obsoletion of 6371 (formerly 'mRNA splicing')

[gocentral]

In reannotating some things following on from the recent changes to 'RNA splicing ; GO:0008380' and children, it became very clear that the term GO:0006371, which was formerly 'mRNA splicing' but which was changed to 'nuclear mRNA splicing, via spliceosome' in the recent reorganization must be obsoleted with suggestions to consider any of these 4 terms:

Group I intron splicing ; GO:0000372 Group II intron splicing ; GO:0000373 Group III intron splicing ; GO:0000374 nuclear mRNA splicing, via spliceosome ; GO:new ID

Apologies, it was my oversight that this change did not get made the first time around. All of the previous children of 6371 referred to spliceosomal splicing, but 6371 itself has been used to annotate things involved in both Group I and II splicing in SGD, and would have been legitimate for Group III intron splicing for organisms which possess this class of introns.

-Karen

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/1030":https://sourceforge.net/p/geneontology/ontology-requests/1030

[gocentral]

Logged In: YES user_id=579762

Hey Karen,

Does Group I/II/III intron splicing occur in mRNAs?

Do we have really have to obsolete this term (6371) instead of moving the annotations that were really meant to be Group I/II/III annotations to the right term?

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473890

Hey Tanya,

Yes, Group I, II, and III intron splicing does occur in mRNAs, though at least Group I and II intron splicing also occurs in tRNAs and rRNAs. I've included the comments for each of the three process terms that provides info on the scope of locations of each of these 3 intron types. Because of the broad localization of Group I and II intron splicing, both of these terms need to be directly under 'RNA splicing (8380)' and not under the former 'mRNA splicing (6371)'.

So, unfortunately, I think we do have to obsolete this term (6371) according to our rules because I think that changing it from 'mRNA splicing' to 'nuclear mRNA splicing, via spliceosome' narrows the meaning from "splicing of any mRNA" to "splicing of nuclear mRNAs by the spliceosome". Prior to the existence of the newly added terms for Group I, II, and III splicing, 'mRNA splicing ; GO:0006371' could definitely have been the most appropriate term for annotation of gene products involved in this.

... and I know it's a pain because I've just spent a day and a half going through our annotations to 6371 reannotating things which should be annotated to Group I or II splicing. Of course now, if 6371 does get obsoleted, we can just do an automated transfer of everything remaining to the new GOid for 'nuclear mRNA splicing via spliceosome'.

term: Group I intron splicing goid: GO:0000372 comment: Note that Group I introns are known to be found in 1) rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; 2) tRNA and mRNA of bacteria and bacteriophage; 3) rRNA of protists and fungi; and 4) occasionally in mRNA of animal mitochondria (e.g. sea anemone).

term: Group II intron splicing goid: GO:0000373 comment: Note that Group II introns are known to be found in 1) rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; 2) mRNA of bacteria.

term: Group III intron splicing goid: GO:0000374 comment: Note that Group III introns are known to be found in mRNA of plastids of euglenoid protists.

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=579762

Hey again,

OK. You've convinced me. 8-)

>Of course now, if 6371 does get obsoleted, we can just do >an automated transfer of everything remaining to the new >GOid for 'nuclear mRNA splicing via spliceosome'.

We don't have that many annotations so I can go through them and see if any of them need to be moved to another term.

Was there an old definition of 6371 that was updated to be specific for the spliceosome? If so, why didn't the id change at that point?

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473890

Hi again,

Um, yes, I would be the culprit for changing the definition of 6371 without obsoleting it, hence my apology in the original posting. Because all of it's children were spliceosomal-related, I assumed that 6371 was also spliceosomal specific.

The previous definition is below. It isn't actually very accurate because it indicates cleavage and then ligation of two free ends, which is an incorrect description of the mechanism of all splicing except that which is the mechanism by which most tRNAs are spliced.

term: mRNA splicing goid: GO:0006371 definition: The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, so that mRNA consisting only of the joined exons is produced. definition_reference: ISBN:0198506732

-Karen

Original comment by: krchristie

[gocentral]

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Aha. Okey-dokey, will get on with checking the annotations then.

You could change the term string of 6371 back to 'mRNA splicing' before/when you get rid of it. That way there won't be two 'nuclear mRNA blah, blah' (primary name) terms in the db.

T

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473890

Hi again,

Um, yes, I would be the culprit for changing the definition of 6371 without obsoleting it, hence my apology in the original posting. Because all of it's children were spliceosomal-related, I assumed that 6371 was also spliceosomal specific.

The previous definition is below. It isn't actually very accurate because it indicates cleavage and then ligation of two free ends, which is an incorrect description of the mechanism of all splicing except that which is the mechanism by which most tRNAs are spliced.

term: mRNA splicing goid: GO:0006371 definition: The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, so that mRNA consisting only of the joined exons is produced. definition_reference: ISBN:0198506732

-Karen

Original comment by: krchristie

[gocentral]

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absolutely agree that the term name of 6371 should be changed back to 'mRNA splicing' and I'll put the original definition back in for the record as well before obsoleting it.

-Karen

Original comment by: krchristie

[gocentral]

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If I hear no objections by Tuesday Sept 2nd, I will obsolete GO:0006371 (as 'mRNA splicing' and with its original def) and add a new term for 'nuclear mRNA splicing, via spliceosome' with a new GOid.

-Karen

Original comment by: krchristie

[gocentral]

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Since at least one mRNA that I know of is spliced via the tRNA type reactions, I agree that we do have to be more specific for the totality of mRNAs; hence, we do need a "nuclear mRNA splicing via splicesosome" term. This will effect about 60 genes annotated, but I'd rather like to revisit these anyways.

Original comment by: hdrabkin

[gocentral]

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In the comment for obsoletion, I also suggested 'RNA splicing, via endonucleolytic cleavage and ligation ; GO:0000394', as per Harold's comment.

Original comment by: krchristie

[gocentral]

• status: open --> closed-accepted

Original comment by: krchristie