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Add gene table version to the api version endpoint? #10299

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rmadupuri opened this issue Jul 26, 2023 · 5 comments · May be fixed by #10925
Open

Add gene table version to the api version endpoint? #10299

rmadupuri opened this issue Jul 26, 2023 · 5 comments · May be fixed by #10925
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enhancement good first issue

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@rmadupuri
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rmadupuri commented Jul 26, 2023 •
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The gene tables are updated every 6 months. The 4th round of update went in recently and the versions are archived here - https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/gene-table-update/build-input-for-importer/gene-table-release-archives and they are specific to cBioPortal.

Can we also add these versions to https://www.cbioportal.org/api/info? cc @inodb

NOTE: The DB schema needs to be extended to include the gene table version in the info Table.
@MrChatterjee98
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@inodb @rmadupuri is this issue still open? I would like to contribute can you please assign it to me?

@inodb
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inodb commented Jul 29, 2024

@MrChatterjee98 still open - feel free to work on it, thank you!

@MrChatterjee98
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MrChatterjee98 commented Jul 31, 2024 •
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hi @inodb , as I went through the docs and the datahub repo I couldn't find any semantic version which indicates the version of the gene table , I am keeping the version as 5.0.0 as per the last update mentioned in the following pr cBioPortal/datahub-study-curation-tools#57

@rmadupuri
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rmadupuri commented Jul 31, 2024 •
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Hi @MrChatterjee98, thank you for working on this. We've been using internal versioning such as v5 and v4 for our documentation, but I believe we can version this better for the database and api, similar to the GENESET_VERSION for HGNC. For example, we could use a format like hgnc_v2023.10.1 to indicate the HGNC release date of the data used to create the tables. hgnc_v2023.10.1 would be the latest gene table version.

@inodb any thoughts?

@MrChatterjee98 MrChatterjee98 linked a pull request Aug 3, 2024 that will close this issue
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@MrChatterjee98
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@inodb @rmadupuri I have done the changes please review the pr, thanks

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fix #10229 added genetable version to info MrChatterjee98/cbioportal
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@inodb @rmadupuri @MrChatterjee98