Remove GARD (#681)

* Remove GARD
Remove GARD as non-EMC source
- ODK setup: metadata/gard.yml & mondo-ingest-odk.yaml
- Specific files: docs, outputs, and intermediaries.
- Refs within files: mondo-ingest.Makefile, gitignore, mkdocs.yml, Makefile (after running update_repo)

* Re-ran update_repo after merging develop

.gitignore

@@ -108,7 +108,4 @@ src/scripts/mondo_unmapped.tsv
 tests/output/*
 !tests/output/.gitkeep
 src/scripts/dataframes/*
-src/ontology/reports/gard.subclass.added-obsolete.robot.tsv
-src/ontology/reports/gard.subclass.added.robot.tsv
-src/ontology/reports/gard.subclass.confirmed.robot.tsv
 src/ontology/reports/basic-report.tsv

docs/odk-workflows/RepositoryFileStructure.md

@@ -31,7 +31,6 @@ These are the components in MONDO-INGEST
 | Filename | URL |
 | -------- | --- |
 | doid.owl | http://purl.obolibrary.org/obo/doid.owl |
-| gard.owl | https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl |
 | icd10cm.owl | https://data.bioontology.org/ontologies/ICD10CM/submissions/23/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb |
 | icd10who.owl | https://github.com/monarch-initiative/icd10who/releases/latest/download/icd10who.ttl |
 | icd11foundation.owl | https://github.com/monarch-initiative/icd11/releases/latest/download/icd11foundation.owl |

mkdocs.yaml

@@ -25,7 +25,6 @@ nav:
     - Mondo sources:
       - Overview: sources.md
       - DO: sources/doid.md
-      - GARD: sources/gard.md
       - ICD10CM: sources/icd10cm.md
       - ICD10WHO: sources/icd10who.md
       - ICD11Foundation: sources/icd11foundation.md
@@ -38,7 +37,6 @@ nav:
     - Mondo source metrics:
       - Overview: metrics.md
       - DO: metrics/doid.md
-      - GARD: metrics/gard.md
       - ICD10CM: metrics/icd10cm.md
       - ICD10WHO: metrics/icd10who.md
       - ICD11Foundation: metrics/icd11foundation.md

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                1f779a242dc046d5c98b39bde1a60c2488195d1ad6e0a21ee94bac1ae0f05b98
+CONFIG_HASH=                96106b155c56dcf985ea2dc716aaaeb0cb34f47bbe55cb1cae81a9895138f6bf
 
 
 # ----------------------------------------
@@ -54,7 +54,7 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(COMPONENTSDIR)/doid.owl $(COMPONENTSDIR)/gard.owl $(COMPONENTSDIR)/icd10cm.owl $(COMPONENTSDIR)/icd10who.owl $(COMPONENTSDIR)/icd11foundation.owl $(COMPONENTSDIR)/ncit.owl $(COMPONENTSDIR)/omim.owl $(COMPONENTSDIR)/ordo.owl 
+OTHER_SRC =                 $(COMPONENTSDIR)/doid.owl $(COMPONENTSDIR)/icd10cm.owl $(COMPONENTSDIR)/icd10who.owl $(COMPONENTSDIR)/icd11foundation.owl $(COMPONENTSDIR)/ncit.owl $(COMPONENTSDIR)/omim.owl $(COMPONENTSDIR)/ordo.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
@@ -443,20 +443,6 @@ $(COMPONENTSDIR)/doid.owl: component-download-doid.owl
 .PRECIOUS: $(COMPONENTSDIR)/doid.owl
 
 
-.PHONY: component-download-gard.owl
-component-download-gard.owl: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl \
-	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
-
-$(COMPONENTSDIR)/gard.owl: component-download-gard.owl
-	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-gard.owl.owl $(TMPDIR)/component-download-gard.owl.tmp.owl ; then echo "Component identical."; \
-      else echo "Component is different, updating." &&\
-		cp $(TMPDIR)/component-download-gard.owl.owl $(TMPDIR)/component-download-gard.owl.tmp.owl &&\
-		$(ROBOT) annotate -i $(TMPDIR)/component-download-gard.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
-
-.PRECIOUS: $(COMPONENTSDIR)/gard.owl
-
-
 .PHONY: component-download-icd10cm.owl
 component-download-icd10cm.owl: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I https://data.bioontology.org/ontologies/ICD10CM/submissions/23/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb \

src/ontology/mondo-ingest-odk.yaml

@@ -27,8 +27,6 @@ components:
   products:
     - filename: doid.owl
       source: http://purl.obolibrary.org/obo/doid.owl
-    - filename: gard.owl
-      source: https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl
     - filename: icd10cm.owl
       source: https://data.bioontology.org/ontologies/ICD10CM/submissions/23/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
     - filename: icd10who.owl

src/ontology/mondo-ingest.Makefile

@@ -175,11 +175,6 @@ $(COMPONENTSDIR)/icd11foundation.owl: $(TMPDIR)/icd11foundation_relevant_signatu
 		remove -T config/properties.txt --select complement --select properties --trim true \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/icd11foundation.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd11foundation.owl -o $@; fi
 
-$(COMPONENTSDIR)/gard.owl: $(TMPDIR)/gard_relevant_signature.txt | component-download-gard.owl
-	if [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-gard.owl.owl --select imports \
-		remove -T $(TMPDIR)/gard_relevant_signature.txt --select complement --select "classes individuals" --trim false \
-		annotate --ontology-iri $(URIBASE)/mondo/sources/gard.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/gard.owl -o $@; fi
-
 $(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT) merge $(patsubst %, -i %, $^) \
 		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \