Invitation to a Meeting to discuss Ontologies for Phenotypes
Pankaj Jaiswal
pj37 at cornell.edu
Fri Sep 6 11:07:38 EDT 2002
Sue Rhee wrote:
>
> That's great that you were able to do it. Did you introduce both GO and
> POC? What was the response/reaction like?
>
> Sue
>
First of all there was a session on Gene Ontology (Gene Ontology: how should
genes be named? How can they be compared between genomes? Homology versus
function.) in which mainly Dina Mandoli (by way of Mark Wilkinson's
presentation) and Daphne Preuss introduced the GO concepts, in a generic way.
Then I made a small presentation on application of ontologies, by giving a
couple of examples and tried to initiate a discussion on how ontologies are
becoming important in the curation work. I presented both the GO and POC (PO and
TO). As far as GO was concerned the reaction was its Okay to have a
GO-function/process/component defined for a gene product in the pair wise terms
but it does not reflect the vision of a plant systematist on how will it explain
the particular gene product's acquiring of these GO concepts (as part of its
biological role) in an organism on an evolutionary aspect. Though we have a
granularity at organismal level (sensu terms) for distinction but still on a
wider aspect it does not explain the phylogenetics. This is important in
understanding the basic difference in genetic variation. Also Most of the
variation does not come from the coding regions (curated by GO) but from the non
coding, inter or intra genic genic regions, which the GO does not handle.
Therefore the PO can infact jump into this wagon to take care of the variation
atleast at the level of morphological/anatomical variation resulting due to the
various factors such as genetic/epigenetic/enviroment. The concept of PO and
its DAG structure was appreciated since it helps in making multiple
relationships of derived and children terms. We (POC) need to have a very smart
idea on how are we going to handle the micro organisms where there is no
anatomy. There were some concerns raised by the group on how we define
morphology and anatomy, should we have them separate or have it combined form as
of now. I think we need to convince the community on this issue before we go on
to have something concrete on this, because a
taxonomist/paleontologist/systematist views it is a different perspective than a
biochemist/molecular biologist. I had a good discussion with Andrew Doust (from
Toby Kellogg's group) and Geeta Bharathan and was able to convince them to an
extent on POC concepts, but it still needs more exposure and some good examples
to convince.
After coming back Susan and myself presented an overview of the ontology work
(GO and PO) as well as Gramene to Andrew Doust and Toby over a conference call
while sharing the desktop. We are yet to hear their comments though they were
excited about the work.
At the deep Gene workshop, everyone felt that this is the right time to have the
ontologies working specially the PO and TO, otherwise its going to be too late
since a lot of high throughput projects on plants will start (some have already
started) churning out the mutant collections and it will be really hard to go
back and score the phenotypes again. As far as pairwise similarity is there GO
is doing a fine job.
May be Brent can comment more on this, I am copying the mail to him.
Pankaj
> On Wed, 4 Sep 2002, Pankaj Jaiswal wrote:
>
> > Hi Sue,
> >
> > I went to the Deep Gene meeting at Wisconsin last month and introduced the
> > ontologies to the group of Brent and his colleagues.
> > It seems they are going to hold their next workshop at PAG this time. Though I
> > am not so sure if he said anything on holding a joint session with Ontology
> > workshop.
> >
> > Pankaj
> >
> > Sue Rhee wrote:
> > >
> > > Hi, Richard
> > >
> > > Yes, I could do that, if I can go to the meeting. Do you know what the
> > > dates are? Also, Brent Mishler <bmishler at socrates.Berkeley.EDU> from the
> > > Deep Green project was deeply interested in holding a joint 'ontologies'
> > > session, but I am not sure if anyone from the POC has been responsive
> > > enough to organize this with him. Would you be willing to communicate with
> > > him and see if his group would be interested in contributing a talk in
> > > your session please?
> > >
> > > CHeers,
> > > Sue
> > >
> > > On Wed, 4 Sep 2002, Bruskiewich, Richard wrote:
> > >
> > > > Sue,
> > > >
> > > > Would you like to talk about the TAIR interface this year at PAMG-XI? I'd be
> > > > more than pleased to slot you in. Can Pankaj/Tanya coordinate a report on
> > > > the plant ontology development efforts?
> > > >
> > > > Cheers,
> > > > Richard
> > > >
> > > > -----Original Message-----
> > > > From: Vincent, Leszek [mailto:Leszek at missouri.edu]
> > > > Sent: Thursday, September 05, 2002 6:13 AM
> > > > To: Sue Rhee
> > > > Cc: lreiser at acoma.Stanford.EDU; pj37 at cornell.edu; srm4 at cornell.edu;
> > > > R.BRUSKIEWICH at CGIAR.ORG; tberardi at acoma.Stanford.EDU
> > > > Subject: RE: Invitation to a Meeting to discuss Ontologies for
> > > > Phenotypes
> > > >
> > > >
> > > > Hi Sue,
> > > >
> > > > Thanks for your reply & helpful input in all the points of your
> > > > contribution. Let's see what gets put into the email 'melting pot' during
> > > > the next few weeks as others contribute their comments/suggestions. Having a
> > > > coherent perspective amongst us plant-based folk would be very helpful for
> > > > us & a good constructive contribution to the meeting.
> > > >
> > > > I understand that Graham McLaren (IRRI) will be attending. I'll contact him
> > > > separately about this dialogue.
> > > >
> > > > - Leszek
> > > >
> > > > > -----Original Message-----
> > > > > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > > > Sent: Tuesday, September 03, 2002 3:14 PM
> > > > > To: Vincent, Leszek
> > > > > Cc: lreiser at acoma.Stanford.EDU; pj37 at cornell.edu; srm4 at cornell.edu;
> > > > > R.BRUSKIEWICH at CGIAR.ORG; tberardi at acoma.Stanford.EDU
> > > > > Subject: RE: Invitation to a Meeting to discuss Ontologies for
> > > > > Phenotypes
> > > > >
> > > > >
> > > > > Hi, all
> > > > >
> > > > > Sorry for the delay.
> > > > >
> > > > > On Wed, 28 Aug 2002, Vincent, Leszek wrote:
> > > > >
> > > > > > Dear colleagues,
> > > > > >
> > > > > > Michael Ashburner sent an invite recently: "the purpose of
> > > > > this meeting
> > > > > > is to discuss schema for the representation of phenotype
> > > > > and trait data
> > > > > > in model organism databases (plant, animal and microbial),
> > > > > and an agreed
> > > > > > mechanism for how to proceed from there."
> > > > > >
> > > > > > Regarding Michael's invite I have several comments:
> > > > > >
> > > > > > 1. I think it would be important for at least one
> > > > > representative from
> > > > > > each research group (Gramene, IRRI, MaizeDB & TAIR) to be present at
> > > > > > this meeting. That would mean 4 out of 30 people would be
> > > > > plant folk -
> > > > > > still only ~13% but an important 13% for such a
> > > > > 'grassroots' meeting.
> > > > > > Will it be possible for someone from each of the above groups to
> > > > > > participate in the meeting??
> > > > >
> > > > > Yes. TAIR will send two people: Sue Rhee and Tanya Beradini.
> > > > >
> > > > > > 2. I suspect that the challenges being experienced by
> > > > > non-plant people
> > > > > > regarding the representation of phenotypic data will be/ are fairly
> > > > > > similar/'identical' to ours - comments/thoughts??
> > > > >
> > > > > Yes. At least we should focus on the commonality and not the
> > > > > differences.
> > > > > Fundamentally the large issues of describing phenotypes should be the
> > > > > same, hense the coming together of the groups.
> > > > >
> > > > > > 3. I note that Michael is going to call for papers to be distributed
> > > > > > before the meeting. Would you like to 'brainstorm' this
> > > > > topic via email
> > > > > > (or phone conf call) - to help us each perceive the 'issues' more
> > > > > > clearly. I know I could benefit from some form of
> > > > > provocation/nucleating
> > > > > > thoughts in this area. This dialogue could contribute to either
> > > > > > providing individual 'papers' to Michael for distribution
> > > > > or a synthesis
> > > > > > of our views into a single brief doc. - I'd be happy to
> > > > > co-ordinate this
> > > > > > dialogue etc. What are your thoughts - comments??
> > > > >
> > > > > Sounds like a great idea. It would be great if the plant
> > > > > groups could come
> > > > > up with a coherent perspective. I wonder if we could all come up with
> > > > > issues/questions we want to bring out and perhaps after the
> > > > > discussions
> > > > > via email have brewed up some, we could talk over the phone?
> > > > >
> > > > > Here are a few questions I had:
> > > > >
> > > > > 1. What is/should be the distinction between a biological
> > > > > process and a
> > > > > phenotype?
> > > > >
> > > > > 2. Does the description of phenotype require several
> > > > > ontologies or should
> > > > > it be one ontology?
> > > > >
> > > > > 3. What is the difference between a trait and a phenotype?
> > > > >
> > > > > In responding to these, it would be great to include references and
> > > > > examples. I think it's less productive to have the dicussions
> > > > > at the level
> > > > > of personal feelings. At least, that is my 2 cents.
> > > > >
> > > > > Cheers!
> > > > > Sue
> > > > >
> > > > >
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > - Leszek
> > > > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > > > P. Leszek D. Vincent Ph.D., FLS
> > > > > > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> > > > > > University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
> > > > > > Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
> > > > > > Ph/Fax (Home): (573) 441-1228;
> > > > > > Email: Leszek at missouri.edu
> > > > > > Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> > > > > > (http://www.maizemap.org/ and http://www.agron.missouri.edu/)
> > > > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > > >
> > > > > > =======================
> > > > > > > -----Original Message-----
> > > > > > > From: Michael Ashburner (Genetics) [mailto:ma11 at gen.cam.ac.uk]
> > > > > > > Sent: Friday, August 23, 2002 1:12 PM
> > > > > > > To: <snip>
> > > > > >
> > > > > > > Subject: Invitation to a Meeting to discuss Ontologies
> > > > > for Phenotypes
> > > > > > >
> > > > > > >
> > > > > > > Cambridge August 23 2002.
> > > > > > >
> > > > > > > Dear colleague,
> > > > > > >
> > > > > > > A short working meeting to discuss the representation of
> > > > > phenotypic
> > > > > > > data in genomic/genetic databases will be held Dec 6 - 8,
> > > > > 2002 (See
> > > > > > > my email of May 16 2002; let me know if you have lost it or
> > > > > > > never received
> > > > > > > it).
> > > > > > >
> > > > > > > The meeting will be hosted by The Institute of Genomic
> > > > > > > Research (TIGR):
> > > > > > >
> > > > > > > The Institute for Genomic Research
> > > > > > > 9712 Medical Center Drive
> > > > > > > Rockville, MD 20850
> > > > > > > 301-838-0200
> > > > > > >
> > > > > > > I am very grateful to Owen White and Jennifer Wortman of TIGR for
> > > > > > > facilitating this and for the offer of facilities.
> > > > > > >
> > > > > > > The meeting will start at 8.30 am on Saturday December 7
> > > > > and finish
> > > > > > > after lunch on Sunday December 8. We will have a group
> > > > > dinner at a
> > > > > > > local hostelry on the evening of Saturday; TIGR have very
> > > > > generously
> > > > > > > offered provide lunch and refreshments in the meeting room.
> > > > > > >
> > > > > > > We are strictly limited to 30 people. I attach a list of
> > > > > > > those to whom
> > > > > > > this email is being sent. If there are any very obvious
> > > > > ommissions
> > > > > > > please let me know.
> > > > > >
> > > > > > > <snip>
> > > > > >
> > > > > > > To repeat, the purpose of this meeting is to discuss
> > > > > schema for the
> > > > > > > representation of phenotype and trait data in model
> > > > > organism databases
> > > > > > > (plant, animal and microbial), and an agreed mechanism for
> > > > > > > how to proceed
> > > > > > > from there.
> > > > > > >
> > > > > > > Please let me know if you will attend.
> > > > > > >
> > > > > > > I thank Jennifer Wortmann and Owen White of TIGR for their help.
> > > > > > >
> > > > > > > Best wishes,
> > > > > > >
> > > > > > > Michael Ashburner
> > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > > > > >
> > > > > > <snip>
> > > > > >
> > > > >
> > > > > --------------------------------------------------------------
> > > > > ---------------
> > > > > 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.
> > > > > --------------------------------------------------------------
> > > > > ---------------
> > > > >
> > > > >
> > > >
> > >
> > > -----------------------------------------------------------------------------
> > > 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.
> > > -----------------------------------------------------------------------------
> >
> > --
> >
> > ******************************************
> > Pankaj Jaiswal, Ph.D.
> > Postdoctoral 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
> > ******************************************
> >
>
> -----------------------------------------------------------------------------
> 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.
> -----------------------------------------------------------------------------
--
******************************************
Pankaj Jaiswal, Ph.D.
Postdoctoral 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
******************************************
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