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

[<jld...@se...>]

Jian,

None of the rows created by the plugin should be empty.  Have you checked the
'text' column?  Not every row will have a source_id because not everything
entered into GOSynonym has a secondary identifier, but they should all have
'text,' which is the column that holds the actual synonym.

Jennifer

Quoting 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
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
> >>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> >>>>Practices
> >>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> >>>>& QA
> >>>>Security * Process Improvement & Measurement * 
> >>>>http://www.sqe.com/bsce5sf
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>        
> >>>>
> >>    
> >>
> >
> >
> >
> >
> >-------------------------------------------------------
> >SF.Net email is sponsored by:
> >Tame your development challenges with Apache's Geronimo App Server. 
> >Download it for free - -and be entered to win a 42" plasma tv or your very
> >own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >  
> >
> 
>