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

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

Hi Jennifer,

That makes sense now. It really helps understand this plugin.

However, I have a new question, why the plugin loads so many empty 
records on SRes.GOSynonym while loading those secondary identifiers?


Thank you very much.

Jian

jld...@se... wrote:

>Jian,
>
>I beleive that the behavior we are observing is actually a designed behavior. 
>The pattern that I observed in my last email indicated that everything that was
>missing from the SRes.GOTerm table was a secondary identifier.  After further
>investigation we noticed that secondary identifiers are stored in the
>SRes.GOSynonym table as source_ids.
>
>Please let us know if this resolves your problem, or if you encounter any
>further issues when dealing with the plugin.
>
>
>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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