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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Ontology: integrate Mondo ontology #162

Closed AlanSimmons closed 1 year ago

AlanSimmons commented 1 year ago

Per Jonathan in Slack:

Can we please add mondo.owl to our ingests - i think its much like DOID - but would add more translation - here it is: and shoud be MONDO as the SAB (and i think it could be fairly early in the process - perhaps just after DOID? https://obofoundry.org/ontology/mondo.htm

This should be as straightforward as updating the ontologies.json and build_csv.sh files.

AlanSimmons commented 1 year ago

Although it was straightforward to ingest the MONDO OWL, there is an issue with the resulting OWLNETS files. MONDO identifies gene nodes in format http://identifiers.org/hgnc/ID. These identifiers will need to be converted to the format HGNC HGNC:ID. Because this is a post-OWLNETS conversion like for EDAM , the enhancements for EDAM and MONDO will be made together.

AlanSimmons commented 1 year ago

The ingestion script now correctly formats genes identified in MONDO via identifers.org. I validated by generating a new knowledge graph.