Re: [GUSDEV] how do I load GO terms

[Chris S. <sto...@pc...>]

Hi Isabelle.
A timely request- sorry that we did not get to it before you ran into  
the error. It was on our to do list to address this. John B., can you  
move the plugin and respond to Isabelle.
Thanks,
Chris
On Dec 11, 2008, at 4:41 PM, 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 The wiki information is outdated.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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