Manual curation for 2024.09 release

[apriltuesday]

Refer to documentation for full description of steps.
Estimated submission deadline is beginning of August.

Checklist:

• Step 1 — Process
• Step 2 — Curate
  • Curation
  • Review 1
  • Review 2
• Step 3 — Export
• Step 4 — EFO feedback

[apriltuesday]

@Dona094 @tcezard Spreadsheet is ready here. Some notes:

• Please ignore "gene-related condition" terms as non-informative, these will be removed in the future.
• Just a reminder, we've now combined the NEW term curation with the general curation step, documented here. Let me know if anything is unclear in the SOP or if any spreadsheet formulas don't work properly.

[Dona094]

35 DONE

96 IMPORT

2 NEW

2 SKIP

[apriltuesday]

Thank you both!

Just a note on the drug response terms (I also put a note in the comment column so we remember next time): Historically the policy has been to curate drug responses in ClinVar like any others, but I think we should discuss whether we want to change that given the PGKB pipeline and PGx widget (though keep in mind most drug response data in ClinVar originates from submitters besides PGKB). It really comes down to whether an association like this is at all useful, or whether we should be feeding that evidence to the PGx widget instead.

Regardless, for a term like eculizumab, poor response to I don't think we've ever had a good approach to how to map this; there are EFO terms for "response to __" but the "poor" modifier makes things complicated... so the SKIP is fine here anyway.

[apriltuesday]

Moved 3 terms from IMPORT to SKIP, new counts are:

• 35 DONE
• 93 IMPORT
• 2 NEW
• 5 SKIP

EFO issue created here.