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Source ontology files for the Gene Ontology
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NTR: to decribe DNA damage localizations #8667

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

I have a couple of free text annotations which I haven't previously captured in GO because I wasn't sure if the terms existed.

After talking to Midori there is a precedent for these types of terms, and

"DNA damage focus" (related synonym, DNA damage foci for searching) would this be described as a under nuclear body? if so a nuclear body associated with chromosomal regions with DNA damage?

"site of double-strand break" a chromosomal region associated with a double strand break in DNA?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/8455

gocentral commented 13 years ago

Val asked me to try to improve the suggested definitions …

name: site of double-strand break def: "A region of a chromosome at which a double-strand break has occurred." [GOC:mah] is_a: GO:0044427 ! chromosomal part

name: DNA damage focus def: "A nuclear body that forms at the site of a DNA double-strand break and contains DNA damage signaling and repair proteins." [PMID: 21035408 , PMID: 20096808] synonym: "DNA damage foci" EXACT [GOC:vw] synonym: "ionizing radiation-induced foci" RELATED [PMID: 21035408 , PMID: 20096808] synonym: "IRIF" RELATED [PMID:] is_a: GO:0016604 ! nuclear body [maybe also is_a 'site of double-strand break' ?]

Related synonyms refer to the same thing, so could be considered 'exact'; I put 'related' because the foci can form no matter what caused the ds break.

Other papers - I've looked mainly at abstracts for these: PMIDs 19806024, 12956959, 18725402, 17660715

Actually, some of the papers suggest there's a lot of overlap between repair foci and ds breaks ... not sure whether, or how, you may want to relate the terms to each other ... or if both are actually needed ...

cheers, m

Original comment by: mah11

gocentral commented 13 years ago

Original comment by: mah11

gocentral commented 13 years ago

Yep I wondered afterwards if we needed both, maybe we do only need a single term for this, because I think it's probably same observations used to make the inference, its only the interpretation which is different.?

val

Original comment by: ValWood

gocentral commented 13 years ago

Original comment by: rebeccafoulger

gocentral commented 13 years ago

I agree that one term makes most sense, so I added:

[Term] id: GO:0035861 name: site of double-strand break namespace: cellular_component def: "A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix." [GOC:bf, GOC:mah, GOC:vw, PMID:20096808, PMID:21035408] synonym: "DNA damage foci" RELATED [GOC:vw] synonym: "DNA damage focus" RELATED [GOC:mah, PMID:20096808, PMID:21035408] synonym: "ionizing radiation-induced foci" RELATED [PMID:20096808, PMID:21035408] synonym: "IRIF" RELATED [PMID:20096808, PMID:21035408] synonym: "site of DSB" EXACT [PMID:21035408] is_a: GO:0044427 ! chromosomal part

I put the foci synonyms as related (was toying with narrow) but feel free to pipe-up/edit if you disagree.

thanks, Becky

Original comment by: rebeccafoulger

gocentral commented 13 years ago

Original comment by: rebeccafoulger

gocentral commented 13 years ago

Maybe it should be 2 terms with a parent child relationship? I think damage foci can also form when replication forks collapse and with single stranded DNA damage so there is some specificity to capture here.

Original comment by: ValWood

gocentral commented 13 years ago

Original comment by: mah11