From a644a124066be94eceeadf595c14de7851385ff2 Mon Sep 17 00:00:00 2001 From: goodb Date: Sat, 18 Apr 2020 14:03:01 -0700 Subject: [PATCH] add build for reacto.owl and go-lego-reacto.owl to stage_release addresses https://github.com/geneontology/pipeline/issues/35 --- src/ontology/Makefile | 15 ++++++++++++++- src/ontology/catalog-v001.xml | 2 ++ src/ontology/extensions/go-lego-reacto-edit.ofn | 13 +++++++++++++ 3 files changed, 29 insertions(+), 1 deletion(-) create mode 100644 src/ontology/extensions/go-lego-reacto-edit.ofn diff --git a/src/ontology/Makefile b/src/ontology/Makefile index cc89cda120..b5729f6390 100644 --- a/src/ontology/Makefile +++ b/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 # ---------------------------------------- diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 9366c76dec..57f6d742e7 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -41,4 +41,6 @@ + + diff --git a/src/ontology/extensions/go-lego-reacto-edit.ofn b/src/ontology/extensions/go-lego-reacto-edit.ofn new file mode 100644 index 0000000000..577dfd2557 --- /dev/null +++ b/src/ontology/extensions/go-lego-reacto-edit.ofn @@ -0,0 +1,13 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( +Import() +Import() +Annotation(rdfs:comment "This ontology extends go-lego (the core ontology underlying GO-CAMs, with classes representing entities in Reactome.)") +)