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

[Michael S. <msa...@pc...>]

Has a bug been filed for this?  If not, please do so.

--Mike



On 8/18/05 5:25 PM, "jld...@se..." <jld...@se...>
wrote:

> I'm looking into the issue, and will let you know what I find as soon as
> possible.
> 
> Jennifer
> 
> Quoting Jian Lu <jl...@vb...>:
> 
>> Steve,
>> 
>> After further investigation of GO files and comparison of the database,
>> here is the report:
>> 
>> GO file information:
>> !autogenerated-by:     DAG-Edit version 1.419 rev 3
>> !saved-by:             gocvs
>> !date:                 Fri Aug 12 21:00:17 PDT 2005
>> !version: $Revision: 3.306 $
>> 
>> unique GO terms in component.ontology: 1745
>> unique GO terms in function.ontology: 7902
>> unique GO terms in process.ontology: 10370
>> unique GO terms in all three files: 20015
>> 
>> total loaded GO terms: 19395
>> total missing GO terms: 620
>> 
>> 
>> steve wrote:
>> 
>>> 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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>> 
>> 
> 
> 
> 
> 
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