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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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add taxon constraints on apoptosis #12041

Closed cmungall closed 8 years ago

cmungall commented 8 years ago

Currently:

relationship: never_in_taxon NCBITaxon:33090 {id="GOTAX:0000490"} ! Viridiplantae

That's it, including inherited. So it's valid to annotate E coli with apoptosis in GO.

I suggest Opisthokontes conservatively

paolaroncaglia commented 8 years ago

Hi Chris,

Yes, restricting ‘apoptotic process’ to Opisthokonta (Fungi/Metazoa group - Taxonomy ID: 33154) sounds like a good idea. If that’s ok with you, I’ll keep this edit for next week when Melanie is on her first GH/TG rotation, so I can show her an example of taxon rule edit - and one best done with OBO-Edit at the moment ;-)

Note that while the use of ‘apoptosis’ is indeed discouraged in bacteria (http://www.sciencedirect.com/science/article/pii/S1286457913001044), there is growing evidence of programmed cell death events in prokaryotes (http://www.nature.com/nrmicro/journal/v12/n1/full/nrmicro3136.html). But we’re good - ‘programmed cell death’ doesn’t have any taxon restriction.

Paola

paolaroncaglia commented 8 years ago

Edited taxon rule for GO:0006915 'apoptotic process' as follows:

-relationship: never_in_taxon NCBITaxon:33090 {id="GOTAX:0000490"} ! Viridiplantae +relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta

Thanks,

Paola