Steven Marygold
Steven Marygold
(original ticket to improve lncRNA definition is #575.) @blakesweeney just alerted me to this new 'consensus statement' paper that tries to define and classify lncRNAs better: https://www.nature.com/articles/s41580-022-00566-8 Relevant passages: _lncRNAs...
@pgaudet will you be obsoleting GO:0005966 as per comment above? If not, can you remove the partial EC xref from the definition line? [Term] id: GO:0005966 name: cyclic-nucleotide phosphodiesterase complex...
Update: QuickGO now says there are just 4 annotations to this term - 2 IEA via EnsemblPlants, 1 TAS, and 1 IDA to Arabidopsis GRXC5 (as mentioned above).
On the other hand, Amigo (but not QuickGO) still shows all the InterPro2GO mappings to this term, which were removed from InterPro months ago...
_just double checking that there isn't somewhere else that we need to be referring people to when it comes to this term?_ Hi @egchristensen No, I think it can just...
> @sjm41 I've emailed Adam Frankish and asked him to confirm in this thread. If I don't hear back from him in a couple days we'll go ahead and obsolete....
@blakesweeney Does Rfam use/need these snoRNA SO terms: U3_snoRNA (SO:0001179) U3_snoRNA_gene (SO:0002378) U14_snoRNA (SO:0000403) U14_snoRNA_primary_transcript (SO:0005837) U14_snoRNA_gene (SO:0002377) Proposal in original post is to obsolete them as 'out of scope'...
_Maybe we can find out if there is any usage of these terms and let people know the better way to annotate?_ I don't know of the best way of...
methylation_guide_snoRNA (SO:0005841) = GO:0030561 methylation_guide_snoRNA_primary_transcript (SO:0000580) = GO:0030561 methylation_guide_snoRNA_gene (SO:0002379) = GO:0030561 pseudouridylation_guide_snoRNA (SO:0001187) = GO:0030558 pseudouridylation_guide_snoRNA_gene (SO:0002380) = GO:0030558 U3_snoRNA (SO:0001179) = RF00012 U3_snoRNA_gene (SO:0002378) = n/a or RF00012...
@egchristensen Yes, the list of 10 SO terms above is the complete list of Rfam-mirrored SO terms we think should be obsoleted (though there are other snoRNA terms suggested for...