Re: [Gusdev-gusdev] Controlled Vocabularies data

[Arnaud K. <ax...@sa...>]

I have one rectification to make, see below.

On Mon, 1 Dec 2003, Arnaud Kerhornou wrote:

> Hi Steve
>
> Steve Fischer wrote:
>
> > Arnaud-
> >
> > first, about DoTS::GeneInstanceCategory.  we don't seem to be using
> > this table.  its empty in our instance.
>
> We want to generate gene, RNA and protein entries and link them to
> corresponding gene, RNA and protein feature entries. This is done using
> the Gene, RNA and Protein Instance entries.
> There is a FK to a GeneInstanceCategory entry in GeneInstance and this
> can not be null. The same for RNAInstance and for ProteinInstance, I'm
> not sure what they are for.
>
> >
> >
> > second, about the other vocabs.  there is no central resource
> > available. each is dealt with individually.  for example, sres.taxon
> > has a plugin which loads data from ncbi.  sres.anatomy exists uniquely
> > in our db and was created manually.
>
> I'm thinking of CVs such as Taxon with has its own plugin and that the
> data can be retrieve from NCBI.

I meant I'm not thinking of CVs such as Taxon.

> There are a few ones, GUS specific, that we could share, e.g.
> SRes::OntologyRelationshipType
> <http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType>
> (AFAIR two entries "part_of" and "is_a"). They could be stored in XML
> format or as SQL statements. I'm thinking of others CVs, I'll prepare a
> list.
>
> >
> > so, to best answer your question we would need to know which CVs you
> > want to populate.
> >
> > steve
> >
> > Arnaud Kerhornou wrote:
> >
> >> Hi
> >>
> >> We would like to populate some of the GUS Controlled Vocabulary
> >> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of
> >> SRes tables.
> >> Are these resources available in XML format or in SQL statements from
> >> gusdb website or from CVS ?
> >>
> >> cheers and happy thanksgiving !!
> >> Arnaud
> >>
> >>
>