IRIS linking back to the Plant Ontology Consortium Plant Onto logies

[Bruskiewich, Richard]

Hi Pankaj,

As I mentioned at PAMG-X, I have a new database curator on staff, Mr. Victor
"Jun" Ulat, working with me since January 2nd. I've assigned him to deal
with controlled vocabularies and ontologies as a major part of his mandate.
To start with, he's been wrestling with setting up a CVS client at IRRI and
simply connecting to gorgonzola with CVS, so that we can start to
participate the CV/O development.  I believe that he has finally ironed out
the bugs of this over the past day or so...

Second, Arllet, Jun and some local UPLB students have been working on
embedding the GO database schema directly into IRIS. Because IRIS already
has some existing "controlled vocabulary" setup and application code written
to it, this is a tricky affair; however, we hope to have the job done over
the coming month, or soon thereafter. Once this is done, we will directly
synchronize our gene, phenotype, anatomy, developmental and trait ontologies
with the non-string CV/O node identifiers (not the strings) of the community
consensus CV/O's that we are all developing together.

BTW, "Trait" in IRIS is not all "Genetic Trait" in the sense that we
commonly use the term in biology. Unfortunately, IRIS has used the term
"trait" in a loose way in the past. That was one of my first complaints when
I started working with it and asked that the terminology be changed. We
renamed it to "properties", however, some use of the old term prevails.
Otherwise said, IRIS "traits" are not all genetic, so we'll need to be
intelligent about how we go about mapping them onto the POC CV/O's.

I trust that this clarifies where we are at present at IRRI. 

BTW, is someone from Gramene coming to the next ICIS workshop in Brisbane
(http://www.icis.org/icis) in April?

Cheers
Richard

PS Like a broken record, may I once again reiterate the opinion that "Trait
Ontologies" be subsumed into "Plant Ontologies" and not be an independent
ontology hierarchy (or DAG, for the purists)? :-))

-----Original Message-----
From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
Sent: Wednesday, February 27, 2002 3:41 AM
To: Doreen Ware; Zhaow Wei; brie
Cc: Susan McCouch; Graham Mclaren; Richard Bruskiewich
Subject: IRIS linking back to our TO



Hi Doreen, Wei and Kuan,

The International rice information system (IRIS) at IRRI, Philippines are
trying
to link back the trait (TO) terms to us. Its great but, the way they are
linking
does not return the exact match or the query in our Ontology database.

I just happend to browse through 
http://202.164.190.105/iris/showGermData.asp?GID=410238&Study=186

and figured out that they have the trait terms that link back to us.

For an example on this page see for trait term "Plant height"

returns a URL 
http://www.gramene.org/perl/ontology/search?query=Plant
height&btn=Ontology+Search

the results of this query is very generic.

whereas according to me it should be
http://www.gramene.org/perl/ontology/search?query=plant+height

Could you please give a do write-up on how to make links to our Protein
database
and Ontology database query. 

Thanks
Pankaj



******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************