monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Update alliance gene expression to capture assay as qualifier, xref as publication #497

Closed kevinschaper closed 1 year ago

kevinschaper commented 1 year ago

Right now it's using the has_evidence field to capture the assay and crossReference.id from the Alliance json format, but it probably makes more sense to use qualifier for assay and put the crossReference field into the publication slot.

Looking at the model definition for has_evidence and evidence_type, I think we initially followed the definition of has evidence - a connection to supporting evidence - rather than the range of evidence type, which points to this being a slot for evidence codes.

 has evidence:
    is_a: association slot
    range: evidence type
    description: >-
      connects an association to an instance of supporting evidence
    exact_mappings:
      - RO:0002558
    multivalued: true

  evidence type:
    is_a: information content entity
    aliases: ['evidence code']
    description: >-
      Class of evidence that supports an association
    values_from:
      - eco
    exact_mappings:
      - ECO:0000000