Re: [GUSDEV] how do I load GO terms

[Jian Lu <jl...@vb...>]

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 The wiki information is outdated.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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