format-version: 1.2
remark: Includes Ontology(OntologyID(Anonymous-3)) [Axioms: 754 Logical Axioms: 212]
ontology: go/extensions/legorel

[Typedef]
id: capable_of
name: capable of
def: "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. " []
subset: ro-eco
xref: RO:0002215
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: 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)\"." xsd:string
domain: BFO:0000004
range: BFO:0000015
is_a: capable_of_part_of ! capable of part of
expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" []

[Typedef]
id: capable_of_negatively_regulating
name: capable of negatively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." []
xref: RO:0002597
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: capable_of negatively_regulates
is_a: capable_of_regulating ! capable of regulating

[Typedef]
id: capable_of_part_of
name: capable of part of
def: "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." []
xref: RO:0002216
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: causal_agent_in ! causal agent in
is_a: functionally_related_to ! functionally related to
expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" []

[Typedef]
id: capable_of_positively_regulating
name: capable of positively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." []
xref: RO:0002598
property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: capable_of positively_regulates
is_a: capable_of_regulating ! capable of regulating

[Typedef]
id: capable_of_regulating
name: capable of regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." []
xref: RO:0002596
property_value: IAO:0000112 "pyrethroid -> growth" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: capable_of regulates
is_a: causal_agent_in ! causal agent in

[Typedef]
id: causal_agent_in
name: causal agent in
def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" []
xref: RO:0002500
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process
inverse_of: has_causal_agent ! has causal agent

[Typedef]
id: causal_relation_between_material_entities
name: causal relation between material entities
xref: RO:0002506
property_value: 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" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: 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." xsd:string
domain: BFO:0000040
range: BFO:0000040
is_a: causally_related_to ! causally related to

[Typedef]
id: causal_relation_between_material_entity_and_a_process
name: causal relation between material entity and a process
def: "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." []
xref: RO:0002595
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
domain: BFO:0000040
range: BFO:0000015
is_a: causally_related_to ! causally related to

[Typedef]
id: causal_relation_between_processes
name: causal relation between processes
def: "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." []
xref: RO:0002501
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: 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." xsd:string
domain: BFO:0000003
range: BFO:0000003
is_a: causally_related_to ! causally related to

[Typedef]
id: causally_downstream_of
name: causally downstream of
def: "inverse of upstream of" []
xref: RO:0002404
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: causally_downstream_of_or_within ! causally downstream of or within
is_a: preceded_by ! preceded by
inverse_of: causally_upstream_of ! causally upstream of

[Typedef]
id: causally_downstream_of_or_within
name: causally downstream of or within
xref: RO:0002427
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_transitive: true
is_a: causal_relation_between_processes ! causal relation between processes

[Typedef]
id: causally_influenced_by
name: causally influenced by
xref: RO:0002559
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string
is_a: causal_relation_between_material_entities ! causal relation between material entities
inverse_of: causally_influences ! causally influences

[Typedef]
id: causally_influences
name: causally influences
def: "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" []
xref: RO:0002566
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string
is_a: causal_relation_between_material_entities ! causal relation between material entities

[Typedef]
id: causally_related_to
name: causally related to
def: "This relation groups causal relations between material entities and causal relations between processes" []
xref: RO:0002410
property_value: IAO:0000114 IAO:0000428
property_value: 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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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." xsd:string
is_a: related_via_dependence_to ! related via dependence to

[Typedef]
id: causally_upstream_of
name: causally upstream of
def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
xref: RO:0002411
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: causally_upstream_of_or_within ! causally upstream of or within
is_a: precedes ! precedes

[Typedef]
id: causally_upstream_of_or_within
name: causally upstream of or within
def: "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." []
synonym: "affects" RELATED []
xref: RO:0002418
property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "influences (processual)" xsd:string
is_transitive: true
is_a: causal_relation_between_processes ! causal relation between processes
inverse_of: causally_downstream_of_or_within ! causally downstream of or within

[Typedef]
id: contains_process
name: contains process
def: "[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" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
xref: BFO:0000067
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Typedef]
id: directly_activates
name: directly activates
def: "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" []
xref: RO:0002406
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly positively regulates" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly activates (process to process)" xsd:string
is_a: directly_positively_regulates ! directly positively regulates
is_a: lego_relation ! lego relation

[Typedef]
id: directly_inhibits
name: directly inhibits
xref: RO:0002408
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly negatively regulates" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string
is_a: directly_negatively_regulates ! directly negatively regulates
is_a: lego_relation ! lego relation

[Typedef]
id: directly_negatively_regulates
name: directly negatively regulates
def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" []
xref: RO:0002630
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
is_a: directly_regulates ! directly regulates
is_a: negatively_regulates ! negatively regulates

[Typedef]
id: directly_positively_regulates
name: directly positively regulates
def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" []
xref: RO:0002629
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
is_a: directly_regulates ! directly regulates
is_a: positively_regulates ! positively regulates

[Typedef]
id: directly_provides_input_for
name: directly provides input for
def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" []
xref: RO:0002413
property_value: IAO:0000114 IAO:0000428
property_value: 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" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string
is_a: immediately_causally_upstream_of ! immediately causally upstream of
is_a: lego_relation ! lego relation
is_a: transitively_provides_input_for ! transitively provides input for

[Typedef]
id: directly_regulates
name: directly regulates
def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" []
xref: RO:0002578
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly regulates (processual)" xsd:string
property_value: RO:0002575 RO:0002211
is_a: immediately_causally_upstream_of ! immediately causally upstream of
is_a: regulates ! regulates

[Typedef]
id: enabled_by
name: enabled by
def: "inverse of enables" []
xref: RO:0002333
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: functionally_related_to ! functionally related to
is_a: lego_relation ! lego relation

[Typedef]
id: enables
name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"}
xref: RO:0002327
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
property_value: 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." xsd:string
property_value: 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." xsd:string
is_a: capable_of ! capable of
inverse_of: enabled_by ! enabled by

[Typedef]
id: enables_activity_in
name: enables activity in
def: "c executes activity in d if and only if c enables p and p occurs_in d" []
xref: RO:0002432
property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "executes activity in" xsd:string
holds_over_chain: enables occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: functionally_related_to ! functionally related to

[Typedef]
id: ends
name: ends
def: "inverse of ends with" []
subset: ro-eco
xref: RO:0002229
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: part_of ! part of
is_a: temporally_related_to ! temporally related to
inverse_of: ends_with ! ends with

[Typedef]
id: ends_after
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
xref: RO:0002086
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_transitive: true
is_a: temporally_related_to ! temporally related to

[Typedef]
id: ends_with
name: ends with
def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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." []
subset: ro-eco
xref: RO:0002230
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "finished by" xsd:string
is_transitive: true
is_a: has_part ! has part
is_a: lego_relation ! lego relation
is_a: temporally_related_to ! temporally related to

[Typedef]
id: functionally_related_to
name: functionally related to
xref: RO:0002328
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string

[Typedef]
id: has_causal_agent
name: has causal agent
def: "Inverse of 'causal agent in'" []
xref: RO:0002608
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: causally_related_to ! causally related to

[Typedef]
id: has_end_location
name: has end location
def: "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" []
subset: ro-eco
xref: RO:0002232
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "ends with process that occurs in" xsd:string
domain: BFO:0000015
range: BFO:0000004
holds_over_chain: ends_with occurs_in
is_a: has_part_that_occurs_in ! has part that occurs in

[Typedef]
id: has_input
name: has input
def: "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." []
subset: ro-eco
xref: RO:0002233
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
holds_over_chain: starts_with has_input
is_a: has_participant ! has participant
is_a: lego_relation ! lego relation
inverse_of: input_of ! input of

[Typedef]
id: has_output
name: has output
def: "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." []
subset: ro-eco
xref: RO:0002234
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "produces" xsd:string
holds_over_chain: ends_with has_output
is_a: has_participant ! has participant
is_a: lego_relation ! lego relation
inverse_of: output_of ! output of

[Typedef]
id: has_part
name: has part
def: "a core relation that holds between a whole and its part" []
xref: BFO:0000051
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
is_a: overlaps ! overlaps

[Typedef]
id: has_part_structure_that_is_capable_of
name: has part structure that is capable of
def: "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" []
xref: RO:0002584
property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: has_part capable_of
is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process
is_a: functionally_related_to ! functionally related to

[Typedef]
id: has_part_that_occurs_in
name: has part that occurs in
def: "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." []
subset: ro-eco
xref: RO:0002479
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000003
range: BFO:0000004
holds_over_chain: has_part occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"}

[Typedef]
id: has_participant
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
xref: RO:0000057
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
domain: BFO:0000003
range: BFO:0000002
holds_over_chain: has_part has_participant

[Typedef]
id: has_start_location
name: has start location
def: "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" []
subset: ro-eco
xref: RO:0002231
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "starts with process that occurs in" xsd:string
domain: BFO:0000015
range: BFO:0000004
holds_over_chain: starts_with occurs_in
is_a: has_part_that_occurs_in ! has part that occurs in

[Typedef]
id: immediately_causally_downstream_of
name: immediately causally downstream of
xref: RO:0002405
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: causally_downstream_of ! causally downstream of
is_a: immediately_preceded_by ! immediately preceded by
inverse_of: immediately_causally_upstream_of ! immediately causally upstream of

[Typedef]
id: immediately_causally_upstream_of
name: immediately causally upstream of
def: "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." []
xref: RO:0002412
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0002575 RO:0002411
is_a: causally_upstream_of ! causally upstream of
is_a: immediately_precedes ! immediately precedes

[Typedef]
id: immediately_preceded_by
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
xref: RO:0002087
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
holds_over_chain: starts_with ends_with
is_a: preceded_by ! preceded by
inverse_of: immediately_precedes ! immediately precedes

[Typedef]
id: immediately_precedes
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
xref: RO:0002090
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
holds_over_chain: ends_with starts_with
is_a: precedes ! precedes

[Typedef]
id: indirectly_activates
name: indirectly activates
def: "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" []
xref: RO:0002407
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "indirectly positively regulates" xsd:string
property_value: RO:0002579 RO:0002213
holds_over_chain: directly_activates directly_activates
holds_over_chain: directly_activates indirectly_activates
holds_over_chain: indirectly_inhibits indirectly_inhibits
is_transitive: true
is_a: positively_regulates ! positively regulates
transitive_over: directly_activates ! directly activates

[Typedef]
id: indirectly_inhibits
name: indirectly inhibits
xref: RO:0002409
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "indirectly negatively regulates" xsd:string
property_value: RO:0002579 RO:0002212
holds_over_chain: directly_inhibits directly_inhibits
holds_over_chain: directly_inhibits indirectly_inhibits
is_transitive: true
is_a: negatively_regulates ! negatively regulates
transitive_over: directly_inhibits ! directly inhibits

[Typedef]
id: input_of
name: input of
subset: ro-eco
xref: RO:0002352
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: functionally_related_to ! functionally related to
is_a: participates_in ! participates in

[Typedef]
id: interacts_with
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
subset: ro-eco
synonym: "in pairwise interaction with" EXACT []
xref: RO:0002434
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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." xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI
domain: BFO:0000040
range: BFO:0000040
is_symmetric: true

[Typedef]
id: involved_in
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
xref: RO:0002331
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
holds_over_chain: enables part_of
is_a: involved_in_or_regulates ! involved in or regulates
transitive_over: part_of ! part of

[Typedef]
id: involved_in_negative_regulation_of
name: involved in negative regulation of
xref: RO:0002430
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: enables negatively_regulates
holds_over_chain: involved_in negatively_regulates
is_a: involved_in_regulation_of ! involved in regulation of

[Typedef]
id: involved_in_or_regulates
name: involved in or regulates
def: "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" []
xref: RO:0002431
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "involved in or involved in regulation of" xsd:string
is_a: causal_agent_in ! causal agent in
is_a: functionally_related_to ! functionally related to

[Typedef]
id: involved_in_positive_regulation_of
name: involved in positive regulation of
xref: RO:0002429
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: enables positively_regulates
holds_over_chain: involved_in positively_regulates
is_a: involved_in_regulation_of ! involved in regulation of

[Typedef]
id: involved_in_regulation_of
name: involved in regulation of
def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" []
xref: RO:0002428
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: enables regulates
holds_over_chain: involved_in regulates
is_a: involved_in_or_regulates ! involved in or regulates

[Typedef]
id: is_evidence_with_support_from
name: is evidence with support from
def: "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
xref: RO:0002614
property_value: IAO:0000112 "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." xsd:string
is_a: lego_relation ! lego relation
is_a: related_via_evidence_or_inference_to ! related via evidence or inference to

[Typedef]
id: lego_relation
name: lego relation
xref: LEGOREL:0000000

[Typedef]
id: mereotopologically_related_to
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
xref: RO:0002323
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: molecularly_controls
name: molecularly controls
def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" []
xref: RO:0002448
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: causally_influences ! causally influences
is_a: molecularly_interacts_with ! molecularly interacts with

[Typedef]
id: molecularly_decreases_activity_of
name: molecularly decreases activity of
def: "Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b." []
xref: RO:0002449
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "inhibits" xsd:string
is_a: molecularly_controls ! molecularly controls

[Typedef]
id: molecularly_increases_activity_of
name: molecularly increases activity of
def: "Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b." []
xref: RO:0002450
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "activates" xsd:string
is_a: molecularly_controls ! molecularly controls

[Typedef]
id: molecularly_interacts_with
name: molecularly interacts with
def: "An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected." []
xref: RO:0002436
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "binds" xsd:string
property_value: IAO:0000118 "molecularly binds with" xsd:string
property_value: seeAlso ECO:0000353
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI
is_symmetric: true
is_a: interacts_with ! interacts with

[Typedef]
id: negatively_regulated_by
name: negatively regulated by
xref: RO:0002335
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: regulated_by ! regulated by

[Typedef]
id: negatively_regulates
name: negatively regulates
def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" []
xref: RO:0002212
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
holds_over_chain: ends_with negatively_regulates
is_a: regulates ! regulates
inverse_of: negatively_regulated_by ! negatively regulated by

[Typedef]
id: occurs_in
name: occurs in
def: "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" []
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
xref: BFO:0000066
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003
range: BFO:0000004
holds_over_chain: part_of occurs_in
is_a: lego_relation ! lego relation
inverse_of: contains_process ! contains process
transitive_over: part_of ! part of

[Typedef]
id: output_of
name: output of
subset: ro-eco
xref: RO:0002353
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: functionally_related_to ! functionally related to
is_a: participates_in ! participates in

[Typedef]
id: overlaps
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: ro-eco
xref: RO:0002131
property_value: IAO:0000114 IAO:0000125
property_value: RO:0001900 RO:0001901
holds_over_chain: has_part overlaps
holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: part_of part_of
is_a: mereotopologically_related_to ! mereotopologically related to
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []

[Typedef]
id: part_of
name: part of
def: "a core relation that holds between a part and its whole" []
xref: BFO:0000050
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
is_transitive: true
is_a: lego_relation ! lego relation
is_a: overlaps ! overlaps
inverse_of: has_part ! has part

[Typedef]
id: part_of_structure_that_is_capable_of
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
xref: RO:0002329
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: functionally_related_to ! functionally related to

[Typedef]
id: participates_in
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
xref: RO:0000056
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
domain: BFO:0000002
range: BFO:0000003
inverse_of: has_participant ! has participant

[Typedef]
id: positively_regulated_by
name: positively regulated by
xref: RO:0002336
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: regulated_by ! regulated by

[Typedef]
id: positively_regulates
name: positively regulates
def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" []
xref: RO:0002213
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
holds_over_chain: ends_with positively_regulates
holds_over_chain: negatively_regulates negatively_regulates
is_a: regulates ! regulates
inverse_of: positively_regulated_by ! positively regulated by

[Typedef]
id: preceded_by
name: preceded by
def: "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." []
subset: ro-eco
xref: BFO:0000062
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
domain: BFO:0000003
range: BFO:0000003
holds_over_chain: part_of preceded_by
is_transitive: true
is_a: ends_after ! ends after
inverse_of: precedes ! precedes

[Typedef]
id: precedes
name: precedes
def: "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." []
subset: ro-eco
xref: BFO:0000063
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003
range: BFO:0000003
holds_over_chain: part_of precedes
is_transitive: true
is_a: temporally_related_to ! temporally related to

[Typedef]
id: produced_by
name: produced by
def: "a produced_by b iff some process that occurs_in b has_output a." []
subset: ro-eco
xref: RO:0003001
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Melissa Haendel" xsd:string
domain: BFO:0000040
range: BFO:0000040

[Typedef]
id: produces
name: produces
def: "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." []
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.
subset: ro-eco
xref: RO:0003000
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Melissa Haendel" xsd:string
domain: BFO:0000040
range: BFO:0000040
inverse_of: produced_by ! produced by

[Typedef]
id: regulated_by
name: regulated by
def: "inverse of regulates" []
xref: RO:0002334
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
domain: BFO:0000015
range: BFO:0000015
is_transitive: true
is_a: causally_downstream_of_or_within ! causally downstream of or within

[Typedef]
id: regulates
name: regulates
def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" []
xref: RO:0002211
property_value: IAO:0000114 IAO:0000125
property_value: 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" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
domain: BFO:0000015
range: BFO:0000015
holds_over_chain: directly_regulates directly_regulates
holds_over_chain: ends_with regulates
is_transitive: true
is_a: causally_upstream_of ! causally upstream of
inverse_of: regulated_by ! regulated by

[Typedef]
id: related_via_dependence_to
name: related via dependence to
def: "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." []
xref: RO:0002609
property_value: 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." xsd:string

[Typedef]
id: related_via_evidence_or_inference_to
name: related via evidence or inference to
xref: RO:0002616

[Typedef]
id: starts
name: starts
def: "inverse of starts with" []
subset: ro-eco
xref: RO:0002223
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 "Allen" xsd:string
is_a: part_of ! part of
is_a: temporally_related_to ! temporally related to
inverse_of: starts_with ! starts with

[Typedef]
id: starts_with
name: starts with
def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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." []
subset: ro-eco
xref: RO:0002224
property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "started by" xsd:string
is_transitive: true
is_a: has_part ! has part
is_a: lego_relation ! lego relation
is_a: temporally_related_to ! temporally related to

[Typedef]
id: temporally_related_to
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
xref: RO:0002222
property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: 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." xsd:string
domain: BFO:0000003
range: BFO:0000003

[Typedef]
id: transitively_provides_input_for
name: transitively provides input for
def: "transitive form of directly_provides_input_for" []
xref: RO:0002414
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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')" xsd:string
property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string
domain: BFO:0000015
range: BFO:0000015
is_transitive: true
is_a: causally_upstream_of ! causally upstream of