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PomBase website v2
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ortholog references #2192

Closed ValWood closed 2 months ago

ValWood commented 3 months ago

Are we displaying references for orthologs? I ask because

SPBC354.10 UBAP2 PMID:35633597

reference is not showing

kimrutherford commented 3 months ago

The ortholog loader only reads 2 columns - the 2 gene IDs. It ignores any other columns.

The orthologs from Compara and the pombe-japonicus orthologs have publications attached because we set the publication for all orthologs in those files with a command line argument on the loader.

ValWood commented 3 months ago

Does the loader read the db_xrefs for the ones curated in Artemis?

kimrutherford commented 2 months ago

Does the loader read the db_xrefs for the ones curated in Artemis?

Yep, it does.

I've never added the same code for the TSV ortholog file reader.

ValWood commented 2 months ago

OK I will migrate this one , I usually put them there I forgot

ValWood commented 2 months ago

This worked, but the reference only appears on one of the orthologs, but it supports both:

Screenshot 2024-07-16 at 09 09 51
kimrutherford commented 2 months ago

Looks like a very old bug! There are other cases too: https://www.pombase.org/gene/SPBC25H2.09

The reference was only being applied to the first ortholog from /controlled_curation. I think I've fixed this. I'm doing a test load on my desktop to confirm.

kimrutherford commented 2 months ago

I think I've fixed this. I'm doing a test load on my desktop to confirm.

The test worked so that fix should be on the main site in the morning.

kimrutherford commented 2 months ago

The test worked so that fix should be on the main site in the morning.

Now fixed:

image