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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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query - ribosome biogenesis & subunit export #9667

Closed gocentral closed 7 years ago

gocentral commented 12 years ago

Hi,

At present, 'ribosomal subunit export from nucleus' (GO:0000054) is part_of ribosome biogenesis (GO:0042254). The generic ancestor 'cellular component biogenesis' doesn't have anything about transporting an assembled component, though, so we want to make sure the current arrangement is actually optimal.

Val tell me that a number of genes whose products are involved in RNA processing have mutants with ribosomal subunit export defects, which looks very much like a downstream effect.

So we're wondering whether there's any reason other than those phenotypes for including the export parent (and the bit of the ribosomal subunit biogenesis defs that says "includes transport to the sites of protein synthesis"). If not, it may be best not to have the GO:0000054 part_of GO:0042254 link in the ontology. Can anyone shed any light?

thanks, Midori & Val

(Val also suggests assigning this to David because he's worked on this part of go before.)

Reported by: mah11

Original Ticket: geneontology/ontology-requests/9460

gocentral commented 12 years ago

p.s. another thing about the mutant phenotypes: can't tell from a subunit export defect whether the gene product's direct involvement is in RNA processing, subunit export, or both

Original comment by: mah11

gocentral commented 12 years ago

Hi David,

See Val's suggestion - Would you be ok with looking into this request? In case it's useful, the QuickGO change log shows that 'ribosomal subunit export from nucleus' (GO:0000054) was made part_of ribosome biogenesis (GO:0042254) on April 1st 2008 http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000054\#term=history

Thanks, Paola

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Original comment by: paolaroncaglia

gocentral commented 12 years ago

I had another thought on the way home. This organization may be because you can't separate because the modification and export as they happen concurrently. Is this the case?

Original comment by: ValWood

ValWood commented 8 years ago

@ukemi any thoughts? Val

ukemi commented 8 years ago

@hdrabkin you would know more about this than I would.

pgaudet commented 7 years ago

Hi @valwood @mah11

According to the wikipedia article cited in the GO term definition (https://en.wikipedia.org/wiki/Ribosome_biogenesis) PMID:26404467 and PMID:17509569 it seems like export can be considered part of the ribosome biogenesis.

Can this be closed ?

Thanks, Pascale

ValWood commented 7 years ago

OK....I remember older discussions that people call processing export and assembly biogenesis