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

Fri Oct 17 20:36:01 EDT 2003

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
> >>-------------------------------------------------------------------------
> >>-- ----

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)