ENZYME nomenclature database in chado

[Victor de Jager-2]

Dear all,

I would like to use the EC numbering scheme for one of my databases, but before I'm staring to write a script,does anyone have a script or experience with loading the ENZYME nomenclature database from Swissprot into the Chado scheme?

best regards

Victor de Jager

 

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[Sam Angiuoli]

Victor,
We have a version of the nomenclature from 2004 in OBO format
(attached) that we've been loading into the cvterm tables of Chado.
In this scheme, the EC numbers are stored as dbxrefs for a cvterm that
has the name and description of the enzyme.

Sam Angiuoli
Institute for Genome Sciences
University of Maryland School of Medicine

2008/6/26 Victor de Jager <victor.de.jager@...>:

> Dear all,
>
> I would like to use the EC numbering scheme for one of my databases, but
> before I'm staring to write a script,does anyone have a script or experience
> with loading the ENZYME nomenclature database from Swissprot into the Chado
> scheme?
>
> best regards
>
> Victor de Jager
>
>
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
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> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>

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[Victor de Jager-2]

Thanks Sam,

I was about to write a script that converts the files from the
repository in a similar way as in your obo scheme. Woould you still have
a copy of th ecMaker.pl script mentioned in the file somewhere?

Victor

-----Original Message-----
From: Sam Angiuoli [mailto:angiuoli@...]
Sent: Thursday, June 26, 2008 4:02 PM
To: Victor de Jager
Cc: gmod-schema@...
Subject: Re: [Gmod-schema] ENZYME nomenclature database in chado

Victor,
We have a version of the nomenclature from 2004 in OBO format
(attached) that we've been loading into the cvterm tables of Chado.
In this scheme, the EC numbers are stored as dbxrefs for a cvterm that
has the name and description of the enzyme.

Sam Angiuoli
Institute for Genome Sciences
University of Maryland School of Medicine

2008/6/26 Victor de Jager <victor.de.jager@...>:

> Dear all,
>
> I would like to use the EC numbering scheme for one of my databases,
> but before I'm staring to write a script,does anyone have a script or
> experience with loading the ENZYME nomenclature database from
> Swissprot into the Chado scheme?
>
> best regards
>
> Victor de Jager
>
>
>
> ----------------------------------------------------------------------
> --- Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for just about anything
> Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> Gmod-schema mailing list
> Gmod-schema@...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>

 

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[Robson Francisco de Souza]

2008/6/27 Victor de Jager <victor.de.jager@...>:
> Thanks Sam,
>
> I was about to write a script that converts the files from the
> repository in a similar way as in your obo scheme. Woould you still have
> a copy of th ecMaker.pl script mentioned in the file somewhere?

The GO websites distributes a file mapping EC numbers to GO terms.
Perhaps you could use this file to add dbxref entries for the GO terms?

Still I don't know if there is any standadized to load this sort of
annotation fot cvterm entries. Does anyone know anything about this?
Robson

> Victor
>
> -----Original Message-----
> From: Sam Angiuoli [mailto:angiuoli@...]
> Sent: Thursday, June 26, 2008 4:02 PM
> To: Victor de Jager
> Cc: gmod-schema@...
> Subject: Re: [Gmod-schema] ENZYME nomenclature database in chado
>
> Victor,
> We have a version of the nomenclature from 2004 in OBO format
> (attached) that we've been loading into the cvterm tables of Chado.
> In this scheme, the EC numbers are stored as dbxrefs for a cvterm that
> has the name and description of the enzyme.
>
> Sam Angiuoli
> Institute for Genome Sciences
> University of Maryland School of Medicine
>
> 2008/6/26 Victor de Jager <victor.de.jager@...>:
>> Dear all,
>>
>> I would like to use the EC numbering scheme for one of my databases,
>> but before I'm staring to write a script,does anyone have a script or
>> experience with loading the ENZYME nomenclature database from
>> Swissprot into the Chado scheme?
>>
>> best regards
>>
>> Victor de Jager
>>
>>
>>
>> ----------------------------------------------------------------------
>> --- Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for just about anything
>> Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmod-schema@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>
>
> __________ Information from ESET NOD32 Antivirus, version of virus
> signature database 3223 (20080627) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>
>
> __________ Information from ESET NOD32 Antivirus, version of virus
> signature database 3223 (20080627) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
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> _______________________________________________
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>

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