diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 77b4c72..ec0efec 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.2 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/imports/merged_import.owl b/imports/merged_import.owl index 17ae597..21c5567 100644 --- a/imports/merged_import.owl +++ b/imports/merged_import.owl @@ -7,20 +7,18 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-04-26") + +Annotation(owl:versionInfo "2024-09-19") +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -47,9 +45,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -59,7 +54,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -71,128 +65,35 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -204,37 +105,22 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ -# Annotation Property: (definition) - -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - # Annotation Property: (is a defining property chain axiom where second argument is reflexive) AnnotationAssertion( "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.") @@ -280,18 +166,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (subset_property) - -AnnotationAssertion(rdfs:label "subset_property") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (in_subset) - -AnnotationAssertion(rdfs:label "in_subset") - ############################ # Object Properties @@ -332,58 +206,50 @@ AnnotationAssertion(rdfs:label "rea ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (preceded by) - -AnnotationAssertion( "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."@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (precedes) - -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "precedes"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (has_specified_input) AnnotationAssertion( "The inverse property of is_specified_input_of"@en) AnnotationAssertion(rdfs:label "has_specified_input"@en) -EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_input_of) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) AnnotationAssertion(rdfs:label "is_specified_input_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (has_specified_output) AnnotationAssertion( "The inverse property of is_specified_output_of"@en) AnnotationAssertion(rdfs:label "has_specified_output"@en) -EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_output_of) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion(rdfs:label "is_specified_output_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (achieves_planned_objective) AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") AnnotationAssertion(rdfs:label "achieves_planned_objective") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (objective_achieved_by) + +AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion(rdfs:label "objective_achieved_by") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) # Object Property: (characteristic of) @@ -431,21 +297,6 @@ AnnotationAssertion(rdfs:label "conc ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (function of) - -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (quality of) - -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - # Object Property: (role of) AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) @@ -453,21 +304,6 @@ AnnotationAssertion(rdfs:label "role SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (has function) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has quality) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - # Object Property: (has role) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) @@ -476,101 +312,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulated by) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - # Object Property: (in register with) AnnotationAssertion(Annotation( ) "A relationship that holds between two images, A and B, where: @@ -588,25 +329,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (ends after) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ends after"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately preceded by) - -AnnotationAssertion(rdfs:label "immediately preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately precedes) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately precedes"@en) -SubObjectPropertyOf( ) - # Object Property: (overlaps) AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") @@ -634,116 +356,12 @@ ObjectPropertyDomain( ObjectUnionOf( )) ObjectPropertyRange( ) -# Object Property: (regulates) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (positively regulates) - -AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (capable of) - -AnnotationAssertion( "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. ") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of part of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "capable of part of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (temporally related to) - -AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "temporally related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has input) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has input"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (acts upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within") -SubObjectPropertyOf( ) - # Object Property: (expresses) AnnotationAssertion( "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") AnnotationAssertion(rdfs:label "expresses"@en) SubObjectPropertyOf( ) -# Object Property: (causally upstream of, positive effect) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, negative effect) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (characteristic of part of) AnnotationAssertion( "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.") @@ -755,25 +373,6 @@ SubObjectPropertyOf( "A mereological relationship or a topological relationship") AnnotationAssertion(rdfs:label "mereotopologically related to"@en) -# Object Property: (enables) - -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enables"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (functionally related to) - -AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion(rdfs:label "functionally related to"@en) - -# Object Property: (part of structure that is capable of) - -AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) -SubObjectPropertyOf( ) - # Object Property: (genomically related to) AnnotationAssertion( "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.") @@ -781,45 +380,6 @@ AnnotationAssertion(rdfs:label "geno ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion(rdfs:label "involved in"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulated by) - -AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulated by"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulated by) - -AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (positively regulated by) - -AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulated by"@en) -SubObjectPropertyOf( ) - # Object Property: (member of) AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") @@ -832,367 +392,11 @@ InverseObjectProperties( "has member is a mereological relation between a collection and an item.") AnnotationAssertion(rdfs:label "has member"@en) SubObjectPropertyOf( ) -IrreflexiveObjectProperty() - -# Object Property: (input of) - -AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "input of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally downstream of) - -AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion(rdfs:label "causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately causally downstream of) - -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (causally related to) - -AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "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.") -AnnotationAssertion(rdfs:label "causally related to"@en) - -# Object Property: (causally upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "causally upstream of or within") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (causally downstream of or within) - -AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of or within") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interacts with") -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "molecularly interacts with") -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - -# Object Property: (is kinase activity) - -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - -# Object Property: (causal agent in process) - -AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion(rdfs:label "causal agent in process") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (causal relation between processes) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "causal relation between processes") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (depends on) AnnotationAssertion(rdfs:label "depends on") -# Object Property: (causal relation between entities) - -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (causally influenced by) - -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion(rdfs:label "interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (causally influences) - -AnnotationAssertion( "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).") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has part structure that is capable of) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "has part structure that is capable of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causal relation between material entity and a process) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "causal relation between material entity and a process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion(rdfs:label "capable of regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of negatively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion(rdfs:label "capable of negatively regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of positively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion(rdfs:label "capable of positively regulating") -SubObjectPropertyOf( ) - -# Object Property: (process has causal agent) - -AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion(rdfs:label "process has causal agent") -SubObjectPropertyOf( ) - -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly positively regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly negatively regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (realized in response to stimulus) - -AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "realized in response to stimulus") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -SubObjectPropertyOf( ) - -# Object Property: (realized in response to) - -AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") -AnnotationAssertion(rdfs:label "realized in response to"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (generically depends on) AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") @@ -1208,142 +412,64 @@ AnnotationAssertion(rdfs:label "is c ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (device utilizes material) - -AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "device utilizes material"@en) - -# Object Property: (regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) - ############################ # Classes ############################ +# Class: (entity) + +AnnotationAssertion(rdfs:label "entity"@en) + # Class: (continuant) -AnnotationAssertion( "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."@en) AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ) DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) # Class: (occurrent) -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) # Class: (independent continuant) -AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:label "independent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) DisjointClasses( ) # Class: (process) -AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - # Class: (realizable entity) -AnnotationAssertion( "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."@en) AnnotationAssertion(rdfs:label "realizable entity"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) # Class: (specifically dependent continuant) -AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) # Class: (role) -AnnotationAssertion( "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."@en) AnnotationAssertion(rdfs:label "role"@en) SubClassOf( ) # Class: (generically dependent continuant) -AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) AnnotationAssertion(rdfs:label "generically dependent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) # Class: (material entity) -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) AnnotationAssertion(rdfs:label "material entity"@en) SubClassOf( ) DisjointClasses( ) @@ -1566,15 +692,6 @@ AnnotationAssertion(rdfs:label "a EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) - -# Class: () - -DisjointClasses( ) - -# Class: () - -SubClassOf( ObjectHasSelf()) # Class: (planned process) @@ -1620,83 +737,16 @@ EquivalentClasses( ObjectIntersectio SubClassOf( ) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) DisjointClasses( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/Makefile b/src/ontology/Makefile index b224877..7f18799 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for vfbext # Generated using ontology-development-kit -# ODK Version: v1.5 +# ODK Version: v1.5.2 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 11643cc79293c3aa48319672aa04a650c744220372aba01fe8124783bf56a725 +CONFIG_HASH= f536379bcd203347d28185a6c0c3abdac1af3338ef70a92870fa1c31ea32920f # ---------------------------------------- @@ -45,8 +45,8 @@ REPORT_LABEL = -l true REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties -SPARQL_EXPORTS = basic-report edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.5 +SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +ODK_VERSION_MAKEFILE = v1.5.2 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -159,7 +159,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro caro fbbt obi +IMPORTS = bfo ro caro fbbt obi IMPORT_ROOTS = $(IMPORTDIR)/merged_import IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -416,6 +416,14 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports ifeq ($(strip $(MIR)),true) +## ONTOLOGY: bfo +.PHONY: mirror-bfo +.PRECIOUS: $(MIRRORDIR)/bfo.owl +mirror-bfo: | $(TMPDIR) + curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(TMPDIR)/bfo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/bfo-download.owl --base-iri http://purl.obolibrary.org/obo/BFO_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + ## ONTOLOGY: ro .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl diff --git a/src/ontology/imports/bfo_terms.txt b/src/ontology/imports/bfo_terms.txt new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/src/ontology/imports/bfo_terms.txt @@ -0,0 +1 @@ + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 17ae597..21c5567 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,20 +7,18 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-04-26") + +Annotation(owl:versionInfo "2024-09-19") +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -47,9 +45,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -59,7 +54,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -71,128 +65,35 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -204,37 +105,22 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ -# Annotation Property: (definition) - -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - # Annotation Property: (is a defining property chain axiom where second argument is reflexive) AnnotationAssertion( "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.") @@ -280,18 +166,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (subset_property) - -AnnotationAssertion(rdfs:label "subset_property") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (in_subset) - -AnnotationAssertion(rdfs:label "in_subset") - ############################ # Object Properties @@ -332,58 +206,50 @@ AnnotationAssertion(rdfs:label "rea ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (preceded by) - -AnnotationAssertion( "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."@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (precedes) - -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "precedes"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (has_specified_input) AnnotationAssertion( "The inverse property of is_specified_input_of"@en) AnnotationAssertion(rdfs:label "has_specified_input"@en) -EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_input_of) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) AnnotationAssertion(rdfs:label "is_specified_input_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (has_specified_output) AnnotationAssertion( "The inverse property of is_specified_output_of"@en) AnnotationAssertion(rdfs:label "has_specified_output"@en) -EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_output_of) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion(rdfs:label "is_specified_output_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (achieves_planned_objective) AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") AnnotationAssertion(rdfs:label "achieves_planned_objective") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (objective_achieved_by) + +AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion(rdfs:label "objective_achieved_by") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) # Object Property: (characteristic of) @@ -431,21 +297,6 @@ AnnotationAssertion(rdfs:label "conc ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (function of) - -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (quality of) - -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - # Object Property: (role of) AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) @@ -453,21 +304,6 @@ AnnotationAssertion(rdfs:label "role SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (has function) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has quality) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - # Object Property: (has role) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) @@ -476,101 +312,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulated by) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - # Object Property: (in register with) AnnotationAssertion(Annotation( ) "A relationship that holds between two images, A and B, where: @@ -588,25 +329,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (ends after) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ends after"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately preceded by) - -AnnotationAssertion(rdfs:label "immediately preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately precedes) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately precedes"@en) -SubObjectPropertyOf( ) - # Object Property: (overlaps) AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") @@ -634,116 +356,12 @@ ObjectPropertyDomain( ObjectUnionOf( )) ObjectPropertyRange( ) -# Object Property: (regulates) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (positively regulates) - -AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (capable of) - -AnnotationAssertion( "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. ") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of part of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "capable of part of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (temporally related to) - -AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "temporally related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has input) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has input"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (acts upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within") -SubObjectPropertyOf( ) - # Object Property: (expresses) AnnotationAssertion( "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") AnnotationAssertion(rdfs:label "expresses"@en) SubObjectPropertyOf( ) -# Object Property: (causally upstream of, positive effect) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, negative effect) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (characteristic of part of) AnnotationAssertion( "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.") @@ -755,25 +373,6 @@ SubObjectPropertyOf( "A mereological relationship or a topological relationship") AnnotationAssertion(rdfs:label "mereotopologically related to"@en) -# Object Property: (enables) - -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enables"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (functionally related to) - -AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion(rdfs:label "functionally related to"@en) - -# Object Property: (part of structure that is capable of) - -AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) -SubObjectPropertyOf( ) - # Object Property: (genomically related to) AnnotationAssertion( "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.") @@ -781,45 +380,6 @@ AnnotationAssertion(rdfs:label "geno ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion(rdfs:label "involved in"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulated by) - -AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulated by"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulated by) - -AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (positively regulated by) - -AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulated by"@en) -SubObjectPropertyOf( ) - # Object Property: (member of) AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") @@ -832,367 +392,11 @@ InverseObjectProperties( "has member is a mereological relation between a collection and an item.") AnnotationAssertion(rdfs:label "has member"@en) SubObjectPropertyOf( ) -IrreflexiveObjectProperty() - -# Object Property: (input of) - -AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "input of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally downstream of) - -AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion(rdfs:label "causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately causally downstream of) - -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (causally related to) - -AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "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.") -AnnotationAssertion(rdfs:label "causally related to"@en) - -# Object Property: (causally upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "causally upstream of or within") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (causally downstream of or within) - -AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of or within") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interacts with") -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "molecularly interacts with") -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - -# Object Property: (is kinase activity) - -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - -# Object Property: (causal agent in process) - -AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion(rdfs:label "causal agent in process") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (causal relation between processes) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "causal relation between processes") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (depends on) AnnotationAssertion(rdfs:label "depends on") -# Object Property: (causal relation between entities) - -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (causally influenced by) - -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion(rdfs:label "interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (causally influences) - -AnnotationAssertion( "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).") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has part structure that is capable of) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "has part structure that is capable of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causal relation between material entity and a process) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "causal relation between material entity and a process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion(rdfs:label "capable of regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of negatively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion(rdfs:label "capable of negatively regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of positively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion(rdfs:label "capable of positively regulating") -SubObjectPropertyOf( ) - -# Object Property: (process has causal agent) - -AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion(rdfs:label "process has causal agent") -SubObjectPropertyOf( ) - -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly positively regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly negatively regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (realized in response to stimulus) - -AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "realized in response to stimulus") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -SubObjectPropertyOf( ) - -# Object Property: (realized in response to) - -AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") -AnnotationAssertion(rdfs:label "realized in response to"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (generically depends on) AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") @@ -1208,142 +412,64 @@ AnnotationAssertion(rdfs:label "is c ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (regulates activity of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (device utilizes material) - -AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "device utilizes material"@en) - -# Object Property: (regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) - ############################ # Classes ############################ +# Class: (entity) + +AnnotationAssertion(rdfs:label "entity"@en) + # Class: (continuant) -AnnotationAssertion( "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."@en) AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ) DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) # Class: (occurrent) -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) # Class: (independent continuant) -AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:label "independent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) DisjointClasses( ) # Class: (process) -AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - # Class: (realizable entity) -AnnotationAssertion( "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."@en) AnnotationAssertion(rdfs:label "realizable entity"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) # Class: (specifically dependent continuant) -AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) # Class: (role) -AnnotationAssertion( "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."@en) AnnotationAssertion(rdfs:label "role"@en) SubClassOf( ) # Class: (generically dependent continuant) -AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) AnnotationAssertion(rdfs:label "generically dependent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) # Class: (material entity) -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) AnnotationAssertion(rdfs:label "material entity"@en) SubClassOf( ) DisjointClasses( ) @@ -1566,15 +692,6 @@ AnnotationAssertion(rdfs:label "a EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) - -# Class: () - -DisjointClasses( ) - -# Class: () - -SubClassOf( ObjectHasSelf()) # Class: (planned process) @@ -1620,83 +737,16 @@ EquivalentClasses( ObjectIntersectio SubClassOf( ) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) DisjointClasses( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index c745bd7..79107ac 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -1,14 +1,13 @@ ?cls ?def ?xrefs "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." - "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."@en "A objective specification to obtain a material entity for potential use as an input during an investigation." "An individual member of a clade of cellular organisms." "An anatomical structure that has more than one cell as a part." "Anatomical entity that has no mass." "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " + "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." - "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en @@ -19,47 +18,42 @@ "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." "An anatomical structure that has no cells or cell parts as a part." + "An anatomical entity that has mass." - "An entity that has temporal parts and that happens, unfolds or develops through time."@en + "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." "CL:0000000 GO:0005623" - "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])"@en - "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." - "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."@en - "Anatomical entity which is part_of Drosophila melanogaster." "UBERON:0001062" "A material entity that has two or more specimens as its parts."@en + + "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." - + "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." "A planned process with the objective of collecting a specimen." "An anatomical structure consisting of one or more cells." - "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."@en "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." - "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])"@en "Anatomical structure that has multiple cells as parts." "UBERON:0010000" "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." - "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])"@en - "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." "UBERON:0000061 CARO:0000003" - + - + + + "A material entity that has the specimen role."@en "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." - "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en "UBERON:0000465 CARO:0000006" - diff --git a/src/ontology/reports/class-count-by-prefix.tsv b/src/ontology/reports/class-count-by-prefix.tsv new file mode 100644 index 0000000..5d78978 --- /dev/null +++ b/src/ontology/reports/class-count-by-prefix.tsv @@ -0,0 +1,13 @@ +?prefix ?numberOfClasses +"OBI" 6 +"CARO" 20 +"FBbt" 4 +"IAO" 2 +"BFO" 11 +"fbbt/vfb/VFBext" 5 +"NCBITaxon" 1 +"fbbt/vfb/VFB" 1 +"SO" 1 +"UBERON" 1 +"PATO" 5 +"" 1 diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv index 3805936..9df4352 100644 --- a/src/ontology/reports/edges.tsv +++ b/src/ontology/reports/edges.tsv @@ -1,29 +1,28 @@ ?x ?p ?y - - - - - + + + - + _:Bdc27f7d2X2D59cfX2D47b2X2Db233X2De06e1623c4a4genid103 + - - _:Bb1c3f966X2D3bfaX2D40deX2Da782X2Df38093fb7481genid218 + + + - _:Bb1c3f966X2D3bfaX2D40deX2Da782X2Df38093fb7481genid176 + - @@ -35,9 +34,7 @@ - - @@ -51,9 +48,11 @@ + _:Bdc27f7d2X2D59cfX2D47b2X2Db233X2De06e1623c4a4genid62 + diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv index f31c57a..3d94180 100644 --- a/src/ontology/reports/synonyms.tsv +++ b/src/ontology/reports/synonyms.tsv @@ -12,7 +12,6 @@ "multi-cell-part structure" "specifically dependent continuant"@en "process"@en - "quality"@en "biological entity" "independent continuant"@en "cell" @@ -21,7 +20,6 @@ "cellular anatomical structure"@en "anatomical entity" "immaterial anatomical entity" - "function"@en "anatomical structure" "realizable entity"@en "continuant"@en @@ -37,6 +35,7 @@ "specimen collection process" "cellular organism" "specimen"@en + "entity"@en "planned process"@en "disconnected anatomical group" "material anatomical entity" @@ -46,5 +45,4 @@ "specimen collection objective" "collection of specimens"@en "gross anatomical part"@en - "disposition"@en "multicellular structure" diff --git a/src/ontology/vfbext-odk.yaml b/src/ontology/vfbext-odk.yaml index 013529e..1e85f71 100644 --- a/src/ontology/vfbext-odk.yaml +++ b/src/ontology/vfbext-odk.yaml @@ -28,6 +28,10 @@ import_group: - rdfs:label - IAO:0000115 products: + - id: bfo + make_base: TRUE + base_iris: + - http://purl.obolibrary.org/obo/BFO_ - id: ro use_base: TRUE - id: caro diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql index 0c4d284..a6a4851 100644 --- a/src/sparql/class-count-by-prefix.sparql +++ b/src/sparql/class-count-by-prefix.sparql @@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE FILTER (!isBlank(?cls)) BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) } -GROUP BY ?prefix +GROUP BY ?prefix \ No newline at end of file diff --git a/vfbext-base.json b/vfbext-base.json index beabf2e..4c56480 100644 --- a/vfbext-base.json +++ b/vfbext-base.json @@ -16,32 +16,32 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "26:04:2024 11:54" + "val" : "19:09:2024 09:19" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-26" + "val" : "2024-09-19" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-04-26/vfbext-base.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-09-19/vfbext-base.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", - "lbl" : "cell cluster", + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000001", - "lbl" : "has_channel", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/CARO_0030002", + "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000002", - "lbl" : "has_background_channel", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", + "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000003", - "lbl" : "has_signal_channel", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", + "lbl" : "cell cluster", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", "lbl" : "expression pattern fragment", @@ -56,10 +56,6 @@ "val" : "2018-03-04T10:55:59Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000005", - "lbl" : "source_data_link", - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006", "lbl" : "multi channel image", @@ -78,10 +74,54 @@ "val" : "2018-05-15T15:53:38Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", + "lbl" : "intersectional expression pattern", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:54:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", + "lbl" : "channel", + "type" : "CLASS" + }, { + "id" : "http://xmlns.com/foaf/0.1/image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000001", + "lbl" : "has_channel", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000002", + "lbl" : "has_background_channel", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000003", + "lbl" : "has_signal_channel", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000008", "lbl" : "has hemidriver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.", @@ -99,6 +139,7 @@ "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000009", "lbl" : "has driver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.", @@ -113,22 +154,46 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", - "lbl" : "intersectional expression pattern", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-26T07:54:17Z" - } ] - } + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", - "lbl" : "channel", - "type" : "CLASS" + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000005", + "lbl" : "source_data_link", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", @@ -178,6 +243,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/CARO_0030002" } ] + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000008", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000009", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0030002" ] } ] } ] } \ No newline at end of file diff --git a/vfbext-base.obo b/vfbext-base.obo index c584939..6c1cb68 100644 --- a/vfbext-base.obo +++ b/vfbext-base.obo @@ -1,13 +1,16 @@ format-version: 1.2 -data-version: vfbext/releases/2024-04-26/vfbext-base.owl -date: 26:04:2024 11:54 +data-version: vfbext/releases/2024-09-19/vfbext-base.owl +date: 19:09:2024 09:19 +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: terms http://purl.org/dc/terms/ remark: VFB extension ontology ontology: vfbext/vfbext-base -property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string -property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 -property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2024-04-26" xsd:string +property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string +property_value: dc:title "VFB Extension Ontology" xsd:string +property_value: dc:type IAO:8000001 +property_value: owl:versionInfo "2024-09-19" xsd:string +property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] id: VFB:10000005 @@ -68,6 +71,7 @@ is_a: VFBext:0000001 ! has_channel id: VFBext:0000008 name: has hemidriver def: "A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements." [PMID:17088209] +domain: VFBext:0000010 ! intersectional expression pattern created_by: dos creation_date: 2018-09-26T07:48:55Z @@ -75,6 +79,7 @@ creation_date: 2018-09-26T07:48:55Z id: VFBext:0000009 name: has driver def: "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements." [PMID:8223268, Wikipedia:GAL4/UAS_system] +domain: CARO:0030002 is_a: RO:0002292 created_by: dos creation_date: 2018-09-26T07:49:10Z diff --git a/vfbext-base.owl b/vfbext-base.owl index 435faa7..790572f 100644 --- a/vfbext-base.owl +++ b/vfbext-base.owl @@ -13,14 +13,14 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 26:04:2024 11:54 + 19:09:2024 09:19 VFB extension ontology - 2024-04-26 + 2024-09-19 @@ -150,6 +150,7 @@ + A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements. dos 2018-09-26T07:48:55Z @@ -168,6 +169,7 @@ + A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements. dos 2018-09-26T07:49:10Z @@ -304,5 +306,5 @@ - + diff --git a/vfbext-full.json b/vfbext-full.json index c13fb9e..c321239 100644 --- a/vfbext-full.json +++ b/vfbext-full.json @@ -13,169 +13,60 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "26:04:2024 11:54" + "val" : "19:09:2024 09:19" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-26" + "val" : "2024-09-19" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-04-26/vfbext-full.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-09-19/vfbext-full.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "lbl" : "entity", + "type" : "CLASS" + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "lbl" : "occurrent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "lbl" : "independent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "lbl" : "process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl" : "disposition", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000017", "lbl" : "realizable entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl" : "quality", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "lbl" : "specifically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000031", "lbl" : "generically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl" : "function", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000040", "lbl" : "material entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000054", - "lbl" : "realized in", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000055", - "lbl" : "realizes", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", - "lbl" : "has_exemplar", - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0000000", "lbl" : "anatomical entity", @@ -434,9 +325,14 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000005", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000104", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000011", "lbl" : "planned process", @@ -455,51 +351,6 @@ "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" } } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000293", - "lbl" : "has_specified_input", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_input_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000295", - "lbl" : "is_specified_input_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000299", - "lbl" : "has_specified_output", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_output_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000312", - "lbl" : "is_specified_output_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000417", - "lbl" : "achieves_planned_objective", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." - } - } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000659", "lbl" : "specimen collection process", @@ -537,281 +388,268 @@ } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "id" : "http://purl.obolibrary.org/obo/PATO_0000125", + "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PATO_0001993", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0002266", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0010000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0010001", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000110", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", + "lbl" : "cell cluster", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", + "lbl" : "expression pattern fragment", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Inverse of characteristic_of" - } + "comments" : [ "A multicellular structure that is part of an expression pattern." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-04T10:55:59Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006", + "lbl" : "multi channel image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007", + "lbl" : "template image", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" - } + "comments" : [ "A single channel image that is used as a template for image registration." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-15T15:53:38Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", + "lbl" : "intersectional expression pattern", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:54:17Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000058", - "lbl" : "is concretized as", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", + "lbl" : "channel", + "type" : "CLASS" + }, { + "id" : "http://xmlns.com/foaf/0.1/image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." - } + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000059", - "lbl" : "concretizes", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." - } + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000079", - "lbl" : "function of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" - } - } + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000081", - "lbl" : "role of", + "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", + "lbl" : "has_exemplar", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000085", - "lbl" : "has function", + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "lbl" : "has_specified_input", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + "val" : "The inverse property of is_specified_input_of" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "lbl" : "is_specified_input_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000087", - "lbl" : "has role", + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "lbl" : "has_specified_output", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + "val" : "The inverse property of is_specified_output_of" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000091", - "lbl" : "has disposition", + "id" : "http://purl.obolibrary.org/obo/OBI_0000312", + "lbl" : "is_specified_output_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000092", - "lbl" : "disposition of", + "id" : "http://purl.obolibrary.org/obo/OBI_0000417", + "lbl" : "achieves_planned_objective", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "inverse of has disposition" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002013", - "lbl" : "has regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/OBI_0000833", + "lbl" : "objective_achieved_by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" - } ] + "val" : "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", - "lbl" : "has negative regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:01Z" - } ] + "val" : "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." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002015", - "lbl" : "has positive regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:17Z" - } ] + "val" : "Inverse of characteristic_of" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002017", - "lbl" : "has component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:44:33Z" - } ] + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002018", - "lbl" : "has component process", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:49:21Z" + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", - "lbl" : "directly regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:24Z" - } ] + "definition" : { + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002023", - "lbl" : "directly negatively regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:38Z" - } ] + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002024", - "lbl" : "directly positively regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:47Z" - } ] + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002025", - "lbl" : "has effector activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-22T14:14:36Z" - } ] + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002026", "lbl" : "in register with", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", @@ -825,28 +663,11 @@ "val" : "2017-12-07T12:58:06Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002086", - "lbl" : "ends after", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", - "lbl" : "immediately preceded by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002090", - "lbl" : "immediately precedes", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002131", "lbl" : "overlaps", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" @@ -857,6 +678,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002180", "lbl" : "has component", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -867,1752 +689,641 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002206", "lbl" : "expressed in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "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." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "A mereological relationship or a topological relationship" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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. " - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable of part of", + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "is member of is a mereological relation between a item and a collection." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", - "lbl" : "has input", + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "val" : "has member is a mereological relation between a collection and an item." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002263", - "lbl" : "acts upstream of", + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002264", - "lbl" : "acts upstream of or within", + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002292", - "lbl" : "expresses", + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "lbl" : "is carrier of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002304", - "lbl" : "causally upstream of, positive effect", + "id" : "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", + "lbl" : "exemplar_of", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", - "lbl" : "causally upstream of, negative effect", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000001", + "lbl" : "has_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002314", - "lbl" : "characteristic of part of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000002", + "lbl" : "has_background_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002323", - "lbl" : "mereotopologically related to", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000003", + "lbl" : "has_signal_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A mereological relationship or a topological relationship" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002327", - "lbl" : "enables", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000008", + "lbl" : "has hemidriver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "c enables p iff c is capable of p and c acts to execute p." + "val" : "A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.", + "xrefs" : [ "PMID:17088209" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002328", - "lbl" : "functionally related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - } + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:48:55Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002329", - "lbl" : "part of structure that is capable of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000009", + "lbl" : "has driver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - } + "val" : "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.", + "xrefs" : [ "PMID:8223268", "Wikipedia:GAL4/UAS_system" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:49:10Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002330", - "lbl" : "genomically related to", + "id" : "http://xmlns.com/foaf/0.1/depicts", + "lbl" : "depicts", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - } - } + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002331", - "lbl" : "involved in", + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + "val" : "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." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002333", - "lbl" : "enabled by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of enables" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002334", - "lbl" : "regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002335", - "lbl" : "negatively regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of negatively regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002336", - "lbl" : "positively regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of positively regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002350", - "lbl" : "member of", + "id" : "http://purl.obolibrary.org/obo/caro#core", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "is member of is a mereological relation between a item and a collection." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002351", - "lbl" : "has member", + "id" : "http://purl.obolibrary.org/obo/caro#plus", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "has member is a mereological relation between a collection and an item." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002352", - "lbl" : "input of", + "id" : "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of has input" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", - "lbl" : "causally downstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt#cur", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of upstream of" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002405", - "lbl" : "immediately causally downstream of", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/fbbt#larval_OF", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002407", - "lbl" : "indirectly positively regulates", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#clone", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002409", - "lbl" : "indirectly negatively regulates", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#neuron", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", - "lbl" : "causally related to", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#ns_part", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#synaptic_neuropil", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002412", - "lbl" : "immediately causally upstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#tract", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" }, { - 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"meta" : { - "definition" : { - "val" : "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" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002434", - "lbl" : "interacts with", + "id" : "http://purl.org/dc/terms/references", + "lbl" : "has_reference", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002436", - "lbl" : "molecularly interacts with", + "id" : "http://purl.org/dc/terms/source", + "lbl" : "has_source", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. 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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)." - } - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002578", - "lbl" : "directly regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000141", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002584", - "lbl" : "has part structure that is capable of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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" - } - } + "sub" : "http://purl.obolibrary.org/obo/CARO_0000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0030000" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002595", - "lbl" : "causal relation between material entity and a process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - 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}, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002212" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004034", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002304" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004035", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002305" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002263", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002233" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002264", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002418" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002450", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002449", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004033", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004046" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004032", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004047" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002331", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002212" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] } ] } ] } \ No newline at end of file diff --git a/vfbext-full.obo b/vfbext-full.obo index 0d725e5..34a28b1 100644 --- a/vfbext-full.obo +++ b/vfbext-full.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-04-26/vfbext-full.owl -date: 26:04:2024 11:54 +data-version: vfbext/releases/2024-09-19/vfbext-full.owl +date: 19:09:2024 09:19 subsetdef: clone "" subsetdef: core "" subsetdef: cur "" @@ -14,94 +14,70 @@ subsetdef: neuron "" subsetdef: ns_part "" subsetdef: plus "" subsetdef: ro-eco "" -subsetdef: RO:0002259 "" subsetdef: synaptic_neuropil "" subsetdef: tract "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: terms http://purl.org/dc/terms/ remark: VFB extension ontology ontology: vfbext/vfbext-full -property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string -property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2024-04-26" xsd:string +property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string +property_value: dc:title "VFB Extension Ontology" xsd:string +property_value: owl:versionInfo "2024-09-19" xsd:string +property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string + +[Term] +id: BFO:0000001 +name: entity [Term] id: BFO:0000002 name: continuant -def: "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." [] +is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant [Term] id: BFO:0000003 name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent +is_a: BFO:0000001 ! entity [Term] id: BFO:0000004 name: independent continuant -def: "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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000015 name: process -def: "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])" [] is_a: BFO:0000003 ! occurrent -[Term] -id: BFO:0000016 -name: disposition -is_a: BFO:0000017 ! realizable entity -disjoint_from: BFO:0000023 ! role - [Term] id: BFO:0000017 name: realizable entity -def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000019 ! quality -relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity - -[Term] -id: BFO:0000019 -name: quality -is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 name: specifically dependent continuant -def: "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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 name: role -def: "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." [] is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 name: generically dependent continuant -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant - -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition [Term] id: BFO:0000040 name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity @@ -329,16 +305,8 @@ xref: UBERON:0001062 is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity intersection_of: BFO:0000050 NCBITaxon:7227 ! part of -disjoint_from: PATO:0000001 relationship: BFO:0000050 NCBITaxon:7227 ! part of -[Term] -id: GO:0008150 -disjoint_from: OBI:0000011 ! planned process - -[Term] -id: GO:0016301 - [Term] id: OBI:0000011 name: planned process @@ -408,7 +376,7 @@ creation_date: 2018-03-04T10:55:59Z [Term] id: VFBext:0000006 name: multi channel image -is_a: http://xmlns.com/foaf/0.1/image +is_a: foaf:image [Term] id: VFBext:0000007 @@ -428,7 +396,7 @@ creation_date: 2018-09-26T07:54:17Z [Term] id: VFBext:0000014 name: channel -is_a: http://xmlns.com/foaf/0.1/image +is_a: foaf:image [Typedef] id: BFO:0000050 @@ -465,58 +433,50 @@ name: realizes domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity -[Typedef] -id: BFO:0000062 -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 -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -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 -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - [Typedef] id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] +domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is_specified_input_of [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] +domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] +domain: OBI:0000011 ! planned process +range: IAO:0000005 +inverse_of: OBI:0000833 ! objective_achieved_by + +[Typedef] +id: OBI:0000833 +name: objective_achieved_by +def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] +domain: IAO:0000005 +range: OBI:0000011 ! planned process [Typedef] id: RO:0000052 @@ -545,7 +505,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -565,21 +525,6 @@ def: "A relationship between a specifically dependent continuant and a generical domain: BFO:0000020 ! specifically dependent continuant range: BFO:0000031 ! generically dependent continuant -[Typedef] -id: RO:0000079 -name: function of -def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] -domain: BFO:0000034 ! function -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000085 ! has function - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000086 ! has quality - [Typedef] id: RO:0000081 name: role of @@ -587,21 +532,6 @@ def: "a relation between a role and an independent continuant (the bearer), in w is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role -[Typedef] -id: RO:0000085 -name: has function -def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000034 ! function -is_a: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -range: BFO:0000019 ! quality -is_a: RO:0000053 ! has characteristic - [Typedef] id: RO:0000087 name: has role @@ -610,130 +540,16 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! has characteristic -[Typedef] -id: RO:0000091 -name: has disposition -def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000016 ! disposition -is_a: RO:0000053 ! has characteristic -inverse_of: RO:0000092 ! disposition of - -[Typedef] -id: RO:0000092 -name: disposition of -def: "inverse of has disposition" [] -subset: RO:0002259 -is_a: RO:0000052 ! characteristic of - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "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." [] -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "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." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "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." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -is_a: RO:0002018 ! has component process -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "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." [] -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:49:21Z - -[Typedef] -id: RO:0002022 -name: directly regulated by -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:24Z - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:38Z - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:47Z - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_functional: true -is_a: RO:0002017 ! has component activity -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002026 name: in register with def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] -domain: http://xmlns.com/foaf/0.1/image -range: http://xmlns.com/foaf/0.1/image +domain: foaf:image +range: foaf:image is_a: RO:0002323 ! mereotopologically related to created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z -[Typedef] -id: RO:0002086 -name: ends after -subset: ro-eco -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002090 -name: immediately precedes -subset: ro-eco -is_a: BFO:0000063 ! precedes - [Typedef] id: RO:0002131 name: overlaps @@ -765,122 +581,12 @@ is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of -[Typedef] -id: RO:0002211 -name: regulates -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by -transitive_over: RO:0002025 ! has effector activity - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -holds_over_chain: RO:0002212 RO:0002212 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002215 -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 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: RO:0002216 ! capable of part of - -[Typedef] -id: RO:0002216 -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." [] -holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002222 -name: temporally related to -subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent - -[Typedef] -id: RO:0002233 -name: has input -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -domain: BFO:0000015 ! process -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - [Typedef] id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] is_a: RO:0002330 ! genomically related to -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - [Typedef] id: RO:0002314 name: characteristic of part of @@ -894,28 +600,6 @@ id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -[Typedef] -id: RO:0002327 -name: enables -def: "c enables p iff c is capable of p and c acts to execute p." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] - -[Typedef] -id: RO:0002329 -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." [] -holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002330 name: genomically related to @@ -923,47 +607,6 @@ def: "holds between two entities when some genome-level process such as gene exp domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0000056 ! participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -subset: RO:0002259 -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -subset: RO:0002259 -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -subset: RO:0002259 -is_a: RO:0002334 ! regulated by - [Typedef] id: RO:0002350 name: member of @@ -977,385 +620,10 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] is_a: BFO:0000051 ! has part -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002407 -name: indirectly positively regulates -def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -holds_over_chain: RO:0002409 RO:0002409 -holds_over_chain: RO:0002629 RO:0002407 -holds_over_chain: RO:0002629 RO:0002629 -is_transitive: true -is_a: RO:0002213 ! positively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002409 -name: indirectly negatively regulates -def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -holds_over_chain: RO:0002630 RO:0002409 -holds_over_chain: RO:0002630 RO:0002630 -is_transitive: true -is_a: RO:0002212 ! negatively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002410 -name: causally related to -def: "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." [https://en.wikipedia.org/wiki/Causality] - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "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." [] -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "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." [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -subset: RO:0002259 -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -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" [] -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002434 -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 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_symmetric: true - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "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." [] -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: directly regulates activity of -def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0011002 ! regulates activity of - -[Typedef] -id: RO:0002449 -name: directly negatively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002450 -name: directly positively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) - -[Typedef] -id: RO:0002481 -name: is kinase activity -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -is_a: RO:0002410 ! causally related to - [Typedef] id: RO:0002502 name: depends on -[Typedef] -id: RO:0002506 -name: causal relation between entities -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002559 -name: causally influenced by -is_a: RO:0002506 ! causal relation between entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002566 -name: causally influences -def: "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)." [] -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002506 ! causal relation between entities - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002584 -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" [] -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002595 -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." [] -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -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." [] -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -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." [] -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -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." [] -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0004028 -name: realized in response to stimulus -def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000040 ! material entity -holds_over_chain: RO:0009501 RO:0002233 -is_a: RO:0002410 ! causally related to -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2017-12-26T19:45:49Z - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-25T23:20:13Z - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:49:30Z - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:49:51Z - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "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" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:53:14Z - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "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" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:53:22Z - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -is_a: RO:0002418 ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-03-13T23:55:05Z - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -is_a: RO:0002418 ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-03-13T23:55:19Z - -[Typedef] -id: RO:0009501 -name: realized in response to -def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process -holds_over_chain: BFO:0000054 RO:0002404 -is_a: RO:0002410 ! causally related to - [Typedef] id: RO:0010001 name: generically depends on @@ -1373,62 +641,6 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000031 ! generically dependent continuant holds_over_chain: RO:0000059 RO:0000053 -[Typedef] -id: RO:0011002 -name: regulates activity of -def: "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." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0012011 -name: indirectly causally upstream of -def: "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." [] -is_a: RO:0002411 ! causally upstream of -created_by: https://orcid.org/0000-0003-1813-6857 -creation_date: 2022-09-26T06:07:17Z - -[Typedef] -id: RO:0012012 -name: indirectly regulates -def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] -is_a: RO:0002211 ! regulates -is_a: RO:0012011 ! indirectly causally upstream of -created_by: https://orcid.org/0000-0003-1813-6857 -creation_date: 2022-09-26T06:08:01Z - -[Typedef] -id: RO:0017001 -name: device utilizes material -def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -holds_over_chain: RO:0002215 RO:0002233 -creation_date: 2021-11-08T12:00:00Z - -[Typedef] -id: RO:0019000 -name: regulates characteristic -def: "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." [] -domain: BFO:0000015 ! process -range: PATO:0000001 -holds_over_chain: RO:0002211 RO:0019000 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0019001 -name: positively regulates characteristic -def: "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." [] -holds_over_chain: RO:0002213 RO:0019001 -is_a: RO:0019000 ! regulates characteristic - -[Typedef] -id: RO:0019002 -name: negatively regulates characteristic -def: "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." [] -holds_over_chain: RO:0002212 RO:0019001 -holds_over_chain: RO:0002213 RO:0019002 -is_a: RO:0019000 ! regulates characteristic - [Typedef] id: VFBext:0000001 name: has_channel @@ -1460,6 +672,10 @@ is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z +[Typedef] +id: foaf:depicts +name: depicts + [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -1469,7 +685,3 @@ id: http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0 name: exemplar_of is_a: RO:0002350 ! member of -[Typedef] -id: http://xmlns.com/foaf/0.1/depicts -name: depicts - diff --git a/vfbext-full.owl b/vfbext-full.owl index dd9ab7d..e9995f8 100644 --- a/vfbext-full.owl +++ b/vfbext-full.owl @@ -12,20 +12,18 @@ xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:vfb2="http://purl.obolibrary.org/obo/fbbt/vfb#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 26:04:2024 11:54 + 19:09:2024 09:19 VFB extension ontology - 2024-04-26 + 2024-09-19 @@ -43,26 +41,13 @@ - - definition - - - - - - - - - + - + - - 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 - + @@ -203,27 +188,21 @@ - - - - + - - - - + - + - + - + - + @@ -251,17 +230,9 @@ - - - - - - - - subset_property - + @@ -285,29 +256,25 @@ - - database_cross_reference - + - - in_subset - + - + - + - + - + @@ -373,44 +340,6 @@ - - - - - - - - - - - - - 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. - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - 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. - - precedes - - - - @@ -422,12 +351,9 @@ - - - - - + + The inverse property of is_specified_input_of has_specified_input @@ -438,6 +364,7 @@ + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. is_specified_input_of @@ -447,12 +374,9 @@ - - - - - + + The inverse property of is_specified_output_of has_specified_output @@ -463,6 +387,7 @@ + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. is_specified_output_of @@ -472,12 +397,26 @@ + + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. achieves_planned_objective + + + + + + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + objective_achieved_by + + + + @@ -557,29 +496,6 @@ - - - - - - - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - function of - - - - - - - - - - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - quality of - - - - @@ -591,29 +507,6 @@ - - - - - - - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - has function - - - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - has quality - - - - @@ -626,163 +519,6 @@ - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - disposition of - - - - - - - - - - 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. - - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - 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. - - 2017-05-24T09:31:01Z - has negative regulatory component activity - - - - - - - - - - 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. - - 2017-05-24T09:31:17Z - has positive regulatory component activity - - - - - - - - - - 2017-05-24T09:44:33Z - has component activity - - - - - - - - - - - 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. - - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - - 2017-09-17T13:52:24Z - directly regulated by - - - - - - - - - - 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. - - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - 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. - - - - - - - - - - - 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. - - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - 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. - - - - - - - - - - - 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. - - 2017-09-22T14:14:36Z - has effector activity - - - - - 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. - - - - - @@ -817,37 +553,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - ends after - - - - - - - - - - immediately preceded by - - - - - - - - - - immediately precedes - - - - @@ -923,1059 +628,88 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - - 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. - - - - regulates - - - - - - - - - - - p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - - negatively regulates - - - - - - - - - - - - - - - - p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - - positively regulates - - - - - + - - - - - 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 + + + y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. + expresses - + - - - + + - + - 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. - capable of part of - - - - - - - - - true - - - - - - - - - - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - temporally related to - - - - - - - - - - - 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 input - - - - - - - - - - - - - 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 - - - - - - - - - - - - - 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. - - acts upstream of or within - - - - - - - - - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses - - - - - - - - - - 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, positive effect - - - - - - - - - - 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. - - - causally upstream of, negative effect - - - - - - - - - - - - - - - - - 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. - characteristic of part of - - - - - - - - - true - - - - - - - - A mereological relationship or a topological relationship - mereotopologically related to - - - - - - - - - - - - - - - - - - c enables p iff c is capable of p and c acts to execute p. - - enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - genomically related to - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - involved in - - - - - - - - - - inverse of enables - - enabled by - - - - - - - - - - - - inverse of regulates - - regulated by - - - - - - - - - inverse of negatively regulates - - negatively regulated by - - - - - - - - - inverse of positively regulates - - positively regulated by - - - - - - - - - - is member of is a mereological relation between a item and a collection. - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - has member - - - - - - - - - - inverse of has input - - - input of - - - - - - - - - - - inverse of upstream of - causally downstream of - - - - - - - - - - - immediately causally downstream of - - - - - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - indirectly positively regulates - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - indirectly negatively regulates - - - - - - - - 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. - causally related to - - - - - 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. - https://en.wikipedia.org/wiki/Causality - - - - - - - - - - - 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. - - - causally upstream of - - - - - - - - - - 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. - immediately causally upstream of - - - - - - - - - - - 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. - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of - - - - - - - - - - - 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 - involved in or involved in regulation of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - - interacts with - - - - - - - - - - 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. - molecularly interacts with - - - - - - - - - phosphorylates - - - - - - - - - - - - - - - - - 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. - directly regulates activity of - - - - - - - - - - - - - - - - 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. - directly negatively regulates activity of - - - - - - - - - - - - - - - - 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. - directly positively regulates activity of - - - - - - - - helper property (not for use in curation) - - - - - - - - - is kinase activity - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process - - - - - - - - - - - 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. - causal relation between processes - - - - - - - - depends on - - - - - - - - - - - causal relation between entities - - - - - - - - - - causally influenced by - - - - - - - - - interaction relation helper property - - - - - - - - - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - - - 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). - causally influences - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - - directly regulates - - - - - - - - - - - - - - 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 - has part structure that is capable of - - - - - - - - - - - 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. - causal relation between material entity and a process - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - process has causal agent - - - - - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - - - directly positively regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - - - directly negatively regulates - - - - - - - - - - - - - - - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - 2017-12-26T19:45:49Z - realized in response to stimulus - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - - 2018-01-25T23:20:13Z - enables subfunction - - - - - - - - - - - - - - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - - - - - - - - - - + + - - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect + 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. + characteristic of part of + + + + + + + + true + - + - - - - - - - - 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 - - 2018-01-26T23:53:14Z - - acts upstream of, positive effect + + A mereological relationship or a topological relationship + mereotopologically related to - + - - - - - - - - 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 - - 2018-01-26T23:53:22Z - - acts upstream of, negative effect + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + genomically related to - + - - - - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect + + + + is member of is a mereological relation between a item and a collection. + member of - + - - - - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect + + + has member is a mereological relation between a collection and an item. + has member - + - - - - - - - - - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - realized in response to + + depends on @@ -2011,105 +745,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - 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. - regulates activity of - - - - - - - - - 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. - - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - - 2022-09-26T06:08:01Z - indirectly regulates - - - - - - - - - - - - X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - 2021-11-08T12:00:00Z - device utilizes material - - - - - - - - - - - - - - - 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. - regulates characteristic - - - - - - - - - - - - - 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. - positively regulates characteristic - - - - - - - - - - - - - - - - - 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. - negatively regulates characteristic - - - - @@ -2202,15 +837,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + entity + + + + - - - - - - + @@ -2218,7 +856,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. continuant @@ -2227,19 +864,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - + - An entity that has temporal parts and that happens, unfolds or develops through time. occurrent @@ -2249,15 +880,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - 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]) independent continuant @@ -2267,66 +891,25 @@ For example, A and B may be gene products and binding of B by A positively regul - 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]) process - - - - - - disposition - - - - - - - - - - - - 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. realizable entity - - - - - - - - - - - quality - - - - - - - - - - - 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]) specifically dependent continuant @@ -2336,7 +919,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. role @@ -2346,27 +928,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) generically dependent continuant - - - - - function - - - - @@ -2378,7 +944,6 @@ For example, A and B may be gene products and binding of B by A positively regul - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity @@ -2777,14 +1342,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure - + @@ -2796,7 +1361,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell @@ -2900,7 +1465,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Anatomical entity which is part_of Drosophila melanogaster. UBERON:0001062 @@ -2917,33 +1481,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - true - - - - - - @@ -3117,12 +1654,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3260,39 +1791,6 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -3301,1006 +1799,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/vfbext-non-classified.json b/vfbext-non-classified.json index ba7c4a7..e5b5dd5 100644 --- a/vfbext-non-classified.json +++ b/vfbext-non-classified.json @@ -13,169 +13,60 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "26:04:2024 11:54" + "val" : "19:09:2024 09:19" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-26" + "val" : "2024-09-19" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-04-26/vfbext-non-classified.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-09-19/vfbext-non-classified.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "lbl" : "entity", + "type" : "CLASS" + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "lbl" : "occurrent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "lbl" : "independent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "lbl" : "process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl" : "disposition", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000017", "lbl" : "realizable entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl" : "quality", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "lbl" : "specifically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000031", "lbl" : "generically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl" : "function", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000040", "lbl" : "material entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000054", - "lbl" : "realized in", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000055", - "lbl" : "realizes", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", - "lbl" : "has_exemplar", - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0000000", "lbl" : "anatomical entity", @@ -434,9 +325,14 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000005", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000104", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000011", "lbl" : "planned process", @@ -455,51 +351,6 @@ "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" } } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000293", - "lbl" : "has_specified_input", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_input_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000295", - "lbl" : "is_specified_input_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000299", - "lbl" : "has_specified_output", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_output_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000312", - "lbl" : "is_specified_output_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000417", - "lbl" : "achieves_planned_objective", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." - } - } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000659", "lbl" : "specimen collection process", @@ -537,281 +388,268 @@ } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "id" : "http://purl.obolibrary.org/obo/PATO_0000125", + "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PATO_0001993", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0002266", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0010000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0010001", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000110", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", + "lbl" : "cell cluster", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", + "lbl" : "expression pattern fragment", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Inverse of characteristic_of" - } + "comments" : [ "A multicellular structure that is part of an expression pattern." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-04T10:55:59Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006", + "lbl" : "multi channel image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007", + "lbl" : "template image", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" - } + "comments" : [ "A single channel image that is used as a template for image registration." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-15T15:53:38Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", + "lbl" : "intersectional expression pattern", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:54:17Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000058", - "lbl" : "is concretized as", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", + "lbl" : "channel", + "type" : "CLASS" + }, { + "id" : "http://xmlns.com/foaf/0.1/image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." - } + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000059", - "lbl" : "concretizes", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." - } + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000079", - "lbl" : "function of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" - } - } + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000081", - "lbl" : "role of", + "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", + "lbl" : "has_exemplar", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000085", - "lbl" : "has function", + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "lbl" : "has_specified_input", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + "val" : "The inverse property of is_specified_input_of" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "lbl" : "is_specified_input_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000087", - "lbl" : "has role", + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "lbl" : "has_specified_output", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + "val" : "The inverse property of is_specified_output_of" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000091", - "lbl" : "has disposition", + "id" : "http://purl.obolibrary.org/obo/OBI_0000312", + "lbl" : "is_specified_output_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000092", - "lbl" : "disposition of", + "id" : "http://purl.obolibrary.org/obo/OBI_0000417", + "lbl" : "achieves_planned_objective", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "inverse of has disposition" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002013", - "lbl" : "has regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/OBI_0000833", + "lbl" : "objective_achieved_by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" - } ] + "val" : "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", - "lbl" : "has negative regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:01Z" - } ] + "val" : "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." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002015", - "lbl" : "has positive regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:17Z" - } ] + "val" : "Inverse of characteristic_of" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002017", - "lbl" : "has component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:44:33Z" - } ] + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002018", - "lbl" : "has component process", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:49:21Z" + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", - "lbl" : "directly regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:24Z" - } ] + "definition" : { + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002023", - "lbl" : "directly negatively regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:38Z" - } ] + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002024", - "lbl" : "directly positively regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:47Z" - } ] + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002025", - "lbl" : "has effector activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-22T14:14:36Z" - } ] + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002026", "lbl" : "in register with", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", @@ -825,28 +663,11 @@ "val" : "2017-12-07T12:58:06Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002086", - "lbl" : "ends after", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", - "lbl" : "immediately preceded by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002090", - "lbl" : "immediately precedes", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002131", "lbl" : "overlaps", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" @@ -857,6 +678,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002180", "lbl" : "has component", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -867,1736 +689,625 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002206", "lbl" : "expressed in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "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." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "A mereological relationship or a topological relationship" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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. " - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable of part of", + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "is member of is a mereological relation between a item and a collection." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", - "lbl" : "has input", + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "val" : "has member is a mereological relation between a collection and an item." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002263", - "lbl" : "acts upstream of", + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002264", - "lbl" : "acts upstream of or within", + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002292", - "lbl" : "expresses", + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "lbl" : "is carrier of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002304", - "lbl" : "causally upstream of, positive effect", + "id" : "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", + "lbl" : "exemplar_of", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", - "lbl" : "causally upstream of, negative effect", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000001", + "lbl" : "has_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002314", - "lbl" : "characteristic of part of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000002", + "lbl" : "has_background_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002323", - "lbl" : "mereotopologically related to", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000003", + "lbl" : "has_signal_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A mereological relationship or a topological relationship" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002327", - "lbl" : "enables", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000008", + "lbl" : "has hemidriver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "c enables p iff c is capable of p and c acts to execute p." + "val" : "A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.", + "xrefs" : [ "PMID:17088209" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002328", - "lbl" : "functionally related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - } + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:48:55Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002329", - "lbl" : "part of structure that is capable of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000009", + "lbl" : "has driver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - } + "val" : "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.", + "xrefs" : [ "PMID:8223268", "Wikipedia:GAL4/UAS_system" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:49:10Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002330", - "lbl" : "genomically related to", + "id" : "http://xmlns.com/foaf/0.1/depicts", + "lbl" : "depicts", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - } - } + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002331", - "lbl" : "involved in", + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + "val" : "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." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002333", - "lbl" : "enabled by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of enables" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002334", - "lbl" : "regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002335", - "lbl" : "negatively regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of negatively regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002336", - "lbl" : "positively regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of positively regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002350", - "lbl" : "member of", + "id" : "http://purl.obolibrary.org/obo/caro#core", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "is member of is a mereological relation between a item and a collection." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002351", - "lbl" : "has member", + "id" : "http://purl.obolibrary.org/obo/caro#plus", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "has member is a mereological relation between a collection and an item." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002352", - "lbl" : "input of", + "id" : "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of has input" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", - "lbl" : "causally downstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt#cur", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of upstream of" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002405", - "lbl" : "immediately causally downstream of", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/fbbt#larval_OF", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002407", - "lbl" : "indirectly positively regulates", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#clone", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002409", - "lbl" : "indirectly negatively regulates", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#neuron", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", - "lbl" : "causally related to", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#ns_part", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#synaptic_neuropil", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002412", - "lbl" : "immediately causally upstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#tract", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002418", - "lbl" : "causally upstream of or within", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000005", + "lbl" : "source_data_link", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002427", - "lbl" : "causally downstream of or within", + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of causally upstream of or within" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", - "lbl" : "involved in regulation of", + "id" : "http://purl.org/dc/elements/1.1/contributor", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002429", - "lbl" : "involved in positive regulation of", + "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002430", - "lbl" : "involved in negative regulation of", + "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", - "lbl" : "involved in or involved in regulation of", + "id" : "http://purl.org/dc/terms/license", + "lbl" : "has_license", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002434", - "lbl" : "interacts with", + "id" : "http://purl.org/dc/terms/references", + "lbl" : "has_reference", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002436", - "lbl" : "molecularly interacts with", + "id" : "http://purl.org/dc/terms/source", + "lbl" : "has_source", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002447", - "lbl" : "phosphorylates", - "type" : "PROPERTY" + "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002448", - "lbl" : "directly regulates activity of", + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. 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"predicateId" : "http://purl.obolibrary.org/obo/BFO_0000063", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] + "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000299", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000417", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000005" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000833", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000005" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -2831,25 +1457,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000059", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0000085", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000087", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002018", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002026", "domainClassIds" : [ "http://xmlns.com/foaf/0.1/image" ], @@ -2858,69 +1469,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] - 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"domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002434", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002448", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002449", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002450", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002501", - 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}, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] } ], "propertyChainAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000062", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000062" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000063", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000063" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -2974,12 +1512,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002131" ] - 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}, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004033", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004046" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004032", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004047" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002331", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002212" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] } ] } ] } \ No newline at end of file diff --git a/vfbext-non-classified.obo b/vfbext-non-classified.obo index 9ad872f..ef8b64a 100644 --- a/vfbext-non-classified.obo +++ b/vfbext-non-classified.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-04-26/vfbext-non-classified.owl -date: 26:04:2024 11:54 +data-version: vfbext/releases/2024-09-19/vfbext-non-classified.owl +date: 19:09:2024 09:19 subsetdef: clone "" subsetdef: core "" subsetdef: cur "" @@ -14,94 +14,70 @@ subsetdef: neuron "" subsetdef: ns_part "" subsetdef: plus "" subsetdef: ro-eco "" -subsetdef: RO:0002259 "" subsetdef: synaptic_neuropil "" subsetdef: tract "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: terms http://purl.org/dc/terms/ remark: VFB extension ontology ontology: vfbext/vfbext-non-classified -property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string -property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2024-04-26" xsd:string +property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string +property_value: dc:title "VFB Extension Ontology" xsd:string +property_value: owl:versionInfo "2024-09-19" xsd:string +property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string + +[Term] +id: BFO:0000001 +name: entity [Term] id: BFO:0000002 name: continuant -def: "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." [] +is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant [Term] id: BFO:0000003 name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent +is_a: BFO:0000001 ! entity [Term] id: BFO:0000004 name: independent continuant -def: "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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000015 name: process -def: "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])" [] is_a: BFO:0000003 ! occurrent -[Term] -id: BFO:0000016 -name: disposition -is_a: BFO:0000017 ! realizable entity -disjoint_from: BFO:0000023 ! role - [Term] id: BFO:0000017 name: realizable entity -def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000019 ! quality -relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity - -[Term] -id: BFO:0000019 -name: quality -is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 name: specifically dependent continuant -def: "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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 name: role -def: "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." [] is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 name: generically dependent continuant -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant - -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition [Term] id: BFO:0000040 name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity @@ -329,16 +305,8 @@ xref: UBERON:0001062 is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity intersection_of: BFO:0000050 NCBITaxon:7227 ! part of -disjoint_from: PATO:0000001 relationship: BFO:0000050 NCBITaxon:7227 ! part of -[Term] -id: GO:0008150 -disjoint_from: OBI:0000011 ! planned process - -[Term] -id: GO:0016301 - [Term] id: OBI:0000011 name: planned process @@ -404,7 +372,7 @@ creation_date: 2018-03-04T10:55:59Z [Term] id: VFBext:0000006 name: multi channel image -is_a: http://xmlns.com/foaf/0.1/image +is_a: foaf:image [Term] id: VFBext:0000007 @@ -424,7 +392,7 @@ creation_date: 2018-09-26T07:54:17Z [Term] id: VFBext:0000014 name: channel -is_a: http://xmlns.com/foaf/0.1/image +is_a: foaf:image [Typedef] id: BFO:0000050 @@ -461,58 +429,50 @@ name: realizes domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity -[Typedef] -id: BFO:0000062 -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 -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -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 -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - [Typedef] id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] +domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is_specified_input_of [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] +domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] +domain: OBI:0000011 ! planned process +range: IAO:0000005 +inverse_of: OBI:0000833 ! objective_achieved_by + +[Typedef] +id: OBI:0000833 +name: objective_achieved_by +def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] +domain: IAO:0000005 +range: OBI:0000011 ! planned process [Typedef] id: RO:0000052 @@ -541,7 +501,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -561,21 +521,6 @@ def: "A relationship between a specifically dependent continuant and a generical domain: BFO:0000020 ! specifically dependent continuant range: BFO:0000031 ! generically dependent continuant -[Typedef] -id: RO:0000079 -name: function of -def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] -domain: BFO:0000034 ! function -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000085 ! has function - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000086 ! has quality - [Typedef] id: RO:0000081 name: role of @@ -583,21 +528,6 @@ def: "a relation between a role and an independent continuant (the bearer), in w is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role -[Typedef] -id: RO:0000085 -name: has function -def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000034 ! function -is_a: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -range: BFO:0000019 ! quality -is_a: RO:0000053 ! has characteristic - [Typedef] id: RO:0000087 name: has role @@ -606,130 +536,16 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! has characteristic -[Typedef] -id: RO:0000091 -name: has disposition -def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000016 ! disposition -is_a: RO:0000053 ! has characteristic -inverse_of: RO:0000092 ! disposition of - -[Typedef] -id: RO:0000092 -name: disposition of -def: "inverse of has disposition" [] -subset: RO:0002259 -is_a: RO:0000052 ! characteristic of - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "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." [] -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "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." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "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." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -is_a: RO:0002018 ! has component process -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "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." [] -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:49:21Z - -[Typedef] -id: RO:0002022 -name: directly regulated by -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:24Z - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:38Z - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:47Z - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_functional: true -is_a: RO:0002017 ! has component activity -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002026 name: in register with def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] -domain: http://xmlns.com/foaf/0.1/image -range: http://xmlns.com/foaf/0.1/image +domain: foaf:image +range: foaf:image is_a: RO:0002323 ! mereotopologically related to created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z -[Typedef] -id: RO:0002086 -name: ends after -subset: ro-eco -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002090 -name: immediately precedes -subset: ro-eco -is_a: BFO:0000063 ! precedes - [Typedef] id: RO:0002131 name: overlaps @@ -761,122 +577,12 @@ is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of -[Typedef] -id: RO:0002211 -name: regulates -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by -transitive_over: RO:0002025 ! has effector activity - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -holds_over_chain: RO:0002212 RO:0002212 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002215 -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 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: RO:0002216 ! capable of part of - -[Typedef] -id: RO:0002216 -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." [] -holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002222 -name: temporally related to -subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent - -[Typedef] -id: RO:0002233 -name: has input -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -domain: BFO:0000015 ! process -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - [Typedef] id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] is_a: RO:0002330 ! genomically related to -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - [Typedef] id: RO:0002314 name: characteristic of part of @@ -890,28 +596,6 @@ id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -[Typedef] -id: RO:0002327 -name: enables -def: "c enables p iff c is capable of p and c acts to execute p." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] - -[Typedef] -id: RO:0002329 -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." [] -holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002330 name: genomically related to @@ -919,47 +603,6 @@ def: "holds between two entities when some genome-level process such as gene exp domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0000056 ! participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -subset: RO:0002259 -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -subset: RO:0002259 -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -subset: RO:0002259 -is_a: RO:0002334 ! regulated by - [Typedef] id: RO:0002350 name: member of @@ -973,385 +616,10 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] is_a: BFO:0000051 ! has part -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002407 -name: indirectly positively regulates -def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -holds_over_chain: RO:0002409 RO:0002409 -holds_over_chain: RO:0002629 RO:0002407 -holds_over_chain: RO:0002629 RO:0002629 -is_transitive: true -is_a: RO:0002213 ! positively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002409 -name: indirectly negatively regulates -def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -holds_over_chain: RO:0002630 RO:0002409 -holds_over_chain: RO:0002630 RO:0002630 -is_transitive: true -is_a: RO:0002212 ! negatively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002410 -name: causally related to -def: "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." [https://en.wikipedia.org/wiki/Causality] - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "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." [] -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "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." [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -subset: RO:0002259 -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -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" [] -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002434 -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 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_symmetric: true - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "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." [] -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: directly regulates activity of -def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0011002 ! regulates activity of - -[Typedef] -id: RO:0002449 -name: directly negatively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002450 -name: directly positively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) - -[Typedef] -id: RO:0002481 -name: is kinase activity -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -is_a: RO:0002410 ! causally related to - [Typedef] id: RO:0002502 name: depends on -[Typedef] -id: RO:0002506 -name: causal relation between entities -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002559 -name: causally influenced by -is_a: RO:0002506 ! causal relation between entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002566 -name: causally influences -def: "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)." [] -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002506 ! causal relation between entities - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002584 -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" [] -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002595 -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." [] -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -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." [] -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -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." [] -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -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." [] -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0004028 -name: realized in response to stimulus -def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000040 ! material entity -holds_over_chain: RO:0009501 RO:0002233 -is_a: RO:0002410 ! causally related to -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2017-12-26T19:45:49Z - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-25T23:20:13Z - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:49:30Z - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:49:51Z - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "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" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:53:14Z - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "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" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:53:22Z - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -is_a: RO:0002418 ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-03-13T23:55:05Z - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -is_a: RO:0002418 ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-03-13T23:55:19Z - -[Typedef] -id: RO:0009501 -name: realized in response to -def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process -holds_over_chain: BFO:0000054 RO:0002404 -is_a: RO:0002410 ! causally related to - [Typedef] id: RO:0010001 name: generically depends on @@ -1369,62 +637,6 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000031 ! generically dependent continuant holds_over_chain: RO:0000059 RO:0000053 -[Typedef] -id: RO:0011002 -name: regulates activity of -def: "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." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0012011 -name: indirectly causally upstream of -def: "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." [] -is_a: RO:0002411 ! causally upstream of -created_by: https://orcid.org/0000-0003-1813-6857 -creation_date: 2022-09-26T06:07:17Z - -[Typedef] -id: RO:0012012 -name: indirectly regulates -def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] -is_a: RO:0002211 ! regulates -is_a: RO:0012011 ! indirectly causally upstream of -created_by: https://orcid.org/0000-0003-1813-6857 -creation_date: 2022-09-26T06:08:01Z - -[Typedef] -id: RO:0017001 -name: device utilizes material -def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -holds_over_chain: RO:0002215 RO:0002233 -creation_date: 2021-11-08T12:00:00Z - -[Typedef] -id: RO:0019000 -name: regulates characteristic -def: "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." [] -domain: BFO:0000015 ! process -range: PATO:0000001 -holds_over_chain: RO:0002211 RO:0019000 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0019001 -name: positively regulates characteristic -def: "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." [] -holds_over_chain: RO:0002213 RO:0019001 -is_a: RO:0019000 ! regulates characteristic - -[Typedef] -id: RO:0019002 -name: negatively regulates characteristic -def: "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." [] -holds_over_chain: RO:0002212 RO:0019001 -holds_over_chain: RO:0002213 RO:0019002 -is_a: RO:0019000 ! regulates characteristic - [Typedef] id: VFBext:0000001 name: has_channel @@ -1456,6 +668,10 @@ is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z +[Typedef] +id: foaf:depicts +name: depicts + [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -1465,7 +681,3 @@ id: http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0 name: exemplar_of is_a: RO:0002350 ! member of -[Typedef] -id: http://xmlns.com/foaf/0.1/depicts -name: depicts - diff --git a/vfbext-non-classified.owl b/vfbext-non-classified.owl index ec66584..8575329 100644 --- a/vfbext-non-classified.owl +++ b/vfbext-non-classified.owl @@ -12,20 +12,18 @@ xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:vfb2="http://purl.obolibrary.org/obo/fbbt/vfb#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 26:04:2024 11:54 + 19:09:2024 09:19 VFB extension ontology - 2024-04-26 + 2024-09-19 @@ -43,26 +41,13 @@ - - definition - - - - - - - - - + - + - - 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 - + @@ -203,27 +188,21 @@ - - - - + - - - - + - + - + - + - + @@ -251,17 +230,9 @@ - - - - - - - - subset_property - + @@ -285,29 +256,25 @@ - - database_cross_reference - + - - in_subset - + - + - + - + - + @@ -373,44 +340,6 @@ - - - - - - - - - - - - - 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. - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - 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. - - precedes - - - - @@ -422,12 +351,9 @@ - - - - - + + The inverse property of is_specified_input_of has_specified_input @@ -438,6 +364,7 @@ + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. is_specified_input_of @@ -447,12 +374,9 @@ - - - - - + + The inverse property of is_specified_output_of has_specified_output @@ -463,6 +387,7 @@ + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. is_specified_output_of @@ -472,12 +397,26 @@ + + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. achieves_planned_objective + + + + + + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + objective_achieved_by + + + + @@ -557,29 +496,6 @@ - - - - - - - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - function of - - - - - - - - - - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - quality of - - - - @@ -591,29 +507,6 @@ - - - - - - - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - has function - - - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - has quality - - - - @@ -626,163 +519,6 @@ - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - disposition of - - - - - - - - - - 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. - - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - 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. - - 2017-05-24T09:31:01Z - has negative regulatory component activity - - - - - - - - - - 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. - - 2017-05-24T09:31:17Z - has positive regulatory component activity - - - - - - - - - - 2017-05-24T09:44:33Z - has component activity - - - - - - - - - - - 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. - - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - - 2017-09-17T13:52:24Z - directly regulated by - - - - - - - - - - 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. - - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - 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. - - - - - - - - - - - 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. - - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - 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. - - - - - - - - - - - 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. - - 2017-09-22T14:14:36Z - has effector activity - - - - - 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. - - - - - @@ -817,37 +553,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - ends after - - - - - - - - - - immediately preceded by - - - - - - - - - - immediately precedes - - - - @@ -923,1059 +628,88 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - - 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. - - - - regulates - - - - - - - - - - - p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - - negatively regulates - - - - - - - - - - - - - - - - p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - - positively regulates - - - - - + - - - - - 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 + + + y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. + expresses - + - - - + + - + - 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. - capable of part of - - - - - - - - - true - - - - - - - - - - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - temporally related to - - - - - - - - - - - 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 input - - - - - - - - - - - - - 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 - - - - - - - - - - - - - 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. - - acts upstream of or within - - - - - - - - - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses - - - - - - - - - - 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, positive effect - - - - - - - - - - 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. - - - causally upstream of, negative effect - - - - - - - - - - - - - - - - - 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. - characteristic of part of - - - - - - - - - true - - - - - - - - A mereological relationship or a topological relationship - mereotopologically related to - - - - - - - - - - - - - - - - - - c enables p iff c is capable of p and c acts to execute p. - - enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - genomically related to - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - involved in - - - - - - - - - - inverse of enables - - enabled by - - - - - - - - - - - - inverse of regulates - - regulated by - - - - - - - - - inverse of negatively regulates - - negatively regulated by - - - - - - - - - inverse of positively regulates - - positively regulated by - - - - - - - - - - is member of is a mereological relation between a item and a collection. - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - has member - - - - - - - - - - inverse of has input - - - input of - - - - - - - - - - - inverse of upstream of - causally downstream of - - - - - - - - - - - immediately causally downstream of - - - - - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - indirectly positively regulates - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - indirectly negatively regulates - - - - - - - - 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. - causally related to - - - - - 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. - https://en.wikipedia.org/wiki/Causality - - - - - - - - - - - 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. - - - causally upstream of - - - - - - - - - - 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. - immediately causally upstream of - - - - - - - - - - - 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. - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of - - - - - - - - - - - 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 - involved in or involved in regulation of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - - interacts with - - - - - - - - - - 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. - molecularly interacts with - - - - - - - - - phosphorylates - - - - - - - - - - - - - - - - - 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. - directly regulates activity of - - - - - - - - - - - - - - - - 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. - directly negatively regulates activity of - - - - - - - - - - - - - - - - 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. - directly positively regulates activity of - - - - - - - - helper property (not for use in curation) - - - - - - - - - is kinase activity - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process - - - - - - - - - - - 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. - causal relation between processes - - - - - - - - depends on - - - - - - - - - - - causal relation between entities - - - - - - - - - - causally influenced by - - - - - - - - - interaction relation helper property - - - - - - - - - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - - - 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). - causally influences - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - - directly regulates - - - - - - - - - - - - - - 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 - has part structure that is capable of - - - - - - - - - - - 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. - causal relation between material entity and a process - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - process has causal agent - - - - - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - - - directly positively regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - - - directly negatively regulates - - - - - - - - - - - - - - - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - 2017-12-26T19:45:49Z - realized in response to stimulus - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - - 2018-01-25T23:20:13Z - enables subfunction - - - - - - - - - - - - - - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - - - - - - - - - - + + - - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect + 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. + characteristic of part of + + + + + + + + true + - + - - - - - - - - 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 - - 2018-01-26T23:53:14Z - - acts upstream of, positive effect + + A mereological relationship or a topological relationship + mereotopologically related to - + - - - - - - - - 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 - - 2018-01-26T23:53:22Z - - acts upstream of, negative effect + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + genomically related to - + - - - - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect + + + + is member of is a mereological relation between a item and a collection. + member of - + - - - - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect + + + has member is a mereological relation between a collection and an item. + has member - + - - - - - - - - - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - realized in response to + + depends on @@ -2011,105 +745,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - 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. - regulates activity of - - - - - - - - - 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. - - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - - 2022-09-26T06:08:01Z - indirectly regulates - - - - - - - - - - - - X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - 2021-11-08T12:00:00Z - device utilizes material - - - - - - - - - - - - - - - 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. - regulates characteristic - - - - - - - - - - - - - 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. - positively regulates characteristic - - - - - - - - - - - - - - - - - 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. - negatively regulates characteristic - - - - @@ -2202,15 +837,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + entity + + + + - - - - - - + @@ -2218,7 +856,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. continuant @@ -2227,19 +864,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - + - An entity that has temporal parts and that happens, unfolds or develops through time. occurrent @@ -2249,15 +880,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - 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]) independent continuant @@ -2267,66 +891,25 @@ For example, A and B may be gene products and binding of B by A positively regul - 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]) process - - - - - - disposition - - - - - - - - - - - - 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. realizable entity - - - - - - - - - - - quality - - - - - - - - - - - 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]) specifically dependent continuant @@ -2336,7 +919,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. role @@ -2346,27 +928,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) generically dependent continuant - - - - - function - - - - @@ -2378,7 +944,6 @@ For example, A and B may be gene products and binding of B by A positively regul - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity @@ -2777,14 +1342,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure - + @@ -2796,7 +1361,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell @@ -2900,7 +1465,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Anatomical entity which is part_of Drosophila melanogaster. UBERON:0001062 @@ -2917,33 +1481,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - true - - - - - - @@ -3094,12 +1631,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3230,39 +1761,6 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -3271,1006 +1769,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/vfbext-simple.json b/vfbext-simple.json index 3f66076..cc0fd3b 100644 --- a/vfbext-simple.json +++ b/vfbext-simple.json @@ -13,20 +13,74 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "26:04:2024 11:54" + "val" : "19:09:2024 09:19" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-26" + "val" : "2024-09-19" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-04-26/vfbext-simple.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-09-19/vfbext-simple.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", + "lbl" : "cell cluster", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", + "lbl" : "expression pattern fragment", + "type" : "CLASS", + "meta" : { + "comments" : [ "A multicellular structure that is part of an expression pattern." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-04T10:55:59Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006", + "lbl" : "multi channel image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007", + "lbl" : "template image", + "type" : "CLASS", + "meta" : { + "comments" : [ "A single channel image that is used as a template for image registration." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-15T15:53:38Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", + "lbl" : "intersectional expression pattern", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:54:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", + "lbl" : "channel", + "type" : "CLASS" + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "lbl" : "part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" @@ -36,15 +90,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", "lbl" : "has_exemplar", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." @@ -54,6 +106,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002350", "lbl" : "member of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." @@ -62,63 +115,28 @@ }, { "id" : "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", "lbl" : "exemplar_of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", - "lbl" : "cell cluster", - "type" : "CLASS" + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000001", "lbl" : "has_channel", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000002", "lbl" : "has_background_channel", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000003", "lbl" : "has_signal_channel", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", - "lbl" : "expression pattern fragment", - "type" : "CLASS", - "meta" : { - "comments" : [ "A multicellular structure that is part of an expression pattern." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-04T10:55:59Z" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000005", - "lbl" : "source_data_link", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006", - "lbl" : "multi channel image", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007", - "lbl" : "template image", - "type" : "CLASS", - "meta" : { - "comments" : [ "A single channel image that is used as a template for image registration." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-05-15T15:53:38Z" - } ] - } + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000008", "lbl" : "has hemidriver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.", @@ -136,6 +154,7 @@ "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000009", "lbl" : "has driver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.", @@ -150,50 +169,102 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", - "lbl" : "intersectional expression pattern", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-26T07:54:17Z" - } ] - } + "id" : "http://xmlns.com/foaf/0.1/depicts", + "lbl" : "depicts", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", - "lbl" : "channel", - "type" : "CLASS" + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#clone", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#neuron", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#ns_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#synaptic_neuropil", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#tract", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000005", + "lbl" : "source_data_link", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "lbl" : "has_license", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/references", "lbl" : "has_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/source", "lbl" : "has_source", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", - "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", - "lbl" : "in_subset", - "type" : "PROPERTY" - }, { - "id" : "http://xmlns.com/foaf/0.1/depicts", - "lbl" : "depicts", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007", diff --git a/vfbext-simple.obo b/vfbext-simple.obo index 23a60c7..5a687a2 100644 --- a/vfbext-simple.obo +++ b/vfbext-simple.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-04-26/vfbext-simple.owl -date: 26:04:2024 11:54 +data-version: vfbext/releases/2024-09-19/vfbext-simple.owl +date: 19:09:2024 09:19 subsetdef: clone "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -10,12 +10,15 @@ subsetdef: neuron "" subsetdef: ns_part "" subsetdef: synaptic_neuropil "" subsetdef: tract "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: terms http://purl.org/dc/terms/ remark: VFB extension ontology ontology: vfbext/vfbext-simple -property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string -property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2024-04-26" xsd:string +property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string +property_value: dc:title "VFB Extension Ontology" xsd:string +property_value: owl:versionInfo "2024-09-19" xsd:string +property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] id: VFB:10000005 diff --git a/vfbext-simple.owl b/vfbext-simple.owl index d29c177..24baedf 100644 --- a/vfbext-simple.owl +++ b/vfbext-simple.owl @@ -13,13 +13,13 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 26:04:2024 11:54 + 19:09:2024 09:19 VFB extension ontology - 2024-04-26 + 2024-09-19 @@ -37,9 +37,7 @@ - - definition - + @@ -161,9 +159,7 @@ - - subset_property - + @@ -187,17 +183,13 @@ - - database_cross_reference - + - - in_subset - + @@ -402,5 +394,5 @@ - + diff --git a/vfbext.json b/vfbext.json index 7612844..8221f00 100644 --- a/vfbext.json +++ b/vfbext.json @@ -13,169 +13,60 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "26:04:2024 11:54" + "val" : "19:09:2024 09:19" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-26" + "val" : "2024-09-19" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-04-26/vfbext.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-09-19/vfbext.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "lbl" : "entity", + "type" : "CLASS" + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "lbl" : "occurrent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "lbl" : "independent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "lbl" : "process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl" : "disposition", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000017", "lbl" : "realizable entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl" : "quality", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "lbl" : "specifically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000031", "lbl" : "generically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl" : "function", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000040", "lbl" : "material entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000054", - "lbl" : "realized in", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000055", - "lbl" : "realizes", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", - "lbl" : "has_exemplar", - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0000000", "lbl" : "anatomical entity", @@ -434,9 +325,14 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000005", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000104", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000011", "lbl" : "planned process", @@ -455,51 +351,6 @@ "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" } } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000293", - "lbl" : "has_specified_input", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_input_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000295", - "lbl" : "is_specified_input_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000299", - "lbl" : "has_specified_output", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_output_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000312", - "lbl" : "is_specified_output_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000417", - "lbl" : "achieves_planned_objective", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." - } - } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000659", "lbl" : "specimen collection process", @@ -537,281 +388,268 @@ } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "id" : "http://purl.obolibrary.org/obo/PATO_0000125", + "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PATO_0001993", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0002266", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0010000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0010001", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000110", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", + "lbl" : "cell cluster", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", + "lbl" : "expression pattern fragment", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Inverse of characteristic_of" - } + "comments" : [ "A multicellular structure that is part of an expression pattern." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-04T10:55:59Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006", + "lbl" : "multi channel image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007", + "lbl" : "template image", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" - } + "comments" : [ "A single channel image that is used as a template for image registration." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-15T15:53:38Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010", + "lbl" : "intersectional expression pattern", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:54:17Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000058", - "lbl" : "is concretized as", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", + "lbl" : "channel", + "type" : "CLASS" + }, { + "id" : "http://xmlns.com/foaf/0.1/image", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." - } + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000059", - "lbl" : "concretizes", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." - } + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000079", - "lbl" : "function of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" - } - } + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000081", - "lbl" : "role of", + "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", + "lbl" : "has_exemplar", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000085", - "lbl" : "has function", + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "lbl" : "has_specified_input", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + "val" : "The inverse property of is_specified_input_of" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "lbl" : "is_specified_input_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000087", - "lbl" : "has role", + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "lbl" : "has_specified_output", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + "val" : "The inverse property of is_specified_output_of" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000091", - "lbl" : "has disposition", + "id" : "http://purl.obolibrary.org/obo/OBI_0000312", + "lbl" : "is_specified_output_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000092", - "lbl" : "disposition of", + "id" : "http://purl.obolibrary.org/obo/OBI_0000417", + "lbl" : "achieves_planned_objective", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "inverse of has disposition" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002013", - "lbl" : "has regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/OBI_0000833", + "lbl" : "objective_achieved_by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" - } ] + "val" : "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", - "lbl" : "has negative regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:01Z" - } ] + "val" : "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." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002015", - "lbl" : "has positive regulatory component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:17Z" - } ] + "val" : "Inverse of characteristic_of" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002017", - "lbl" : "has component activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:44:33Z" - } ] + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002018", - "lbl" : "has component process", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:49:21Z" + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", - "lbl" : "directly regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:24Z" - } ] + "definition" : { + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002023", - "lbl" : "directly negatively regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:38Z" - } ] + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002024", - "lbl" : "directly positively regulated by", + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:47Z" - } ] + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002025", - "lbl" : "has effector activity", + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-22T14:14:36Z" - } ] + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002026", "lbl" : "in register with", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", @@ -825,28 +663,11 @@ "val" : "2017-12-07T12:58:06Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002086", - "lbl" : "ends after", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", - "lbl" : "immediately preceded by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002090", - "lbl" : "immediately precedes", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002131", "lbl" : "overlaps", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" @@ -857,6 +678,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002180", "lbl" : "has component", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -867,1752 +689,641 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002206", "lbl" : "expressed in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "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." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "val" : "A mereological relationship or a topological relationship" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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. " - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable of part of", + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "is member of is a mereological relation between a item and a collection." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", - "lbl" : "has input", + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "val" : "has member is a mereological relation between a collection and an item." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002263", - "lbl" : "acts upstream of", + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002264", - "lbl" : "acts upstream of or within", + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002292", - "lbl" : "expresses", + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "lbl" : "is carrier of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002304", - "lbl" : "causally upstream of, positive effect", + "id" : "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", + "lbl" : "exemplar_of", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", - "lbl" : "causally upstream of, negative effect", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000001", + "lbl" : "has_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002314", - "lbl" : "characteristic of part of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000002", + "lbl" : "has_background_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002323", - "lbl" : "mereotopologically related to", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000003", + "lbl" : "has_signal_channel", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A mereological relationship or a topological relationship" - } - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002327", - "lbl" : "enables", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000008", + "lbl" : "has hemidriver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "c enables p iff c is capable of p and c acts to execute p." + "val" : "A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.", + "xrefs" : [ "PMID:17088209" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002328", - "lbl" : "functionally related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - } + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:48:55Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002329", - "lbl" : "part of structure that is capable of", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000009", + "lbl" : "has driver", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - } + "val" : "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.", + "xrefs" : [ "PMID:8223268", "Wikipedia:GAL4/UAS_system" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T07:49:10Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002330", - "lbl" : "genomically related to", + "id" : "http://xmlns.com/foaf/0.1/depicts", + "lbl" : "depicts", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - } - } + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002331", - "lbl" : "involved in", + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + "val" : "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." } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002333", - "lbl" : "enabled by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of enables" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002334", - "lbl" : "regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002335", - "lbl" : "negatively regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of negatively regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002336", - "lbl" : "positively regulated by", + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of positively regulates" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002350", - "lbl" : "member of", + "id" : "http://purl.obolibrary.org/obo/caro#core", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "is member of is a mereological relation between a item and a collection." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002351", - "lbl" : "has member", + "id" : "http://purl.obolibrary.org/obo/caro#plus", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "has member is a mereological relation between a collection and an item." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002352", - "lbl" : "input of", + "id" : "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of has input" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", - "lbl" : "causally downstream of", + "id" : "http://purl.obolibrary.org/obo/fbbt#cur", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of upstream of" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002405", - "lbl" : "immediately causally downstream of", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/fbbt#larval_OF", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002407", - "lbl" : "indirectly positively regulates", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#clone", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002409", - "lbl" : "indirectly negatively regulates", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#neuron", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", - "lbl" : "causally related to", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb#ns_part", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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.", - 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"id" : "http://purl.obolibrary.org/obo/RO_0002418", - "lbl" : "causally upstream of or within", + "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000005", + "lbl" : "source_data_link", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002427", - "lbl" : "causally downstream of or within", + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of causally upstream of or within" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", - "lbl" : "involved in regulation of", + "id" : "http://purl.org/dc/elements/1.1/contributor", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002429", - "lbl" : "involved in positive regulation of", + "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002430", - "lbl" : "involved in negative regulation of", + "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", - "lbl" : "involved in or involved in regulation of", + "id" : "http://purl.org/dc/terms/license", + "lbl" : "has_license", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002434", - "lbl" : "interacts with", + "id" : "http://purl.org/dc/terms/references", + "lbl" : "has_reference", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002436", - "lbl" : "molecularly interacts with", + "id" : "http://purl.org/dc/terms/source", + "lbl" : "has_source", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002447", - "lbl" : "phosphorylates", - "type" : "PROPERTY" + "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002448", - "lbl" : "directly regulates activity of", + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002449", - "lbl" : "directly negatively regulates activity of", + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002450", - "lbl" : "directly positively regulates activity of", + "id" : "http://www.geneontology.org/formats/oboInOwl#date", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002464", - "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY" + "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002481", - "lbl" : "is kinase activity", - "type" : "PROPERTY" + "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002500", - "lbl" : "causal agent in process", + "id" : "http://xmlns.com/foaf/0.1/homepage", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - } - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002501", - "lbl" : "causal relation between processes", + "id" : "http://xmlns.com/foaf/0.1/mbox", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "propertyType" : "ANNOTATION" + } ], + "edges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002502", - "lbl" : "depends on", - "type" : "PROPERTY" + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002506", - "lbl" : "causal relation between entities", - "type" : "PROPERTY" + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002559", - "lbl" : "causally influenced by", - "type" : "PROPERTY" + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002563", - "lbl" : "interaction relation helper property", - "type" : "PROPERTY" + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002564", - "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY" + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002566", - "lbl" : "causally influences", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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)." - } - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002578", - "lbl" : "directly regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } + "sub" : "http://purl.obolibrary.org/obo/BFO_0000141", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002584", - "lbl" : "has part structure that is capable of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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" - } - } + "sub" : "http://purl.obolibrary.org/obo/CARO_0000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0030000" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002595", - "lbl" : "causal relation between material entity and a process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - } - } + "sub" : "http://purl.obolibrary.org/obo/CARO_0000003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000006" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002596", - "lbl" : "capable of regulating", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - } - } + "sub" : "http://purl.obolibrary.org/obo/CARO_0000003", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002597", - "lbl" : "capable of negatively regulating", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - } - } + "sub" : "http://purl.obolibrary.org/obo/CARO_0000003", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0010000" }, { - 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"chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002211" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002448", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002212" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004034", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002304" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004035", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002305" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002263", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002233" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002264", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002418" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002450", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002449", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002333" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004033", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004046" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004032", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004047" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002331", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002212" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] } ] } ] } \ No newline at end of file diff --git a/vfbext.obo b/vfbext.obo index 0eea2de..5530c44 100644 --- a/vfbext.obo +++ b/vfbext.obo @@ -1,5 +1,5 @@ format-version: 1.2 -date: 26:04:2024 11:54 +date: 19:09:2024 09:19 subsetdef: clone "" subsetdef: core "" subsetdef: cur "" @@ -13,94 +13,70 @@ subsetdef: neuron "" subsetdef: ns_part "" subsetdef: plus "" subsetdef: ro-eco "" -subsetdef: RO:0002259 "" subsetdef: synaptic_neuropil "" subsetdef: tract "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: terms http://purl.org/dc/terms/ remark: VFB extension ontology ontology: http://virtualflybrain.org/data/VFB/OWL/vfbext.owl -property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string -property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2024-04-26" xsd:string +property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string +property_value: dc:title "VFB Extension Ontology" xsd:string +property_value: owl:versionInfo "2024-09-19" xsd:string +property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string + +[Term] +id: BFO:0000001 +name: entity [Term] id: BFO:0000002 name: continuant -def: "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." [] +is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant [Term] id: BFO:0000003 name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent +is_a: BFO:0000001 ! entity [Term] id: BFO:0000004 name: independent continuant -def: "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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000015 name: process -def: "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])" [] is_a: BFO:0000003 ! occurrent -[Term] -id: BFO:0000016 -name: disposition -is_a: BFO:0000017 ! realizable entity -disjoint_from: BFO:0000023 ! role - [Term] id: BFO:0000017 name: realizable entity -def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000019 ! quality -relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity - -[Term] -id: BFO:0000019 -name: quality -is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 name: specifically dependent continuant -def: "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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 name: role -def: "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." [] is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 name: generically dependent continuant -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant - -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition [Term] id: BFO:0000040 name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity @@ -328,16 +304,8 @@ xref: UBERON:0001062 is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity intersection_of: BFO:0000050 NCBITaxon:7227 ! part of -disjoint_from: PATO:0000001 relationship: BFO:0000050 NCBITaxon:7227 ! part of -[Term] -id: GO:0008150 -disjoint_from: OBI:0000011 ! planned process - -[Term] -id: GO:0016301 - [Term] id: OBI:0000011 name: planned process @@ -407,7 +375,7 @@ creation_date: 2018-03-04T10:55:59Z [Term] id: VFBext:0000006 name: multi channel image -is_a: http://xmlns.com/foaf/0.1/image +is_a: foaf:image [Term] id: VFBext:0000007 @@ -427,7 +395,7 @@ creation_date: 2018-09-26T07:54:17Z [Term] id: VFBext:0000014 name: channel -is_a: http://xmlns.com/foaf/0.1/image +is_a: foaf:image [Typedef] id: BFO:0000050 @@ -464,58 +432,50 @@ name: realizes domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity -[Typedef] -id: BFO:0000062 -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 -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -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 -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - [Typedef] id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] +domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is_specified_input_of [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] +domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] +domain: OBI:0000011 ! planned process +range: IAO:0000005 +inverse_of: OBI:0000833 ! objective_achieved_by + +[Typedef] +id: OBI:0000833 +name: objective_achieved_by +def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] +domain: IAO:0000005 +range: OBI:0000011 ! planned process [Typedef] id: RO:0000052 @@ -544,7 +504,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -564,21 +524,6 @@ def: "A relationship between a specifically dependent continuant and a generical domain: BFO:0000020 ! specifically dependent continuant range: BFO:0000031 ! generically dependent continuant -[Typedef] -id: RO:0000079 -name: function of -def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] -domain: BFO:0000034 ! function -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000085 ! has function - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000086 ! has quality - [Typedef] id: RO:0000081 name: role of @@ -586,21 +531,6 @@ def: "a relation between a role and an independent continuant (the bearer), in w is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role -[Typedef] -id: RO:0000085 -name: has function -def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000034 ! function -is_a: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -range: BFO:0000019 ! quality -is_a: RO:0000053 ! has characteristic - [Typedef] id: RO:0000087 name: has role @@ -609,130 +539,16 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! has characteristic -[Typedef] -id: RO:0000091 -name: has disposition -def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000016 ! disposition -is_a: RO:0000053 ! has characteristic -inverse_of: RO:0000092 ! disposition of - -[Typedef] -id: RO:0000092 -name: disposition of -def: "inverse of has disposition" [] -subset: RO:0002259 -is_a: RO:0000052 ! characteristic of - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "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." [] -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "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." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "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." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -is_a: RO:0002018 ! has component process -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "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." [] -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-05-24T09:49:21Z - -[Typedef] -id: RO:0002022 -name: directly regulated by -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:24Z - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:38Z - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-17T13:52:47Z - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "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." [https://orcid.org/0000-0002-7073-9172] -is_functional: true -is_a: RO:0002017 ! has component activity -created_by: https://orcid.org/0000-0002-7073-9172 -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002026 name: in register with def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] -domain: http://xmlns.com/foaf/0.1/image -range: http://xmlns.com/foaf/0.1/image +domain: foaf:image +range: foaf:image is_a: RO:0002323 ! mereotopologically related to created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z -[Typedef] -id: RO:0002086 -name: ends after -subset: ro-eco -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002090 -name: immediately precedes -subset: ro-eco -is_a: BFO:0000063 ! precedes - [Typedef] id: RO:0002131 name: overlaps @@ -764,122 +580,12 @@ is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of -[Typedef] -id: RO:0002211 -name: regulates -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by -transitive_over: RO:0002025 ! has effector activity - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -holds_over_chain: RO:0002212 RO:0002212 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002215 -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 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: RO:0002216 ! capable of part of - -[Typedef] -id: RO:0002216 -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." [] -holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002222 -name: temporally related to -subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent - -[Typedef] -id: RO:0002233 -name: has input -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -domain: BFO:0000015 ! process -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - [Typedef] id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] is_a: RO:0002330 ! genomically related to -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - [Typedef] id: RO:0002314 name: characteristic of part of @@ -893,28 +599,6 @@ id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -[Typedef] -id: RO:0002327 -name: enables -def: "c enables p iff c is capable of p and c acts to execute p." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] - -[Typedef] -id: RO:0002329 -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." [] -holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002330 name: genomically related to @@ -922,47 +606,6 @@ def: "holds between two entities when some genome-level process such as gene exp domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0000056 ! participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -subset: RO:0002259 -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -subset: RO:0002259 -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -subset: RO:0002259 -is_a: RO:0002334 ! regulated by - [Typedef] id: RO:0002350 name: member of @@ -976,385 +619,10 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] is_a: BFO:0000051 ! has part -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002407 -name: indirectly positively regulates -def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -holds_over_chain: RO:0002409 RO:0002409 -holds_over_chain: RO:0002629 RO:0002407 -holds_over_chain: RO:0002629 RO:0002629 -is_transitive: true -is_a: RO:0002213 ! positively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002409 -name: indirectly negatively regulates -def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -holds_over_chain: RO:0002630 RO:0002409 -holds_over_chain: RO:0002630 RO:0002630 -is_transitive: true -is_a: RO:0002212 ! negatively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002410 -name: causally related to -def: "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." [https://en.wikipedia.org/wiki/Causality] - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "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." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "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." [] -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "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." [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -subset: RO:0002259 -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -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" [] -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002434 -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 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_symmetric: true - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "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." [] -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: directly regulates activity of -def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0011002 ! regulates activity of - -[Typedef] -id: RO:0002449 -name: directly negatively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002450 -name: directly positively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) - -[Typedef] -id: RO:0002481 -name: is kinase activity -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -is_a: RO:0002410 ! causally related to - [Typedef] id: RO:0002502 name: depends on -[Typedef] -id: RO:0002506 -name: causal relation between entities -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002559 -name: causally influenced by -is_a: RO:0002506 ! causal relation between entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002566 -name: causally influences -def: "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)." [] -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002506 ! causal relation between entities - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002584 -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" [] -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002595 -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." [] -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -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." [] -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -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." [] -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -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." [] -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0004028 -name: realized in response to stimulus -def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000040 ! material entity -holds_over_chain: RO:0009501 RO:0002233 -is_a: RO:0002410 ! causally related to -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2017-12-26T19:45:49Z - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-25T23:20:13Z - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:49:30Z - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:49:51Z - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "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" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:53:14Z - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "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" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-01-26T23:53:22Z - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -is_a: RO:0002418 ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-03-13T23:55:05Z - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -is_a: RO:0002418 ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 -creation_date: 2018-03-13T23:55:19Z - -[Typedef] -id: RO:0009501 -name: realized in response to -def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process -holds_over_chain: BFO:0000054 RO:0002404 -is_a: RO:0002410 ! causally related to - [Typedef] id: RO:0010001 name: generically depends on @@ -1372,62 +640,6 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000031 ! generically dependent continuant holds_over_chain: RO:0000059 RO:0000053 -[Typedef] -id: RO:0011002 -name: regulates activity of -def: "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." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0012011 -name: indirectly causally upstream of -def: "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." [] -is_a: RO:0002411 ! causally upstream of -created_by: https://orcid.org/0000-0003-1813-6857 -creation_date: 2022-09-26T06:07:17Z - -[Typedef] -id: RO:0012012 -name: indirectly regulates -def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] -is_a: RO:0002211 ! regulates -is_a: RO:0012011 ! indirectly causally upstream of -created_by: https://orcid.org/0000-0003-1813-6857 -creation_date: 2022-09-26T06:08:01Z - -[Typedef] -id: RO:0017001 -name: device utilizes material -def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -holds_over_chain: RO:0002215 RO:0002233 -creation_date: 2021-11-08T12:00:00Z - -[Typedef] -id: RO:0019000 -name: regulates characteristic -def: "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." [] -domain: BFO:0000015 ! process -range: PATO:0000001 -holds_over_chain: RO:0002211 RO:0019000 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0019001 -name: positively regulates characteristic -def: "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." [] -holds_over_chain: RO:0002213 RO:0019001 -is_a: RO:0019000 ! regulates characteristic - -[Typedef] -id: RO:0019002 -name: negatively regulates characteristic -def: "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." [] -holds_over_chain: RO:0002212 RO:0019001 -holds_over_chain: RO:0002213 RO:0019002 -is_a: RO:0019000 ! regulates characteristic - [Typedef] id: VFBext:0000001 name: has_channel @@ -1459,6 +671,10 @@ is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z +[Typedef] +id: foaf:depicts +name: depicts + [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -1468,7 +684,3 @@ id: http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0 name: exemplar_of is_a: RO:0002350 ! member of -[Typedef] -id: http://xmlns.com/foaf/0.1/depicts -name: depicts - diff --git a/vfbext.owl b/vfbext.owl index 326be60..b19a299 100644 --- a/vfbext.owl +++ b/vfbext.owl @@ -12,9 +12,7 @@ xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:vfb2="http://purl.obolibrary.org/obo/fbbt/vfb#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -22,9 +20,9 @@ An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 26:04:2024 11:54 + 19:09:2024 09:19 VFB extension ontology - 2024-04-26 + 2024-09-19 @@ -42,26 +40,13 @@ - - definition - - - - - - - - - + - + - - 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 - + @@ -202,27 +187,21 @@ - - - - + - - - - + - + - + - + - + @@ -250,17 +229,9 @@ - - - - - - - - subset_property - + @@ -284,29 +255,25 @@ - - database_cross_reference - + - - in_subset - + - + - + - + - + @@ -372,44 +339,6 @@ - - - - - - - - - - - - - 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. - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - 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. - - precedes - - - - @@ -421,12 +350,9 @@ - - - - - + + The inverse property of is_specified_input_of has_specified_input @@ -437,6 +363,7 @@ + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. is_specified_input_of @@ -446,12 +373,9 @@ - - - - - + + The inverse property of is_specified_output_of has_specified_output @@ -462,6 +386,7 @@ + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. is_specified_output_of @@ -471,12 +396,26 @@ + + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. achieves_planned_objective + + + + + + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + objective_achieved_by + + + + @@ -556,29 +495,6 @@ - - - - - - - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - function of - - - - - - - - - - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - quality of - - - - @@ -590,29 +506,6 @@ - - - - - - - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - has function - - - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - has quality - - - - @@ -625,163 +518,6 @@ - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - disposition of - - - - - - - - - - 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. - - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - 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. - - 2017-05-24T09:31:01Z - has negative regulatory component activity - - - - - - - - - - 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. - - 2017-05-24T09:31:17Z - has positive regulatory component activity - - - - - - - - - - 2017-05-24T09:44:33Z - has component activity - - - - - - - - - - - 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. - - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - - 2017-09-17T13:52:24Z - directly regulated by - - - - - - - - - - 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. - - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - 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. - - - - - - - - - - - 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. - - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - 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. - - - - - - - - - - - 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. - - 2017-09-22T14:14:36Z - has effector activity - - - - - 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. - - - - - @@ -816,37 +552,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - ends after - - - - - - - - - - immediately preceded by - - - - - - - - - - immediately precedes - - - - @@ -922,1059 +627,88 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - - 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. - - - - regulates - - - - - - - - - - - p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - - negatively regulates - - - - - - - - - - - - - - - - p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - - positively regulates - - - - - + - - - - - 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 + + + y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. + expresses - + - - - + + - + - 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. - capable of part of - - - - - - - - - true - - - - - - - - - - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - temporally related to - - - - - - - - - - - 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 input - - - - - - - - - - - - - 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 - - - - - - - - - - - - - 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. - - acts upstream of or within - - - - - - - - - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses - - - - - - - - - - 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, positive effect - - - - - - - - - - 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. - - - causally upstream of, negative effect - - - - - - - - - - - - - - - - - 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. - characteristic of part of - - - - - - - - - true - - - - - - - - A mereological relationship or a topological relationship - mereotopologically related to - - - - - - - - - - - - - - - - - - c enables p iff c is capable of p and c acts to execute p. - - enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - genomically related to - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - involved in - - - - - - - - - - inverse of enables - - enabled by - - - - - - - - - - - - inverse of regulates - - regulated by - - - - - - - - - inverse of negatively regulates - - negatively regulated by - - - - - - - - - inverse of positively regulates - - positively regulated by - - - - - - - - - - is member of is a mereological relation between a item and a collection. - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - has member - - - - - - - - - - inverse of has input - - - input of - - - - - - - - - - - inverse of upstream of - causally downstream of - - - - - - - - - - - immediately causally downstream of - - - - - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - indirectly positively regulates - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - indirectly negatively regulates - - - - - - - - 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. - causally related to - - - - - 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. - https://en.wikipedia.org/wiki/Causality - - - - - - - - - - - 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. - - - causally upstream of - - - - - - - - - - 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. - immediately causally upstream of - - - - - - - - - - - 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. - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of - - - - - - - - - - - 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 - involved in or involved in regulation of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - - interacts with - - - - - - - - - - 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. - molecularly interacts with - - - - - - - - - phosphorylates - - - - - - - - - - - - - - - - - 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. - directly regulates activity of - - - - - - - - - - - - - - - - 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. - directly negatively regulates activity of - - - - - - - - - - - - - - - - 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. - directly positively regulates activity of - - - - - - - - helper property (not for use in curation) - - - - - - - - - is kinase activity - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process - - - - - - - - - - - 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. - causal relation between processes - - - - - - - - depends on - - - - - - - - - - - causal relation between entities - - - - - - - - - - causally influenced by - - - - - - - - - interaction relation helper property - - - - - - - - - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - - - 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). - causally influences - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - - directly regulates - - - - - - - - - - - - - - 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 - has part structure that is capable of - - - - - - - - - - - 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. - causal relation between material entity and a process - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - process has causal agent - - - - - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - - - directly positively regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - - - directly negatively regulates - - - - - - - - - - - - - - - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - 2017-12-26T19:45:49Z - realized in response to stimulus - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - - 2018-01-25T23:20:13Z - enables subfunction - - - - - - - - - - - - - - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - - - - - - - - - - + + - - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect + 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. + characteristic of part of + + + + + + + + true + - + - - - - - - - - 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 - - 2018-01-26T23:53:14Z - - acts upstream of, positive effect + + A mereological relationship or a topological relationship + mereotopologically related to - + - - - - - - - - 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 - - 2018-01-26T23:53:22Z - - acts upstream of, negative effect + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + genomically related to - + - - - - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect + + + + is member of is a mereological relation between a item and a collection. + member of - + - - - - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect + + + has member is a mereological relation between a collection and an item. + has member - + - - - - - - - - - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - realized in response to + + depends on @@ -2010,105 +744,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - 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. - regulates activity of - - - - - - - - - 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. - - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - - 2022-09-26T06:08:01Z - indirectly regulates - - - - - - - - - - - - X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - 2021-11-08T12:00:00Z - device utilizes material - - - - - - - - - - - - - - - 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. - regulates characteristic - - - - - - - - - - - - - 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. - positively regulates characteristic - - - - - - - - - - - - - - - - - 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. - negatively regulates characteristic - - - - @@ -2201,15 +836,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + entity + + + + - - - - - - + @@ -2217,7 +855,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. continuant @@ -2226,19 +863,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - + - An entity that has temporal parts and that happens, unfolds or develops through time. occurrent @@ -2248,15 +879,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - 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]) independent continuant @@ -2266,66 +890,25 @@ For example, A and B may be gene products and binding of B by A positively regul - 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]) process - - - - - - disposition - - - - - - - - - - - - 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. realizable entity - - - - - - - - - - - quality - - - - - - - - - - - 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]) specifically dependent continuant @@ -2335,7 +918,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. role @@ -2345,27 +927,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) generically dependent continuant - - - - - function - - - - @@ -2377,7 +943,6 @@ For example, A and B may be gene products and binding of B by A positively regul - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity @@ -2776,14 +1341,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure - + @@ -2795,7 +1360,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell @@ -2899,7 +1464,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Anatomical entity which is part_of Drosophila melanogaster. UBERON:0001062 @@ -2916,33 +1480,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - true - - - - - - @@ -3116,12 +1653,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3259,39 +1790,6 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -3300,1006 +1798,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +