HPOA g2p ingest

[putmantime]

Ingest for human gene to phenotype associations.

http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt

Notes: The headers in this file need some preprocessing AFAIK. OMIM gene id are used.

[RichardBruskiewich]

Synoptic Notes from Monarch Technical Meeting:

• [x] Entrez Genes to HPO terms, with source (mim2gene, orphanet, etc) and associated disease ID
• [x] Need to brainstorm options for representing the relationships to all three concepts: gene, phenotype and disease
  • [x] Option 1: annotate the predicate/edge (reification, disease context of whole statement) with disease term, etc. qualifiers
  • [ ] Option 2: annotate the Association.object with disease qualifier for disease HPO term (i.e. specific context of the phenotype)

[RichardBruskiewich]

For the first iteration, it seems reasonable perhaps to take Option 1 above, and put the disease identifier, plus any HPO frequency term, as edge context qualifiers, into the Association.qualifiers (list value) field, using the source database name (not sure if we should treat these as infores CURIES) in the Association.has_evidence (list value) field.