Makefile updates to publish go-plus, go-gaf, go-lego as standalone fi…

…les (no imports). Fixes #16876.

src/ontology/Makefile

@@ -68,6 +68,8 @@ GO_BASIC_RELATIONS = BFO:0000050 RO:0002211 RO:0002212 RO:0002213
 GO_MAIN_RELATIONS = $(GO_BASIC_RELATIONS) BFO:0000051 BFO:0000066 RO:0002091 RO:0002092 RO:0002093
 
 GO_PLUS = extensions/go-plus
+GO_GAF = extensions/go-gaf
+GO_LEGO = extensions/go-lego
 
 SPARQLDIR = ../sparql
 REPORTDIR = $(RELEASEDIR)/reports
@@ -187,16 +189,25 @@ reasoned.owl: enhanced.owl $(SRC)-check regulates_chains.ofn
 	$(ROBOT) reason -i $< -r ELK -e asserted-only relax reduce annotate -V $(RELEASE_URIBASE)/$(ONT).owl unmerge -i regulates_chains.ofn -o $@
 
 # equivalent to reasoned, but we rename
+# TODO cleanup redundancies with merge here and with go-base
 $(GO_PLUS).owl: reasoned.owl
-	$(ROBOT) annotate -i $< -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@
+	$(ROBOT) merge -i $< --collapse-import-closure true --include-annotations false annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@
 .PRECIOUS: $(GO_PLUS).owl
 
 # Create release file containing GO-asserted axioms, no external axioms, and no inferences.
-# GO artifacts to merge are hardcoded here.
+# GO artifacts to merge are hardcoded here. Would make sense to eventually consolidate go-plus
+# as just the merge of go-base.
 go-base.owl: enhanced.owl
 	$(OWLTOOLS) $(USECAT) $< --remove-imports-declarations -o -f ofn $@.tmp &&\
 	$(ROBOT) merge -i $@.tmp -i extensions/go-gci.owl -i extensions/go-bridge.owl -i extensions/ro_pending.owl -i imports/x-disjoint.owl annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@ && rm $@.tmp
 
+$(GO_GAF).owl: extensions/go-gaf-edit.ofn $(GO_PLUS).owl extensions/gorel.owl mirror/cl-download.owl mirror/taxslim.owl mirror/taxslim-disjoint-over-in-taxon.owl
+	$(ROBOT) merge -i $< --collapse-import-closure true --include-annotations false annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@
+
+# Not all imports are being pre-mirrored; the ones that are should be dependencies
+$(GO_LEGO).owl: extensions/go-lego-edit.ofn $(GO_PLUS).owl mirror/ro-download.owl extensions/legorel.owl extensions/go-bfo-bridge.owl mirror/taxslim.owl mirror/taxslim-disjoint-over-in-taxon.owl
+	$(ROBOT) merge -i $< --collapse-import-closure true --include-annotations false annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@
+
 # ----------------------------------------
 # OBO and subsets
 # ----------------------------------------
@@ -336,6 +347,14 @@ mirror/ncbitaxon-download.owl: imports/ncbitaxon_terms.txt
 #	OWLTOOLS_MEMORY=12G owltools  $< --create-taxon-disjoint-over-in-taxon -s -r NCBITaxon:1 -m --set-ontology-id $OBO/zz -o
 #.PRECIOUS: mirror/ncbitaxon-download-enhanced.owl
 
+mirror/taxslim.owl: $(SRC)
+	wget --no-check-certificate $(OBO)/ncbitaxon/subsets/taxslim.owl $(WGET_OUT)
+.PRECIOUS: mirror/taxslim.owl
+
+mirror/taxslim-disjoint-over-in-taxon.owl: $(SRC)
+	wget --no-check-certificate $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl $(WGET_OUT)
+.PRECIOUS: mirror/taxslim-disjoint-over-in-taxon.owl
+
 # special case: download obo for speed for ncbitaxon
 mirror/pr-download.owl: $(SRC)
 	wget --no-check-certificate $(OBO)/pr.obo $(WGET_OUT)
@@ -369,7 +388,7 @@ mirror/cl-download.owl: $(SRC)
 # see https://github.com/geneontology/go-ontology/issues/12946
 mirror/ro-download.owl: $(SRC)
 	$(OWLTOOLS) $(OBO)/ro.owl --merge-imports-closure -o $@
-.PRECIOUS: mirror/cl-download.owl
+.PRECIOUS: mirror/ro-download.owl
 
 # general case: download remote OWL first
 mirror/%-download.owl: $(SRC)

src/ontology/catalog-v001.xml

@@ -12,6 +12,7 @@
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/chebi_roles.owl" uri="imports/chebi_roles.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/cl_import.owl" uri="imports/cl_import.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/cl-basic.owl" uri="mirror/cl-download.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/po_import.owl" uri="imports/po_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/caro_import.owl" uri="imports/caro_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/fao_import.owl" uri="imports/fao_import.owl"/>
@@ -20,12 +21,15 @@
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/oba_import.owl" uri="imports/oba_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/so_import.owl" uri="imports/so_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/ro_import.owl" uri="imports/ro_import.owl"/>
+   	<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ro.owl" uri="mirror/ro-download.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/annotation_properties.owl" uri="imports/annotation_properties.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/pato_import.owl" uri="imports/pato_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl" uri="mirror/taxslim.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl" uri="mirror/taxslim-disjoint-over-in-taxon.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/fao_import.owl" uri="imports/fao_import.owl"/>
-    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/go-plus.owl" uri="imports/go-plus.owl"/>
-    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/go-gaf.owl" uri="imports/go-gaf.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/go-plus.owl" uri="extensions/go-plus.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl" uri="extensions/go-gaf.owl"/>
    	<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/chebi.owl" uri="mirror/chebi.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/uberon/reasoner_axioms.owl" uri="go_inferences_null.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/go-taxon-groupings.owl" uri="imports/go-taxon-groupings.owl"/>
@@ -34,4 +38,5 @@
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/gorel.owl" uri="imports/gorel.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/x-disjoint.owl" uri="imports/x-disjoint.owl"/>
 	<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/reactome_xrefs_import.owl" uri="imports/reactome_xrefs_import.owl"/>
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-caro.owl" uri="mirror/uberon-bridge-to-caro.owl"/>
 </catalog>

src/ontology/extensions/go-gaf.owl → src/ontology/extensions/go-gaf-edit.ofn

@@ -6,6 +6,7 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl>
+# When adding an import, ensure this dependency is captured in the go-gaf makefile target
 Import(<http://purl.obolibrary.org/obo/go/extensions/gorel.owl>)
 Import(<http://purl.obolibrary.org/obo/cl/cl-basic.owl>)
 Import(<http://purl.obolibrary.org/obo/go/extensions/go-plus.owl>)

src/ontology/extensions/go-lego.owl → src/ontology/extensions/go-lego-edit.ofn

@@ -13,7 +13,7 @@ Import(<http://purl.obolibrary.org/obo/go/extensions/go-plus.owl>)
 Import(<http://purl.obolibrary.org/obo/go/extensions/go-bfo-bridge.owl>)
 Import(<http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl>)
 Import(<http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl>)
-Import(<http://purl.obolibrary.org/obo/eco/eco-base.owl>)
+Import(<http://purl.obolibrary.org/obo/eco/eco-basic.owl>)
 Import(<http://purl.obolibrary.org/obo/wbbt.owl>)
 Import(<http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl>)
 Import(<http://purl.obolibrary.org/obo/wbphenotype/imports/wbls_import.owl>)