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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Taxonomic scope of 'stem cell division' GO:0017145 #23764

Open tberardini opened 1 year ago

tberardini commented 1 year ago

image

There is no taxon restriction but the term is linked to CL term for 'animal stem cell' (synonym).

Stem cells are definitely a thing in plants as well. :) One recent paper: https://www.nature.com/articles/s41467-021-26165-3 Can we go ahead and use this term? Should there be modifications to the linked CL term?

This issue crosses between annotation and ontology. I have opened a ticket only the ontology tracker for now. Thanks for your advice.

balhoff commented 1 year ago

The CL term does have a Metazoa taxon restriction, so I think either the GO logical definition needs to be changed, or the CL term restriction needs to be changed. The taxon restriction doesn't technically propagate over the GO 'has input' relation, but that's just a loophole.

tberardini commented 1 year ago

The CL term does have a Metazoa taxon restriction, so I think either the GO logical definition needs to be changed, or the CL term restriction needs to be changed.

Is there a preference for which one to do? As it stands, I'm holding off on annotating an Arabidopsis gene to this term.

tberardini commented 1 year ago

Any updates? @pgaudet @balhoff