SPKW-nucleotide-excision repair

gocentral commented 18 years ago

exo1 is getting a mapping to nucleotide-excision repair, but it is actually involved in mis-match repair (not NES).

I'm not sure which keyword but its:

IEA (GOA:spkw) with SP_KW:KW-0267

(by the way how do we crosslink to these? I searched the EBI website for this accession number but I didn't retreive anything?)

the word is likely to be

Excision nuclease?

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/305":https://sourceforge.net/p/geneontology/annotation-issues/305

gocentral commented 18 years ago

milestone: --> GOA
assigned_to: nobody --> ecamon

Original comment by: mah11

gocentral commented 17 years ago

Logged In: YES user_id=1647919 Originator: NO

Hi Val,

Im checking out EXO1_SCHPO/P53695

Exonuclease kw is mapped to exonuclease activity in GO Excision nuclease kw is mapped to both nuclease activity and nucleotide-excision repair in GO

Excision nuclease kw def is: Enzyme which excises abnormal or mismatched nucleotides from a DNA DE strand.

so val as part of mismatch repair does your gene no repair mismatched nucleotides?????

are you suggesting I map kw Excision nuclease simply to DNA repair GO:0006281????? Can you confirm the above first?

You can't search KW_IDs yet in UniProtKB but I will investigate this further. You can see the KW_IDS in expasy kw list..

http://ca.expasy.org/cgi-bin/keywlist.pl bookmark that page.

cheers, Evelyn

Original comment by: camon

gocentral commented 17 years ago

Logged In: YES user_id=516865 Originator: YES

Hi Ev,

Nucleotide excision repair is a particular pathway

part of def:

"In nucleotide excision repair a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase."

Exo1 is involved in mismatch repair

"A system for the correction of errors introduced during DNA replication when an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination."

But it is not involved in nucleotide excision repair.

So, either

The keyword mapping of "Excision nuclease" needs removing OR the mapping of "Excision nuclease" to 'nucleotide excision repair' needs removing.

Original comment by: ValWood

gocentral commented 17 years ago

assigned_to: ecamon --> edimmer

Original comment by: mah11

gocentral commented 17 years ago

Logged In: YES user_id=1647919 Originator: NO

Hi Val,

I think for this one as "Excision nuclease" already has a correct mapping i'm going to remove the extra mapping of "Excision nuclease" to 'nucleotide excision repair'

HOWEVER

I also think this may be a kw assignment problem so I'm also passing to Emily to resolve with Claire,Serenella.

If it is a kw assignment problem and that problem gets fixed, emily you can then later on remap.

ok

Evelyn

EMILY CHANGE TO PENDING

Original comment by: camon

gocentral commented 17 years ago

status: open --> pending

Original comment by: edimmer