NCIt Neoplasm Core Module
type: Ontology
version IRI: neoplasm-core.owl
comment: Module extract from NCIt OBO Edition (Plus) based on the NCIt Neoplasm Core. This module is based on the SLME BOT algorithm, starting with the list of Neoplasm Core terms.

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.

comment
type: AnnotationProperty

label
type: AnnotationProperty

part_of
type: ObjectProperty
inverse of: has_part
type: TransitiveProperty
IAO_0000115: a core relation that holds between a part and its whole
has db xref: BFO:0000050
has OBO namespace: uberon
id: part_of
shorthand: part_of
label: part of

has_part
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: a core relation that holds between a whole and its part
has db xref: BFO:0000051
has OBO namespace: uberon
id: has_part
shorthand: has_part
label: has part

preceded_by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part_of
IAO_0000115: X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
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.
has db xref: BFO:0000062
has exact synonym: is preceded by
has exact synonym: takes place after
has OBO namespace: uberon
id: preceded_by
shorthand: preceded_by
label: preceded by

Axiom
annotated source: preceded_by
annotated property: hasExactSynonym
annotated target: is preceded by
has db xref: SIO:000249

Axiom
annotated source: preceded_by
annotated property: hasExactSynonym
annotated target: takes place after
has db xref: Allen:precedes

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
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.
has db xref: BFO:0000063
has OBO namespace: uberon
id: precedes
shorthand: precedes

occurs in
type: ObjectProperty
inverse of: contains process
domain: BFO_0000003
range: BFO_0000004
property chain axiom: part_of
IAO_0000115: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t

contains process
type: ObjectProperty
IAO_0000115: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
has db xref: BFO:0000067
has OBO namespace: uberon
id: contains_process
shorthand: contains_process

participates in
type: ObjectProperty
inverse of: has participant
domain: BFO_0000002
range: BFO_0000003
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: BFO_0000003
range: BFO_0000002
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

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
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.

has ligand
type: ObjectProperty
sub property of: has input
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.

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: 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.

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.

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

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
IAO_0000115: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
UBPROP_0000001: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
has db xref: RO:0002087
has exact synonym: directly preceded by
has exact synonym: is directly preceded by
has exact synonym: is immediately preceded by
has exact synonym: starts_at_end_of
has OBO namespace: uberon
id: immediately_preceded_by
shorthand: immediately_preceded_by
label: immediately preceded by

Axiom
annotated source: immediately_preceded_by
annotated property: UBPROP_0000001
annotated target: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
source: SIO:000251

Axiom
annotated source: immediately_preceded_by
annotated property: hasExactSynonym
annotated target: is immediately preceded by
has db xref: SIO:000251

immediately precedes
type: ObjectProperty
sub property of: precedes

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.
has db xref: RO:0002180
has OBO namespace: uberon
id: has_component
shorthand: has_component

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
property chain axiom: directly regulates
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.
has db xref: RO:0002211
shorthand: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
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.
has db xref: RO:0002212
shorthand: negatively_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
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.
has db xref: RO:0002213
shorthand: positively_regulates

capable of
type: ObjectProperty
sub property of: capable of part of
sub property of: functionally related to
domain: BFO_0000004
range: BFO_0000015
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.
has db xref: RO:0002215
has OBO namespace: uberon
id: capable_of
shorthand: capable_of

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in
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.
has db xref: RO:0002216
has OBO namespace: uberon
id: capable_of_part_of
shorthand: capable_of_part_of

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

temporally related to
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000003

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: BFO_0000015
range: material entity
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.

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 involved in regulation of p if c enables 'p' and p' causally upstream of p

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in
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 'p' and p' causally upstream of or within p

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

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

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has_part
property chain axiom: has component activity

functionally related to
type: ObjectProperty
has db xref: RO:0002328
has OBO namespace: uberon
id: functionally_related_to
shorthand: functionally_related_to

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.
has db xref: RO:0002329
has OBO namespace: uberon
id: part_of_structure_that_is_capable_of
shorthand: part_of_structure_that_is_capable_of

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: 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: functionally related to
sub property of:
  inverse of: capable of
IAO_0000115: inverse of enables

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

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
has db xref: RO:0002352
has OBO namespace: uberon
id: input_of
shorthand: input_of

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

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 if and only if p precedes q and p and q are linked in a causal chain

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 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.

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.

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

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

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
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

is active in
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
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.

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
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

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.

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.

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.

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.

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.

has part that occurs in
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000004
property chain axiom: has_part
property chain axiom: occurs in
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.

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

causal agent in
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: 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
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.

causal relation between material entities
type: ObjectProperty
domain: material entity
range: material entity

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

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

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.

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
domain: material entity
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.

capable of regulating
type: ObjectProperty
sub property of: causal agent in
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.

has causal agent
type: ObjectProperty
IAO_0000115: Inverse of 'causal agent in'

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.

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.

material entity
type: Class
subclass of: BFO_0000004

molecular_function
type: Class

biological_process
type: Class
subclass of: BFO_0000015

negative regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: negatively regulates
    some values from: molecular_function
subclass of: regulation of molecular function
subclass of: Restriction
  on property: negatively regulates
  some values from: molecular_function

positive regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: positively regulates
    some values from: molecular_function
subclass of: regulation of molecular function
subclass of: Restriction
  on property: positively regulates
  some values from: molecular_function

positive regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: positively regulates
    some values from: biological_process
subclass of: regulation of biological process
subclass of: Restriction
  on property: positively regulates
  some values from: biological_process

negative regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: negatively regulates
    some values from: biological_process
subclass of: regulation of biological process
subclass of: Restriction
  on property: negatively regulates
  some values from: biological_process

regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: regulates
    some values from: biological_process
subclass of: biological regulation
subclass of: Restriction
  on property: regulates
  some values from: biological_process

biological regulation
type: Class
subclass of: biological_process

regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: regulates
    some values from: molecular_function
subclass of: biological regulation
subclass of: Restriction
  on property: regulates
  some values from: molecular_function

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

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: occurs in
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: part_of
  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