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

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

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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