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[gofriends] Re: parsing error
erant at psb.ugent.be
Thu Oct 25 07:34:33 PDT 2007
the latest GO file has parsing error in line: 41325 it actually
corresponds to a date:
Wednesday, 24 October 2007 9: 31:13 am
On Oct 2, 2007, at 1:09 PM, Midori Harris wrote:
> Dear Erick,
> Yes, that is another error; thanks again for informing us! I will have
> a correction committed by the end of the day today.
> On Tue, 2 Oct 2007, Erick Antezana wrote:
>> Dear Midori,
>> once again there is a problem related to the dbxref of the term
>> with id: GO:0009703 :
>> id: GO:0009703
>> name: nitrate reductase (NADH) activity
>> namespace: molecular_function
>> def: "Catalysis of the reaction: NO2- (nitrite) + NAD+ + H2O = NO3-
>> (nitrate) + NADH + H+." [EC:184.108.40.206]
>> comment: Note that this function was formerly EC:220.127.116.11.
>> exact_synonym: "assimilatory NADH:nitrate reductase activity"
>> exact_synonym: "NADH-dependent nitrate reductase activity"
>> exact_synonym: "NADH-nitrate reductase activity" [:EC e]
>> exact_synonym: "NADH:nitrate oxidoreductase activity" [EC:18.104.22.168]
>> exact_synonym: "NADH:nitrate reductase" 
>> exact_synonym: "nitrate reductase (NADH(2)) activity" [EC:22.214.171.124]
>> broad_synonym: "assimilatory nitrate reductase activity" [EC:126.96.36.199]
>> xref_analog: EC:188.8.131.52
>> xref_analog: MetaCyc:NITRATE-REDUCTASE-(NADH)-RXN
>> is_a: GO:0046857 ! oxidoreductase activity, acting on other
>> nitrogenous compounds as donors, with NAD or NADP as acceptor
>> In particular the dbxref of the third listed synonym (exact_synonym:
>> "NADH-nitrate reductase activity" [:EC e]) is wrong. I guess it
>> should be EC:184.108.40.206?
>> Erick Antezana wrote:
>>> I just got the latest GO OBO file. And, while parsing it with the
>>> OBO parser from onto-perl
>>> (http://search.cpan.org/~easr/onto-perl-0.32/) we came across the
>>> following line (61699):
>>> ATP: protein-L-histidine N-pros-phosphotransferase
>>> from term:
>>> id: GO:0008256
>>> name: protein histidine pros-kinase activity
>>> it is a typo, isn't it?
Erick Antezana http://www.cellcycleontology.org
Tel:32 (0)9 3313824 Fax:32 (0)9 3313809
VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent
Technologiepark 927, 9052 Gent, BELGIUM
erant at psb.ugent.be http://www.psb.ugent.be
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