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

[Lincoln Stein]

Hi Folks,

Just a warning.  We've started mangling Paulien's name.  I 
might have started it.

Lincoln

On Saturday 18 October 2003 01:14 pm, 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
> >>>>-----------------------------------------------------
> >>>>-------------------- -- ----