Re: [Gusdev-gusdev] GenBank, Gene Ontology questions

[Steve F. <st...@pc...>]

chetna-

I think Dave Barkan can probably answer your question about loading GO 
ontologies.

Dave... can you answer Chetna's question 2) below?

steve

Chetna D. Warade wrote:

>Hi all,
>
>It would be great if I can get insight into following:
>
>1) GenBank
>
>I am trying to load data from GenBank with the  command
>
>ga GUS::Common::Plugin::GBParser --gbRel=133 
>--file=/home/gusdev/GenBank/TcNCBIgenomic.gb
>
>I am getting SQL Error: foreign  key violation for tables SRes.DbRef and 
>DoTS.ExternalNASequence.
>
>I wanted to know more about how to solve the dependencies in these 
>tables.
>
>In order to solve this dependency I might need the 
>InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I 
>was wondering if its up and running.
>
>2) GeneOntology
>
>We have successfully  installed Taxonomy in the gus 3.0 database at this 
>end. I need to know what version and files do I need to put all the 3 
>ontologies in the database.  Also what are the dependencies in loading 
>Gene Ontology in terms of data.
>
>3) Following is the list of tables we have filled in to work with gus:
>Core.Algorithm
>Core.AlgorithmInvocation
>Core.Userinfo
>Core.Projectinfo
>Core.Groupinfo
>Core.Machine
>SRes.Taxon
>SRes.Taxonname
>SRes.GeneticCode
>
>I would be very happy to call you guys over phone (if possible) at a 
>good time if you think that the answers are really long and complex to 
>talk over email.
>
>Hope to hear from you all,
>Thanks,
>Chetna
>
>
>
>
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