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Modularize and update BGee ingest #843

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Tracked by #724 ...
amc-corey-cox opened this issue Oct 10, 2024 · 4 comments
Open
7 tasks
Tracked by #724 ...

Modularize and update BGee ingest #843

amc-corey-cox opened this issue Oct 10, 2024 · 4 comments
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@amc-corey-cox
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amc-corey-cox commented Oct 10, 2024

BGee ingest is one of our longer to run ingests. Moving this to a modular ingest should improve the overall build of the KG because it can be done asynchronously before the build of the new graph.

Also, we should reach out to BGee collaborators to improve our process for selecting edges to import into the Monarch KG.

  • create repo
  • download yaml
  • transform python
  • transform yaml
  • tests
  • documentation
  • import into monarch-ingest
This was referenced Oct 10, 2024
@amc-corey-cox
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As mentioned in #724 we should also look at the evidence capture in this ingest while we are evaluating other parts and moving to modular.

@amc-corey-cox
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There is another BGee ingest update ticket monarch-initiative/monarch-ingest#414 and we should address them both when we do this.

That ticket has more information on the update portion.

@amc-corey-cox
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I sent a summary to @monicacecilia for an introduction to to the Bgee team.

@amc-corey-cox
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I have now passed the summary on to Melissa for an introduction.

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