Closure should be used when querying the genes biotype

geneontology / amigo

AmiGO is the public interface for the Gene Ontology.

http://amigo.geneontology.org

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Closure should be used when querying the genes biotype #713

Open cmungall opened 8 months ago

cmungall commented 8 months ago

If I select "ncRNA" in amigo it should also include the subtypes of ncRNA, however, it doesn't use the closure

(low priority as the type hierarchy is basically flat other than ncRNA and it's easy enough to recapitulate the ncRNA query with a negative query on gene/protein/complex)

cmungall commented 8 months ago

Technically "gene_product" should also have it's closure but this is a useless term and I don't know why we annotate to it

UPDATE this is an upstream pipeline issue: https://github.com/geneontology/go-site/issues/2246

ValWood commented 8 months ago

agreed.

PomBase has used for 8 lncRNAs:

@kimrutherford could you look into this? (I'll transfer this comment to our Chado tracker)