plant ontology, cooperation?

[Leonore Reiser]

Dear Paulien:

This is wonderful. TAIR is part of a recently funded project to develop
plant ontologies called the "Plant Ontology Consortium". The goals of this
project are exactly what you describe.

The project website is http://www.plantontology.org/. So far most of the
ontology development has been done by Gramene (rice), TAIR and Maize DB.
The website describes the project and how to access the ontologies. We are
using the DAGeditor and ontology representation developed by the GO
(directed, acyclic graphs). The plan is to make the ontologies as broadly
applicable as we can to accomodate as many organisms as possible. The
ontologies can be accessed without restriction and the GO has made the
DAGeditor freely available. We are using the CVS repository as a
shared development resource and communicating over email primarily for
development.

It would be fantastic to work with your group to develop the structure and
content of the ontologies.We were planning to have a users meeting in
January, following the PAG meeting in San Diego-will people from your
organization be attending?

I am ccing this email to the group.We have just hired a coordinator (your counterpart here)  who will
be starting soon. She will be based at TAIR but will coordinate the efforts
for the whole group-in the meantime, I am very happy to work with you.
Best Regards
Leonore Reiser



On Thu, 16 Oct 2003, Adamse, Paulien wrote:

> Dear Mrs. Reiser,
>
> I hope you are the right person to write to about this, but I will give it a try. If I should contact somebody else, please let me know.
>
> I am writing on behalf of seven partner labs in Europe, working together to establish a network of plant databases. The project is called PlaNet (at the moment the address is http://mips.gsf.de/proj/planet/). The 7 partners all have databases with information about Arabidopsis (and sometimes other plants). Some are working on prediction-tools, others have collections of mutantlines (or germplasm or accessions, etc.). The goal is to connect them all and build one general access to it, using BioMoby. People will be able to query through this site and do not have to worry about in which database they have to look for their information.
>
> To be able to query multiple databases with one type of question it is very important to standardize the available information as much as possible. One important aspect in this is the description of the mutants. We set up a working group to compare the different ontologies/vocabularies already used by the different partners. I am the coordinator of this group. In Wageningen I am in the process of building a database for our mutants (WAtDB, not online yet), but we already have a wealth of information about mutants, transgenics and natural variants. But no standard terminology (yet) for describing them.
>
> This is where my request to you is coming in. We have a lot of phenotype descriptions and already noticed that not everything has been covered by the TAIR vocabulary. One way to solve that is to send you numerous submissions/update requests. But we thought that it might be more useful to work together more structural. Are you interested in cooperation with our group? If so, what would be a good way to do this? In November our PO working group is meeting again here in Wageningen and I would like to discuss it with them during that meeting. But it would be very useful to know what you think about it and maybe already get some suggestions about how we could work together.
>
> I hope you are interested and have time to reply within a few weeks. That way I can use your information when I am preparing our coming EU PlaNet PO working group meeting.
>
> Thanks in advance!
>
> Best wishes,
> Paulien
>
>
> Dr Paulien Adamse
> BU Bioscience
> Plant Research International,
> P.O. Box 16,
> 6700 AA Wageningen,
> The Netherlands.
>
> Tel: +31 317 477001/476830
> FAX: +31 317 418094
> paulien.adamse at wur.nl
> www.plant.wageningen-ur.nl
>
>

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Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
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