[GUSDEV] how do I load GO terms

[Isabelle P. <isa...@sb...>]

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 The wiki information is outdated.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
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Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113