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ENSCORESW-3553: store RGD separately based on type of link

Marek Szuba requested to merge bugfix/RGD_sources into master

Created by: magaliruffier


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For RGD which have a direct link to an Ensembl stable ID, use a different source than RGD which have an inferred link via RefSeq

Use case

RGD accessions can be linked to a RefSeq accession or directly to an Ensembl stable ID. Storing these links as two separate xref entries means we can treat them separately and prioritise the better link when available. Without the distinction, we can have the same accession mapped to two different stable IDs and one link is arbitrarily chosen over the other. In some cases, the chosen link is invalid and no link to RGD is kept.


More links to RGD, more reproducible, more reliable

Possible Drawbacks



Have you added/modified unit tests to test the changes? NA If so, do the tests pass/fail? NA Have you run the entire test suite and no regression was detected? NA

The xref pipeline currently fails for rat because some links become invalid after loading into the core database. With the proposed fix, the pipeline runs successfully and RGD xrefs are correctly mapped to Ensembl genes

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