Merge pull request #172 from FlyBase/release-2023-07-05

Release 2023 07 05
FlyBase · Jul 5, 2023 · c3ac3ab · c3ac3ab
2 parents 8397225 + 1ce04aa
commit c3ac3ab
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diff --git 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
@@ -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
diff --git 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
@@ -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
@@ -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