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[gofriends] Re: parsing error

Midori Harris midori at ebi.ac.uk
Tue Oct 2 04:09:06 PDT 2007


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
>> 
>
>

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