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geneontology / neo

noctua entity ontology
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Xenbase identifiers are not correct getting labels (in NEO?) #109

Closed kltm closed 1 year ago

kltm commented 2 years ago

This issue seems to have recurred. It only seems to affect some genes and in some cases both gene symbols and URIs are being shown in the same model. image

The issue may be somewhat different as currently the gene symbols are not showing up in the Noctua lookup. image

Originally posted by @malcolmfisher103 in https://github.com/geneontology/noctua/issues/706#issuecomment-1195572742

kltm commented 2 years ago

@malcolmfisher103, let's go through the NEO update cycle this Thursday and if the problem is still occurring we can start running it down.

kltm commented 1 year ago

Noting that this is persisting after update. Also noting that these are indeed the given symbols: http://noctua-amigo.berkeleybop.org/amigo/term/Xenbase:XB-GENE-17329976 http://noctua-amigo.berkeleybop.org/amigo/term/Xenbase:XB-GENE-17345783

kltm commented 1 year ago

@malcolmfisher103 This seems to be an issue with the upstream GPI in the metadata: https://ftp.xenbase.org/pub/GenePageReports/xenbase.gpi.gz The lines for these identifiers do not seem to contain symbols, so the symbol falls back to the identifier.

malcolmfisher103 commented 1 year ago

Thanks for chasing this up @kltm, I was just doing the same thing. There seems to be an issue with the gpi production script that has lead some genes having an empty column for the gene symbol which seems to lead to the XB-GENE-ID being assigned as the symbol. The genes have symbols on Xenbase, I'll work with our DB admins to find out what is up.

kltm commented 1 year ago

Cheers!