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Move L2G gold standard to the curation repo #3463

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ireneisdoomed opened this issue Sep 13, 2024 · 4 comments · May be fixed by opentargets/curation#36
Closed
3 tasks

Move L2G gold standard to the curation repo #3463

ireneisdoomed opened this issue Sep 13, 2024 · 4 comments · May be fixed by opentargets/curation#36
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Data Relates to Open Targets data team Genetics Relates to Open Targets genetics team

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@ireneisdoomed
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ireneisdoomed commented Sep 13, 2024 •
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As a developer I want to have the raw L2G gold standard in the curation repo because it is a static file that is subject to versioning. Having it in the curation repo makes sense. It now lives in GCS, and moving it removes some overhead to deal with it in Gentropy.

Background

This file was initially maintained in its own repo https://github.com/opentargets/genetics-gold-standards/tree/master

Tasks

  • Upload to the curation repo
  • Document
  • Update dependency management in Gentropy
@ireneisdoomed ireneisdoomed added Gentropy Data Relates to Open Targets data team labels Sep 13, 2024
@ireneisdoomed ireneisdoomed linked a pull request Sep 18, 2024 that will close this issue
feat: l2g gold standard freeze opentargets/curation#36
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@addramir
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I think this issue could be/should modified depending on our logic for training the model. Lets make this decision as soon as we have credible set level feature matrix.

@addramir
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addramir commented Sep 20, 2024 •
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Can we close this issue?

@project-defiant
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@addramir we should still maintain old Gold standard somewhere (not exactly on the google bucket). I have done some of this as a part of opentargets/curation#36, but wanted to wait for us to see if the last week workshop will result in some proper feedback on this.

@addramir
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I still consider it as some kind of static asset. We can curate it from sourse as a DAG or simply compile this file manually and store as static asset.

@prashantuniyal02 prashantuniyal02 added Genetics Relates to Open Targets genetics team and removed Gentropy labels Oct 10, 2024
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feat: l2g gold standard freeze opentargets/curation
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@addramir @ireneisdoomed @project-defiant @prashantuniyal02