Implement modular ingests (sup)

[sagehrke]

Super Ticket for tracking the implementation of modular ingests

Look here for detailed tracker --> Modular Ingest Tracking Table 2025 Google Sheet

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In progress

• Add allele->genotype, allele->gene, gene->genotype associations from Alliance #946
• MaveDB (TODO: create issue) #770

Needed

• Documentation cleanup Update "Sources" documentation to be the modular ingests documentation monarch-ingest#622

Notes

• Need to identify QC & reporting strategy for modular ingests.
• Need to identify next batch of modular ingests.
  • Tech Support for next batch: @kevinschaper @AO33 @ptgolden

[sagehrke]

@ptgolden Just a kind reminder that you said you would convert our modularization task into a table we can easily see status. Note, that you can do that here in markdown or if we want to use a google sheet, that would be fine too. Let me know if you need any support and thank you!!!

[ptgolden]

GitHub Flavored Markdown doesn't allow creating interactive checkboxes (aka "task lists") within tables, unfortunately.

Two options. First, I could make a Google Sheet.

Second, we can manually add checkmarks into a table, e.g.

ingest key	download yaml	transform python	transform yaml	tests	documentation	import into monarch ingest	remove code from monarch ingest
alliance_genotype	✅	✅	✅	✅	✅	✅	⬜
alliance_phenotype	✅	✅	✅	✅	✅	✅	⬜

...which would require manually editing the markdown for the table.

I'd tend towards the latter, just to keep everything in the same place, but editing the markdown by hand is a bit of a pain while working on an ingest may be a bit of a pain.

[sagehrke]

Let's go with a document so it's easier to make notes and updates.

Modular Ingest Tracking 2025