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

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

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