Review of Evidence Capture for Monarch Ingests

[RichardBruskiewich]

The Monarch Data meeting of 22nd June 2023, reviewed the need for quality assurance in the capture of Monarch graph edge evidence. We wish to:

• [ ] Clarify how to apply the current Biolink Model (Translator) standards for the capture and annotation of evidence, e.g. annotation of knowledge types and agents; capture of supporting citations
• [ ] Review every Monarch Ingest source for available metadata which can be used to populate the Biolink Model evidence model evidence slot values needed:
  • [ ] alliance
  • [ ] bgee
  • [ ] ctd
  • [ ] dictybase
  • [ ] flybase
  • [ ] goa
  • [ ] hgnc
  • [ ] hpoa
  • [ ] mgi
  • [ ] ncbi
  • [ ] panther
  • [ ] pombase
  • [ ] reactome
  • [ ] rgd
  • [ ] sgd
  • [ ] string
  • [ ] xenbase
  • [ ] zfin

[RichardBruskiewich]

@kevinschaper is this issue already covered somewhere else (maybe @amc-corey-cox is doing most of the needful here?)

[amc-corey-cox]

@RichardBruskiewich I created a Jupyter notebook to look at the evidence in our final QC graph. I haven't dug into anything in the ingests. We were mostly concerned with evidence types and coverage for QC. I think this is tangential to what I'm working on now. With that said... I will try to get some insight on this as well.

[RichardBruskiewich]

Let me know if you need any Biolink Model backup on this issue (could potentially frame as a Translator outreach?)

[monicacecilia]

Hi @amc-corey-cox, did you make any other progress on this back then? We've made progress in displaying evidence in the results tables. Are there any other improvements? If so, what? @kevinschaper 👀 👆