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pombase / canto

The PomBase community curation tool
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Often cannot locate process terms for extentions even with exact string #2826

Closed ValWood closed 3 weeks ago

ValWood commented 3 weeks ago

For example:

Screenshot 2024-04-23 at 12 46 48 Screenshot 2024-04-23 at 12 45 56 Screenshot 2024-04-23 at 11 47 07

@PCarme have you seen this other then for extensions?

kimrutherford commented 3 weeks ago

I can't see any obvious reason for that. Seems like a bug. I'll investigate when I'm back at work later.

kimrutherford commented 3 weeks ago

I think part of the problem is that the "in biological process" extension is restricted to GO:0009987 (cellular process) only.

That explains why "protein catabolic process" and "anaphase-promoting complex-dependent catabolic process".

Should I change the configuration to include all of / more of biological_process?

I can't understand why "RNA capping" isn't found as it's a descendent of "cellular process". I'm still trying to work that out.

ValWood commented 3 weeks ago

Yes use biological process. Some of these should be cellular, and most irrelevant terms should not be blocked by taxon constraints.

kimrutherford commented 3 weeks ago

Yes use biological process. Some of these should be cellular, and most irrelevant terms should not be blocked by taxon constraints.

OK, I'll change that now. Canto will be updated will the new configuration in an hour or two.

I can't understand why "RNA capping" isn't found as it's a descendent of "cellular process". I'm still trying to work that out.

I was misreading the ancestry graph. RNA capping" is a "part_of" descendent of "cellular process" but not an "is_a" descendent, which explains things. Changing to allow any BP term in the extension will fix that.

ValWood commented 3 weeks ago

CC @Pcarme