Merge pull request #93 from FlyBase/release_2024-04-18

release files 2024-04-18

fbdv.obo

@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: fbdv/releases/2024-02-21
-date: 21:02:2024 14:18
+data-version: fbdv/releases/2024-04-18
+date: 18:04:2024 09:08
 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
 subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
 subsetdef: goslim_aspergillus "Aspergillus GO slim"
@@ -14,10 +14,6 @@ subsetdef: goslim_plant "Plant GO slim"
 subsetdef: goslim_pombe "Fission yeast GO slim"
 subsetdef: goslim_yeast "Yeast GO slim"
 subsetdef: gosubset_prok "Prokaryotic GO subset"
-subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
-subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
-subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
-subsetdef: ro-eco ""
 default-namespace: FlyBase_development_CV
 namespace-id-rule: * FBdv:$sequence(8,7000,10000)$
 ontology: fbdv.obo
@@ -32,7 +28,7 @@ property_value: IAO:0000700 FBdv:00000000
 property_value: IAO:0000700 FBdv:00005259
 property_value: IAO:0000700 FBdv:00007013
 property_value: IAO:0000700 FBdv:00007024
-property_value: owl:versionInfo "2024-02-21" xsd:string
+property_value: owl:versionInfo "2024-04-18" xsd:string
 
 [Term]
 id: FBdv:00000000
@@ -2157,32 +2153,16 @@ def: "A part of relation that applies only between occurrents." []
 id: RO:0002087
 name: immediately preceded by
 comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
-property_value: IAO:0000118 "starts_at_end_of" xsd:string
 inverse_of: RO:0002090 ! immediately precedes
 
 [Typedef]
 id: RO:0002090
 name: immediately precedes
 comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
-subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
-property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
-property_value: IAO:0000118 "ends_at_start_of" xsd:string
-property_value: IAO:0000118 "meets" xsd:string
-property_value: RO:0002575 BFO:0000063
 
 [Typedef]
 id: RO:0002092
 name: happens during
 comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
-subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
-subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
-subset: http://purl.obolibrary.org/obo/valid_for_gocam
-subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
-property_value: IAO:0000118 "d" xsd:string
-property_value: IAO:0000118 "during" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI
 is_transitive: true
 

fly_development.obo

@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: 2024-02-21
-date: 21:02:2024 14:18
+data-version: 2024-04-18
+date: 18:04:2024 09:08
 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
 subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
 subsetdef: goslim_aspergillus "Aspergillus GO slim"
@@ -14,10 +14,6 @@ subsetdef: goslim_plant "Plant GO slim"
 subsetdef: goslim_pombe "Fission yeast GO slim"
 subsetdef: goslim_yeast "Yeast GO slim"
 subsetdef: gosubset_prok "Prokaryotic GO subset"
-subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
-subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
-subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
-subsetdef: ro-eco ""
 default-namespace: FlyBase development CV
 namespace-id-rule: * FBdv:$sequence(8,7000,10000)$
 ontology: fbdv/fbdv-simple
@@ -2054,10 +2050,6 @@ relationship: substage_of FBdv:00005369 ! adult stage
 id: happens_during
 name: happens_during
 comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
-subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
-subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
-subset: http://purl.obolibrary.org/obo/valid_for_gocam
-subset: ro-eco
 xref: RO:0002092
 is_transitive: true
 

src/ontology/reports/obo_qc_fbdv.obo.txt

@@ -15,7 +15,6 @@ WARN	missing_definition	oboInOwl:hasOBOFormatVersion	IAO:0000115
 WARN	missing_definition	oboInOwl:hasOBONamespace	IAO:0000115	
 WARN	missing_definition	oboInOwl:hasRelatedSynonym	IAO:0000115	
 WARN	missing_definition	oboInOwl:id	IAO:0000115	
-WARN	missing_definition	oboInOwl:inSubset	IAO:0000115	
 WARN	missing_superclass	FBdv:00000000	rdfs:subClassOf	
 WARN	missing_superclass	FBdv:00005259	rdfs:subClassOf	
 WARN	missing_superclass	FBdv:00007013	rdfs:subClassOf	

src/ontology/reports/obsoletes.tsv

@@ -0,0 +1,13 @@
+?cls	?replCls	?consCls
+<http://purl.obolibrary.org/obo/FBdv_00005305>		
+<http://purl.obolibrary.org/obo/FBdv_00005310>		
+<http://purl.obolibrary.org/obo/FBdv_00005320>		
+<http://purl.obolibrary.org/obo/FBdv_00005326>		
+<http://purl.obolibrary.org/obo/FBdv_00005329>	"FBdv:00005330"	
+<http://purl.obolibrary.org/obo/FBdv_00005373>	<http://purl.obolibrary.org/obo/FBdv_00005370>	
+<http://purl.obolibrary.org/obo/FBdv_00005374>	<http://purl.obolibrary.org/obo/FBdv_00005371>	
+<http://purl.obolibrary.org/obo/FBdv_00005375>	<http://purl.obolibrary.org/obo/FBdv_00006012>	
+<http://purl.obolibrary.org/obo/FBdv_00005412>		
+<http://purl.obolibrary.org/obo/FBdv_00007008>		
+<http://purl.obolibrary.org/obo/FBdv_00007010>	<http://purl.obolibrary.org/obo/FBdv_00005259>	
+<http://purl.obolibrary.org/obo/FBdv_root_00000000>	<http://purl.obolibrary.org/obo/FBdv_00000000>