About (RE: plant ontology, cooperation? (fwd))

Sue Rhee rhee at acoma.Stanford.EDU
Mon Oct 20 12:56:07 EDT 2003 

i totally agree.
sue

On Mon, 20 Oct 2003, Leonore Reiser wrote:

> Haven't yet heard back regarding the last email from
> Paulien. I'll suggest it- but maybe lets see what we can resolve/deal with
> over email first. If we're all going to go to the trrouble of a conference
> call with this many time zones- we should have a very defined agenda
> (IMHO).
> Leonore
>
>
> On Sat, 18 Oct 2003, Pankaj Jaiswal wrote:
>
> > I agree. Leonore, do you want to go ahead and arrange a conf. call with Pauline.
> >
> > Thanks
> > Pankaj
> >
> >
> > Lincoln Stein wrote:
> > > Since Pauline wasn't planning to go to PAG, we can hold off on meeting her
> > > until july.  But we should have a teleconference with her sooner.
> > >
> > > Lincoln
> > >
> > > On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal wrote:
> > >
> > >>Hi Leonore,
> > >>
> > >>Meeting Pauline at the PAG will be a great idea. We can have discussion
> > >>with him and other potential target DBs and projects. However, POC's first
> > >>user meeting is in July next year. In Jan at Stanford it will be a GO users
> > >>meeting, where many of the plant people are trying to come, e.g. Deepgene
> > >>group.
> > >>
> > >>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?).
> > >>
> > >>Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
> > >>Project is at http://mips.gsf.de/proj/thal/phenotype/
> > >>
> > >>
> > >>>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.
> > >>
> > >>I agree with Sue, since their priority is on Arabidopsis.
> > >>
> > >>
> > >>>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
> > >>>>-------------------------------------------------------------------------
> > >>>>-- ----
> > >
> > >
> >
> > --
> > ******************************************
> > Pankaj Jaiswal, Ph.D.
> > Research 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
> > ******************************************
> >
> >
> >
>
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------
>
>

-----------------------------------------------------------------------------
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.
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