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

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

Hi Sucheta,
RAD3.OntologyEntry.table_id points to Core.TableInfo.table_id and 
identifies the table. RAD3.OntologyEntry.row_id points to the primary key 
of the relevant entry in the table corresponding to table_id.
For example, the entry in our current RAD3.OntologyEntry:

ONTOLOGY_ENTRY_ID	PARENT_ID	TABLE_ID	ROW_ID	
EXTERNAL_DATABASE_RELEASE_ID	SOURCE_ID	URI	NAME	CATEGORY	
VALUE	...
460	504	3032	29603	8015	#stimulus_or_stress_design	
(null)	PerturbationalDesign	ExperimentDesignType	
stimulus_or_stress_design...

has table_id=3032 which corresponds to the table SRes.MGEDOntologyTerm 
(that is this is the table in our Core.TableInfo with table_id=3032), the 
row_id=29603 tells us that if we to the query:

select * from SRes.MGEDOntologyTerm where mged_ontology_term_id=29603

we'll get the stimulus_or_stress_design entry.
In other words, the entry in RAD3.OntologyEntry with ontology_entry_id=460 
corresponds to the ontology term stored in SRes.MGEDONtologyTerm with 
primary_key=29603 in that table.

I'll let Trish address your remaining questions (1 and 2), as 
she can probably provide you with more details on that than me.
Elisabetta

On Thu, 13 May 2004, Sucheta Tripathy wrote:

> Hello,
> 
> It may appear little stupid, but I was browsing through all the core tables 
> as well as the sres.ontology group of tables, but could not find a row_id 
> corresponding to a table. Am I missing something? Anyway, this is not an 
> important problem.
> 
> Here are some more important questions.
> 1. Have you downloaded the sres.ontology data from NCBI?
> 2. For the RAD3.ontologyentry how do you generate data?
> 
> Many thanks
> 
> Sucheta
> 
> 
> At 09:56 AM 5/13/2004 -0400, Elisabetta Manduchi wrote:
> 
> >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
> 

-- 
Elisabetta Manduchi

Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021

phone: 215-573-4408
fax: 215 573-3111
email: man...@pc...
web: http://www.cbil.upenn.edu/~manduchi

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