add makefile to generate a synonym csv report from ontologies/rdf

synonyms/Makefile

@@ -0,0 +1,44 @@
+WGET = /usr/bin/wget --timestamping --no-verbose
+
+OBO = http://purl.obolibrary.org/obo
+MONARCH = https://archive.monarchinitiative.org/latest/rdf
+
+
+OBO_SOURCES = mondo.owl \
+	      hp.owl \
+	      chebi.owl
+
+MONARCH_SOURCES = reactome.ttl
+
+ALL_SOURCES = $(OBO_SOURCES) $(MONARCH_SOURCES)
+CSVS = $(ALL_SOURCES:=.csv)
+
+build/:
+	mkdir -p build
+
+build/robot.jar: | build/
+	curl -L -o build/robot.jar \
+		https://build.berkeleybop.org/job/robot/lastSuccessfulBuild/artifact/bin/robot.jar
+
+ROBOT := java -jar build/robot.jar
+
+sources/:
+	mkdir --parents $@
+
+$(OBO_SOURCES): | sources/
+	cd sources && $(WGET) $(OBO)/$@
+
+$(MONARCH_SOURCES): | sources/
+	cd sources && $(WGET) $(MONARCH)/$@
+
+$(CSVS): $(ALL_SOURCES) build/robot.jar
+	$(ROBOT) \
+		filter --input sources/$(patsubst %.csv,%,$@) --axioms annotation \
+	        query -f csv --query ./sparql/synonyms.sparql $@
+
+all-synonyms.csv: $(CSVS)
+	cat *.csv | sort -u >all-synonyms.csv
+
+
+all: $(ALL_SOURCES) build/robot.jar $(CSVS) all-synonyms.csv
+

synonyms/README.md

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+Generates a tsv of synonyms using [robot](http://robot.obolibrary.org/)
+with the fields iri, synonym type, synonym
+
+To run:
+
+  make all
+
+To add ontologies or rdf sources adjust the ALL_SOURCES variable
+

synonyms/sparql/synonyms.sparql

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+prefix owl: <http://www.w3.org/2002/07/owl#>
+prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?cls ?pred ?val
+WHERE 
+  { ?cls ?pred ?val ;
+         a owl:Class .
+    FILTER (
+    ?pred = oboInOwl:hasRelatedSynonym ||
+    ?pred = oboInOwl:hasNarrowSynonym ||
+    ?pred = oboInOwl:hasBroadSynonym ||
+    ?pred = oboInOwl:hasExactSynonym
+    )
+  }