Re: [GUSDEV] how do I load GO terms

[Elisabetta M. <man...@pc...>]

This command will no longer work with the new updates to the plugin 
applied 2 days ago and reflected in the plugin John Brestelli sent to 
Isabelle (also available in the gus svn trunk). The new version takes in 
just one .obo file. The updates were necessary because the former version 
of the plugin was no longer working with the most recent GO files 
released for function, process and component.
Elisabetta

On Fri, 12 Dec 2008, Jian Lu wrote:

> Try this command (use your own filePath)
>
> ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/home/data/go
> --functionExtDbName='GO Function' --processExtDbName='GO Process'
> --componentExtDbName='GO Component' --commit
>
> We have been using it for a long time without any problem. But recently
> it failed and gave a message 'out of memory'. I am not sure it is
> hardware issue, GO file format issue or something else.
>
> Isabelle Phan wrote:
>> Hello
>>
>> how do I load GO terms into GUS? The wiki information is outdated. I read the InsertGeneOntology plugin documentation but I am not sure I understand it. This in particular makes no sense to me:
>>
>> "you must provide either the (component, function, process)ExtDbName argument or set --create and provide the (component, function, process)ExtDbName argument for every branch you are loading."
>>
>> Please can you give an example?
>>
>> After several trial and error, I guessed that this command should load the GO component:
>>
>> ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/core/trypdb/gus-test/data/go/ --createRelease --flatFile=component.ontology --componentExtDbName="GO Component" --commit
>>
>> Is this correct? When I ran that command, the loading did not complete after 2 hours. I suspect locking of foreign key constraints in postgres. Is there a way around this?
>>
>> thanks,
>>
>> Isabelle
>> --
>> Isabelle Phan, DPhil
>> Seattle Biomedical Research Institute
>> +1(206)256 7113
>>
>>
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-- 
Elisabetta Manduchi, Ph.D.

Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021

phone: 215-573-4408
fax: 215 573-3111
email: man...@pc...
web: http://www.cbil.upenn.edu/~manduchi

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