search

geneontology / neo

noctua entity ontology
9 stars 2 forks source link

Check type of mouse ncRNA genes - not recognized in Noctua as valid annotation objects #72

Closed vanaukenk closed 3 years ago

vanaukenk commented 3 years ago

I'm not sure which is the best tracker for this issue, but am starting with NEO.

If a mouse ncRNA gene is used as an enabling entity or an input to a BP or MF, the nodes are being flagged by the ShEx validator because these ncRNA gene identifiers are not recognized as valid annotation objects.

In the MGI gpi file, these genes are typed as ncRNA genes using SO:0001263 according to the GPI2.0 spec.

@hdrabkin @ukemi @kltm @balhoff

Note: if I check one of these gene ids, e.g. MGI:2676885, in noctua-amigo, the graph view seems to show the correct parentage.

hdrabkin commented 3 years ago

This might be the same issue we had with pro ids (PR:xxxxxxx), also in our gpi. Don't know if THAT was even fixed.

balhoff commented 3 years ago

@vanaukenk SO:0001263 does not appear to be in go-lego, so probably the hierarchy isn't connecting.

hdrabkin commented 3 years ago

So that would exclude tRNA, miRNA, rRNA, snRNA, snoRNA, lncRNAs as functional gene products yes?

balhoff commented 3 years ago

@hdrabkin we do have some of those terms already. It's anything you currently see in the GO editor file.

balhoff commented 3 years ago

https://github.com/geneontology/go-ontology/pull/21818

vanaukenk commented 3 years ago

Thanks, @balhoff !

hdrabkin commented 3 years ago

Using two miRNA genes as input, I verify that now no more 'red dots' from ShEx. Thanky @balhoff !