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monarch-initiative / monarch-app

Monarch Initiative website and API
https://monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
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Get modular NCBI gene ingest up and producing releases #712

Open kevinschaper opened 2 months ago

kevinschaper commented 2 months ago

We have options here.

We could just make a Jenkinsfile to automate @hrshdhgd's pyobo based ingest: https://github.com/monarch-initiative/NCBI-gene-pyobo. This is probably the least amount of work.

We could convert https://github.com/monarch-initiative/ncbi-gene to a proper monarch-ingest-cookiecutter repo, and make it fit into a GitHub Actions workflow by limiting to a subset of taxa. This feels like it might be more maintainable (by me, I suppose!) in the long run.

I assume it's also possible to also subset the pyobo version. So, first step here is a decision, next step is an implementation.

kevinschaper commented 1 month ago

Since the modular ingest cookiecutter has been working well for us, let's try going that way for this. Assigning to @glass-ships to convert ncbi-gene to the ingest cookie cutter, adding the taxon filter from monarch-ingest to start, and then we'll expand it.

glass-ships commented 3 weeks ago

https://github.com/monarch-initiative/ncbi-gene/releases/tag/untagged-7e1667250e0bbc290a06