About (RE: plant ontology, cooperation? (fwd))
Leonore Reiser
lreiser at acoma.Stanford.EDU
Fri Oct 17 15:31:50 EDT 2003
Yep- .I assume thats what they were looking for.I think they have been
looking at the ontologies and have some suggestions for improvement.
I'd suggest coming to TAIR to maybe hash out some things as well- but
probably later- see how things go via email.
Any other comments/suggestions before I respond?
On Fri, 17 Oct 2003, Sue Rhee wrote:
> Hi, Leonore,
>
> Yes, it'd be a good agenda item. I like your suggestion of having them
> pick an area of ontology. Since it looks like most of their mutant
> phenotypes are for Arabidopsis, a good place to start may be for them to
> start with one of the Arabidopsis ontologies? They could also start
> learning (or perhaps they are already familiar?) DagEdit and get familiar
> with the existing ontologies.
>
> Sue
>
>
>
> On Fri, 17 Oct 2003, Leonore Reiser wrote:
>
> > Hi Everyone, I assume that ya'll have had a chance to read this email. I'd
> > like to send a response soon but want feedback as to how this should be
> > approached. I dont know anymore about what they are doing than what has
> > been written so obviously need to find out more about the project (Pankaj
> > do you know if this is the one Klaus is working with?).
> >
> > Anyway- can I suggest this for an agenda item on the 22nd. In the
> > meanwhile what is the general feeling about how to proceed. If they have
> > some concrete suggestions/feedback it would be excellent to incorporate
> > this at the outset. It would be great to pick an area of an ontology to
> > work on with them and see how this goes.
> >
> > Best
> > Leonore
> >
> > -------------------------------------------------------------------------------
> > 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
> > -------------------------------------------------------------------------------
> >
> > ---------- Forwarded message ----------
> > Date: Fri, 17 Oct 2003 09:33:42 +0200
> > From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> > To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> > Cc: lstein at cshl.org, po-dev at plantontology.org
> > Subject: RE: plant ontology, cooperation?
> >
> > 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
> > ========================================================================
> >
> >
> >
> >
>
> -----------------------------------------------------------------------------
> Sue Rhee rhee at acoma.stanford.edu
> The Arabidopsis Information Resource URL: www.arabidopsis.org
> Carnegie Institution of Washington FAX: +1-650-325-6857
> Department of Plant Biology Tel: +1-650-325-1521 ext. 251
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> -----------------------------------------------------------------------------
>
>
-------------------------------------------------------------------------------
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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