editor note
type: AnnotationProperty
IAO_0000115: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.

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

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.

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000115: a core relation that holds between a part and its whole

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000115: a core relation that holds between a whole and its part

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000115: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000115: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000115: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: characteristic
IAO_0000115: Inverse of characteristic_of

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000115: a relation between a continuant and a process, in which the continuant is somehow involved in the process

has participant
type: ObjectProperty
domain: occurrent
domain: process
range: continuant
property chain axiom: has part
IAO_0000115: a relation between a process and a continuant, in which the continuant is somehow involved in the process

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000115: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000115: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000115: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000115: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000115: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000115: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
IAO_0000115: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
IAO_0000115: inverse of has disposition

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
IAO_0000115: a relation between two independent continuants, the location and the target, in which the target is entirely within the location

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
property chain axiom: part of
IAO_0000115: a relation between two independent continuants, the target and the location, in which the target is entirely within the location

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

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.

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.

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.

has component activity
type: ObjectProperty
sub property of: has component process

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
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.

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates

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.

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: https://orcid.org/0000-0002-7073-9172

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.

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: https://orcid.org/0000-0002-7073-9172

has effector activity
type: ObjectProperty
sub property of: has component activity
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.

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: https://orcid.org/0000-0002-7073-9172

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes

immediately precedes
type: ObjectProperty
sub property of: precedes

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000115: x overlaps y if and only if there exists some z such that x has part z and z part of y

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

only in taxon
type: ObjectProperty
sub property of: in taxon
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.

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: organism
property chain axiom: part of
property chain axiom: has part
property chain axiom: develops from
property chain axiom: capable of
property chain axiom: has developmental contribution from
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.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000115: A is spatially_disjoint_from B if and only if they have no parts in common

has component
type: ObjectProperty
sub property of: has part
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.

develops from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
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

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_0000115: inverse of develops from

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
IAO_0000115: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
IAO_0000115: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.

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
IAO_0000115: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
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.

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: part of
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.

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

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
IAO_0000115: x adjacent to y if and only if x and y share a boundary.

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
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.

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops from
IAO_0000115: x has developmental contribution from y iff x has some part z such that z develops from y

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: part of
IAO_0000115: inverse of has developmental contribution from

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
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

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
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_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 succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000115: Inverse of developmentally preceded by

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
IAO_0000115: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
IAO_0000115: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
IAO_0000115: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

evolutionarily related to
type: ObjectProperty
IAO_0000115: A relationship that holds via some environmental process

mereotopologically related to
type: ObjectProperty
IAO_0000115: A mereological relationship or a topological relationship

developmentally related to
type: ObjectProperty
IAO_0000115: A relationship that holds between entities participating in some developmental process (GO:0032502)

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000115: c enables p iff c is capable of p and c acts to execute p.

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.

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
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.

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

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

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
IAO_0000115: inverse of enables

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
IAO_0000115: inverse of regulates

negatively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of negatively regulates

positively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of positively regulates

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
IAO_0000115: inverse of has input

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
IAO_0000115: x spatially_coextensive_with y if and inly if x and y have the same location

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
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).

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
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

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

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
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

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000115: inverse of upstream of

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
IAO_0000115: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
IAO_0000115: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.

causally related to
type: ObjectProperty
IAO_0000115: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.

Axiom
annotated source: causally related to
annotated property: IAO_0000115
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
has db xref: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
IAO_0000115: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
IAO_0000115: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.

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 is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
has related synonym: affects

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

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

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

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

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

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
IAO_0000115: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
has exact synonym: in pairwise interaction with

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.

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
has exact synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
has exact synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
has exact synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty

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

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

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.

depends on
type: ObjectProperty

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
IAO_0000115: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
IAO_0000115: p directly regulates q iff p is immediately causally upstream of q and p regulates q.

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: has part
property chain axiom: capable of
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

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
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.

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

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.

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

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

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
IAO_0000115: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
IAO_0000115: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
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.

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

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

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

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

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
IAO_0000115: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
IAO_0000115: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
IAO_0000115: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000115: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
has broad synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
IAO_0000115: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
IAO_0000115: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
IAO_0000115: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.

continuant
type: Class
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
IAO_0000115: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

occurrent
type: Class
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
IAO_0000115: An entity that has temporal parts and that happens, unfolds or develops through time.

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: characteristic
IAO_0000115: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])

spatial region
type: Class
subclass of: immaterial entity

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  all values from: process
IAO_0000115: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])

disposition
type: Class
subclass of: realizable
disjoint with: role

realizable
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: realizable
disjoint with: quality
IAO_0000115: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
label: realizable entity

quality
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: quality

characteristic
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: characteristic
subclass of: Restriction
  on property: has part
  all values from: characteristic
IAO_0000115: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
label: specifically dependent continuant

role
type: Class
subclass of: realizable
IAO_0000115: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
IAO_0000115: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity

molecular_function
type: Class
subclass of: process
disjoint with: biological_process
IAO_0000115: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has exact synonym: molecular function
label: gene product or complex activity

Axiom
annotated source: molecular_function
annotated property: IAO_0000115
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has db xref: GOC:pdt

biological_process
type: Class
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: molecular_function
IAO_0000115: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
IAO_0000115: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
has exact synonym: biological process
has exact synonym: physiological process
has related synonym: single organism process
has related synonym: single-organism process
label: biological process

Axiom
annotated source: biological_process
annotated property: IAO_0000115
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
has db xref: GOC:pdt

kinase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is kinase activity
  has self: true
IAO_0000115: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has exact synonym: phosphokinase activity

Axiom
annotated source: kinase activity
annotated property: IAO_0000115
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has db xref: ISBN:0198506732

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
IAO_0000115: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.

organism
type: Class
subclass of: material entity
IAO_0000115: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.

quality
type: Class
subclass of: characteristic
IAO_0000115: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities

Axiom
annotated source: quality
annotated property: IAO_0000115
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

anatomical entity
type: Class
subclass of: independent continuant
IAO_0000115: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.

Axiom
annotated source: anatomical entity
annotated property: IAO_0000115
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
has db xref: FMA:62955
has db xref: http://orcid.org/0000-0001-9114-8737

example to be eventually removed
type: NamedIndividual

metadata complete
type: NamedIndividual
IAO_0000115: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
IAO_0000115: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
IAO_0000115: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
IAO_0000115: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
IAO_0000115: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
IAO_0000115: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

to be replaced with external ontology term
type: NamedIndividual
IAO_0000115: Terms with this status should eventually replaced with a term from another ontology.

requires discussion
type: NamedIndividual
type: curation status specification
IAO_0000115: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.

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: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  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: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  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: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  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

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

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x