Add HPO<->UMLS and HPO<->MeSH mapping to MedGen release

monarch-initiative / medgen

MedGen ingest.

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Add HPO<->UMLS and HPO<->MeSH mapping to MedGen release #18

Closed joeflack4 closed 7 months ago

joeflack4 commented 8 months ago

addresses #16

Changes

SSSOM outputs
- Add: Code for 2 new outputs: hpo-umls.sssom.tsv and hpo-mesh.sssom.tsv

General
- Add: Python requirement: PyYaml
- Update: ORCID in SSSOM config
- Bug fix: Edge case for missing intermediate file in pipeline
- Remove: Intentionally duplicative, no longer needed 'MEDGENCUI' xrefs
- Add: Refactor to load mapping set using function that handles lots of repetitive stuff: get_mapping_set()

joeflack4 commented 8 months ago

CC @Souzadevinicius Just adding some SSSOM outputs for the MedGen ingest.

joeflack4 commented 7 months ago

@matentzn @twhetzel All's good with this one now as well, I believe.

joeflack4 commented 7 months ago

@matentzn Roger. @twhetzel This has been amply reviewed; merging now.