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Reformat Schema and STRchive loci#262

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hdashnow merged 5 commits intomainfrom
schema-base
Sep 5, 2025
Merged

Reformat Schema and STRchive loci#262
hdashnow merged 5 commits intomainfrom
schema-base

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@hdashnow
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@hdashnow hdashnow commented Sep 4, 2025

Description

This PR will serve as a base for the changes coming in both #238 and #260.

Fixes: #240

Major Changes

  • Reorder fields in schema and STRchive loci json to be more similar to locus pages
  • Automate sorting of STRchive loci json fields so that they match the schema order
  • Remove deprecated fields "type", "flank_motif" and "source" and where necessary integrate their content into other fields
  • Add new locus_structure format and check it against the reference genome for some unusual loci like FAME and XYLT1

Minor Changes

  • Fix citation in one of the ataxias that was pointing to the wrong disease

Checklist

  • All changes are well summarized
  • Check all tests pass
  • Check that the website preview looks good
  • Update the STRchive version in CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.
  • Ask someone to review this PR

@hdashnow hdashnow requested review from Macayla-weiner and Copilot and removed request for Copilot September 4, 2025 14:34
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@hdashnow
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hdashnow commented Sep 4, 2025

@Macayla-weiner would you mind reviewing this change in particular when you get a chance? These are the changes that are most likely to be biologically/diagnostically relevant, so I'd love a second set of eyes on them:

  • all the FAME loci locus_structure
  • XYLT1 locus_struction and location_in_gene

@Macayla-weiner
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@Macayla-weiner would you mind reviewing this change in particular when you get a chance? These are the changes that are most likely to be biologically/diagnostically relevant, so I'd love a second set of eyes on them:

  • all the FAME loci locus_structure
  • XYLT1 locus_struction and location_in_gene

Looks good to me!

@hdashnow
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hdashnow commented Sep 4, 2025

@vincerubinetti, any feedback on this before you try to integrate it with your schema changes?

@vincerubinetti
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I don't see anything in the schema file that will conflict with what I'm doing in my other branch. LGTM.

@hdashnow hdashnow marked this pull request as ready for review September 5, 2025 20:34
@hdashnow hdashnow merged commit 6b83d31 into main Sep 5, 2025
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@hdashnow hdashnow deleted the schema-base branch September 5, 2025 20:41
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Add locus_structure detail forDBQD2_XYLT1

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