Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[steve <sfi...@pc...>]

jian-

yes, we have used the plugin, but it has been changed a little 
recently.  can you do a grep on the file to count how many terms there 
are in it?   have you looked carefully at those entries in the file to 
see if there is something that distinguishes them?    can you count how 
many rows actually are in the database that were put there by that run 
of the plugin?

thanks for your help,
steve

Jian Lu wrote:

> Hi group,
>
> I downloaded Gene Ontology version 3.306 
> (component.ontology,function.ontology, process.ontology) and ran
> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
> database.
> Here is my command:
>
> ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
> /home/data/ontology --functionExtDbName 'GO Function' 
> --processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
> --commit
>
>
> Everything looks fine, no errors. It returned a result as "Created 
> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
> entries in GOSynonym.  Skipped 0 total entries".
>
> But when I was doing other data checking, I found there are three GO 
> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
> They do exist on the GO downloaded files.
> Has anyone used this plugin to load GO and checked its completeness? 
> Please advise. Thanks.
>
> Jian
>
>
>
>
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