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pombase / pombase-config

Shared configuration for PomBase projects
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more explicit FYPO extension relations #65

Closed mah11 closed 3 years ago

mah11 commented 3 years ago

Related to #63 and https://github.com/pombase/pombase-chado/issues/828

I could do a quick fix for the item in the Chado ticket, but I had a bit of a think. Now I wonder if we should make the FYPO extension relations more explicit globally, since Canto treats GeneID, TranscriptID, and ProteinID identically (and I managed to forget that it does that, & jsut looked at the range entries and thought "that oughta be fine"). It would be more consistent overall than futzing around the edges for one case (and then another, and another ...).

We could use assayed_region, assayed_transcript, and assayed_protein for GeneID, TranscriptID, and ProteinID respectively. Some of the SO ranges would also get assayed_region or assayed_transcript.

I've added all three to fypo_extension_relations.obo on spec, and will edit the FYPO extension configuration soon(ish) if you like the idea. @kimrutherford could you remind me whether the website config would need any changes?

Thoughts?

ValWood commented 3 years ago

This sounds much better.

mah11 commented 3 years ago

OK, I've committed a big ol' overhaul, and added relations to the pombase-legacy load-pombase-chado.yaml file. I'll leave this open until Kim has a chance to see if the load goes well.

kimrutherford commented 3 years ago

Thanks. I'll keep an eye on the load.

I think line 8 of load-pombase-chado.yaml is a typo?

assayed_using

https://github.com/pombase/pombase-legacy/commit/e5f1ea15280110dae64c866e7d3448871cdca3f9#diff-0c66eb5b988dac95a4640dd17b66d28c7ba1e0873bfd9ef7a3e1b4dcb6635d0fR8

mah11 commented 3 years ago

I think line 8 of load-pombase-chado.yaml is a typo?

must be - I don't remember editing that line! Could've been a slip of the mouse. Want me to fix it or will you?

kimrutherford commented 3 years ago

I'm happy to fix it. Does "assayed_using" need to be added to the list of allowed extensions?

mah11 commented 3 years ago

I'm happy to fix it.

Thanks!

Does "assayed_using" need to be added to the list of allowed extensions?

It should already be there - we've been using it for literally years.

kimrutherford commented 3 years ago

It should already be there - we've been using it for literally years.

Ah, right. I missed it when I had a look.

I've committed the fix and I'll keep an eye on the load.

mah11 commented 3 years ago

thanks again :)

kimrutherford commented 3 years ago

I think this is done now. https://www.pombase.org/reference/PMID:33771877 looks OK.