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[gofriends] Re: parsing error

Erick Antezana erant at psb.ugent.be
Thu Oct 25 07:34:33 PDT 2007


Dear Midori,

   the latest GO file has parsing error in line: 41325 it actually 
corresponds to a date:

Wednesday, 24 October 2007 9: 31:13 am

cheers,
Erick

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.
>
> Midori
>
> 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 :
>>
>> [Term]
>> 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:1.7.1.1]
>> comment: Note that this function was formerly EC:1.6.6.1.
>> exact_synonym: "assimilatory NADH:nitrate reductase activity" 
>> [EC:1.7.1.1]
>> exact_synonym: "NADH-dependent nitrate reductase activity" 
>> [EC:1.7.1.1]
>> exact_synonym: "NADH-nitrate reductase activity" [:EC e]
>> exact_synonym: "NADH:nitrate oxidoreductase activity" [EC:1.7.1.1]
>> exact_synonym: "NADH:nitrate reductase" []
>> exact_synonym: "nitrate reductase (NADH(2)) activity" [EC:1.7.1.1]
>> broad_synonym: "assimilatory nitrate reductase activity" [EC:1.7.1.1]
>> xref_analog: EC:1.7.1.1
>> 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:1.7.1.1?
>>
>> Erick
>>
>> Erick Antezana wrote:
>>> Hi,
>>>
>>>   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:
>>> [Term]
>>> id: GO:0008256
>>> name: protein histidine pros-kinase activity
>>> ...
>>> it is a typo, isn't it?
>>> cheers,
>>> Erick
>>
>>
>>
--
==============================================
Erick Antezana                     http://www.cellcycleontology.org
PhD Student
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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