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

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

Hi Steve,

By further investigation of GO data, here is the report:

Gene Ontology file info:
!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 $

Total unique GO term in component.ontology: 1745
Total unique GO term in function.ontology: 7902
Total unique GO term in process.ontology: 10370
Total unique GO term in three files: 20015 (note: GO:0003673 exists in 
all three files)

By comparing our database SRes.GOTERM
Total loaded by GUS plugin: 19395

Surprisingly, there are 620 GO terms unloaded!!!

I have attached a file which lists all unqiue GO terms from three 
original files with flag 'loaded' and 'missing'.

Thanks.

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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>