From 1ad2ef7beae84013c088c17a91eb7c5f5773d16d Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 16 Oct 2024 11:55:58 +0100 Subject: [PATCH 1/4] Obsolete neuronal brush cells and adjust logical definition of tanycyte Fixes #2514 #2634 --- src/ontology/cl-edit.owl | 12 +-- src/ontology/imports/merged_import.owl | 116 +++++++++++++------------ 2 files changed, 67 insertions(+), 61 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 588dbc3bf..e246ebd82 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3330,7 +3330,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (preferred_root) +# Annotation Property: obo:IAO_0000700 (has ontology root term) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3424,11 +3424,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -8218,10 +8218,9 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo AnnotationAssertion(rdfs:label obo:CL_0000554 "gastrin stimulating hormone secreting cell") SubClassOf(obo:CL_0000554 obo:CL_0000167) -# Class: obo:CL_0000555 (neuronal brush cell) +# Class: obo:CL_0000555 (obsolete neuronal brush cell) -AnnotationAssertion(rdfs:label obo:CL_0000555 "neuronal brush cell") -SubClassOf(obo:CL_0000555 obo:CL_0000117) +AnnotationAssertion(rdfs:label obo:CL_0000555 "obsolete neuronal brush cell") # Class: obo:CL_0000556 (megakaryocyte) @@ -14590,6 +14589,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002085 "BTO:0001953") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002085 "FMA:54560") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasExactSynonym obo:CL_0002085 "stretch cell") AnnotationAssertion(rdfs:label obo:CL_0002085 "tanycyte") +SubClassOf(obo:CL_0002085 obo:CL_0000065) SubClassOf(obo:CL_0002085 obo:CL_0000683) SubClassOf(obo:CL_0002085 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004670)) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index d1e2a21f9..36a4260a5 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -14325,8 +14325,8 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "definition"@en) # Annotation Property: (editor note) @@ -14347,8 +14347,8 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "term_tracker_item") AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) -AnnotationAssertion(rdfs:label "term tracker item"@en) AnnotationAssertion(rdfs:label "term tracker item") +AnnotationAssertion(rdfs:label "term tracker item"@en) # Annotation Property: (expand expression to) @@ -14363,15 +14363,15 @@ AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion(rdfs:label "has ontology root term"@en) AnnotationAssertion(rdfs:label "has ontology root term") +AnnotationAssertion(rdfs:label "has ontology root term"@en) # Annotation Property: (term replaced by) AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "term replaced by"@en) AnnotationAssertion(rdfs:label "term replaced by") +AnnotationAssertion(rdfs:label "term replaced by"@en) # Annotation Property: (defined by construct) @@ -14870,12 +14870,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of"@en) AnnotationAssertion(rdfs:label "part of") +AnnotationAssertion(rdfs:label "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") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -14895,8 +14895,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part"@en) AnnotationAssertion(rdfs:label "has part") +AnnotationAssertion(rdfs:label "has part"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -14909,8 +14909,8 @@ AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") -AnnotationAssertion(rdfs:label "preceded by"@en) AnnotationAssertion(rdfs:label "preceded by") +AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -14925,8 +14925,8 @@ AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") -AnnotationAssertion(rdfs:label "precedes"@en) AnnotationAssertion(rdfs:label "precedes") +AnnotationAssertion(rdfs:label "precedes"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -14943,8 +14943,8 @@ AnnotationAssertion( ) AnnotationAssertion( "occurs_in") AnnotationAssertion(rdfs:comment "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:label "occurs in"@en) AnnotationAssertion(rdfs:label "occurs in") +AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -14992,8 +14992,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "bearer_of") AnnotationAssertion( "bearer_of") -AnnotationAssertion(rdfs:label "has characteristic"@en) AnnotationAssertion(rdfs:label "bearer of") +AnnotationAssertion(rdfs:label "has characteristic"@en) InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -15004,8 +15004,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") -AnnotationAssertion(rdfs:label "participates in"@en) AnnotationAssertion(rdfs:label "participates in") +AnnotationAssertion(rdfs:label "participates in"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15018,8 +15018,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_participant") AnnotationAssertion( "has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) AnnotationAssertion(rdfs:label "has participant") +AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15126,8 +15126,8 @@ AnnotationAssertion( ) AnnotationAssertion( "bounding_layer_of") AnnotationAssertion(rdfs:comment "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.") -AnnotationAssertion(rdfs:label "bounding layer of"@en) AnnotationAssertion(rdfs:label "bounding layer of") +AnnotationAssertion(rdfs:label "bounding layer of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) @@ -15172,8 +15172,8 @@ AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by"@en) AnnotationAssertion(rdfs:label "immediately preceded by") +AnnotationAssertion(rdfs:label "immediately preceded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15185,8 +15185,8 @@ AnnotationAssertion( ) AnnotationAssertion( "immediately_precedes") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes"@en) AnnotationAssertion(rdfs:label "immediately precedes") +AnnotationAssertion(rdfs:label "immediately precedes"@en) SubObjectPropertyOf( ) # Object Property: (has soma location) @@ -15292,8 +15292,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "overlaps") -AnnotationAssertion(rdfs:label "overlaps"@en) AnnotationAssertion(rdfs:label "overlaps") +AnnotationAssertion(rdfs:label "overlaps"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -15414,8 +15414,8 @@ AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") -AnnotationAssertion(rdfs:label "has component"@en) AnnotationAssertion(rdfs:label "has component") +AnnotationAssertion(rdfs:label "has component"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -15479,8 +15479,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "regulates") -AnnotationAssertion(rdfs:label "regulates"@en) AnnotationAssertion(rdfs:label "regulates") +AnnotationAssertion(rdfs:label "regulates"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -15498,8 +15498,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "negatively_regulates") -AnnotationAssertion(rdfs:label "negatively regulates"@en) AnnotationAssertion(rdfs:label "negatively regulates") +AnnotationAssertion(rdfs:label "negatively regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15514,8 +15514,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "positively_regulates") -AnnotationAssertion(rdfs:label "positively regulates"@en) AnnotationAssertion(rdfs:label "positively regulates") +AnnotationAssertion(rdfs:label "positively regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15529,8 +15529,8 @@ AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") -AnnotationAssertion(rdfs:label "capable of"@en) AnnotationAssertion(rdfs:label "capable of") +AnnotationAssertion(rdfs:label "capable of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15542,8 +15542,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion(rdfs:label "capable of part of"@en) AnnotationAssertion(rdfs:label "capable of part of") +AnnotationAssertion(rdfs:label "capable of part of"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15566,8 +15566,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") -AnnotationAssertion(rdfs:label "adjacent to"@en) AnnotationAssertion(rdfs:label "adjacent to") +AnnotationAssertion(rdfs:label "adjacent to"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15604,8 +15604,8 @@ AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") -AnnotationAssertion(rdfs:label "starts with"@en) AnnotationAssertion(rdfs:label "starts with") +AnnotationAssertion(rdfs:label "starts with"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15640,8 +15640,8 @@ AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") -AnnotationAssertion(rdfs:label "ends with"@en) AnnotationAssertion(rdfs:label "ends with") +AnnotationAssertion(rdfs:label "ends with"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15654,8 +15654,8 @@ AnnotationAssertion( "has_start_location") AnnotationAssertion( ) AnnotationAssertion( "has_start_location") -AnnotationAssertion(rdfs:label "has start location"@en) AnnotationAssertion(rdfs:label "has start location") +AnnotationAssertion(rdfs:label "has start location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15668,8 +15668,8 @@ AnnotationAssertion( "has_end_location") AnnotationAssertion( ) AnnotationAssertion( "has_end_location") -AnnotationAssertion(rdfs:label "has end location"@en) AnnotationAssertion(rdfs:label "has end location") +AnnotationAssertion(rdfs:label "has end location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15685,8 +15685,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_input") -AnnotationAssertion(rdfs:label "has input"@en) AnnotationAssertion(rdfs:label "has input") +AnnotationAssertion(rdfs:label "has input"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15703,8 +15703,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_output") -AnnotationAssertion(rdfs:label "has output"@en) AnnotationAssertion(rdfs:label "has output") +AnnotationAssertion(rdfs:label "has output"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15818,8 +15818,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_developmental_progression_of") AnnotationAssertion( "results_in_developmental_progression_of") -AnnotationAssertion(rdfs:label "results in developmental progression of"@en) AnnotationAssertion(rdfs:label "results in developmental progression of") +AnnotationAssertion(rdfs:label "results in developmental progression of"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15835,8 +15835,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_development_of") -AnnotationAssertion(rdfs:label "results in development of"@en) AnnotationAssertion(rdfs:label "results in development of") +AnnotationAssertion(rdfs:label "results in development of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15849,8 +15849,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) AnnotationAssertion(rdfs:label "results in formation of") +AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15865,8 +15865,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_morphogenesis_of") -AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) AnnotationAssertion(rdfs:label "results in morphogenesis of") +AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15880,8 +15880,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_maturation_of") -AnnotationAssertion(rdfs:label "results in maturation of"@en) AnnotationAssertion(rdfs:label "results in maturation of") +AnnotationAssertion(rdfs:label "results in maturation of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15933,8 +15933,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_acquisition_of_features_of") -AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) AnnotationAssertion(rdfs:label "results in acquisition of features of") +AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -15979,8 +15979,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "regulates_levels_of") AnnotationAssertion( "regulates_levels_of") -AnnotationAssertion(rdfs:label "regulates levels of"@en) AnnotationAssertion(rdfs:label "regulates levels of") +AnnotationAssertion(rdfs:label "regulates levels of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15993,8 +15993,8 @@ AnnotationAssertion( "regulated_by") AnnotationAssertion( ) AnnotationAssertion( "regulated_by") -AnnotationAssertion(rdfs:label "regulated by"@en) AnnotationAssertion(rdfs:label "regulated by") +AnnotationAssertion(rdfs:label "regulated by"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -16008,8 +16008,8 @@ AnnotationAssertion( "negatively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "negatively_regulated_by") -AnnotationAssertion(rdfs:label "negatively regulated by"@en) AnnotationAssertion(rdfs:label "negatively regulated by") +AnnotationAssertion(rdfs:label "negatively regulated by"@en) SubObjectPropertyOf( ) # Object Property: (positively regulated by) @@ -16020,8 +16020,8 @@ AnnotationAssertion( "positively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "positively_regulated_by") -AnnotationAssertion(rdfs:label "positively regulated by"@en) AnnotationAssertion(rdfs:label "positively regulated by") +AnnotationAssertion(rdfs:label "positively regulated by"@en) SubObjectPropertyOf( ) # Object Property: (related via localization to) @@ -16041,8 +16041,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_start_location") -AnnotationAssertion(rdfs:label "has target start location"@en) AnnotationAssertion(rdfs:label "has target start location") +AnnotationAssertion(rdfs:label "has target start location"@en) SubObjectPropertyOf( ) # Object Property: (has target end location) @@ -16055,8 +16055,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_end_location") -AnnotationAssertion(rdfs:label "has target end location"@en) AnnotationAssertion(rdfs:label "has target end location") +AnnotationAssertion(rdfs:label "has target end location"@en) SubObjectPropertyOf( ) # Object Property: (results in transport along) @@ -16066,8 +16066,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_along") AnnotationAssertion( "results_in_transport_along") -AnnotationAssertion(rdfs:label "results in transport along"@en) AnnotationAssertion(rdfs:label "results in transport along") +AnnotationAssertion(rdfs:label "results in transport along"@en) SubObjectPropertyOf( ) # Object Property: (results in transport across) @@ -16078,8 +16078,8 @@ AnnotationAssertion( "results_in_transport_across") AnnotationAssertion( ) AnnotationAssertion( "results_in_transport_across") -AnnotationAssertion(rdfs:label "results in transport across"@en) AnnotationAssertion(rdfs:label "results in transport across") +AnnotationAssertion(rdfs:label "results in transport across"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16089,8 +16089,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_growth_of") AnnotationAssertion( "results_in_growth_of") -AnnotationAssertion(rdfs:label "results in growth of"@en) AnnotationAssertion(rdfs:label "results in growth of") +AnnotationAssertion(rdfs:label "results in growth of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16100,8 +16100,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_to_from_or_in") AnnotationAssertion( "results_in_transport_to_from_or_in") -AnnotationAssertion(rdfs:label "results in transport to from or in"@en) AnnotationAssertion(rdfs:label "results in transport to from or in") +AnnotationAssertion(rdfs:label "results in transport to from or in"@en) SubObjectPropertyOf( ) # Object Property: (member of) @@ -16135,8 +16135,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "output_of") -AnnotationAssertion(rdfs:label "output of"@en) AnnotationAssertion(rdfs:label "output of") +AnnotationAssertion(rdfs:label "output of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16254,8 +16254,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "causally_downstream_of") AnnotationAssertion( "causally_downstream_of") -AnnotationAssertion(rdfs:label "causally downstream of"@en) AnnotationAssertion(rdfs:label "causally downstream of") +AnnotationAssertion(rdfs:label "causally downstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16289,8 +16289,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of") -AnnotationAssertion(rdfs:label "causally upstream of"@en) AnnotationAssertion(rdfs:label "causally upstream of") +AnnotationAssertion(rdfs:label "causally upstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -16645,8 +16645,8 @@ AnnotationAssertion( ) AnnotationAssertion( "produces") AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") -AnnotationAssertion(rdfs:label "produces"@en) AnnotationAssertion(rdfs:label "produces") +AnnotationAssertion(rdfs:label "produces"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16659,8 +16659,8 @@ AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") -AnnotationAssertion(rdfs:label "produced by"@en) AnnotationAssertion(rdfs:label "produced by") +AnnotationAssertion(rdfs:label "produced by"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16740,8 +16740,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_small_molecule_activator") AnnotationAssertion( "has_small_molecule_activator") -AnnotationAssertion(rdfs:label "has small molecule activator"@en) AnnotationAssertion(rdfs:label "has small molecule activator") +AnnotationAssertion(rdfs:label "has small molecule activator"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16757,8 +16757,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "acts_on_population_of") -AnnotationAssertion(rdfs:label "acts on population of"@en) AnnotationAssertion(rdfs:label "acts on population of") +AnnotationAssertion(rdfs:label "acts on population of"@en) SubObjectPropertyOf( ) # Object Property: (is small molecule regulator of) @@ -16790,8 +16790,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_fusion_of") -AnnotationAssertion(rdfs:label "results in fusion of"@en) AnnotationAssertion(rdfs:label "results in fusion of") +AnnotationAssertion(rdfs:label "results in fusion of"@en) SubObjectPropertyOf( ) # Object Property: (has synaptic IO in region) @@ -17074,12 +17074,18 @@ SubClassOf( ) -# Class: () +# Class: (cell) DisjointClasses( ) DisjointClasses( ) DisjointClasses( ) +# Class: (obsolete neuronal brush cell) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "https://github.com/obophenotype/cell-ontology/issues/2634") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) + # Class: (vacuole inheritance) AnnotationAssertion(Annotation( "GOC:mcc") Annotation( "PMID:10873824") Annotation( "PMID:14616069") "The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.") From 9f91f3e35b52bab4412516e628925658df608a6a Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 16 Oct 2024 12:02:06 +0100 Subject: [PATCH 2/4] Update cl-edit.owl --- src/ontology/cl-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index e246ebd82..4fa8a920e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -14590,7 +14590,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002085 "FMA:54560") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasExactSynonym obo:CL_0002085 "stretch cell") AnnotationAssertion(rdfs:label obo:CL_0002085 "tanycyte") SubClassOf(obo:CL_0002085 obo:CL_0000065) -SubClassOf(obo:CL_0002085 obo:CL_0000683) SubClassOf(obo:CL_0002085 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004670)) # Class: obo:CL_0002086 (specialized cardiac myocyte) From 23fd4b8732734980952debc0a00caa8b315c6b05 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 16 Oct 2024 12:10:37 +0100 Subject: [PATCH 3/4] Update merged_import.owl --- src/ontology/imports/merged_import.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 36a4260a5..ce9391f0e 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -17082,7 +17082,7 @@ DisjointClasses( (obsolete neuronal brush cell) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "https://github.com/obophenotype/cell-ontology/issues/2634") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) From 8b40e9a583b6fa2ff6a55cdfb0ca378befa6e1a2 Mon Sep 17 00:00:00 2001 From: dosumis Date: Mon, 16 Dec 2024 15:08:07 +0000 Subject: [PATCH 4/4] Update cl-edit.owl Fixed incomplete obsoletion --- src/ontology/cl-edit.owl | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 00c8a97bd..922b842d9 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3126,6 +3126,7 @@ Declaration(Class(obo:GO_0031045)) Declaration(Class(obo:GO_0036053)) Declaration(Class(obo:GO_0036376)) Declaration(Class(obo:GO_0042599)) +Declaration(Class(obo:GO_0044237)) Declaration(Class(obo:GO_0044316)) Declaration(Class(obo:GO_0070278)) Declaration(Class(obo:GO_0070483)) @@ -3342,7 +3343,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (preferred_root) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3436,11 +3437,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -5118,8 +5119,8 @@ AnnotationAssertion(owl:deprecated obo:CL_0000161 "true"^^xsd:boolean) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "PMID:31613538") Annotation(oboInOwl:hasDbXref "PMID:31670611") obo:IAO_0000115 obo:CL_0000162 "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "BTO:0001780") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "FMA:62901") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") oboInOwl:hasExactSynonym obo:CL_0000162 "gastric parietal cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") Annotation(oboInOwl:hasDbXref "PMID:31613538") rdfs:comment obo:CL_0000162 "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.") AnnotationAssertion(rdfs:label obo:CL_0000162 "parietal cell") SubClassOf(obo:CL_0000162 obo:CL_0000151) @@ -8237,7 +8238,9 @@ SubClassOf(obo:CL_0000554 obo:CL_0000167) # Class: obo:CL_0000555 (obsolete neuronal brush cell) +AnnotationAssertion(obo:IAO_0100001 obo:CL_0000555 obo:CL_4023161) AnnotationAssertion(rdfs:label obo:CL_0000555 "obsolete neuronal brush cell") +AnnotationAssertion(owl:deprecated obo:CL_0000555 "true"^^xsd:boolean) # Class: obo:CL_0000556 (megakaryocyte) @@ -28012,8 +28015,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "HPA:HPA") Annotation(oboInOwl AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001591 "CALOHA:TS-1277") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "fallopian tube glandular cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "fallopian tube glandular cells") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "uterine tube glandular cell") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_1001591 "oviduct glandular cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "uterine tube glandular cell") AnnotationAssertion(rdfs:label obo:CL_1001591 "oviduct secretory cell") EquivalentClasses(obo:CL_1001591 ObjectIntersectionOf(obo:CL_1100001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000993))) SubClassOf(obo:CL_1001591 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004804)) @@ -30506,6 +30509,7 @@ SubClassOf(obo:CL_4023160 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061537)) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9193142") Annotation(oboInOwl:hasDbXref "WikipediaVersioned:Unipolar_brush_cell&oldid=1045937026") obo:IAO_0000115 obo:CL_4023161 "An excitatory glutamatergic interneuron found in the granular layer of the cerebellar cortex and also in the granule cell domain of the cochlear nucleus. Unipolar brush cells have a round or oval cell body with usually a single short dendrite that ends in a brush-like tuft of short dendrites unique to them known as dendrioles.") AnnotationAssertion(terms:contributor obo:CL_4023161 ) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023161 "neuronal brush cell") AnnotationAssertion(rdfs:label obo:CL_4023161 "unipolar brush cell") SubClassOf(obo:CL_4023161 obo:CL_0000099) SubClassOf(obo:CL_4023161 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070025))