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

[Dave B. <db...@pc...>]

Just in case it's not clear, the name of the plugin to load all of this is 
LoadGoOntology; it is located in the GUS/GOPredict component. 

dave

On Tue, 13 May 2003, Dave Barkan wrote:

> Hi Chetna and folks--
> 
> > >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.
> 
> The three ontology files are located at
> 
> ftp://ftp.geneontology.org/pub/go/ontology/
> 
> They are named process.ontology, component.ontology, and 
> function.ontology.
> 
> Whatever is at that ftp site should be the latest version.  Use 
> --createRelease 
> option when running the plugin to automatically generate an External 
> Database Release Id (in SRes.ExternalDatabaseRelease) for these releases 
> of the ontology branches.  Note that there must be entries in 
> SRes.ExternalDatabase with names "GO Function", "GO Component", and 
> "GO Process."  (This could definitely be done better, avoiding hardcoding 
> names like this which are set in our version of GUS.  Let me know if you 
> have trouble with this and I will change it).
> 
> Specify the directory of the files with the --file_path option.  To load a 
> specific branch, specify the corresponding file with the --flat_file 
> option; to load all three just leave this blank.
> 
> You need to have two entries in SRes.GORelationshipType populated; they 
> correspond to the two different types of relationships a GO Term can have 
> with its child in the GO hierarchy, "isa" and "partof."  (These should be 
> set in the 'name' attribute of the GoRelationshipType table and have 
> corresponding ids).  More information on this representation is available 
> at
> 
> http://www.geneontology.org/doc/GO.doc.html#datarep
> 
> The other command lines should be self-explanatory but again let me know 
> if you have any trouble.
> 
> Dave  
> 
> 
> 
> 
> 
> 
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