Updating sssom pipelines and fixing doid

docs/odk-workflows/RepositoryFileStructure.md

@@ -33,6 +33,6 @@ These are the components in MONDO-INGEST
 | omim.owl | https://github.com/monarch-initiative/omim/releases/latest/download/omim.ttl |
 | ordo.owl | http://www.orphadata.org/data/ORDO/ORDO_en_4.0.owl |
 | ncit.owl | http://purl.obolibrary.org/obo/ncit.owl |
-| doid.owl | http://purl.obolibrary.org/obo/ncit.owl |
+| doid.owl | http://purl.obolibrary.org/obo/doid.owl |
 | icd10cm.owl | https://data.bioontology.org/ontologies/ICD10CM/submissions/21/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb |
 | icd10who.owl | https://github.com/monarch-initiative/icd10who/releases/download/latest/icd10who.ttl |

src/ontology/Makefile

@@ -354,7 +354,7 @@ $(COMPONENTSDIR)/ncit.owl:  component-download-ncit.owl
 
 .PHONY: component-download-doid.owl
 component-download-doid.owl: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/ncit.owl \
+	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/doid.owl \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
 $(COMPONENTSDIR)/doid.owl:  component-download-doid.owl

src/ontology/metadata/doid.metadata.sssom.yml

@@ -0,0 +1,33 @@
+mapping_set_id: http://purl.obolibrary.org/obo/mondo/mondo-ingest/mapping/doid.sssom.tsv
+mapping_set_description: >
+  The file `doid.sssom.tsv` is generated from within the mondo-ingest repository (https://github.com/monarch-initiative/mondo-ingest),
+  by running the command `make mappings/doid.sssom.tsv` from within `src/ontology`.
+license: https://creativecommons.org/licenses/by/4.0/
+creator_id: https://orcid.org/0000-0002-2906-7319
+curie_map:
+  ICD10: http://apps.who.int/classifications/icd10/browse/2010/en#/
+  MedDRA: https://identifiers.org/meddra/
+  MESH: https://meshb.nlm.nih.gov/record/ui?ui=
+  OMIM: https://omim.org/entry/
+  Orphanet: http://www.orpha.net/ORDO/Orphanet_
+  UMLS: http://linkedlifedata.com/resource/umls/id/
+  DOID: http://purl.obolibrary.org/obo/DOID_
+  EFO: http://www.ebi.ac.uk/efo/EFO_
+  ENVO: http://purl.obolibrary.org/obo/ENVO_
+  GARD: "https://bioregistry.io/reference/gard:"
+  ICD10CM: https://icd.codes/icd10cm/
+  ICD9CM: https://icd.codes/icd9cm/
+  ICD9CM_2005: https://icd.codes/icd9cm/
+  ICDO: "https://bioregistry.io/reference/gard:"
+  KEGG: http://www.kegg.jp/entry/
+  MEDDRA: https://identifiers.org/meddra/
+  NCI: http://purl.obolibrary.org/obo/NCIT_
+  OMIT: http://purl.obolibrary.org/obo/ENVO_
+  ORDO: http://www.orpha.net/ORDO/Orphanet_
+  SNOMEDCT_US_2020_03_01: http://identifiers.org/snomedct/
+  SNOMEDCT_US_2020_09_01: http://identifiers.org/snomedct/
+  SNOMEDCT_US_2021_07_31: http://identifiers.org/snomedct/
+  SNOMEDCT_US_2021_09_01: http://identifiers.org/snomedct/
+  SYMP: http://purl.obolibrary.org/obo/SYMP_
+  UMLS_CUI: http://linkedlifedata.com/resource/umls/id/
+

src/ontology/mappings/ordo_metadata.sssom.yml → src/ontology/metadata/ordo.metadata.sssom.yml

@@ -6,11 +6,8 @@ license: https://creativecommons.org/licenses/by/4.0/
 creator_id: https://orcid.org/0000-0002-2906-7319
 curie_map:
   ICD10: http://apps.who.int/classifications/icd10/browse/2010/en#/
-  MedDRA: http://purl.bioontology.org/ontology/MEDDRA/
-  MESH: https://meshb.nlm.nih.gov/record/ui?ui=
-  oboInOwl: http://www.geneontology.org/formats/oboInOwl#
+  MedDRA: https://identifiers.org/meddra/
+  MESH: http://identifiers.org/mesh/
   OMIM: https://omim.org/entry/
   Orphanet: http://www.orpha.net/ORDO/Orphanet_
-  skos: http://www.w3.org/2004/02/skos/core#
-  sssom: https://mapping-commons.github.io/sssom/purl/
   UMLS: http://linkedlifedata.com/resource/umls/id/

src/ontology/mondo-ingest-odk.yaml

@@ -32,7 +32,7 @@ components:
     - filename: ncit.owl
       source: http://purl.obolibrary.org/obo/ncit.owl
     - filename: doid.owl
-      source: http://purl.obolibrary.org/obo/ncit.owl
+      source: http://purl.obolibrary.org/obo/doid.owl
     - filename: icd10cm.owl
       source: https://data.bioontology.org/ontologies/ICD10CM/submissions/21/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
     - filename: icd10who.owl

src/ontology/mondo-ingest.Makefile

@@ -66,12 +66,6 @@ $(COMPONENTSDIR)/ordo.owl: $(TMPDIR)/ordo_relevant_signature.txt config/properti
 		rename --mappings config/property-map-2.sssom.tsv --allow-missing-entities true \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/ordo.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/ordo.owl -o $@; fi
 
-$(COMPONENTSDIR)/ordo.json: $(COMPONENTSDIR)/ordo.owl
-	$(ROBOT) convert -i $(COMPONENTSDIR)/ordo.owl -o $(COMPONENTSDIR)/ordo.json
-
-$(MAPPINGSDIR)/ordo.sssom.tsv: $(COMPONENTSDIR)/ordo.json
-	sssom parse $(COMPONENTSDIR)/ordo.json -I obographs-json -m $(MAPPINGSDIR)/ordo_metadata.sssom.yml -o $(MAPPINGSDIR)/ordo.sssom.tsv
-
 $(COMPONENTSDIR)/ncit.owl: $(TMPDIR)/ncit_relevant_signature.txt
 	if [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-ncit.owl.owl --select imports \
 		remove -T $(TMPDIR)/ncit_relevant_signature.txt --select complement --select "classes individuals" --trim false \
@@ -152,6 +146,12 @@ metadata/mondo.sssom.config.yml:
 ../mappings/%.sssom.tsv: $(TMPDIR)/component-%.json metadata/mondo.sssom.config.yml
 	sssom parse $< -I obographs-json -m metadata/mondo.sssom.config.yml -o $@
 
+$(MAPPINGSDIR)/ordo.sssom.tsv: $(TMPDIR)/component-ordo.json
+	sssom parse $(COMPONENTSDIR)/ordo.json -I obographs-json -m metadata/ordo.metadata.sssom.yml -o $@
+
+$(MAPPINGSDIR)/doid.sssom.tsv: $(TMPDIR)/component-doid.json
+	sssom parse $(COMPONENTSDIR)/doid.json -I obographs-json -m metadata/doid.metadata.sssom.yml -o $@
+
 mappings: sssom $(ALL_MAPPINGS)
 
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