regulation of translation, snRNA-mediated - rename terms

[gocentral]

Affected terms are:

positive regulation of translation, snRNA-mediated regulation of translation, snRNA-mediated negative regulation of translation, snRNA-mediated

I think we should rename to sncRNA or something other than snRNA, which refers to small nuclear RNAs.

Tanya

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Based on Ingrid's email:

Hi,

I was just looking over some of my own annotations and was initially disturbed to find an annotation of a small regulatory RNA to GO:0040033, negative regulation of translation, snRNA-mediated. I then read the definition and realized (as I must have when I first annotated the RNA) that snRNA means "small non-coding RNA" here. I think the name of this term could be improved; as far as I know, "snRNA" is most commonly used as an abbreviation for "small nuclear RNA", which is how it is used in many other GO terms. It is confusing to have it used in a different way here; at least I don't think that "small nuclear RNA" is synonymous with "small non-coding RNA". What do you think?

Thanks, Ingrid

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Suzi:

I agree. snRNA is small nuclear RNA to most folks

non-coding RNAs are (I think) usually ncRNA, so perhaps sncRNA might work?

-S

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I agree with Suzi, snRNA, is small nuclear RNA -

Michael

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Reported by: tberardini

Original Ticket: "geneontology/ontology-requests/4760":https://sourceforge.net/p/geneontology/ontology-requests/4760

[gocentral]

Logged In: YES user_id=579762 Originator: YES

From Mike: SO says, this perhaps is the root of the problem. Change the beginning to "Small nuclear RNA ...".

[Term] id: SO:0000274 name: snRNA def: "Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [ems:WB, http://www.ebi.ac.uk/embl/Documentation/FT\_definitions/feature\_table.html , PMID:11733745] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "small nuclear RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000231 ! snRNA_primary_transcript

Can also find "Small nuclear mRNA", that should be RNA not mRNA.

[Term] id: SO:0000231 name: snRNA_primary_transcript def: "A primary transcript encoding a small nuclear mRNA (SO: 0000274)." [SO:ke] is_a: SO:0000483 ! nc_primary_transcript

-Mike

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473890 Originator: NO

Hi,

Unless the term 'sncRNA' is standard in the literature, let's not introduce it. I think 'ncRNA' is pretty standard, so we could either just use that, or if we want the small part, then let's use 'small ncRNA'.

-Karen

Original comment by: krchristie

[gocentral]

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I like that idea, Karen. Thanks!

Tanya

Original comment by: tberardini

[gocentral]

• summary: regulation of translation, snRNA-mediated - rename termsr --> regulation of translation, snRNA-mediated - rename terms

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=546388 Originator: NO

Yes, make this at least ncRNA, or snc, but anything other than snRNA

Original comment by: hdrabkin

[gocentral]

Logged In: YES user_id=1948825 Originator: NO

ncRNA sounds good to me; might as well drop the "small" if it is not going to be defined - how small is small, anyway?

Original comment by: imk07

[gocentral]

Logged In: YES user_id=579762 Originator: YES

sounds like we're converging on:

positive regulation of translation, ncRNA-mediated regulation of translation, ncRNA-mediated negative regulation of translation, ncRNA-mediated

We can have synonyms that have the small ncRNA bit in them.

How does that sound?

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473890 Originator: NO

Hi,

term names sound fine.

not sure it's really even necessary to create the "small ncRNA" synonyms. If you search Pubmed for "ncRNA" you get 151 hits. If you search for the quoted string "small ncRNA", it tells you that the quoted string is not found. It does produce 45 hits which appear to contain both the word 'small' and the word 'ncRNA' non-adjacently. Since it doesn't look like adding the synonyms will add any value, I might just not add them. Not stridently opposed to them either, but in case my earlier email was taken as suggesting that we should have that phrasing too, I just wanted to say that they don't really look particularly useful.

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=579762 Originator: YES

I've made the edits: changed snRNA to ncRNA in all cases.

revision 5.666

Original comment by: tberardini

[gocentral]

• status: open --> closed-accepted

Original comment by: tberardini