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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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log check for incorrectly formatted db_xref #862

Closed ValWood closed 2 years ago

ValWood commented 3 years ago

I spotted this chromosome2.contig:FT db_xref=O_REF:0000024; with=SGD:S000004965; date=20210604" but I didn't see it in the logfile

kimrutherford commented 2 years ago

I've added a check for that. The results will be in the qualifier_problems.txt log file on Thursday.

mah11 commented 2 years ago

Thanks. There seem to be some results now, and I've spotted a few things:

ValWood commented 2 years ago

I fixed typos DDJB --> DDBJ in chromosome1.contig, and left a note about it in the pombase-legacy commit

What is the pombase-legacy commit? (for call tomorrow)

kimrutherford commented 2 years ago

Thanks for checking.

PANTHER:PTHRnnnnn IDs should be allowed

I've fixed that for tonight's load.

and left a note about it in the pombase-legacy commit

And I've fixed the spelling of "DDBJ" in the code.

I can't see what's making the ArrayExpress dbxrefs get flagged - the prefix is in that list at

I noticed that was missing and added it later. Probably it was too late for the load. I'll double check that in the morning.

What is the pombase-legacy commit?

It's: https://github.com/pombase/pombase-legacy/commit/88c0cd4d80527e0924c28f5d63597fb9b99340c3

kimrutherford commented 2 years ago

I'll double check that in the morning.

Looks good to me: https://curation.pombase.org/dumps/latest_build/logs/qualifier_problems.txt

There's just one warning now:

invalid /db_xref: EMD:3522: failed to load qualifier 'term=external_link, the electron microscopy databank; db_xref=EMD:3522' from SPAC18G6.15.1
mah11 commented 2 years ago

Thanks! I had a quick look round yesterday, and I think that EMD:3522 thing is OK - it's this.

kimrutherford commented 2 years ago

I had a quick look round yesterday, and I think that EMD:3522 thing is OK

Thanks, I've added that prefix.