Permanent fix for duplication of merged SNPs on import

EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure

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Permanent fix for duplication of merged SNPs on import #1451

Open ljwh2 opened 5 days ago

ljwh2 commented 5 days ago

Duplicate SNPs cause the data release to break and issues in data presentation, please refer to https://github.com/EBISPOT/goci/issues/1275 for more details. Ala cleaned up all the existing examples in the database but code changes are required to stop it happening in future.

Acceptance criteria for this issue:

Curators can extract merged SNPs using the merged rsID
unpublished SNPs do not break the DR
published SNPs appear only once in the UI & download

ljwh2 commented 5 days ago

On further analysis, this may be a problem on Ensembl side, as none of the duplicated SNPs are found in Ensembl (though they are found in dbSNP). This issue needs a bioinformatician to look at it.