need for GO:0030452 - group I intron catabolic process

[gocentral]

Hi,

I'd like to know the need to specifically single out catabolism of Group I introns for a specific child term:

GO:0030452 - group I intron catabolic process

If we're going to do this thoroughly, we'll end up having catabolism terms for lots of things:

- fragments from pre-rRNA

• spliceosomal type introns
• tRNA introns
• Group II introns
• Group III introns

So far, from what I know of the RNA catabolic processes that occur within the nucleus, it's all the same process no matter what kind of fragment, i.e. they're all degraded by the nuclear exosome.

It's true that Group I introns (in cerevisiae) are clearly not going to be degraded by the nuclear exosome, but that's because all Group I and Group II introns in cerevisiae are in the mitochondrion. I'd guess that whatever occurs in mitochondria to degrade RNA acts on Group I introns, Group II introns, rRNA fragments, etc. In addition, Group I and Group II introns are found in a lot of different places since they're spread across the kingdoms, bacteria, archaea, organelles in eukaryea.

So, if we're going to distinguish different types of catabolic RNA processes, it would probably make more sense to distinguish by location, rather than by RNA "type".

I don't see any annotations to this term in AmiGO. Could we obsolete it? or at least discuss what need this term is really meant to serve?

-Karen

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/5789":https://sourceforge.net/p/geneontology/ontology-requests/5789

[gocentral]

All I can find about GO:0030452 is that it was added back in late 2001, when what was then the Proteome division of Incyte were actively making suggestions. Now, the term isn't used in annotations, and I don't feel any need to keep it separate. I suggest merging it into the parent, mainly to save obsoletion-email hassle.

m

Original comment by: mah11

[gocentral]

merging into the parent sounds fine. We're not maintaining old term names as synonyms anymore are we?

-K

Original comment by: krchristie

[gocentral]

Actually, we do usually keep old names as synonyms, in case any users have gotten used to searching for them. They're not necessarily exact synonyms, though; in fact, usually the synonyms are narrow or related.

m

Original comment by: mah11

[gocentral]

too bad, it seems unnecessary, but I'm not making a case for changing practice on this

-K

Original comment by: krchristie

[gocentral]

done - merged GO:0030452 into parent GO:0000292

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11