
is direct form of: BFO_0000063
in_subset: eco subset

has soma location
type: ObjectProperty
sub property of: overlaps
domain: CL_0000540
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and an anatomical structure that its soma is part of.
IAO_0000117: David Osumi-Sutherland
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
RO_0001900: RO_0001901

fasciculates with
type: ObjectProperty
sub property of: overlaps
inverse of: has fasciculating neuron projection
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
range: CARO_0001001
IAO_0000114: IAO_0000125
IAO_0000115: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: fasciculates with
IAO_0000426: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

axon synapses in
type: ObjectProperty
sub property of: has presynaptic terminal in
inverse of: has postsynaptic terminal in
domain: CL_0000540
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure its axon forms (chemical) synapses in.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed by
type: ObjectProperty
sub property of: upstream in neural circuit with
inverse of: synapsed to
range: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
IAO_0000114: IAO_0000125
IAO_0000115: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has plasma membrane part
type: ObjectProperty
sub property of: BFO_0000051
IAO_0000112: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
IAO_0000114: IAO_0000125
IAO_0000115: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
IAO_0000117: Alexander Diehl
IAO_0000117: Chris Mungall
IAO_0000117: Lindsay Cowell
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19243617
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
RO_0001900: RO_0001901

synapsed_via_type_Ib_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_Ib_bouton
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_via_type_Is_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_Is_bouton
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_via_type_II_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_II_bouton
IAO_0000114: IAO_0000125
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_by_via_type_II_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

synapsed_by_via_type_Ib_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

has postsynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000118: synapsed in
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

releases neurotransmitter
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000114: IAO_0000125
IAO_0000118: has neurotransmitter

synapsed_by_via_type_Is_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Marta Costa
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

has presynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000118: synapses in
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_via_type_III_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_III_bouton
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))

synapsed_by_via_type_III_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))

synapsed to
type: ObjectProperty
sub property of: downstream in neural circuit with
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))

dendrite synapsed in
type: ObjectProperty
sub property of: has postsynaptic terminal in
domain: CL_0000540
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal in
type: ObjectProperty
sub property of: overlaps
domain: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: has synapse in
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: BFO_0000050
property chain axiom: BFO_0000051
IAO_0000114: IAO_0000125
IAO_0000115: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: eco subset

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: BFO_0000051
annotated target: BFO_0000050
RO_0002582: true

has fasciculating neuron projection
type: ObjectProperty
sub property of: overlaps
domain: CARO_0001001
range: Class
  union of: CL_0000540
  union of: Restriction
    on property: BFO_0000050
    some values from: CL_0000540
IAO_0000114: IAO_0000125
IAO_0000115: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: has fasciculating component
IAO_0000426: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

innervates
type: ObjectProperty
sub property of: topObjectProperty
domain: CARO_0001001
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
IAO_0000117: David Osumi-Sutherland
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000004
range: BFO_0000004
IAO_0000114: IAO_0000125
IAO_0000115: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: connected to
IAO_0000232: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO_0001900: RO_0001901

partially overlaps
type: ObjectProperty
sub property of: overlaps
IAO_0000114: IAO_0000125
IAO_0000115: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
IAO_0000116: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
IAO_0000118: proper overlaps
IAO_0000426: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
RO_0001900: RO_0001901
in_subset: eco subset

derived by descent from
type: ObjectProperty
sub property of: evolutionarily related to
inverse of: has derived by descendant
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
IAO_0000118: ancestral_stucture_of
IAO_0000118: evolutionarily_descended_from

has derived by descendant
type: ObjectProperty
sub property of: evolutionarily related to
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: inverse of derived by descent from
in_subset: defined by inverse

shares ancestor with
type: ObjectProperty
sub property of: evolutionarily related to
type: SymmetricProperty
type: TransitiveProperty
property chain axiom: derived by descent from
property chain axiom: has derived by descendant
IAO_0000114: IAO_0000125
IAO_0000115: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
IAO_0000232: Consider obsoleting and merging with child relation, 'in homology relationship with'
comment: VBO calls this homologous_to

serially homologous to
type: ObjectProperty
sub property of: evolutionarily related to
type: SymmetricProperty
type: TransitiveProperty
IAO_0000114: IAO_0000125

only in taxon
type: ObjectProperty
sub property of: in taxon
IAO_0000112: lactation SubClassOf 'only in taxon' some 'Mammalia'
IAO_0000114: IAO_0000125
IAO_0000115: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
IAO_0000116: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: CARO_0001010
property chain axiom: BFO_0000050
property chain axiom: BFO_0000051
property chain axiom: develops from
property chain axiom: expressed in
property chain axiom: has prototype
property chain axiom: capable of
property chain axiom: actively participates in
property chain axiom: develops from part of
property chain axiom: has developmental contribution from
property chain axiom: results in developmental progression of
IAO_0000114: IAO_0000125
IAO_0000115: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
IAO_0000117: Chris Mungall
IAO_0000117: Jennifer Deegan
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
in_subset: eco subset
comment: Connects a biological entity to its taxon of origin.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: IAO_0000125
IAO_0000115: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: eco subset

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: BFO_0000050
  some values from: system
range: Restriction
  on property: BFO_0000050
  some values from: system
property chain axiom:
  inverse of: connects
property chain axiom: connects
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000004
range: Restriction
  on property: BFO_0000050
  some values from: system
IAO_0000112: The M8 connects Glasgow and Edinburgh
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

attached to part of
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: biomechanically related to
domain: CARO_0000003
range: CARO_0000003
property chain axiom: attached to
property chain axiom: BFO_0000050
IAO_0000115: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
IAO_0000589: attached to part of (anatomical structure to anatomical structure)

Axiom
annotated source: attached to part of
annotated property: propertyChainAxiom
annotated target: attached to
annotated target: BFO_0000050
RO_0002582: true

supplies
type: ObjectProperty
sub property of: connected to
IAO_0000115: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

drains
type: ObjectProperty
sub property of: connected to
IAO_0000115: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
sub property of: BFO_0000051
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: 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.
RO_0001900: RO_0001901
in_subset: eco subset

has phenotype
type: ObjectProperty
sub property of: topObjectProperty
inverse of: phenotype of
domain: Class
  union of: BFO_0000031
  union of: CARO_0000006
  union of: OGMS_0000031
range: UPHENO_0001001
IAO_0000114: IAO_0000125
IAO_0000115: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
IAO_0000117: Chris Mungall
in_subset: eco subset

phenotype of
type: ObjectProperty
sub property of: topObjectProperty
type: FunctionalProperty
IAO_0000114: IAO_0000125
IAO_0000115: inverse of has phenotype
IAO_0000117: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: BFO_0000004
range: BFO_0000004
IAO_0000114: IAO_0000125
IAO_0000115: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Melissa Haendel
IAO_0000117: Terry Meehan
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: IAO_0000125
IAO_0000115: inverse of develops from
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
in_subset: defined by inverse

gene product of
type: ObjectProperty
sub property of: genomically related to
inverse of: has gene product
domain: BFO_0000004
range: BFO_0000002
property chain axiom: ribosomal translation of
property chain axiom: transcribed from
IAO_0000114: IAO_0000125
IAO_0000115: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
IAO_0000116: We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
IAO_0000117: Chris Mungall

has gene product
type: ObjectProperty
sub property of: genomically related to
domain: BFO_0000002
range: BFO_0000004
property chain axiom: transcribed to
property chain axiom: ribosomally translates to
IAO_0000112: every HOTAIR lncRNA is the gene product of some HOXC gene
IAO_0000112: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
IAO_0000114: IAO_0000125
IAO_0000115: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
IAO_0000117: Chris Mungall

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: BFO_0000002
range: BFO_0000004
property chain axiom: BFO_0000050
IAO_0000112: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
IAO_0000114: IAO_0000125
IAO_0000115: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
IAO_0000117: Chris Mungall

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
domain: Class
  union of: CARO_0010000
  union of: CL_0000000
range: Class
  union of: CARO_0010000
  union of: CL_0000000
IAO_0000114: IAO_0000125
IAO_0000115: Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: has developmental precursor
IAO_0000119: FBbt
is direct form of: develops from
comment: TODO - add child relations from DOS

parasitoid of
type: ObjectProperty
sub property of: parasite of
inverse of: has parasitoid
IAO_0000115: A parasite that kills or sterilizes its host

has parasitoid
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of parasitoid of
in_subset: defined by inverse

directly develops into
type: ObjectProperty
sub property of: develops into
IAO_0000114: IAO_0000125
IAO_0000115: inverse of directly develops from
IAO_0000118: developmental precursor of
in_subset: defined by inverse

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
property chain axiom: RO_0002230
property chain axiom: directly regulates
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000117: Chris Mungall
IAO_0000117: David Hill
IAO_0000117: Tanya Berardini
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: RO_0002230
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
is negative form of: regulates

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: RO_0002230
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
is positive form of: regulates

has prototype
type: ObjectProperty
domain: Class
  union of: BFO_0000004
  union of: BFO_0000015
IAO_0000112: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
IAO_0000112: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
IAO_0000114: IAO_0000125
IAO_0000115: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
IAO_0000116: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
IAO_0000116: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
IAO_0000117: Chris Mungall

capable of
type: ObjectProperty
sub property of: capable of part of
domain: BFO_0000004
range: BFO_0000015
property chain axiom: has prototype
property chain axiom: actively participates in
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: 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)".
IAO_0000424: RO_0000053 some (RO_0000054 only ?Y)
in_subset: eco subset

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: BFO_0000050
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: has function in
IAO_0000424: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: BFO_0000050
RO_0002582: true

actively participates in
type: ObjectProperty
sub property of: RO_0000056
inverse of: has active participant
IAO_0000115: x actively participates in y if and only if x participates in y and x realizes some active role
IAO_0000117: Chris Mungall
IAO_0000118: agent in

has active participant
type: ObjectProperty
sub property of: RO_0000057
IAO_0000112: 'heart development' has active participant some Shh protein
IAO_0000114: IAO_0000125
IAO_0000115: x has participant y if and only if x realizes some active role that inheres in y
IAO_0000116: This may be obsoleted and replaced by the original 'has agent' relation
IAO_0000117: Chris Mungall
IAO_0000118: has agent
in_subset: eco subset

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
IAO_0000114: IAO_0000125
IAO_0000115: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: BFO_0000004
range: BFO_0000004
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: IAO_0000125
IAO_0000115: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901

Axiom
annotated source: adjacent to
annotated property: IAO_0000112
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

surrounds
type: ObjectProperty
sub property of: adjacent to
IAO_0000114: IAO_0000125
IAO_0000115: inverse of surrounded by
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
in_subset: defined by inverse

RO_0002222
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: 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.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: eco subset

RO_0002223
sub property of: BFO_0000050
IAO_0000117: Chris Mungall
in_subset: eco subset

RO_0002224
sub property of: BFO_0000051
IAO_0000117: Chris Mungall
in_subset: eco subset

develops from part of
type: ObjectProperty
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
IAO_0000117: Chris Mungall

develops in
type: ObjectProperty
sub property of: developmentally preceded by
domain: CARO_0000003
property chain axiom: directly develops from
property chain axiom: RO_0001025
IAO_0000114: IAO_0000125
IAO_0000115: x develops_in y if x is located in y whilst x is developing
IAO_0000117: Chris Mungall
IAO_0000119: EHDAA2
IAO_0000119: Jonathan Bard, EHDAA2

obligate parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.

facultative parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.

RO_0002229
sub property of: BFO_0000050
IAO_0000117: Chris Mungall
in_subset: eco subset

RO_0002230
sub property of: BFO_0000051
IAO_0000117: Chris Mungall
in_subset: eco subset

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: BFO_0000015
range: BFO_0000004
property chain axiom: RO_0002224
property chain axiom: BFO_0000066
IAO_0000114: IAO_0000125
IAO_0000115: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
IAO_0000117: Chris Mungall
IAO_0000118: starts with process that occurs in
in_subset: eco subset

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: BFO_0000015
range: BFO_0000004
property chain axiom: RO_0002230
property chain axiom: BFO_0000066
IAO_0000114: IAO_0000125
IAO_0000115: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
IAO_0000117: Chris Mungall
IAO_0000118: ends with process that occurs in
in_subset: eco subset

has input
type: ObjectProperty
sub property of: RO_0000057
inverse of: input of
domain: BFO_0000015
range: BFO_0000040
property chain axiom: RO_0002224
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: consumes
in_subset: eco subset

has output
type: ObjectProperty
sub property of: RO_0000057
inverse of: output of
property chain axiom: RO_0002230
IAO_0000114: IAO_0000125
IAO_0000115: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
IAO_0000117: Chris Mungall
IAO_0000118: produces
in_subset: eco subset

stem parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)

root parasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)

hemiparasite of
type: ObjectProperty
sub property of: parasite of
IAO_0000115: A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.

has exposure receptor
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
IAO_0000119: ExO:0000001

has exposure stressor
type: ObjectProperty
sub property of: has exposure stimulus
IAO_0000115: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
IAO_0000119: ExO:0000000

has exposure route
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
IAO_0000119: ExO:0000055

has exposure transport path
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A broad relationship between an exposure event or process and the course takes from the source to the target.
IAO_0000119: http://purl.obolibrary.org/obo/ExO_0000004

related via exposure to
type: ObjectProperty
sub property of: causally related to
domain: exposure event or process
IAO_0000115: Any relationship between an exposure event or process and any other entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.

over-expressed in
type: ObjectProperty
sub property of: expressed in
IAO_0000115: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.

under-expressed in
type: ObjectProperty
sub property of: expressed in
IAO_0000115: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

has active ingredient
type: ObjectProperty
sub property of: BFO_0000051
inverse of: active ingredient in'
IAO_0000112: Any portion of roundup 'has active ingredient' some glyphosate
IAO_0000115: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has exact synonym: has active substance
has related synonym: has active pharmaceutical ingredient

active ingredient in'
type: ObjectProperty
sub property of: BFO_0000050
IAO_0000115: inverse of has active ingredient
in_subset: defined by inverse

connecting branch of
type: ObjectProperty
sub property of: in branching relationship with
inverse of: has connecting branch
IAO_0000115: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.

has connecting branch
type: ObjectProperty
sub property of: in branching relationship with
IAO_0000115: inverse of connecting branch of
in_subset: defined by inverse

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: BFO_0000004
range: CARO_0000003
property chain axiom: BFO_0000051
property chain axiom: develops from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: IAO_0000125
IAO_0000115: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: Chris Mungall

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: BFO_0000050
IAO_0000114: IAO_0000125
IAO_0000115: inverse of has developmental contribution from
IAO_0000117: Chris Mungall
in_subset: defined by inverse

developmentally induced by
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally induces
domain: CARO_0000003
range: CARO_0000003
IAO_0000114: IAO_0000125
IAO_0000115: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Melissa Haendel
IAO_0000118: induced by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
IAO_0000119: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
IAO_0000119: GO:0001759
IAO_0000232: We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]

developmentally induces
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally induce
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of developmentally induced by
IAO_0000117: Chris Mungall

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: BFO_0000002
range: BFO_0000002
IAO_0000114: IAO_0000125
IAO_0000115: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
IAO_0000116: false
IAO_0000117: Chris Mungall
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: 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.
IAO_0000115: 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.

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
IAO_0000115: 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.
has related synonym: affects

developmentally replaces
type: ObjectProperty
sub property of: developmentally preceded by
IAO_0000114: IAO_0000125
IAO_0000115: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
IAO_0000116: This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
IAO_0000117: Chris Mungall
IAO_0000118: replaces

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of developmentally preceded by
IAO_0000117: Chris Mungall

part of developmental precursor of
type: ObjectProperty
sub property of: developmentally succeeded by
property chain axiom: BFO_0000050
property chain axiom: directly develops into
IAO_0000112: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall

ubiquitously expressed in
type: ObjectProperty
sub property of: expressed in
inverse of: ubiquitously expresses
IAO_0000114: IAO_0000125
IAO_0000115: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
IAO_0000116: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
IAO_0000117: Chris Mungall

expresses
type: ObjectProperty
sub property of: genomically related to
IAO_0000114: IAO_0000125
IAO_0000115: Inverse of 'expressed in'
IAO_0000117: Chris Mungall

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
IAO_0000114: IAO_0000125
IAO_0000115: inverse of ubiquiotously expressed in
IAO_0000117: Chris Mungall
in_subset: defined by inverse

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: GO_0008150
range: CARO_0000003
IAO_0000114: IAO_0000125
IAO_0000115: 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).
IAO_0000116: 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.
IAO_0000117: Chris Mungall
shorthand: results_in_developmental_progression_of

results in development of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000114: IAO_0000125
IAO_0000115: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
shorthand: results_in_development_of

results in formation of
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
IAO_0000112: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
IAO_0000112: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
shorthand: results_in_formation_of

results in morphogenesis of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000112: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
IAO_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: IAO_0000125
IAO_0000115: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
shorthand: results_in_morphogenesis_of

results in maturation of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000112: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
IAO_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: IAO_0000125
IAO_0000115: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
shorthand: results_in_maturation_of

results in disappearance of
type: ObjectProperty
sub property of: results in ending of
IAO_0000112: foramen ovale closure SubClassOf results in disappearance of foramen ovale
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000232: May be merged into parent relation
shorthand: results_in_disappearance_of

results in developmental regression of
type: ObjectProperty
sub property of: results in ending of
IAO_0000112: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000232: May be merged into parent relation

is treated by substance
type: ObjectProperty
sub property of: causally related to
inverse of: is substance that treats
IAO_0000115: Inverse of 'is substance that treats'
creator: cjm
in_subset: defined by inverse

has habitat
type: ObjectProperty
sub property of: ecologically related to
domain: CARO_0001010
range: ENVO_01000254
IAO_0000112: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
IAO_0000114: IAO_0000428
IAO_0000115: x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
IAO_0000117: Pier Buttigieg
IAO_0000118: adapted for living in
in_subset: eco subset
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
is positive form of: causally upstream of
creator: cjm
comment: 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

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
is negative form of: causally upstream of
creator: cjm
comment: 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

has exposure stimulus
type: ObjectProperty
sub property of: related via exposure to
IAO_0000115: A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
contributor: Austin Meier
contributor: Chris Mungall
contributor: Marie Angelique Laporte
created by: cjm
creation date: 2017-06-05T17:35:04Z

evolutionary variant of
type: ObjectProperty
sub property of: evolutionarily related to
IAO_0000117: Chris Mungall

transports or maintains localization of
type: ObjectProperty
sub property of: RO_0000057
sub property of: related via localization to
property chain axiom: BFO_0000051
IAO_0000115: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
IAO_0000117: Chris Mungall
IAO_0000118: regulates localization of

inheres in part of
type: ObjectProperty
sub property of: depends on
property chain axiom: RO_0000052
property chain axiom: BFO_0000050
IAO_0000115: 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.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: inheres in part of
annotated property: propertyChainAxiom
annotated target: RO_0000052
annotated target: BFO_0000050
RO_0002582: true

results in acquisition of features of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000112: 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.
IAO_0000115: 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
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
shorthand: results_in_acquisition_of_features_of

evolutionarily related to
type: ObjectProperty
IAO_0000115: A relationship that holds via some environmental process
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.

ecologically related to
type: ObjectProperty
IAO_0000115: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in_subset: eco subset

confers advantage in
type: ObjectProperty
sub property of: ecologically related to
range: ENVO_01000254
IAO_0000116: An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
IAO_0000117: Chris Mungall
IAO_0000118: adapted for
in_subset: eco subset

mereotopologically related to
type: ObjectProperty
IAO_0000115: A mereological relationship or a topological relationship
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
IAO_0000115: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

colocalizes with
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000040
IAO_0000112: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
IAO_0000115: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
creator: Gene Ontology Consortium

contributes to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of
IAO_0000112: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
IAO_0000112: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
IAO_0000112: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
IAO_0000116: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: BFO_0000051
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
IAO_0000117: Chris Mungall
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: 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.
IAO_0000232: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.

functionally related to
type: ObjectProperty
IAO_0000115: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: BFO_0000050
property chain axiom: capable of
IAO_0000115: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: Chris Mungall
IAO_0000118: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: BFO_0000050
annotated target: capable of
is a defining property chain axiom: true

genomically related to
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000002
IAO_0000115: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism

involved in
type: ObjectProperty
sub property of: actively participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: BFO_0000050
IAO_0000115: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: Chris Mungall
IAO_0000118: actively involved in
IAO_0000118: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
IAO_0000115: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: regulates levels of (process to entity)

enabled by
type: ObjectProperty
sub property of: functionally related to
IAO_0000115: inverse of enables
IAO_0000117: Chris Mungall

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
IAO_0000115: inverse of regulates
IAO_0000117: Chris Mungall
IAO_0000589: regulated by (processual)
in_subset: defined by inverse

negatively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of negatively regulates
IAO_0000117: Chris Mungall
in_subset: defined by inverse

positively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of positively regulates
IAO_0000117: Chris Mungall
in_subset: defined by inverse

related via localization to
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000002
IAO_0000115: A relationship that holds via some process of localization
IAO_0000117: Chris Mungall

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: BFO_0000050
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
IAO_0000117: Chris Mungall

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: BFO_0000050
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
IAO_0000117: Chris Mungall

imports
type: ObjectProperty
sub property of: transports
property chain axiom: BFO_0000051
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
IAO_0000117: Chris Mungall

results in transport along
type: ObjectProperty
sub property of: related via localization to
IAO_0000115: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
IAO_0000117: Chris Mungall

results in transport across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in
IAO_0000115: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
IAO_0000117: Chris Mungall

results in growth of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000112: 'pollen tube growth' results_in growth_of some 'pollen tube'
IAO_0000117: Chris Mungall

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to
IAO_0000112: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
IAO_0000117: Chris Mungall

exports
type: ObjectProperty
sub property of: transports
property chain axiom: BFO_0000051
IAO_0000117: Chris Mungall

results in commitment to
type: ObjectProperty
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000112: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
IAO_0000115: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate

results in determination of
type: ObjectProperty
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000115: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate

input of
type: ObjectProperty
sub property of: RO_0000056
sub property of: functionally related to
IAO_0000115: inverse of has input
IAO_0000117: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

output of
type: ObjectProperty
sub property of: RO_0000056
sub property of: functionally related to
IAO_0000115: inverse of has output
IAO_0000117: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

formed as result of
type: ObjectProperty
sub property of: output of
IAO_0000117: Chris Mungall

results in structural organization of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000115: A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
IAO_0000117: Chris Mungall

results in specification of
type: ObjectProperty
sub property of: results in developmental progression of
range: CL_0000000
IAO_0000115: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate

results in developmental induction of
type: ObjectProperty
sub property of: results in developmental progression of
IAO_0000115: p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
IAO_0000117: Chris Mungall

has dendrite location
type: ObjectProperty
sub property of: overlaps
IAO_0000117: Chris Mungall
source: http://neurolex.org/wiki/Property:DendriteLocation

attached to
type: ObjectProperty
sub property of: connected to
sub property of: attached to part of
type: SymmetricProperty
IAO_0000115: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
IAO_0000117: Chris Mungall
IAO_0000589: attached to (anatomical structure to anatomical structure)
in_subset: eco subset

has muscle origin
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: CARO_0000003
IAO_0000115: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle origin
annotated property: domain
annotated target: CARO_0000003
comment: We need to import uberon muscle to create a stricter domain constraint

has muscle insertion
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: CARO_0000003
IAO_0000115: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle insertion
annotated property: domain
annotated target: CARO_0000003
IAO_0000116: We need to import uberon muscle into RO to use as a stricter domain constraint

derived from ancestral fusion of
type: ObjectProperty
sub property of: derived by descent from
IAO_0000112: false
IAO_0000114: IAO_0000428
IAO_0000115: x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
has broad synonym: has fused element
comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.

in branching relationship with
type: ObjectProperty
sub property of: BFO_0000050
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000040
IAO_0000114: IAO_0000428
IAO_0000115: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)

tributary of
type: ObjectProperty
sub property of: in branching relationship with
IAO_0000112: Deschutes River tributary_of Columbia River
IAO_0000112: inferior epigastric vein tributary_of external iliac vein
IAO_0000114: IAO_0000428
IAO_0000115: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
IAO_0000117: Chris Mungall
IAO_0000118: drains into
IAO_0000118: drains to
IAO_0000118: tributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Tributary
IAO_0000119: http://www.medindia.net/glossary/venous_tributary.htm
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
in_subset: eco subset

distributary of
type: ObjectProperty
sub property of: in branching relationship with
IAO_0000112: Deschutes River distributary_of Little Lava Lake
IAO_0000114: IAO_0000428
IAO_0000115: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
IAO_0000117: Chris Mungall
IAO_0000118: branch of
IAO_0000118: distributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Distributary
in_subset: eco subset
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes

anabranch of
type: ObjectProperty
sub property of: distributary of
sub property of:
  inverse of: tributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
IAO_0000114: IAO_0000428
IAO_0000115: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
IAO_0000117: Chris Mungall
IAO_0000118: anastomoses with
in_subset: eco subset

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: RO_0001025
property chain axiom:
  inverse of: RO_0001025
IAO_0000112: A lump of clay and a statue
IAO_0000115: x spatially_coextensive_with y if and inly if x and y have the same location
IAO_0000117: Chris Mungall
IAO_0000232: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

branching part of
type: ObjectProperty
sub property of: BFO_0000050
sub property of: in branching relationship with
inverse of: has branching part
range: Restriction
  on property: RO_0000053
  some values from: PATO_0000402
property chain axiom: distributary of
property chain axiom: main stem of
IAO_0000114: IAO_0000428
IAO_0000115: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
IAO_0000117: Chris Mungall
in_subset: eco subset

main stem of
type: ObjectProperty
sub property of: in branching relationship with
IAO_0000114: IAO_0000428
IAO_0000115: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
IAO_0000117: Chris Mungall
in_subset: eco subset

proper distributary of
type: ObjectProperty
sub property of: distributary of
IAO_0000114: IAO_0000428
IAO_0000115: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
IAO_0000117: Chris Mungall
in_subset: eco subset

proper tributary of
type: ObjectProperty
sub property of: tributary of
IAO_0000114: IAO_0000428
IAO_0000115: x proper_tributary_of y iff x tributary_of y and x does not originate from y
IAO_0000117: Chris Mungall
in_subset: eco subset

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
IAO_0000114: IAO_0000428
IAO_0000115: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000117: Chris Mungall

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: Chris Mungall

has potential to developmentally induce
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
IAO_0000117: Chris Mungall

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
IAO_0000115: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: Chris Mungall

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: IAO_0000428
IAO_0000115: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: Chris Mungall

has direct input
type: ObjectProperty
sub property of: has input
property chain axiom: RO_0002224
IAO_0000112: 'protein catabolic process' SubClassOf has_direct_input some protein
IAO_0000114: IAO_0000428
IAO_0000115: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: Chris Mungall
IAO_0000118: directly consumes
IAO_0000232: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'

obsolete has indirect input
type: ObjectProperty
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

obsolete has direct output
type: ObjectProperty
IAO_0000112: translation SubClassOf has_direct_output some protein
IAO_0000114: IAO_0000428
IAO_0000115: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
IAO_0000117: Chris Mungall
IAO_0000118: directly produces
deprecated: true

obsolete has indirect output
type: ObjectProperty
sub property of: has output
property chain axiom: causally upstream of
property chain axiom: obsolete has direct output
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: BFO_0000062
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: IAO_0000428
IAO_0000115: inverse of upstream of
IAO_0000117: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: RO_0002087
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall

directly activates
type: ObjectProperty
sub property of: directly positively regulates
IAO_0000114: IAO_0000428
IAO_0000115: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
IAO_0000117: Chris Mungall
IAO_0000118: directly positively regulates
IAO_0000119: causal-relations
IAO_0000589: directly activates (process to process)

indirectly activates
type: ObjectProperty
sub property of: positively regulates
type: TransitiveProperty
property chain axiom: directly activates
property chain axiom: indirectly inhibits
IAO_0000115: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
IAO_0000117: Chris Mungall
IAO_0000118: indirectly positively regulates
is indirect form of: positively regulates

directly inhibits
type: ObjectProperty
sub property of: directly negatively regulates
IAO_0000117: Chris Mungall
IAO_0000118: directly negatively regulates
IAO_0000119: causal-relations
IAO_0000589: directly inhibits (process to process)

indirectly inhibits
type: ObjectProperty
sub property of: negatively regulates
type: TransitiveProperty
property chain axiom: directly inhibits
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall
IAO_0000118: indirectly negatively regulates
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
IAO_0000114: IAO_0000428
IAO_0000115: This relation groups causal relations between material entities and causal relations between processes
IAO_0000116: 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 yiel…
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally upstream of
type: ObjectProperty
sub property of: BFO_0000063
sub property of: causally upstream of or within
type: TransitiveProperty
IAO_0000114: IAO_0000428
IAO_0000115: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
IAO_0000117: Chris Mungall

immediately causally upstream of
type: ObjectProperty
sub property of: RO_0002090
sub property of: causally upstream of
IAO_0000114: IAO_0000428
IAO_0000115: 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.
IAO_0000117: Chris Mungall
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: obsolete has direct output
property chain axiom: has direct input
IAO_0000114: IAO_0000428
IAO_0000115: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
IAO_0000116: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
IAO_0000114: IAO_0000428
IAO_0000115: transitive form of directly_provides_input_for
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
IAO_0000589: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
IAO_0000115: 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.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: Chris Mungall
IAO_0000118: influences (processual)
has related synonym: affects

differs in
type: ObjectProperty
IAO_0000116: false
IAO_0000117: Chris Mungall
comment: This is an exploratory relation

differs in attribute of
type: ObjectProperty
sub property of: differs in
range: Class
  union of: BFO_0000004
  union of: BFO_0000015
IAO_0000117: Chris Mungall

differs in attribute
type: ObjectProperty
sub property of: differs in
range: BFO_0000020
IAO_0000117: Chris Mungall

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
IAO_0000115: inverse of causally upstream of or within
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
in_subset: defined by inverse

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: Chris Mungall
is positive form of: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: Chris Mungall
is negative form of: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
IAO_0000115: 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
IAO_0000117: Chris Mungall
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: BFO_0000066
IAO_0000112: A protein that enables activity in a cytosol.
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: executes activity in
has exact synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: BFO_0000066
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: IAO_0000115
annotated target: 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.
has db xref: GOC:cjm
has db xref: GOC:dos

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
IAO_0000115: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
IAO_0000117: Chris Mungall

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000116: 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.
IAO_0000117: Chris Mungall
IAO_0000232: 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.
has exact synonym: in pairwise interaction with
in_subset: eco subset

genetically interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
IAO_0000116: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
IAO_0000117: Chris Mungall

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: binds
IAO_0000118: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000117: Chris Mungall
IAO_0000118: interacts with on organism level
in_subset: eco subset

trophically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000115: An interaction relationship in which the partners are related via a feeding relationship.
IAO_0000117: Chris Mungall
in_subset: eco subset

preys on
type: ObjectProperty
sub property of: trophically interacts with
inverse of: preyed upon by
IAO_0000112: A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
IAO_0000112: Baleen whale preys on krill
IAO_0000115: An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
IAO_0000117: Chris Mungall
IAO_0000117: Jorrit Poelen
IAO_0000117: Katja Shulz
IAO_0000118: is subject of predation interaction with
IAO_0000118: preys upon
in_subset: eco subset

symbiotically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
type: SymmetricProperty
property chain axiom: partner in
property chain axiom: is symbiosis
property chain axiom:
  inverse of: partner in
IAO_0000115: A biotic interaction in which the two organisms live together in more or less intimate association.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
is symmetric relational form of process class: GO_0044403
in_subset: eco subset

commensually interacts with
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is commensalism
property chain axiom:
  inverse of: partner in
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
is symmetric relational form of process class: GO_0085031
in_subset: eco subset

mutualistically interacts with
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is mutualism
property chain axiom:
  inverse of: partner in
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
is symmetric relational form of process class: GO_0085030
in_subset: eco subset

interacts with via parasite-host interaction
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is parasitism
property chain axiom:
  inverse of: partner in
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: This relation groups a pair of inverse relations, parasite of and parasitized by
is symmetric relational form of process class: GO_0072519
in_subset: eco subset

parasite of
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: has host
inverse of: parasitized by
property chain axiom: subject participant in
property chain axiom: is parasitism
property chain axiom:
  inverse of: target participant in
IAO_0000112: Pediculus humanus capitis parasite of human
IAO_0000117: Chris Mungall
IAO_0000118: parasitizes
is asymmetric relational form of process class: GO_0072519
has exact synonym: direct parasite of
in_subset: eco subset

parasitized by
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: host of
IAO_0000117: Chris Mungall
IAO_0000118: has parasite
IAO_0000118: parasitised by
has exact synonym: directly parasitized by
in_subset: eco subset

participates in a abiotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
IAO_0000112: Porifiera attaches to substrate
IAO_0000115: A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
IAO_0000117: Chris Mungall
has related synonym: semibiotically interacts with
in_subset: eco subset

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is kinase activity
property chain axiom: has direct input
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

activity directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: causally influences
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
IAO_0000115: 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.
IAO_0000117: Chris Mungall
has exact synonym: molecularly controls

activity directly negatively regulates activity of
type: ObjectProperty
sub property of: activity directly regulates activity of
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: inhibits
has exact synonym: molecularly decreases activity of

activity directly positively regulates activity of
type: ObjectProperty
sub property of: activity directly regulates activity of
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000118: activates
has exact synonym: molecularly increases activity of

transmitted by
type: ObjectProperty
sub property of: ecologically related to
IAO_0000112: all dengue disease transmitted by some mosquito
IAO_0000115: A relationship that holds between a disease and organism
IAO_0000116: Add domain and range constraints
IAO_0000117: Chris Mungall

has symptom
type: ObjectProperty
sub property of: has phenotype
IAO_0000115: A relation that holds between a disease or an organism and a phenotype
IAO_0000117: Chris Mungall

host of
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000117: Chris Mungall
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
in_subset: eco subset

has host
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000117: Chris Mungall
in_subset: eco subset

pollinates
type: ObjectProperty
sub property of: mutualistically interacts with
inverse of: pollinated by
IAO_0000112: Bees pollinate Flowers
IAO_0000116: This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
IAO_0000117: Chris Mungall
IAO_0000118: is subject of pollination interaction with
in_subset: eco subset

pollinated by
type: ObjectProperty
sub property of: mutualistically interacts with
IAO_0000117: Chris Mungall
IAO_0000118: has polinator
IAO_0000118: is target of pollination interaction with
in_subset: eco subset

acquires nutrients from
type: ObjectProperty
sub property of: trophically interacts with
inverse of: provides nutrients for
IAO_0000117: Chris Mungall
IAO_0000232: Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
in_subset: eco subset

preyed upon by
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000115: inverse of preys on
IAO_0000117: Chris Mungall
IAO_0000118: has predator
IAO_0000118: is target of predation interaction with
in_subset: defined by inverse
in_subset: eco subset

is vector for
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: has vector
IAO_0000112: Anopheles is a vector for Plasmodium
IAO_0000117: Chris Mungall
IAO_0000119: a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
in_subset: eco subset

has vector
type: ObjectProperty
sub property of: is vector for
IAO_0000117: Chris Mungall
in_subset: eco subset

partner in
type: ObjectProperty
sub property of: RO_0000056
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target

subject participant in
type: ObjectProperty
sub property of: partner in
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.

target participant in
type: ObjectProperty
sub property of: partner in
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.

helper property
type: ObjectProperty
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is symbiosis
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: Chris Mungall

is commensalism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: Chris Mungall

is mutualism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: Chris Mungall

is parasitism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: Chris Mungall

provides nutrients for
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: Chris Mungall
in_subset: eco subset

eats
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: Chris Mungall
IAO_0000118: is subject of eating interaction with
in_subset: eco subset

is eaten by
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: Chris Mungall
IAO_0000118: eaten by
IAO_0000118: is target of eating interaction with
in_subset: eco subset

is evidence for
type: ObjectProperty
sub property of: related via evidence or inference to
inverse of: has evidence
IAO_0000115: A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
IAO_0000117: Chris Mungall
in_subset: eco subset

composed primarily of
type: ObjectProperty
sub property of: BFO_0000051
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
IAO_0000115: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
RO_0001900: RO_0001901
in_subset: eco subset

child nucleus of
type: ObjectProperty
sub property of: developmentally preceded by
domain: GO_0005634
range: GO_0005634
IAO_0000112: ABal nucleus child nucleus of ABa nucleus (in C elegans)
IAO_0000115: c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
IAO_0000117: Chris Mungall
IAO_0000232: This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.

child nucleus of in hermaphrodite
type: ObjectProperty
sub property of: child nucleus of
IAO_0000115: A child nucleus relationship in which the cells are part of a hermaphroditic organism
IAO_0000117: Chris Mungall

child nucleus of in male
type: ObjectProperty
sub property of: child nucleus of
IAO_0000115: A child nucleus relationship in which the cells are part of a male organism
IAO_0000117: Chris Mungall

has part that occurs in
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000004
property chain axiom: BFO_0000051
property chain axiom: BFO_0000066
IAO_0000115: 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.
IAO_0000117: Chris Mungall
in_subset: eco subset

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: BFO_0000051
annotated target: BFO_0000066
is a defining property chain axiom: true

ubiquitinates
type: ObjectProperty
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is ubiquitination
property chain axiom: has direct input
IAO_0000115: An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: Chris Mungall

is ubiquitination
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: Chris Mungall

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
IAO_0000116: See notes for inverse relation
IAO_0000117: Chris Mungall

sends output to
type: ObjectProperty
sub property of: connected to
IAO_0000116: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
IAO_0000117: Chris Mungall

relation between structure and stage
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000003
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: BFO_0000050
property chain axiom: existence starts at point
IAO_0000115: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: Chris Mungall

existence starts with
type: ObjectProperty
sub property of: existence starts during
IAO_0000115: x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
IAO_0000117: Chris Mungall

existence overlaps
type: ObjectProperty
sub property of: relation between structure and stage
IAO_0000115: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts and ends during
type: ObjectProperty
sub property of: existence starts during
sub property of: existence ends during
IAO_0000115: x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: BFO_0000050
property chain axiom: existence ends at point
IAO_0000115: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends with
type: ObjectProperty
sub property of: existence ends during
IAO_0000115: x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

transformation of
type: ObjectProperty
sub property of: develops from
type: TransitiveProperty
IAO_0000115: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
IAO_0000117: Chris Mungall

immediate transformation of
type: ObjectProperty
sub property of: directly develops from
sub property of: transformation of
IAO_0000115: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
IAO_0000117: Chris Mungall
is direct form of: transformation of

existence starts during or after
type: ObjectProperty
sub property of: relation between structure and stage
property chain axiom: BFO_0000050
property chain axiom: developmentally preceded by
property chain axiom: BFO_0000062
property chain axiom: RO_0002082
property chain axiom: existence starts at point
property chain axiom:
  inverse of: existence starts at point
IAO_0000115: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between structure and stage
property chain axiom: BFO_0000050
property chain axiom: developmentally succeeded by
property chain axiom: BFO_0000063
property chain axiom: RO_0002082
property chain axiom: existence ends at point
property chain axiom:
  inverse of: existence ends at point
IAO_0000115: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
IAO_0000115: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000003
range: BFO_0000003
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
IAO_0000117: Chris Mungall

towards
type: ObjectProperty
sub property of: depends on
IAO_0000115: 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
IAO_0000116: 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.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
sub property of: RO_0000057
IAO_0000112: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
IAO_0000115: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
IAO_0000117: Chris Mungall
IAO_0000118: has intermediate product
in_subset: eco subset

causal relation between material entities
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000040
range: BFO_0000040
IAO_0000116: 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
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

determined by
type: ObjectProperty
sub property of: BFO_0000050
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
domain: system
range: BFO_0000040
IAO_0000112: A coral reef environment is determined by a particular coral reef
IAO_0000115: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
IAO_0000116: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/24330602
IAO_0000589: determined by (system to material entity)
creator: Chris Mungall
creator: Pier Buttigieg
in_subset: eco subset

determines
type: ObjectProperty
sub property of: causally influences
IAO_0000115: inverse of determined by
IAO_0000117: Chris Mungall
IAO_0000589: determines (material entity to system)
in_subset: defined by inverse
in_subset: eco subset

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between material entities
domain: system
range: BFO_0000040
property chain axiom: determined by
property chain axiom: BFO_0000050
IAO_0000115: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
IAO_0000117: Chris Mungall
in_subset: eco subset

Axiom
annotated source: determined by part of
annotated property: propertyChainAxiom
annotated target: determined by
annotated target: BFO_0000050
RO_0002582: true

transcribed from
type: ObjectProperty
sub property of: genomically related to
inverse of: transcribed to
IAO_0000115: x is transcribed from y if and only if x is synthesized from template y
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

transcribed to
type: ObjectProperty
sub property of: genomically related to
IAO_0000115: inverse of transcribed from
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
in_subset: defined by inverse

ribosomal translation of
type: ObjectProperty
sub property of: genomically related to
IAO_0000115: x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

ribosomally translates to
type: ObjectProperty
sub property of: genomically related to
IAO_0000115: inverse of ribosomal translation of
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

sequentially related to
type: ObjectProperty
domain: sequentially ordered entity
range: sequentially ordered entity
IAO_0000115: A relation that holds between two entities that have the property of being sequences or having sequences.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000232: The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
cites as authority: 006650.abstract

sequentially adjacent to
type: ObjectProperty
sub property of: does not overlap sequence of
IAO_0000112: Every UTR is adjacent to a CDS of the same transcript
IAO_0000112: Two consecutive DNA residues are sequentially adjacent
IAO_0000112: Two exons on a processed transcript that were previously connected by an intron are adjacent
IAO_0000115: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

has start sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is start sequence of
type: TransitiveProperty
IAO_0000112: Every CDS has as a start sequence the start codon for that transcript
IAO_0000115: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
IAO_0000117: Chris Mungall
IAO_0000118: started by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is start sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
IAO_0000115: inverse of has start sequence
IAO_0000117: Chris Mungall
IAO_0000118: starts
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

has end sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is end sequence of
type: TransitiveProperty
IAO_0000112: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
IAO_0000115: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
IAO_0000117: Chris Mungall
IAO_0000118: ended by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is end sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
IAO_0000115: inverse of has end sequence
IAO_0000117: Chris Mungall
IAO_0000118: ends
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

is consecutive sequence of
type: ObjectProperty
sub property of: has subsequence
IAO_0000115: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
IAO_0000116: In the SO paper, this was defined as an instance-type relation
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is sequentially aligned with
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
IAO_0000112: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
IAO_0000115: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract

bounds sequence of
type: ObjectProperty
sub property of: sequentially related to
inverse of: is bound by sequence of
type: TransitiveProperty
IAO_0000112: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
IAO_0000115: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract

is bound by sequence of
type: ObjectProperty
sub property of: sequentially related to
type: TransitiveProperty
IAO_0000115: inverse of bounds sequence of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
in_subset: defined by inverse

has subsequence
type: ObjectProperty
sub property of: BFO_0000051
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of
type: TransitiveProperty
IAO_0000115: x has subsequence y iff all of the sequence parts of x are sequence parts of y
IAO_0000117: Chris Mungall
IAO_0000118: contains
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is subsequence of
type: ObjectProperty
sub property of: BFO_0000050
sub property of: is bound by sequence of
sub property of: overlaps sequence of
type: TransitiveProperty
IAO_0000115: inverse of has subsequence
IAO_0000117: Chris Mungall
IAO_0000118: contained by
cites as authority: 006650.abstract
in_subset: defined by inverse

overlaps sequence of
type: ObjectProperty
sub property of: overlaps
sub property of: sequentially related to
type: SymmetricProperty
property chain axiom: has subsequence
property chain axiom: is subsequence of
IAO_0000115: x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract

does not overlap sequence of
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
IAO_0000115: x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
IAO_0000117: Chris Mungall
IAO_0000118: disconnected from
cites as authority: 006650.abstract

is upstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
IAO_0000115: inverse of downstream of sequence of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract

is downstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
IAO_0000115: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract

is immediately downstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of
IAO_0000112: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
IAO_0000117: Chris Mungall
is direct form of: is downstream of sequence of
cites as authority: 006650.abstract

is immediately upstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of
IAO_0000112: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: inverse of immediately downstream of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract

has skeleton
type: ObjectProperty
sub property of: BFO_0000051
inverse of: skeleton of
IAO_0000112: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
IAO_0000115: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
IAO_0000117: Chris Mungall
IAO_0000118: has supporting framework
IAO_0000232: The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).

results in ending of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000115: p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
IAO_0000117: Chris Mungall

hyperparasite of
type: ObjectProperty
sub property of: has host
inverse of: hyperparasitized by
property chain axiom: parasite of
IAO_0000115: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000116: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
IAO_0000117: Chris Mungall
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
has related synonym: epiparasite of
has related synonym: hyperparasitoid of
in_subset: eco subset

hyperparasitized by
type: ObjectProperty
sub property of: host of
property chain axiom: parasitized by
IAO_0000115: inverse of hyperparasite of
IAO_0000117: Chris Mungall
has related synonym: has epiparasite
has related synonym: has hyperparasite
has related synonym: hyperparasitoidized by
in_subset: defined by inverse
in_subset: eco subset

allelopath of
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000117: Chris Mungall
IAO_0000119: http://en.wikipedia.org/wiki/Allelopathy
in_subset: eco subset
see also: x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y

pathogen of
type: ObjectProperty
sub property of: has host
inverse of: has pathogen
IAO_0000117: Chris Mungall
in_subset: eco subset

has pathogen
type: ObjectProperty
sub property of: host of
IAO_0000117: Chris Mungall
in_subset: eco subset

has evidence
type: ObjectProperty
sub property of: related via evidence or inference to
IAO_0000115: inverse of is evidence for
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/25052702
in_subset: defined by inverse
in_subset: eco subset
comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.

causally influenced by
type: ObjectProperty
sub property of: causal relation between material entities
inverse of: causally influences
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (material entity to material entity)

interaction relation helper property
type: ObjectProperty
sub property of: helper property
IAO_0000117: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: Chris Mungall

results in movement of
type: ObjectProperty
sub property of: RO_0000057
IAO_0000115: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
IAO_0000117: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between material entities
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
IAO_0000115: 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
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: causally influences (material entity to material entity)

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
domain: CARO_0000003
range: CARO_0000003
IAO_0000115: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.

has muscle antagonist
type: ObjectProperty
sub property of: biomechanically related to
IAO_0000115: m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Antagonist_(muscle)

has branching part
type: ObjectProperty
sub property of: in branching relationship with
IAO_0000115: inverse of branching part of
IAO_0000117: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

conduit for
type: ObjectProperty
sub property of: overlaps
domain: BFO_0000040
range: BFO_0000040
IAO_0000115: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
IAO_0000117: Chris Mungall
IAO_0000119: UBERON:cjm
IAO_0000232: This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
in_subset: eco subset

lumen of
type: ObjectProperty
sub property of: BFO_0000050
range: BFO_0000040
IAO_0000115: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:cjm
in_subset: eco subset

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: BFO_0000141
IAO_0000115: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
IAO_0000117: Chris Mungall
in_subset: eco subset

has modifier
type: ObjectProperty
domain: BFO_0000020
IAO_0000115: A relation that holds between an attribute or a qualifier and another attribute.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
IAO_0000232: 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.
in_subset: eco subset

participates in a biotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
domain: CARO_0001010
range: CARO_0001010
IAO_0000117: Chris Mungall
in_subset: eco subset

skeleton of
type: ObjectProperty
sub property of: BFO_0000050
domain: CARO_0000003
range: CARO_0000003
IAO_0000115: inverse of has skeleton
IAO_0000117: Chris Mungall
in_subset: defined by inverse

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
IAO_0000115: 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.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
is direct form of: regulates

existence starts at point
type: ObjectProperty
sub property of: relation between structure and stage
IAO_0000115: x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: BFO_0000051
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
IAO_0000115: 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
IAO_0000117: Chris Mungall

results in closure of
type: ObjectProperty
sub property of: RO_0000057
sub property of: results in developmental progression of
IAO_0000116: p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.

results in breakdown of
type: ObjectProperty
sub property of: has input
IAO_0000115: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p

results in synthesis of
type: ObjectProperty
sub property of: results in formation of

results in assembly of
type: ObjectProperty
sub property of: results in formation of
sub property of: results in organization of

results in catabolism of
type: ObjectProperty
sub property of: results in breakdown of
IAO_0000115: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.

results in disassembly of
type: ObjectProperty
sub property of: results in breakdown of
sub property of: results in organization of

results in remodeling of
type: ObjectProperty
sub property of: has input
sub property of: results in organization of

results in organization of
type: ObjectProperty
sub property of: RO_0000057
IAO_0000115: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c

existence ends at point
type: ObjectProperty
sub property of: relation between structure and stage
IAO_0000115: x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000040
range: BFO_0000015
IAO_0000115: 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.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations

capable of inhibiting or preventing pathological process
type: ObjectProperty
sub property of: capable of negatively regulating
IAO_0000112: pazopanib -> pathological angiogenesis
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
IAO_0000118: treats
IAO_0000119: causal-relations
IAO_0000232: The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.

Axiom
annotated source: capable of inhibiting or preventing pathological process
annotated property: IAO_0000118
annotated target: treats
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship

capable of upregulating or causing pathological process
type: ObjectProperty
sub property of: capable of positively regulating
IAO_0000112: benzene -> cancer [CHEBI]
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
IAO_0000118: causes disease
IAO_0000119: causal-relations

is substance that treats
type: ObjectProperty
sub property of: capable of inhibiting or preventing pathological process
IAO_0000115: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
IAO_0000118: treats
IAO_0000119: causal-relations

is marker for
type: ObjectProperty
sub property of: correlated with
IAO_0000115: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
IAO_0000116: May be ceded to OBI

process has causal agent
type: ObjectProperty
sub property of: causally related to
IAO_0000115: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

obsolete related via dependence to
type: ObjectProperty
IAO_0000115: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
deprecated: true

correlated with
type: ObjectProperty
IAO_0000115: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
IAO_0000232: Groups both positive and negative correlation

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
IAO_0000112: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
IAO_0000115: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
comment: In the Gene Ontology association model, this corresponds to the With/From field

has model
type: ObjectProperty
inverse of: is model of
IAO_0000115: Inverse of is-model-of

related via evidence or inference to
type: ObjectProperty

visits
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: visited by

visited by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

visits flowers of
type: ObjectProperty
sub property of: visits
inverse of: has flowers visited by

has flowers visited by
type: ObjectProperty
sub property of: visited by

lays eggs in
type: ObjectProperty
sub property of: parasite of
sub property of: visits
inverse of: has eggs laid in by

has eggs laid in by
type: ObjectProperty
sub property of: parasitized by
sub property of: visited by

kills
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: is killed by
IAO_0000119: https://github.com/jhpoelen/eol-globi-data/issues/143

is killed by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
IAO_0000115: 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.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
is positive form of: directly regulates

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
IAO_0000115: 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.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
is negative form of: directly regulates

ectoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has ectoparasite
IAO_0000115: A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
IAO_0000119: Types

has ectoparasite
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of ectoparasite of
in_subset: defined by inverse

endoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has endoparasite
IAO_0000119: Types
IAO_0000119: A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
has related synonym: lives inside of

has endoparasite
type: ObjectProperty
sub property of: parasitized by

mesoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has mesoparasite
IAO_0000115: A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite

has mesoparasite
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of mesoparasite of
in_subset: defined by inverse

intercellular endoparasite of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intercellular endoparasite
IAO_0000115: A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
IAO_0000119: Types

has intercellular endoparasite
type: ObjectProperty
sub property of: has endoparasite
IAO_0000115: inverse of intercellular endoparasite of
in_subset: defined by inverse

intracellular endoparasite of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intracellular endoparasite
IAO_0000115: A sub-relation of endoparasite-of in which the parasite inhabits host cells.
IAO_0000119: Types

has intracellular endoparasite
type: ObjectProperty
sub property of: has endoparasite
IAO_0000115: inverse of intracellular endoparasite of
in_subset: defined by inverse

produces
type: ObjectProperty
inverse of: produced by
domain: BFO_0000040
range: BFO_0000040
property chain axiom:
  inverse of: BFO_0000066
property chain axiom: has output
IAO_0000114: IAO_0000125
IAO_0000115: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
IAO_0000117: Melissa Haendel
in_subset: eco subset
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.

produced by
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000114: IAO_0000125
IAO_0000115: a produced_by b iff some process that occurs_in b has_output a.
IAO_0000117: Melissa Haendel
in_subset: eco subset

represses expression of
type: ObjectProperty
sub property of: activity directly negatively regulates activity of
IAO_0000115: Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
IAO_0000116: Logical axioms to be added after the relevant branch of GO is MIREOTed in

increases expression of
type: ObjectProperty
sub property of: activity directly positively regulates activity of
IAO_0000115: Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
IAO_0000116: Logical axioms to be added after the relevant branch of GO is MIREOTed in

is model of
type: ObjectProperty
IAO_0000115: Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
IAO_0000116: To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?
IAO_0000117: Matthew Brush
comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.

causes or contributes to condition
type: ObjectProperty
sub property of: causally related to
IAO_0000112: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
IAO_0000116: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

causes condition
type: ObjectProperty
sub property of: causes or contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.

contributes to condition
type: ObjectProperty
sub property of: causes or contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.

contributes to severity of condition
type: ObjectProperty
sub property of: contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
IAO_0000118: contributes to expressivity of condition

contributes to frequency of condition
type: ObjectProperty
sub property of: contributes to condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
IAO_0000118: contributes to penetrance of condition

ameliorates condition
type: ObjectProperty
sub property of: contributes to severity of condition
IAO_0000115: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
IAO_0000118: is preventative for condition
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

correlated with condition
type: ObjectProperty
sub property of: correlated with
IAO_0000115: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

exacerbates condition
type: ObjectProperty
sub property of: contributes to severity of condition
IAO_0000115: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.

condition ameliorated by
type: ObjectProperty
sub property of: causally related to
IAO_0000115: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.

condition exacerbated by
type: ObjectProperty
sub property of: causally related to
IAO_0000115: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.

condition has genetic basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is genetic basis for condition
domain: BFO_0000017
range: Class
  union of: BFO_0000015
  union of: BFO_0000019
  union of: BFO_0000040
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:38:20Z

has material basis in gain of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal gain of function germline mutation of in
created by: cjm
creation date: 2017-11-05T02:45:20Z

has material basis in loss of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal loss of function germline mutation of in
created by: cjm
creation date: 2017-11-05T02:45:37Z

has material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation in
created by: cjm
creation date: 2017-11-05T02:45:54Z

has material basis in somatic mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal somatic mutation in
created by: cjm
creation date: 2017-11-05T02:46:07Z

has major susceptibility factor
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal susceptibility factor for
created by: cjm
creation date: 2017-11-05T02:46:26Z

has partial material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation partially giving rise to
created by: cjm
creation date: 2017-11-05T02:46:57Z

is genetic basis for condition
type: ObjectProperty
sub property of: is basis for realizable
range: BFO_0000017
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:53:08Z

is causal gain of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:55:51Z

is causal loss of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:56:06Z

is causal germline mutation in
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:56:40Z

is causal somatic mutation in
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:57:07Z

is causal susceptibility factor for
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:57:43Z

is causal germline mutation partially giving rise to
type: ObjectProperty
sub property of: is genetic basis for condition
IAO_0000115: Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:58:43Z

realizable has basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is basis for realizable
created by: cjm
creation date: 2017-11-05T03:20:01Z

is basis for realizable
type: ObjectProperty
sub property of: causally related to
created by: cjm
creation date: 2017-11-05T03:20:29Z

disease has basis in
type: ObjectProperty
sub property of: realizable has basis in
sub property of: causal relationship with disease as subject
domain: OGMS_0000031
created by: cjm
creation date: 2017-11-05T03:26:47Z

disease has basis in dysfunction of
type: ObjectProperty
sub property of: disease has basis in
range: CARO_0000006
IAO_0000115: A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
IAO_0000589: disease has basis in dysfunction of (disease to anatomical structure)
created by: cjm
creation date: 2017-11-05T03:29:32Z

disease has basis in disruption of
type: ObjectProperty
sub property of: disease has basis in
range: BFO_0000015
IAO_0000115: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
IAO_0000589: disease has basis in disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:37:52Z

disease has basis in feature
type: ObjectProperty
sub property of: has phenotype
sub property of: disease has basis in
domain: OGMS_0000031
range: Class
  union of: OGMS_0000031
  union of: UPHENO_0001001
IAO_0000115: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
created by: cjm
creation date: 2017-11-05T03:46:07Z

causal relationship with disease as subject
type: ObjectProperty
sub property of: causally related to
sub property of: disease relationship
domain: OGMS_0000031
IAO_0000116: After import upper level from OGMS, make domain more specific.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
created by: cjm
creation date: 2017-11-05T03:50:54Z

disease causes disruption of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: OGMS_0000031
range: BFO_0000015
property chain axiom: BFO_0000050
IAO_0000115: A relationship between a disease and a process where the disease process disrupts the execution of the process.
IAO_0000589: disease causes disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:51:09Z

disease causes dysfunction of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: OGMS_0000031
range: CARO_0000006
property chain axiom: BFO_0000050
IAO_0000589: disease causes dysfunction of (disease to anatomical entity)
created by: cjm
creation date: 2017-11-05T03:58:20Z

disease has location
type: ObjectProperty
sub property of: disease relationship
domain: OGMS_0000031
range: BFO_0000004
range: Class
  union of: CARO_0000006
  union of: CARO_0000007
IAO_0000115: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
IAO_0000116: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
IAO_0000232: This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
created by: cjm
creation date: 2017-11-05T04:06:02Z

disease has inflammation site
type: ObjectProperty
sub property of: disease has location
domain: OGMS_0000031
range: CARO_0000003
IAO_0000115: A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
created by: cjm
creation date: 2017-12-26T19:37:31Z

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000017
range: BFO_0000040
property chain axiom: realized in response to
property chain axiom: has input
IAO_0000115: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: cjm
creation date: 2017-12-26T19:45:49Z

disease has feature
type: ObjectProperty
sub property of: disease relationship
domain: OGMS_0000031
range: Class
  union of: OGMS_0000031
  union of: UPHENO_0001001
IAO_0000115: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
created by: cjm
creation date: 2017-12-26T19:50:53Z

disease arises from structure
type: ObjectProperty
sub property of: disease has basis in
range: CARO_0000003
IAO_0000115: A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
created by: cjm
creation date: 2017-12-26T19:58:44Z

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: BFO_0000051
IAO_0000115: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: cjm
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
is positive form of: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
is negative form of: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
IAO_0000115: 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
is positive form of: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
IAO_0000115: 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
is negative form of: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
is negative form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
is positive form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

epiphyte of
type: ObjectProperty
sub property of: symbiotically interacts with
inverse of: has epiphyte
IAO_0000115: An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
IAO_0000119: https://en.wikipedia.org/wiki/Epiphyte

has epiphyte
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000115: inverse of epiphyte of
in_subset: defined by inverse

kleptoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: kleptoparasitized by
IAO_0000115: A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
IAO_0000119: https://en.wikipedia.org/wiki/Kleptoparasitism

kleptoparasitized by
type: ObjectProperty
sub property of: parasitized by
IAO_0000115: inverse of kleptoparasite of
in_subset: defined by inverse

creates habitat for
type: ObjectProperty
sub property of: ecologically related to
domain: CARO_0001010
range: CARO_0001010
IAO_0000115: An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.

ecologically co-occurs with
type: ObjectProperty
sub property of: ecologically related to
type: SymmetricProperty
domain: CARO_0001010
range: CARO_0001010
IAO_0000115: An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.

lays eggs on
type: ObjectProperty
sub property of: visits
inverse of: has eggs laid on by
IAO_0000115: An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.

has eggs laid on by
type: ObjectProperty
sub property of: visited by
IAO_0000115: An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.

has substance added
type: ObjectProperty
type: IrreflexiveProperty
IAO_0000112: muffin 'has substance added' some 'baking soda'
IAO_0000114: IAO_0000428
IAO_0000115: "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
IAO_0000116: The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
IAO_0000117: Damion Dooley

has substance removed
type: ObjectProperty
type: IrreflexiveProperty
IAO_0000112: 'egg white' 'has substance removed' some 'egg yolk'
IAO_0000114: IAO_0000428
IAO_0000115: "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
IAO_0000117: Damion Dooley

immersed in
type: ObjectProperty
type: IrreflexiveProperty
IAO_0000112: sardines 'immersed in' some 'oil and mustard'
IAO_0000114: IAO_0000428
IAO_0000115: "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
IAO_0000117: Damion Dooley

has primary substance added
type: ObjectProperty
sub property of: has substance added
type: IrreflexiveProperty
IAO_0000112: bread 'has primary substance added' some 'flour'
IAO_0000114: IAO_0000428
IAO_0000115: 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
IAO_0000117: Damion Dooley

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000017
range: BFO_0000015
property chain axiom: BFO_0000054
property chain axiom: causally downstream of
IAO_0000112: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
IAO_0000112: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
IAO_0000112: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
IAO_0000115: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: Austin Meier
contributor: Chris Mungall
contributor: David Osumi-Sutherland
contributor: Marie Angelique Laporte
has exact synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: hasExactSynonym
annotated target: triggered by process
has db xref: RO:cjm

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: BFO_0000031
range: BFO_0000004
property chain axiom: RO_0000052
property chain axiom: RO_0000058
IAO_0000112: Genetic information generically depend on molecules of DNA.
IAO_0000112: The novel *War and Peace* generically depends on this copy of the novel.
IAO_0000112: The pattern shared by chess boards generically depends on any chess board.
IAO_0000112: The score of a symphony g-depends on a copy of the score.
IAO_0000112: This pdf file generically depends on this server.
IAO_0000115: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
IAO_0000119: [072-ISO]
has exact synonym: g-depends on

is carrier of
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000031
property chain axiom: RO_0000059
property chain axiom: RO_0000053
IAO_0000112: Molecules of DNA are carriers of genetic information.
IAO_0000112: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
IAO_0000112: This hard drive is carrier of these data items.
IAO_0000115: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
IAO_0000119: [072-ISO]

disease relationship
type: ObjectProperty
IAO_0000115: This relation groups relations between diseases and any other kind of entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
created by: cjm
creation date: 2018-09-26T00:00:32Z

has increased age-specific mortality rate
type: DatatypeProperty
range: Datatype
  on datatype: short
  with restrictions:
    min inclusive: 0
  with restrictions:
    max inclusive: 100
IAO_0000115: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
creation date: 2018-05-22T16:43:28Z
comment: This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.
created by: dos

Axiom
annotated source: has increased age-specific mortality rate
annotated property: IAO_0000115
annotated target: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
has db xref: PMID:24138933
has db xref: Wikipedia:Infant_mortality

GO_0004842
subclass of: Restriction
  on property: is ubiquitination
  has self: true

GO_0016301
subclass of: Restriction
  on property: is kinase activity
  has self: true

GO_0044403
subclass of: Restriction
  on property: is symbiosis
  has self: true

GO_0072519
subclass of: Restriction
  on property: is parasitism
  has self: true

GO_0085030
subclass of: Restriction
  on property: is mutualism
  has self: true

GO_0085031
subclass of: Restriction
  on property: is commensalism
  has self: true

exposure event or process
type: Class
subclass of: BFO_0000015
IAO_0000112: An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
IAO_0000112: An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
IAO_0000115: A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
IAO_0000116: This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
creator: Chris Mungall
created by: cjm
creation date: 2017-06-05T17:55:39Z

sequentially ordered entity
type: Class
subclass of: Restriction
  on property: has subsequence
  some values from: sequence atomic unit
IAO_0000115: Any entity that is ordered in discrete units along a linear axis.
IAO_0000117: Chris Mungall

sequence atomic unit
type: Class
subclass of: sequentially ordered entity
IAO_0000115: Any individual unit of a collection of like units arranged in a linear order
IAO_0000117: Chris Mungall
IAO_0000232: An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.

sequence bearer
type: Class
subclass of: sequentially ordered entity
IAO_0000115: Any entity that can be divided into parts such that each part is an atomical unit of a sequence
IAO_0000117: Chris Mungall
IAO_0000232: Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.

system
subclass of: BFO_0000040
IAO_0000115: A material entity consisting of multiple components that are causally integrated.
IAO_0000116: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
IAO_0000117: Chris Mungall
IAO_0000119: http://www.jbiomedsem.com/content/4/1/43

RO_0000092
IAO_0000115: inverse of has disposition
in_subset: defined by inverse

RO_0001000
in_subset: eco subset
IAO_0000232: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.

isDefinedBy
IAO_0000589: is defined by

Axiom
annotated source: isDefinedBy
annotated property: IAO_0000589
annotated target: is defined by
comment: This is an experimental annotation

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: GO_0003674
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: GO_0003674
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: GO_0003674
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: BFO_0000051
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: GO_0008150
  argument1: z
body: IndividualPropertyAtom
  property predicate: BFO_0000050
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

From ligand activity to has_ligand
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: z
  argument2: x
body: ClassAtom
  class predicate: GO_0048018
  argument1: z
head: IndividualPropertyAtom
  property predicate: has ligand
  argument1: x
  argument2: y

Imp
comment: This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: BFO_0000066
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: BFO_0000050
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

From has_ligand to ligand activity
type: Imp
body: IndividualPropertyAtom
  property predicate: has ligand
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: z
  argument2: x
head: ClassAtom
  class predicate: GO_0048018
  argument1: z

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2