Alternate format for OLS

- Add: Goal for medgen.owl.gz, along with additional intermediate goals and updates to build goals and GH action for this.

.github/workflows/buid_and_release.yml

@@ -31,10 +31,11 @@ jobs:
         automatic_release_tag: "${{ steps.current-time.outputs.formattedTime }}"
         title: "${{ steps.current-time.outputs.formattedTime }}"
         prerelease: false
-        # todo: add back `release/medgen-disease-extract.owl`, pending https://github.com/monarch-initiative/medgen/issues/11
+        # todo: add back `release/medgen-disease-extract.owl`?, pending https://github.com/monarch-initiative/medgen/issues/11
 #          output/release/medgen-disease-extract.owl
         files: |
           output/release/medgen.obo
+          output/release/medgen.owl.gz
           output/release/medgen-disease-extract.obo
           output/release/medgen-xrefs.robot.template.tsv
           output/release/medgen-xrefs-mesh.robot.template.tsv

makefile

@@ -6,7 +6,8 @@
 .PHONY: all build stage stage-% analyze clean deploy-release build-lite minimal sssom sssom-validate
 
 OBO=http://purl.obolibrary.org/obo
-PRODUCTS=medgen-disease-extract.obo medgen-disease-extract.owl
+# todo: medgen-disease-extract.owl.gz?
+PRODUCTS=medgen-disease-extract.obo medgen-disease-extract.owl medgen.owl.gz
 TODAY ?=$(shell date +%Y-%m-%d)
 VERSION=$(TODAY)
 
@@ -15,9 +16,10 @@ minimal: build-lite stage-lite clean
 stage-lite: | output/release/
 #	mv medgen-disease-extract.owl output/release/
 	mv *.obo output/release/
+	mv medgen.owl.gz output/release/
 	mv *.robot.template.tsv output/release/
 	mv *.sssom.tsv output/release/
-build-lite: medgen-disease-extract.obo medgen-xrefs.robot.template.tsv umls-hpo.sssom.tsv sssom-validate
+build-lite: medgen.owl.gz medgen-disease-extract.obo medgen-xrefs.robot.template.tsv umls-hpo.sssom.tsv sssom-validate
 
 all: build stage clean analyze
 # analyze: runs more than just this file; that goal creates multiple files
@@ -68,6 +70,12 @@ ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt: ftp.ncbi.nlm.nih.gov/
 medgen.obo: ftp.ncbi.nlm.nih.gov/ uid2cui.tsv
 	./src/medgen2obo.pl > $@.tmp && mv $@.tmp $@
 
+medgen.owl: medgen.obo
+	robot convert --input $< --output $@ --format owl
+
+medgen.owl.gz: medgen.owl
+	gzip -c $< > $@
+
 # We only care about diseases for now
 # - NOTE: some cancers seem to appear under Neoplastic-Process
 x-%.obo: medgen.obo