Synchronization: SubClassOf

Pipeline to keep subclass relationships in sync between Mondo and sources.
- Add: makefile goals: sync, sync-subclassof, reports/sync-subclassof.robot.template.tsv
- Update: makefile goal: build-mondo-ingest
- Add: src/scripts/sync_subclassof.py

General
- Bugfix: utils.py remove_angle_brackets(): Now correctly returns a str if receives a str.
- Update: config/prefixes.csv: Add: New entries
- Add: utils.py: get_monarch_curies_converter()

Author: joeflack4

src/ontology/config/prefixes.csv

@@ -224,8 +224,19 @@ PLANP,http://purl.obolibrary.org/obo/PLANP_
 CARO,http://purl.obolibrary.org/obo/CARO_
 NPO,http://purl.bioontology.org/ontology/npo#NPO_
 ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/
+ICD10CM2,https://icd.codes/icd10cm/
 ICD10WHO,https://icd.who.int/browse10/2019/en#/
+ICD10WHO2010,http://apps.who.int/classifications/icd10/browse/2010/en#/
 OMIMPS,https://www.omim.org/phenotypicSeries/PS
+OMIMPS2,https://omim.org/phenotypicSeries/
 OMIM,https://omim.org/entry/
 Orphanet,http://www.orpha.net/ORDO/Orphanet_
-GARD,http://purl.obolibrary.org/obo/GARD_
+GARD,http://purl.obolibrary.org/obo/GARD_
+MEDRA,http://identifiers.org/meddra/
+MESH,http://identifiers.org/mesh/
+SCTID,http://identifiers.org/snomedct/
+MEDGEN,http://purl.obolibrary.org/obo/MEDGEN_
+MEDGEN2,http://identifiers.org/medgen/
+MEDGENCUI,http://purl.obolibrary.org/obo/MEDGENCUI_
+UMLS,http://purl.obolibrary.org/obo/UMLS_
+UMLS2,http://linkedlifedata.com/resource/umls/id/

src/ontology/mondo-ingest.Makefile

@@ -321,7 +321,7 @@ documentation: j2 $(ALL_DOCS) unmapped-terms-docs mapped-deprecated-terms-docs s
 build-mondo-ingest:
 	$(MAKE) refresh-imports exclusions-all mondo-ingest.db slurp-all mappings matches \
 		mapped-deprecated-terms mapping-progress-report \
-		recreate-unmapped-components documentation
+		recreate-unmapped-components sync documentation
 	$(MAKE) prepare_release
 
 .PHONY: build-mondo-ingest-no-imports
@@ -502,6 +502,19 @@ slurp-all-no-updates: $(foreach n,$(ALL_COMPONENT_IDS), slurp-no-updates-$(n))
 .PHONY: slurp-all
 slurp-all: $(foreach n,$(ALL_COMPONENT_IDS), slurp-$(n))
 
+
+#############################
+###### Synchronization ######
+#############################
+.PHONY: sync
+sync: sync-subclassof
+
+.PHONY: sync-subclassof
+sync-subclassof: reports/sync-subclassof.robot.template.tsv
+
+reports/sync-subclassof.robot.template.tsv: tmp/merged.db
+	python3 $(SCRIPTSDIR)/sync_subclassof.py --ontology-db-path tmp/merged.db --prefixes-csv-path config/prefixes.csv --outpath $@
+
 #############################
 ######### Analysis ##########
 #############################