diff --git a/dpo.obo b/dpo.obo index 24a22dd..dc5f672 100644 --- a/dpo.obo +++ b/dpo.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: dpo/releases/2023-05-03 -date: 03:05:2023 17:45 +data-version: dpo/releases/2023-07-05 +date: 05:07:2023 14:34 subsetdef: abnormal_slim "Abnormal/normal slim" subsetdef: absent_slim "Absent/present slim" subsetdef: attribute_slim "Attribute slim" @@ -44,7 +44,7 @@ property_value: http://purl.org/dc/elements/1.1/description "An ontology for the property_value: http://purl.org/dc/elements/1.1/title "Drosophila Phenotype Ontology (DPO)" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: IAO:0000700 FBcv:0000347 -property_value: owl:versionInfo "2023-05-03" xsd:string +property_value: owl:versionInfo "2023-07-05" xsd:string [Term] id: FBcv:0000002 @@ -2388,12 +2388,15 @@ property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 property_value: RO:0040042 BFO:0000017 property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true inverse_of: BFO:0000051 ! has part @@ -2490,8 +2493,9 @@ property_value: IAO:0000232 "This relation is intended to be used in combination [Typedef] id: substage_of -name: substage_of +name: substage of namespace: relationship +def: "A relation between a developmental stage and another, larger developmental stage during which it happens." [FBC:DPG] comment: Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO. xref: FBdv:00018001 is_transitive: true diff --git a/src/ontology/dpo.Makefile b/src/ontology/dpo.Makefile index bc2768a..f451b33 100644 --- a/src/ontology/dpo.Makefile +++ b/src/ontology/dpo.Makefile @@ -48,26 +48,10 @@ mirror-fbdv: | $(TMPDIR) curl -L $(OBOBASE)/fbdv/fbdv-base.owl --create-dirs \ -o $(TMPDIR)/fbdv.owl --retry 4 --max-time 200 && \ $(ROBOT) remove -i $(TMPDIR)/fbdv.owl \ - --term RO:0002012 --term RO:0002087 --term RO:0002090 \ + --term RO:0002087 --term RO:0002090 \ --term RO:0002092 --axioms annotation \ convert -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi -# RO's base contains duplicated definitions for several BFO classes that -# presumably do *not* belong in RO. And here, using 'make_base' is not -# an option since RO also happens to contain terms that have a BFO -# prefix but actually *do* belong in RO (if that sounds insane, it's -# because it is), so a blanket filter based on prefixes won't work. -# So again, we use a precision approach in which we just remove the -# annotations of the offending classes. -mirror-ro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then \ - curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs \ - -o $(TMPDIR)/ro.owl --retry 4 --max-time 200 && \ - $(ROBOT) remove -i $(TMPDIR)/ro.owl \ - --term BFO:0000004 --term BFO:0000015 --term BFO:0000020 \ - --axioms annotation \ - convert -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi - ####################################################### ##### Code for removing patternised classes ########### diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index ec06949..78d194e 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-05-03") + +Annotation(owl:versionInfo "2023-07-05") Declaration(Class()) Declaration(Class()) @@ -747,8 +747,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -958,7 +956,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1328,6 +1325,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -1485,7 +1483,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -1742,10 +1739,6 @@ AnnotationAssertion(rdfs:label "has_related_synonym") -# Annotation Property: (has_scope) - -AnnotationAssertion(rdfs:label "has_scope") - # Annotation Property: (in_subset) AnnotationAssertion(rdfs:label "in_subset") @@ -1781,8 +1774,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -1791,6 +1786,7 @@ AnnotationAssertion( "part of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -1857,6 +1853,7 @@ AnnotationAssertion( "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -1874,14 +1871,15 @@ AnnotationAssertion(rdfs:label "con AnnotationAssertion( "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity."@en) AnnotationAssertion(rdfs:label "derives from part of"@en) -# Object Property: (substage_of) +# Object Property: (substage of) +AnnotationAssertion(Annotation( "FBC:DPG") "A relation between a developmental stage and another, larger developmental stage during which it happens.") AnnotationAssertion( "FBdv:00018001") AnnotationAssertion( "relationship") AnnotationAssertion( "substage_of") AnnotationAssertion( "substage_of") AnnotationAssertion(rdfs:comment "Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO.") -AnnotationAssertion(rdfs:label "substage_of") +AnnotationAssertion(rdfs:label "substage of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -2049,6 +2047,10 @@ ObjectPropertyRange( (occurrent part of) AnnotationAssertion( "A part of relation that applies only between occurrents.") +AnnotationAssertion( "RO:0002012") +AnnotationAssertion( "FlyBase_development_CV") +AnnotationAssertion( "occurrent_part_of") +AnnotationAssertion( "occurrent_part_of") AnnotationAssertion(rdfs:label "occurrent part of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2058,7 +2060,7 @@ ObjectPropertyRange( (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( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has regulatory component activity") SubObjectPropertyOf( ) @@ -2067,7 +2069,7 @@ SubObjectPropertyOf( (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( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") AnnotationAssertion(rdfs:label "has negative regulatory component activity") @@ -2077,7 +2079,7 @@ SubObjectPropertyOf( (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( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") AnnotationAssertion(rdfs:label "has positive regulatory component activity") @@ -2086,7 +2088,7 @@ SubObjectPropertyOf( (has component activity) -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") AnnotationAssertion(rdfs:label "has component activity") @@ -2095,7 +2097,7 @@ SubObjectPropertyOf( (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( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has component process") SubObjectPropertyOf( ) @@ -2104,17 +2106,17 @@ ObjectPropertyRange( (directly regulated by) -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( "GOC:dos") rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") AnnotationAssertion(rdfs:label "directly regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (directly negatively regulated by) -AnnotationAssertion(Annotation( "GOC:dos") "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( "dos") +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( ) @@ -2122,8 +2124,8 @@ InverseObjectProperties( (directly positively regulated by) -AnnotationAssertion(Annotation( "GOC:dos") "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( "dos") +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( ) @@ -2131,8 +2133,8 @@ InverseObjectProperties( (has effector activity) -AnnotationAssertion(Annotation( "GOC:dos") "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( "dos") +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:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") AnnotationAssertion(rdfs:label "has effector activity") @@ -2237,6 +2239,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))"@en) AnnotationAssertion(rdfs:label "happens during"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Happens_during"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -2462,6 +2465,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -2477,6 +2481,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -2489,8 +2494,6 @@ AnnotationAssertion( "has developmental contribution from"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (developmentally contributes to) @@ -2532,7 +2535,7 @@ AnnotationAssertion( "affects") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (developmentally succeeded by) @@ -2553,7 +2556,6 @@ AnnotationAssertion(rdfs:label "resu AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (results in formation of) @@ -2579,6 +2581,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2590,6 +2593,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2633,6 +2637,7 @@ AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enables"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -2658,7 +2663,7 @@ AnnotationAssertion( "actively involved in") AnnotationAssertion( "enables part of") AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2668,6 +2673,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -2753,8 +2759,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has developmental potential involving"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (has potential to developmentally contribute to) @@ -2806,6 +2810,7 @@ AnnotationAssertion( "indirectly activates") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -2817,6 +2822,7 @@ AnnotationAssertion( "indirectly inhibits") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -2923,12 +2929,13 @@ SubObjectPropertyOf( (is active in) AnnotationAssertion( "A protein that enables activity in a cytosol.") -AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dos") "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") +AnnotationAssertion(Annotation( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") AnnotationAssertion( ) AnnotationAssertion( "executes activity in") AnnotationAssertion( "enables activity in") AnnotationAssertion(rdfs:comment "") AnnotationAssertion(rdfs:label "is active in") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3253,6 +3260,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly positively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3266,6 +3274,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly negatively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3306,7 +3315,7 @@ AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (acts upstream of or within, negative effect) @@ -3316,6 +3325,7 @@ AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (acts upstream of, positive effect) @@ -3326,7 +3336,7 @@ AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3338,7 +3348,7 @@ AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -3348,6 +3358,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (causally upstream of or within, positive effect) @@ -3356,6 +3367,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (regulates activity of) @@ -3370,7 +3382,7 @@ ObjectPropertyRange( (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( "pg") +AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) SubObjectPropertyOf( ) @@ -3378,7 +3390,7 @@ SubObjectPropertyOf( (indirectly regulates) AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( "pg") +AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "indirectly regulates"@en) SubObjectPropertyOf( ) @@ -3427,6 +3439,16 @@ AnnotationAssertion( AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) +# Object Property: (positively correlated with) + +AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) +AnnotationAssertion( "directly correlated with"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively correlated with"@en) +SubObjectPropertyOf( ) +SymmetricObjectProperty() +ReflexiveObjectProperty() + # 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.") @@ -3462,7 +3484,7 @@ AnnotationAssertion(rdfs:label (has increased age-specific mortality rate) AnnotationAssertion(Annotation( "PMID:24138933") Annotation( "Wikipedia:Infant_mortality") "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2018-05-22T16:43:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.") AnnotationAssertion(rdfs:label "has increased age-specific mortality rate"@en) @@ -3550,6 +3572,7 @@ AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "independent continuant"@en) SubClassOf( ) @@ -3570,6 +3593,7 @@ 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( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) @@ -3608,7 +3632,6 @@ AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) @@ -3629,7 +3652,6 @@ AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -3651,6 +3673,7 @@ 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(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) @@ -3812,7 +3835,6 @@ AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) SubClassOf( ) DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) @@ -3824,7 +3846,6 @@ AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "immaterial entity"@en) -SubClassOf( ) SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) @@ -9933,6 +9954,7 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (oogenesis) +AnnotationAssertion(Annotation( "GO:0048477") "The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.") AnnotationAssertion( "GO:0048477") AnnotationAssertion( "oogenesis stage") AnnotationAssertion( "FlyBase_development_CV") @@ -10240,6 +10262,7 @@ SubClassOf( (unfertilized egg stage) +AnnotationAssertion(Annotation( "FlyBase:FBrf0158848") "Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.") AnnotationAssertion( "FlyBase_development_CV") AnnotationAssertion( "FBdv:00005287") AnnotationAssertion(rdfs:comment "Temporal ordering number - 10300.") @@ -10251,6 +10274,7 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (fertilized egg stage) +AnnotationAssertion(Annotation( "FlyBase:FBrf0229233") "Developmental stage that starts with sperm entry until the first mitotic division of the zygote.") AnnotationAssertion( "FlyBase_development_CV") AnnotationAssertion( "FBdv:00005288") AnnotationAssertion(rdfs:comment "Temporal ordering number - 10.") @@ -11234,6 +11258,7 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (developmental process) +AnnotationAssertion(Annotation( "GO:0032502") "A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition.") AnnotationAssertion( ) AnnotationAssertion( "2009-10-01T05:56:42Z") AnnotationAssertion( "GO:0032502") @@ -11372,6 +11397,7 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (biological process) +AnnotationAssertion(Annotation( "GO:0008150") "The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module.") AnnotationAssertion( "GO:0008150") AnnotationAssertion( "FlyBase_development_CV") AnnotationAssertion( "FBdv:00007024") @@ -12011,12 +12037,9 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:PO_curators") "OBSOLETE. A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24930"^^xsd:anyURI) AnnotationAssertion( "GO:0016280") -AnnotationAssertion( "Wikipedia:Aging") AnnotationAssertion( "ageing") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0007568") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The reason for obsoletion is that this represents a phenotype.") AnnotationAssertion(rdfs:label "obsolete aging") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -12885,27 +12908,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of cell death) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010941") -AnnotationAssertion(rdfs:label "regulation of cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cell death) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010942") -AnnotationAssertion(rdfs:label "positive regulation of cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of cell cycle process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.") @@ -12993,6 +12995,7 @@ SubClassOf( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:pf") Annotation( "Wikipedia:Cell_migration") "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24787"^^xsd:anyURI) +AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Cell_migration") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016477") @@ -13708,6 +13711,7 @@ AnnotationAssertion( "kinase inhibitor") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033673") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -13725,6 +13729,7 @@ AnnotationAssertion( "stimulation of kinase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033674") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -14083,6 +14088,7 @@ AnnotationAssertion( "upregulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043085") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -14106,6 +14112,7 @@ AnnotationAssertion( "negative regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043086") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -14143,6 +14150,7 @@ SubClassOf( "GOC:bf") "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043549") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -14166,6 +14174,7 @@ AnnotationAssertion( "2009-04-21T04:07:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044092") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -14178,6 +14187,7 @@ AnnotationAssertion( "2009-04-21T04:11:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044093") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -15055,6 +15065,7 @@ AnnotationAssertion( "regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050790") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -15518,6 +15529,7 @@ AnnotationAssertion(Annotation( "transferase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051338") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "regulation of transferase activity") @@ -15536,6 +15548,7 @@ AnnotationAssertion( "stimulation of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051347") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "positive regulation of transferase activity") @@ -15554,6 +15567,7 @@ AnnotationAssertion( "inhibition of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051348") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "negative regulation of transferase activity") @@ -15845,19 +15859,6 @@ AnnotationAssertion( "epithelium development") SubClassOf( ) -# Class: (negative regulation of cell death) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.") -AnnotationAssertion( "dph") -AnnotationAssertion( "2009-04-13T01:56:10Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0060548") -AnnotationAssertion(rdfs:label "negative regulation of cell death") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (developmental growth involved in morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.") @@ -19167,17 +19168,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct 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 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:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") 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()))) +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:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") 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/chado_load_check_simple.txt b/src/ontology/reports/chado_load_check_simple.txt index 92e6f7f..1eeb0f3 100644 --- a/src/ontology/reports/chado_load_check_simple.txt +++ b/src/ontology/reports/chado_load_check_simple.txt @@ -1,3 +1,3 @@ FBcv:0000680 ! abnormal proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924 -FBcv:0007533 ! increased rate of proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924 FBcv:0007545 ! decreased rate of proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924 +FBcv:0007533 ! increased rate of proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924 diff --git a/src/ontology/reports/obo_qc_dpo.obo.txt b/src/ontology/reports/obo_qc_dpo.obo.txt index d58d6cd..c0e2756 100644 --- a/src/ontology/reports/obo_qc_dpo.obo.txt +++ b/src/ontology/reports/obo_qc_dpo.obo.txt @@ -4,7 +4,6 @@ WARN missing_definition FBcv:0000347 IAO:0000115 WARN missing_definition FBcv:0006003 IAO:0000115 WARN missing_definition FBcv:0006007 IAO:0000115 WARN missing_definition FBcv:0008000 IAO:0000115 -WARN missing_definition FBdv:00018001 IAO:0000115 WARN missing_definition IAO:0000115 IAO:0000115 WARN missing_definition IAO:0100001 IAO:0000115 WARN missing_definition RO:0002083 IAO:0000115 diff --git a/src/ontology/reports/obo_qc_dpo.owl.txt b/src/ontology/reports/obo_qc_dpo.owl.txt index 81dadc8..cf0ecbe 100644 --- a/src/ontology/reports/obo_qc_dpo.owl.txt +++ b/src/ontology/reports/obo_qc_dpo.owl.txt @@ -229,12 +229,6 @@ WARN missing_definition FBcv:0000347 IAO:0000115 WARN missing_definition FBcv:0006003 IAO:0000115 WARN missing_definition FBcv:0006007 IAO:0000115 WARN missing_definition FBcv:0008000 IAO:0000115 -WARN missing_definition FBdv:00004886 IAO:0000115 -WARN missing_definition FBdv:00005287 IAO:0000115 -WARN missing_definition FBdv:00005288 IAO:0000115 -WARN missing_definition FBdv:00007009 IAO:0000115 -WARN missing_definition FBdv:00007024 IAO:0000115 -WARN missing_definition FBdv:00018001 IAO:0000115 WARN missing_definition IAO:0000115 IAO:0000115 WARN missing_definition IAO:0000700 IAO:0000115 WARN missing_definition IAO:0100001 IAO:0000115 diff --git a/src/ontology/reports/robot_simple_diff.txt b/src/ontology/reports/robot_simple_diff.txt index e333e17..fb6ae7c 100644 --- a/src/ontology/reports/robot_simple_diff.txt +++ b/src/ontology/reports/robot_simple_diff.txt @@ -1,133 +1,15 @@ -22 axioms in left ontology but not in right ontology: -- Annotation( "03:05:2023 17:45"^^xsd:string) -- Annotation(owl:versionInfo "2023-05-03"^^xsd:string) -- AnnotationAssertion( ) -- AnnotationAssertion( ) -- AnnotationAssertion( ) -- AnnotationAssertion( "FlyBase miscellaneous CV"^^xsd:string) -- AnnotationAssertion( "FlyBase miscellaneous CV"^^xsd:string) -- AnnotationAssertion( "FlyBase miscellaneous CV"^^xsd:string) -- AnnotationAssertion( "FlyBase miscellaneous CV"^^xsd:string) -- AnnotationAssertion( "FlyBase miscellaneous CV"^^xsd:string) -- AnnotationAssertion( "BFO:0000050"^^xsd:string) -- AnnotationAssertion( "BFO:0000051"^^xsd:string) -- AnnotationAssertion( "BFO:0000063"^^xsd:string) -- AnnotationAssertion( "RO:0000052"^^xsd:string) -- AnnotationAssertion( "RO:0002351"^^xsd:string) -- AnnotationAssertion(Annotation( "FBC:DOC"^^xsd:string) "A phenotype in which the aging process is slower than in wild-type."^^xsd:string) -- AnnotationAssertion(Annotation( "FBC:DOC"^^xsd:string) "A phenotype in which the aging process is accelerated compared to wild-type."^^xsd:string) -- AnnotationAssertion(Annotation( "FBC:DOS"^^xsd:string) Annotation( "GOC:cjm"^^xsd:string) Annotation( "GOC:dph"^^xsd:string) Annotation( "GOC:ems"^^xsd:string) Annotation( "GOC:pf"^^xsd:string) Annotation( "Wikipedia:Cell_migration"^^xsd:string) "Phenotype that is any abnormality in cell migration (GO:0016477). 'cell migration' is defined as: 'The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.'"^^xsd:string) -- AnnotationAssertion(Annotation( "FBC:TEMJ"^^xsd:string) Annotation( "GOC:ems"^^xsd:string) Annotation( "PMID:18050396"^^xsd:string) Annotation( "PMID:31164023"^^xsd:string) "Phenotype that is any abnormality in oviposition (GO:0018991) despite production of eggs. 'oviposition' is defined as: 'A reproductive behavior that results in the deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.'."^^xsd:string) -- AnnotationAssertion(Annotation( "GOC:PO_curators"^^xsd:string) "Phenotype that is any abnormality in aging."^^xsd:string) -- AnnotationAssertion(Annotation( "ISBN:978-0-19-850673-7"^^xsd:string) "Phenotype that is an increase in the number of cells in a tissue or organ, usually associated with an increase in size, where the affected tissue or organ maintains its normal form."^^xsd:string) -- OntologyID(OntologyIRI() VersionIRI()) +8 axioms in left ontology but not in right ontology: +- Annotation( "05:07:2023 14:34"^^xsd:string) +- Annotation(owl:versionInfo "2023-07-05"^^xsd:string) +- AnnotationAssertion( ) +- AnnotationAssertion( ) +- AnnotationAssertion( "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +- AnnotationAssertion(Annotation( "FBC:DPG"^^xsd:string) "A relation between a developmental stage and another, larger developmental stage during which it happens."^^xsd:string) +- AnnotationAssertion(rdfs:label "substage of"^^xsd:string) +- OntologyID(OntologyIRI() VersionIRI()) -108 axioms in right ontology but not in left ontology: -+ Annotation( "09:02:2023 12:00"^^xsd:string) -+ Annotation(owl:versionInfo "2023-02-09"^^xsd:string) -+ AnnotationAssertion( "has ontology root term"^^xsd:string) -+ AnnotationAssertion( "this fragility inheres in this vase"^^xsd:string) -+ AnnotationAssertion( "this red color inheres in this apple"^^xsd:string) -+ AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."^^xsd:string) -+ AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"^^xsd:string) -+ AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"^^xsd:string) -+ AnnotationAssertion( "A dependent inheres in its bearer at all times for which the dependent exists."^^xsd:string) -+ AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of inheres in part of"^^xsd:string) -+ AnnotationAssertion( "Nicolas Matentzoglu"^^xsd:string) -+ AnnotationAssertion( "Chris Mungall"^^xsd:string) -+ AnnotationAssertion( "Chris Mungall"^^xsd:string) -+ AnnotationAssertion( "Chris Mungall"^^xsd:string) -+ AnnotationAssertion( ) -+ AnnotationAssertion( ) -+ AnnotationAssertion( ) -+ AnnotationAssertion( ) -+ AnnotationAssertion( "BFO:0000050"^^xsd:string) -+ AnnotationAssertion( "OBO_REL:part_of"^^xsd:string) -+ AnnotationAssertion( "BFO:0000051"^^xsd:string) -+ AnnotationAssertion( "OBO_REL:has_part"^^xsd:string) -+ AnnotationAssertion( "BFO:0000063"^^xsd:string) -+ AnnotationAssertion( "IAO:0000700"^^xsd:string) -+ AnnotationAssertion( "RO:0000052"^^xsd:string) -+ AnnotationAssertion( "RO:0002351"^^xsd:string) -+ AnnotationAssertion( "http://purl.org/dc/elements/1.1/creator"^^xsd:string) -+ AnnotationAssertion( "http://purl.org/dc/elements/1.1/description"^^xsd:string) -+ AnnotationAssertion( "http://purl.org/dc/elements/1.1/title"^^xsd:string) -+ AnnotationAssertion( "http://purl.org/dc/terms/contributor"^^xsd:string) -+ AnnotationAssertion( "http://purl.org/dc/terms/date"^^xsd:string) -+ AnnotationAssertion( "http://purl.org/dc/terms/license"^^xsd:string) -+ AnnotationAssertion( "external"^^xsd:string) -+ AnnotationAssertion( "quality"^^xsd:string) -+ AnnotationAssertion( "relationship"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "chebi_ontology"^^xsd:string) -+ AnnotationAssertion( "external"^^xsd:string) -+ AnnotationAssertion( "quality"^^xsd:string) -+ AnnotationAssertion( "relationship"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "external"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "fly_anatomy.ontology"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "uberon"^^xsd:string) -+ AnnotationAssertion( "part_of"^^xsd:string) -+ AnnotationAssertion( "has_part"^^xsd:string) -+ AnnotationAssertion( "precedes"^^xsd:string) -+ AnnotationAssertion( "has_ontology_root_term"^^xsd:string) -+ AnnotationAssertion( "characteristic_of"^^xsd:string) -+ AnnotationAssertion( "has_member"^^xsd:string) -+ AnnotationAssertion( "dc-creator"^^xsd:string) -+ AnnotationAssertion( "dc-description"^^xsd:string) -+ AnnotationAssertion( "dc-title"^^xsd:string) -+ AnnotationAssertion( "dc-contributor"^^xsd:string) -+ AnnotationAssertion( "dcterms-date"^^xsd:string) -+ AnnotationAssertion( "dcterms-license"^^xsd:string) -+ AnnotationAssertion( "false"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "true"^^xsd:boolean) -+ AnnotationAssertion( "part_of"^^xsd:string) -+ AnnotationAssertion( "has_part"^^xsd:string) -+ AnnotationAssertion( "precedes"^^xsd:string) -+ AnnotationAssertion( "has_ontology_root_term"^^xsd:string) -+ AnnotationAssertion( "characteristic_of"^^xsd:string) -+ AnnotationAssertion( "has_member"^^xsd:string) -+ AnnotationAssertion( "dc-creator"^^xsd:string) -+ AnnotationAssertion( "dc-description"^^xsd:string) -+ AnnotationAssertion( "dc-title"^^xsd:string) -+ AnnotationAssertion( "dc-contributor"^^xsd:string) -+ AnnotationAssertion( "dcterms-date"^^xsd:string) -+ AnnotationAssertion( "dcterms-license"^^xsd:string) -+ AnnotationAssertion(Annotation( "FBC:DOC"^^xsd:string) "A phenotype in which the aging process (GO:0007568) is slower than in wild-type."^^xsd:string) -+ AnnotationAssertion(Annotation( "FBC:DOC"^^xsd:string) "A phenotype in which the aging process (GO:0007568) is accelerated compared to wild-type."^^xsd:string) -+ AnnotationAssertion(Annotation( "FBC:DOS"^^xsd:string) Annotation( "GOC:cjm"^^xsd:string) Annotation( "GOC:dph"^^xsd:string) Annotation( "GOC:ems"^^xsd:string) Annotation( "GOC:pf"^^xsd:string) Annotation( "Wikipedia:Cell_migration"^^xsd:string) "Phenotype that is any abnormality in cell migration (GO:0016477). 'cell migration' is defined as: 'The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.'"^^xsd:string) -+ AnnotationAssertion(Annotation( "FBC:TEMJ"^^xsd:string) Annotation( "GOC:ems"^^xsd:string) "Phenotype that is any abnormality in oviposition (GO:0018991) despite production of eggs. 'oviposition' is defined as: 'The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.'."^^xsd:string) -+ AnnotationAssertion(Annotation( "GOC:PO_curators"^^xsd:string) "Phenotype that is any abnormality in aging (GO:0007568). 'aging' is defined as: 'A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).'"^^xsd:string) -+ AnnotationAssertion(Annotation( "ISBN:9780198506737"^^xsd:string) "Phenotype that is an increase in the number of cells in a tissue or organ, usually associated with an increase in size, where the affected tissue or organ maintains its normal form."^^xsd:string) -+ AnnotationAssertion(rdfs:comment "We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'."^^xsd:string) -+ AnnotationAssertion(rdfs:label "has ontology root term"^^xsd:string) -+ AnnotationAssertion(rdfs:label "creator"^^xsd:string) -+ AnnotationAssertion(rdfs:label "description"^^xsd:string) -+ AnnotationAssertion(rdfs:label "title"^^xsd:string) -+ AnnotationAssertion(rdfs:label "contributor"^^xsd:string) -+ AnnotationAssertion(rdfs:label "date"^^xsd:string) -+ AnnotationAssertion(rdfs:label "license"^^xsd:string) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ Declaration(AnnotationProperty()) -+ OntologyID(OntologyIRI() VersionIRI()) +4 axioms in right ontology but not in left ontology: ++ Annotation( "03:05:2023 17:45"^^xsd:string) ++ Annotation(owl:versionInfo "2023-05-03"^^xsd:string) ++ AnnotationAssertion(rdfs:label "substage_of"^^xsd:string) ++ OntologyID(OntologyIRI() VersionIRI()) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 66a2632..ce1d08a 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-05-03") + +Annotation(owl:versionInfo "2023-07-05") Declaration(Class()) Declaration(Class())