redefine repairosome - Githubissues

geneontology / go-ontology

Source ontology files for the Gene Ontology

http://geneontology.org/page/download-ontology

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redefine repairosome #6817

Closed gocentral closed 9 years ago

gocentral commented 14 years ago

I was trying to figure out what "repairosome" refers to in the contect it has neeb used in annotations:

Def: A stable complex of proteins that carry out the DNA damage recognition and incision reactions characteristic of nucleotide excision repair (NER), such as DNA damage recognition, DNA helix unwinding, and endonucleolytic cleavage at sites flanking damaged DNA; includes TFIIH subunits and additional polypeptides; may form in the absence of DNA damage.

I think, minimally this complex should be renamed NER repairosome or similar (there are repairosomes implicated in mis-match repair.

Should this be a parent of other NER complexes? I have seen a def which says it contains the "majority of NER proteins" (no provenence), but is this really a grouping term? what should be annotated to it ? at present it only has 4 annotations from SGD and 13 in total.

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/6837

gocentral commented 14 years ago

I found email to the effect that Eurie suggested a name change back in 2002. It got swamped out by a different issue in the same thread, so apparently never got done.

I don't think it's meant to be a grouping term … can't really help with what should be annotated. Ask Eurie??

http://fafner.stanford.edu/pipermail/go/2002-July/003964.html

Original comment by: mah11

gocentral commented 14 years ago

emailed Eurie

Original comment by: mah11

gocentral commented 14 years ago

Sorry guys. Val emailed soon after she posted this and it slipped through my email.

Thanks for finding that thread, Midori. Wow, what a blast from the past - how funny that folks were loathe to combine component and function. ;)

Repairosome is not a commonly used phrase. In sc, there does appear to be some controversy whether the NER complexes are sequentially assembled or exist as a giant 'repairosome' (PMID 8621533, PMID 7813015). But that was in the mid 90s, and nothing seems to have been published following up on the existence of a 'repairosome'.

Because of its limited use in the literature and confusion in annotation, I could vote for obsoleting it.

Another (crazy) thought would be to keep 'repairosome' but have 'has_part' children of each of the NEF terms??

Original comment by: eurie

gocentral commented 14 years ago

Thanks ... and I have no preference about what to do with the repairosome term. It's up to you guys whether it's worth keeping. If it is, adding has_part links will do no harm.

Original comment by: mah11