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

Sat Oct 18 13:14:19 EDT 2003

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
******************************************