[Gusdev-rad-issues] Re: [Gusdev-gusdev] about uploading RAD data problem

[Elisabetta M. <man...@pc...>]

Sucheta,
I'm cc-ing the rad-issues list as this is a point of general interest.
The point is that the ontology terms are actually stored in the SRes name 
space. There you'll find a variety of tables, both for the MGED ontologies 
and for Taxon, etc. RAD3.OntologyEntry is merely used to pull in those 
ontology terms that are actually used frequently in RAD, so that most RAD 
tables point to RAD3.OntologyEntry rather than directly to the SRes 
ontology tables (the exception is RAD3.BioSource that for taxon points 
directly to SRes). Thus, a typical term in RAD3.OntologyEntry is actually 
coming from one of the terms stored in an appropriate SRes table, 
precisely in the table pointed by table_id and from the term in that 
table pointed by row_id.
(As an aside, there is an additional component: for the 
StudyAnnotator we have pull-down menus for those fields coming from 
ontologies and since for some categories there are many terms even in 
RAD3.OntologyEntry we use RAD3.ProjectLink to link to each Project those 
OntologyEntry terms that are relevant to that project, so that only those 
would be displayed in the StudyAnnotator when one logs in for a certain 
project.)
Elisabetta

On Thu, 13 May 2004, Sucheta Tripathy wrote:

> Hi Elisabetta,
> 
> Many thanks for pointing me to the dump file. Got it. However, while having 
> a cursory look I could not understand what the row_id in the table means.
> 
> Here is a snippet of the first few lines of the dump file.
> 
> ONTOLOGY_ENTRY_ID       PARENT_ID       TABLE_ID        ROW_ID 
> EXTERNAL_DATABASE_RELEASE_ID    SOURCE_ID       URI     NAME    CATEGORY 
>      VALUE   DEFINITION
> 217     (null)  3032    1185    7054    #cell_lysate    (null)  (null) 
> MaterialType    cell_lysate     cell lysate, a collection of cells whose 
> membranes have been disrupted
> 
> Thanks again
> 
> Sucheta
> 
> At 05:52 PM 5/12/2004 -0400, you wrote:
> 
> >Hi Sucheta,
> >in the StudyAnnotator tarball available at the RAD download site (follow
> >link from RAD website under GetRAD) we have a dump of RAD3.OntologyEntry
> >but it's kind of old. I'm cc-ing Trish Whetzel who is in our group and
> >part of the MGED Ontology group, she can probably point you to a more
> >recent dump.
> >Elisabetta
> >
> >
> >On Wed, 12 May 2004, Sucheta Tripathy wrote:
> >
> > > Hi Elisabetta,
> > >
> > > I am back to bother you again!!
> > > Now that we are going to upload real data to the module, I was 
> > wondering if
> > > I can get hold of a template file for OntologyEntry. This is just to 
> > get an
> > > idea how the terms are defined.
> > > Do you have a template data file that goes to RAD3.OntologyEntry?
> > >
> > > Thanks
> > >
> > > Sucheta