add build for reacto.owl and go-lego-reacto.owl to stage_release

addresses geneontology/pipeline#35

src/ontology/Makefile

@@ -71,6 +71,7 @@ GO_MAIN_RELATIONS = $(GO_BASIC_RELATIONS) BFO:0000051 BFO:0000066 RO:0002091 RO:
 GO_PLUS = extensions/go-plus
 GO_GAF = extensions/go-gaf
 GO_LEGO = extensions/go-lego
+GO_LEGO_REACTO = extensions/go-lego-reacto
 
 SPARQLDIR = ../sparql
 REPORTDIR = $(RELEASEDIR)/reports
@@ -79,7 +80,7 @@ REPORTDIR = $(RELEASEDIR)/reports
 # TOP LEVEL TARGETS
 # ----------------------------------------
 
-stage_release: imports/reactome_xrefs_import.owl test $(ONT).owl $(ONT).obo $(ONT).json.gz $(GO_PLUS).owl $(GO_PLUS).json.gz go-base.owl $(GO_GAF).owl $(GO_LEGO).owl go-basic.obo go-basic.json.gz subset-reports generate-mappings
+stage_release: imports/reactome_xrefs_import.owl test $(ONT).owl $(ONT).obo $(ONT).json.gz $(GO_PLUS).owl $(GO_PLUS).json.gz go-base.owl $(GO_GAF).owl $(GO_LEGO).owl $(GO_LEGO_REACTO).owl go-basic.obo go-basic.json.gz subset-reports generate-mappings
 
 test: $(SRC)-check sparql_test change-report.txt reasoned.owl unsatisfiable
 
@@ -216,6 +217,18 @@ $(GO_GAF).owl: extensions/go-gaf-edit.ofn $(GO_PLUS).owl extensions/gorel.owl mi
 $(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 reason -r ELK --exclude-duplicate-axioms true --remove-redundant-subclass-axioms true --exclude-tautologies structural relax reduce --named-classes-only true annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@
 
+extensions/reacto.owl: $(GO_LEGO).owl mirror/chebi.owl
+	mkdir -p reacto-tmp
+	wget -O ./reacto-tmp/biopax2go.jar --no-check-certificate https://github.com/geneontology/pathways2GO/releases/download/v0.1.0/biopax2go.jar
+	wget -O ./reacto-tmp/biopax.zip --no-check-certificate https://reactome.org/download/current/biopax.zip
+	unzip -o ./reacto-tmp/biopax.zip -d ./reacto-tmp/
+	java -jar -Xmx8G ./reacto-tmp/biopax2go.jar -b ./reacto-tmp/Homo_sapiens.owl -reacto ./extensions/reacto -lego $(GO_LEGO).owl -chebi ./mirror/chebi.owl
+	rm ./reacto-tmp/*
+	rmdir ./reacto-tmp
+
+$(GO_LEGO_REACTO).owl: extensions/go-lego-reacto-edit.ofn $(GO_LEGO).owl extensions/reacto.owl
+	$(ROBOT) merge -i $< --collapse-import-closure true --include-annotations false reason -r ELK --exclude-duplicate-axioms true --remove-redundant-subclass-axioms true --exclude-tautologies structural relax reduce --named-classes-only true annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@
+
 # ----------------------------------------
 # OBO and subsets
 # ----------------------------------------

src/ontology/catalog-v001.xml

@@ -41,4 +41,6 @@
     <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/go/extensions/go-lego.owl" uri="extensions/go-lego.owl"/>
+  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/reacto.owl" uri="extensions/reacto.owl"/>
 </catalog>

src/ontology/extensions/go-lego-reacto-edit.ofn

@@ -0,0 +1,13 @@
+Prefix(:=<http://purl.obolibrary.org/obo/go/extensions/go-lego.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl>
+Import(<http://purl.obolibrary.org/obo/go/extensions/go-lego.owl>)
+Import(<http://purl.obolibrary.org/obo/go/extensions/reacto.owl>)
+Annotation(rdfs:comment "This ontology extends go-lego (the core ontology underlying GO-CAMs, with classes representing entities in Reactome.)")
+)