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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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HuBMAP Application Ontology: Organs #90

Closed ChuckKollar closed 1 year ago

ChuckKollar commented 3 years ago

We need support the various HuBMAP specific organ enums to the ontology. [@computationdoc do you have links to the multiple organ definition yaml files?]

Jonathan has started a spreadsheet (https://docs.google.com/spreadsheets/d/1OChRIHy5DnMI4CBesc9XsNs8TLrEmDiPViEV1gt8r2s/edit#gid=0) that we can directly export 2 csv files for direct use by the Neo4j import step when creating the KG database. [@computationdoc Need Link To Spreadsheet]. This spreadsheet will need to be finished, files exported and added to KG build (and KG built!).

======================= Previously titled: Mapping HubMap Enum sets to ontology terms with this information: From Jonathan: I would give him the cypher for enum thing - but it's basically possibly just the existing term->code Endpoint?

Mapping the codes from these files to actual ontology terms (non-programming task): https://github.com/hubmapconsortium/search-api/tree/test-release/src/search-schema/data/definitions/enums organ_types.yml is the subject here.

NOTE: Find a UBERON URL to map to the same Concept that the description is mapped.

AlanSimmons commented 2 years ago

Organ data from organ_types.yaml incorporated into https://github.com/hubmapconsortium/ontology-api/tree/main/scripts/skowlnets