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

Mon Oct 20 08:17:02 EDT 2003

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
-------------------------------------------------------------------------------