plant ontology, cooperation?

Fri Oct 17 15:54:07 EDT 2003

Dear Paulien:
It would be great if you can come to San Diego. Turns out the users
meeting is planned for July,not January- but POC collaborators will meet.

As a start- you mentioned that there were some specific areas of the
ontologies that were in need of work. What might be best is to start
working on one of these areas to correct/update the structure and content.
Are you familiar with the DAG structure used by GO and other ontologies??
The GO website has some great information/tutorials about this.
(www.arabidopsis.org). You can also access the DAG editor from there and
download a copy from SourceForge
(http://sourceforge.net/project/showfiles.php?group_id=36855).

Since its easiest to see changes in structure using the DAG editor its a
nice way to change things around and then see how it looks. WE can take a
segment of the ontology and refine the structure and share the flat files
(send them back and forth). Email has been a good mode of communication
and we can certainly arrange to speak on the phone if we need to hash out
a particularly difficult area. It would also  be great if you are coming
to SanDiego to spend some time up at Stanford if your schedule allows.

So bottom line is I think it would be a good idea to start with one node
of the ontologies and move on from there. Are you alright with downloading
DagEdit and working this way?

Best
Leonore

On Fri, 17 Oct 2003, Adamse, Paulien wrote:

> Dear Leonore (and others),
>
> Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?
>
> Bye,
> Paulien
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.edu]
> Sent: Thursday, October 16, 2003 16:23
> To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> Cc: po-dev at plantontology.org
> Subject: Re: plant ontology, cooperation?
>
>
> Hello Paulien,
>
> As PI of the POC project, I would like to personally express my enthusiasm for
> building a collaboration with your group to develop plant-wide ontologies to
> describe plant anatomy and developmental stages.  It would be very good for
> our groups to meet at the San Diego users' meeting.
>
> Lincoln
>
> On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> > 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
> >
> > ---------------------------------------------------------------------------
> >---- 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
> > ---------------------------------------------------------------------------
> >----
>
> --
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>
>
>

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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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