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[gofriends] Re: parsing error

Erick Antezana erant at psb.ugent.be
Tue Oct 2 03:29:19 PDT 2007


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)9 331 38 24                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
erant at psb.ugent.be                  http://www.psb.ugent.be/~erant
==================================================================

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