Panther Ingest

[putmantime]

Ingest based on the Dipper ingest of Panther

[RichardBruskiewich]

• [x] 1) The Biolink Model Pydantic fix the Pydantic curie regext parse to accept periods in the namespace (see PR https://github.com/monarch-initiative/biolink-model-pydantic/pull/23 patch of code line https://github.com/monarch-initiative/biolink-model-pydantic/blob/RichardBruskiewich-patch-1/pydanticgen/pydanticgen.py#L176)

• [ ] 2) figure out how to make iterative rows in mockkoza unit tests to work (iteration doesn't happen in Panther unit test test_rows at https://github.com/monarch-initiative/monarch-ingest/blob/orthology-ingest/tests/unit/panther/test_ref_genome_orthologs.py#L122 ?)

• [x] 3) review node.source field usage in Monarch Ingests(?).

  • [ ] 3a) For full Biolink Model compliance, fix all ingests to emit provided_by slots instead, and (eventually) aggregating_knowledge_source of edges (note: this is a general recommendation for all Monarch ingests, not just the Panther ingest)
  • [ ] 3b) Fix KGX duplication of provenance (e.g. infores) labels in provided_by (etc.) piped lists during KGX data loading and/or KGX merge operations (created sister issue in KGX: https://github.com/biolink/kgx/issues/373).
  • [ ] 3c) Set the value of provided_by (and aggregating_knowledge_source?) to be the ingest source infores (e.g. infores:panther for the Panther ingest, etc.) (note: again, this is probably a general recommendation for all Monarch ingests, not just the Panther ingest)

• [x] 4) Formally resolve the question of ingest species selection in a future Monarch project meeting? i.e. who will decide whether or not we have gene-phenotype data of interest for a given species, and whether or not outlier species (e.g. Arabidopsis, Dictylostelium?) should be ingested?

[RichardBruskiewich]

@putmantime and @kevinschaper, I added you both into this issue as assignees, simply to point you to the check list of issues above, which although inspired by the Panther ingest, does have action items of cross-Monarch Ingest (and KGX) consequence.

[putmantime]

Re: Which species to include. For now, include what is currently in this ingest. For future, we need to Review our g2p associations and create a set of species based on those.

[RichardBruskiewich]

Reopened issue to add new species listed in Red https://docs.google.com/spreadsheets/d/1XrljI1Dk2Tg0teJSbQls5Iq_KCGXMCdyWvqAMfMgJ-M/edit#gid=0

[RichardBruskiewich]

Superseded by issue #343