From rwing at Ag.arizona.edu  Tue Dec  3 04:45:37 2002
From: rwing at Ag.arizona.edu (Rod Wing)
Date: Tue, 03 Dec 2002 17:45:37 +0800
Subject: email address
Message-ID: <5.0.0.25.2.20021203174509.02530430@ag.arizona.edu>

Hi Doreen,
What is you email address.
Thanks,
Rod




From matthes at cshl.edu  Wed Dec  4 14:26:21 2002
From: matthes at cshl.edu (Matthes, Anita)
Date: Wed, 4 Dec 2002 14:26:21 -0500 
Subject: email address
Message-ID: <39FDE54A4920D411AE0C0090274602F201E1FDC8@exch01.cshl.org>

Doreen's email address is ware at cshl.edu

-----Original Message-----
From: Rod Wing [mailto:rwing at Ag.arizona.edu]
Sent: Tuesday, December 03, 2002 4:46 AM
To: gramene at gramene.org
Subject: email address


Hi Doreen,
What is you email address.
Thanks,
Rod



From pj37 at cornell.edu  Thu Dec  5 18:11:18 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 05 Dec 2002 18:11:18 -0500
Subject: [Fwd: Redundant sequences !]
Message-ID: <3DEFDD16.A0610DC3@cornell.edu>

FYI
Pankaj

-------- Original Message --------
From: Tao Tao <tao at ncbi.nlm.nih.gov>
Subject: Redundant sequences !
To: pj37 at cornell.edu
CC: tao at ncbi.nlm.nih.gov

Hi,

None of the primary sequence databases are non-redudant.
So there will be redundant records.  Even if the sequences
are the same, they may contain different annotations with
additional information and reference that may be useful.

The two entries are from different sources, one
from swissprot and the other from the translation
of and CDS annotation of an existing nucleotide record. 

For BLAST, we do collapse sequences with 100% identity into
one record.  This practice is limited to blast databases
only.  

REgards,

Tao Tao
NCBI User SErvice

------------- Begin Forwarded Message -------------

Date: Thu, 05 Dec 2002 14:51:08 -0500
From: Pankaj Jaiswal <pj37 at cornell.edu>
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MIME-Version: 1.0
To: info at ncbi.nlm.nih.gov
CC: Gramene at gramene.org
Subject: Redundant sequences !
Content-Transfer-Encoding: 7bit
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version=2.01

Hi,

Why do I see two entries for the same thing? I guess GenBank needs to weed out
such entries which are the same but considered different since they come from
two different database sources, DBJ and SP. It creates more confusion for the
user on which is what. More so as in this particular instance the
name/description has an ambiguity.

1: BAA21547 
RFL [Oryza sativa]
gi|2274790|dbj|BAA21547.1|[2274790]

2: O24175 
Putative transcription factor FL (RFL)
gi|7227890|sp|O24175|FL_ORYSA[7227890]


Pankaj

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


------------- End Forwarded Message -------------



------------- End Forwarded Message -------------


From pj37 at cornell.edu  Thu Dec  5 14:51:08 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 05 Dec 2002 14:51:08 -0500
Subject: Redundant sequences !
Message-ID: <3DEFAE2C.71B73DC9@cornell.edu>

Hi,

Why do I see two entries for the same thing? I guess GenBank needs to weed out
such entries which are the same but considered different since they come from
two different database sources, DBJ and SP. It creates more confusion for the
user on which is what. More so as in this particular instance the
name/description has an ambiguity.

1: BAA21547 
RFL [Oryza sativa]
gi|2274790|dbj|BAA21547.1|[2274790]

2: O24175 
Putative transcription factor FL (RFL)
gi|7227890|sp|O24175|FL_ORYSA[7227890]


Pankaj

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


From jwhit at melbpc.org.au  Mon Dec  9 16:49:42 2002
From: jwhit at melbpc.org.au (Jan Whitaker)
Date: Tue, 10 Dec 2002 08:49:42 +1100
Subject: Website Selected for Agrigate - Gramene
Message-ID: <5.0.2.1.0.20021210084856.022cc870@popa.melbpc.org.au>


Dear Gramene representative,

Congratulations! Your information materials:

Gramene: a comparative mapping resource for grains
	http://www.gramene.org/


have been chosen for listing in Agrigate, the Australian web-based gateway 
to agricultural research information. A listing in Agrigate includes a site 
description and a link to your materials. The resources are selected by an 
editorial review process consisting of specialist librarians and members of 
the agriculture research community. The purpose of Agrigate is to support 
identification and dissemination of high quality research materials.

Agrigate is a project of the libraries of the Universities of Melbourne, 
Adelaide and Queensland and the CSIRO. It has been funded in part by a 
grant from the Australian Research Council. A reference group, including 
representatives from CSIRO, the Universities of Melbourne, Adelaide and 
Queensland, the National Library of Australia and Agriculture Fisheries and 
Forests Australia, has developed the service.

For more information on Agrigate go to:  http://www.agrigate.edu.au

You may wish to include the Agrigate logo 
<http://www.agrigate.edu.au/logo.gif> on your site to indicate your 
material has been selected for Agrigate. We would be grateful if the logo 
linked back to the Agrigate homepage to help information seekers on the 
web. If you want to include a description of Agrigate, we would appreciate 
the use of the following piece of standard text:

"Agrigate - a subject gateway for agricultural information in Australia, 
highlighting links to quality sites located in Australia and internationally."

Agrigate would welcome your suggestions for sites and materials that would 
be suitable for inclusion in Agrigate. We are particularly interested in 
locating information reflecting and supporting Australian research, such as 
conference papers, research reports, data sets, etc. If you feel that you 
have any suggestions please let us know.

If you would like to be added to a "What's New" announcement email list, 
please contact:
AGRIGATE, agrigate at agrigate.edu.au.

Sincerely,

Jan Whitaker
Data Custodian
Agrigate
c/o The Baillieu Library
The University of Melbourne
Parkville  Vic  3052
Email: jwhit at primenet.com




From lewin at ergito.com  Wed Dec 11 09:45:30 2002
From: lewin at ergito.com (Benjamin Lewin)
Date: Wed, 11 Dec 2002 09:45:30 -0500 (EST)
Subject: Ergito Site
Message-ID: <200212111445.gBBEjUsO020485@wally.ergito.com>


I expect you know that since I left Cell I have been working on the web site I established at www.ergito.com. We intend to offer an integrated approach to the biological sciences at several levels. The site started with a molecular biology module based on my book GENES, and we have begun to expand it into other areas and levels. When complete, the site will contain sections on biochemistry, genetics, molecular biology, cell biology, immunology, etc,  each with the scope of a major text on the subject. I would just like to let you know that the first chapters of several modules are now available, including: 

Genetics module: "Yeast Genetics" by Fred Winston (http://www.ergito.com/main.jsp?book_abbrev=genetics&chap_aso=6)
Cell Biology module: "Membrane targeting of proteins" by Tom Rutkowski and Vishu Lingappa (http://www.ergito.com/main.jsp?book_abbrev=cellbio&chap_aso=2)
Introductory Biology: several chapters on basic molecular and cell biology by Douglas and Zarelda Fambrough (http://www.ergito.com/main.jsp?book_abbrev=intro). 

Cell Biology: "Nuclear Structure and Transport" by Pam Silver and Chuck Cole will be available December 15.

If you use one of the links above, you will need to register, but after that will go straight through to the chapter. These chapters are available without charge for the present. We will be adding further chapters to each module in the coming months, until they are complete next year. 

In addition, there are several new essays in the Great Experiments series, in which scientists write about the significance of their discoveries. We are also about to introduce two new series, dealing with Techniques and with Protein Structures. 

If you find this email to be a nuisance, please click on the link http://www.ergito.com/remove.jsp?email=gramene at gramene.org, and I will make sure we do not send you any further emails.  


Regards



From pmp5 at cs.nyu.edu  Wed Dec 11 09:35:57 2002
From: pmp5 at cs.nyu.edu (Peter Palenchar)
Date: Wed, 11 Dec 2002 09:35:57 -0500 (EST)
Subject: No subject
Message-ID: <Pine.GSO.4.44.0212110934530.2104-100000@griffin.cs.nyu.edu>

	I'm looking for a information that links an Arabidopsis gene to
it's Rice ortholog.  Are you or do you know somebody that is doing that
sort of analysis?

Thank you for any help you can provide.

Peter Palenchar



From jn66 at cornell.edu  Tue Dec 10 16:45:43 2002
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Tue, 10 Dec 2002 16:45:43 -0500
Subject: message from Arwa
References: <000501c2a091$52212080$750a040a@haiyan>
Message-ID: <3DF66087.C2AB53CC@cornell.edu>

Dear Arwa,

Thank you for your message.

As an open source database, we are pleased to help users and also hope
to get some feedback, suggestions from the community.

As to reprints, unfortunately we are not able to give you them due to
copyright issue. Please contact with the original authors
for those papers. You can try to contact with the corresponding author,
or
first author if necessary. Please let's know if you have further
questions.

Junjian Ni
Curator in Gramene


haiyan wrote:

>  Dear Junjian Ni how could I thank you ? I appreciate sending me very
> useful abstracts I realy need and I would like to introduce
> myself      I am a postgraduated student from the university of
> Al-Mustansireah - Baghdad . My field work is" the production of salt
> tolerance plantlets of rice using tissue culture technique ".     I
> would appreciate receiving from you any reprints concerning and
> related to my subject .I am waiting for your answer as soon as
> possible . Thank you for your courtesy .  Sincerely yoursArwa
> Abdul-Kareem Tawfiq E-mail : haiyan at warkaa.nethome address :IRAQ -
> BAGHDAD                      Al-khadraa area
> quarter  641                      street  15                      home
> no.  27
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From pj37 at cornell.edu  Wed Dec 11 16:50:13 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 11 Dec 2002 16:50:13 -0500
Subject: 
References: <Pine.GSO.4.44.0212110934530.2104-100000@griffin.cs.nyu.edu>
Message-ID: <3DF7B315.A0BC4042@cornell.edu>

Dear Peter,

We don't have any information about anyone else doing this. However from Gramene
protein entry pages we definitely allow the user to query for respective
arabidopsis homologs.

An example from Gramene is for Adenylate kinase A

http://www.gramene.org/perl/protein_search?protein_id=77852

Once on this protein entry page click on the menu section 
[ Similarity to Other Proteins ] 
and then select for "Arabidopsis". It will do the query for respective
Arabidopsis homologs.


Sincerely
Pankaj
www.gramene.org

Peter Palenchar wrote:
> 
>         I'm looking for a information that links an Arabidopsis gene to
> it's Rice ortholog.  Are you or do you know somebody that is doing that
> sort of analysis?
> 
> Thank you for any help you can provide.
> 
> Peter Palenchar

--


From pj37 at cornell.edu  Fri Dec 13 17:03:05 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 13 Dec 2002 17:03:05 -0500
Subject: Environment Ontology
References: <E18GO0A-0004vR-00@ma11>
Message-ID: <3DFA5919.F55CAD43@cornell.edu>

Hello Everyone,

As we discussed at last weekend's phenotype ontology meeting at TIGR, Gramene
Environment Ontology (GEO) is now available via GOBO site at
http://www.geneontology.org/doc/gobo.html
Pl. see the section on Environment.

The GEO is in the developing stage, thus it needs your feedback.

Cheers
Pankaj

******************************************
Pankaj Jaiswal, Ph.D.                                   
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   
******************************************


From rwinter at ich.ucl.ac.uk  Sat Dec 14 07:02:56 2002
From: rwinter at ich.ucl.ac.uk (Robin Winter)
Date: Sat, 14 Dec 2002 12:02:56 +0000
Subject: Environment Ontology
In-Reply-To: <3DFA5919.F55CAD43@cornell.edu>
References: <E18GO0A-0004vR-00@ma11>
Message-ID: <5.2.0.9.0.20021214115735.02fb9310@pop-smtp.ich.ucl.ac.uk>

Thanks,
I am not sure if people got the attached musings on syndromes/diseases etc.
Robin

At 17:03 13/12/02 -0500, you wrote:
>Hello Everyone,
>
>As we discussed at last weekend's phenotype ontology meeting at TIGR, Gramene
>Environment Ontology (GEO) is now available via GOBO site at
>http://www.geneontology.org/doc/gobo.html
>Pl. see the section on Environment.
>
>The GEO is in the developing stage, thus it needs your feedback.
>
>Cheers
>Pankaj
>
>******************************************
>Pankaj Jaiswal, Ph.D.
>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
>******************************************

Prof. RM Winter
Dept Clinical and Molecular Genetics
Institute of Child Health
30 Guilford Street
London WC1N  1EH
Tel: 0207 242 9789 ext. 2108
Fax: 0207 813 8141
Email: Rwinter at ich.ucl.ac.uk
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From pj37 at cornell.edu  Tue Dec 17 10:28:56 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 17 Dec 2002 10:28:56 -0500
Subject: [Fwd: [Fwd: Re: Environment Ontology]]
Message-ID: <3DFF42B8.1972C84C@cornell.edu>

Hi Folks,
There is some more from Robin.

-Pankaj



-------- Original Message --------
   From: Robin Winter <rwinter at ich.ucl.ac.uk>
Subject: Re: Environment Ontology
     To: Pankaj Jaiswal <pj37 at cornell.edu>
     CC: pj37 at cornell.edu, rd120 at gen.cam.ac.uk

Dear Pankaj,

Looking at your scheme
a) The term 'genetic environment' is a bit confusing (unless you are trying to
bring in maternal effects etc.). Why not just 'genotype'

I think the two examples you give just reflect how the phenotype descriptors
(built into phenotypes) can be used.
Thus


> Pankaj - 1-In most of your cases that a physician records one may not know the
> genetic
> component
> So it will follow the path of A-B-F

Robin - This is the situation where a clinician is asking 'I wonder if phenotype
A in environment X has a genetic component ? ' (ie: it is a hypothetical
phenotype - the clinician needs to prove there is a genetic component)



> Pankaj - 2-In cases, where the genetic component is known then the path would
> depend on
> how a person proceeds. A-(C+B)-E or D-E.

Robin - In this case the clinicician will be saying 'the effect of genotype Q in
environment X is phenoype A'

We are just giving people the controlled vocabularies (phenotype
descriptor/environment/genotype) to build these statements
Robin


-------- Original Message --------


Hi Everyone,

For the last couple of days Robin, Pete, Rachel  and myself were discussing some
of the phenotype ontology details.
Please see the attached file phenotype_robin.txt, where Robin has tried to
outline some of his thoughts on phenotype ontology.


The text from our discussions is as follows....

Cheers

-Pankaj

-------- Original Message --------
   From: Robin Winter <rwinter at ich.ucl.ac.uk>
Subject: Re: Environment Ontology
     To: Pankaj Jaiswal <pj37 at cornell.edu>

Thanks for this,
I am glad I have started some debate !
Give me a bit of time to digest this and I will get back to you.
Robin


At 13:17 16/12/02 -0500, you wrote:

> Thanks Robin and Pete,
>
> If you remember, I presented the same upcoming strategy from Gramene, that a
> phenotype description is a collection of descriptors with its own attributes
> and
> values, instead of a one single phenotype term.
> Here is how we started curating the rice phenotypes associated to various
> genes
> and their alleles
> http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-present.png
>
> But as we progressed, the strategies got modified based on the complexity and
> type of data that we were curating. This resulted in a modified approach,
> which
> we presented at the TIGR meeting.
> http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-new.png
> In this scheme you will see that there are 2 types of phenotypes, simple and
> complex, which is the same as you have in your databases. Simple ones with
> only
> one descriptor where as the complex ones with one to many descriptors and a
> possible one-many gene interaction in a  given set of genetic and physical
> environments.
>
> Based on these modifications we can certainly create a multi dimensional or
> dynamic matrix comprising of
> -type of interaction among
> -genetic to genetic components AND/OR
> - genetic to environment components
> -the observable features
> -Anatomy
> -growth stage/ontogeny/developmental time line
> -Biochemical profiles (mol function/process/cellular component)
>
> Both of them will have their own attributes, values and scores, which
> determines
> the net observations for a phenotype.
>
> In that way you are right, we don't need a phenotype ontology. In order to
> build
> the various dynamic phenotype relationships every, database should have an
> anatomy to describe the organism on which it presents the data, the growth
> stages, various physical (biotic/abiotic) environments under which the
> responses/behavior/diseases for instance are recorded. The biochemical
> components will come from Gene Ontology. After identifying these components
> the
> question is how do we assess them, i.e. the attributes associated with them.
>
> e.g. for an enzyme, it could be its
> enzymatic activity/ Km
> inhibition/ Ki
> activation/ Ka
> structure (molecules structural integrity)
> sequence (modified sequence)
> etc.
>
> These attributes will have values of high/low/more/less on a comparative scale
>
> or on absolute scale of mM (milli molar) numerical values for Km etc. Similar
> to
> one records in biochemical analyses of Blood serum, urine samples. If I am not
>
> wrong, what we want is a uniform vocabulary of attributes and values that we
> want to associate to an observable feature.
>
> such as
>
> function and appearance
>
> Given this background here is the strategy, that I can think of
>
> http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype.png
>
> 1-In most of your cases that a physician records one may not know the genetic
> component
> So it will follow the path of A-B-F
>
> 2-In cases, where the genetic component is known then the path would depend on
>
> how a person proceeds. A-(C+B)-E or D-E.
>
> I think the situation #1 will solve the problem you suggested in meeting,
> about
> phalanges etc. Whereas in cases of syndrome you suggested, the situation #2
> should work.
>
> In plants #2 is certainly the case. #1 will appear only in cases where a
> randomly mutagenized population of individuals is present.
>
> By going through your notes it seems that you need to put up a controlled
> vocabulary of diseases and syndromes. The vocabulary already exists, all you
> may
> need is to put it in a DAG
> (http://www.geneontology.org/doc/GO.usage.html#General) to show multiple
> relationships for a complex disease.
>
> Best regards
> Pankaj
>
> Robin Winter wrote:
> >
> > Thanks,
> > I am not sure if people got the attached musings on syndromes/diseases etc.
> > Robin
> >
> > At 17:03 13/12/02 -0500, you wrote:
> >
> > > Hello Everyone,
> > >
> > > As we discussed at last weekend's phenotype ontology meeting at TIGR,
> > > Gramene
> > > Environment Ontology (GEO) is now available via GOBO site at
> > > http://www.geneontology.org/doc/gobo.html
> > > Pl. see the section on Environment.
> > >
> > > The GEO is in the developing stage, thus it needs your feedback.
> > >
> > > Cheers
> > > Pankaj
> > >
> > > ******************************************
> > > Pankaj Jaiswal, Ph.D.
> > > 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
> > > ******************************************
> >
> > Prof. RM Winter
> > Dept Clinical and Molecular Genetics
> > Institute of Child Health
> > 30 Guilford Street
> > London WC1N  1EH
> > Tel: 0207 242 9789 ext. 2108
> > Fax: 0207 813 8141
> > Email: Rwinter at ich.ucl.ac.uk
> >
> >                      Name: Phenotypes.doc
> >    Phenotypes.doc    Type: Microsoft Word Document (application/msword)
> >                  Encoding: base64
>
> --
>
>

Prof. RM Winter
Dept Clinical and Molecular Genetics
Institute of Child Health
30 Guilford Street
London WC1N  1EH
Tel: 0207 242 9789 ext. 2108
Fax: 0207 813 8141
Email: Rwinter at ich.ucl.ac.uk
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!From Robin White. 
!Email: Rwinter at ich.ucl.ac.uk
!Copied from his original file sent to Pankaj on Saturday, 12/13/2002
____________________________________________________


Some thoughts on Phenotypes/Diseases/Syndromes etc.   

I was thinking about compound/complex phenotypes and don?t think we need these terms.

Presumably we would agree that the definition of a phenotype should be something like ?the effect on an organism of an allele, or group of alleles, given a specific genetic background, and a specific environment?.

However, what we were actually trying to construct controlled vocabularies for are phenotype descriptors.  
These are individual units that can be put together to make up a phenotype.  
A phenotype is made up of one or more phenotype descriptor.
Different groups call phenotype descriptors different things (traits, symptoms, signs etc.). Confusion arises because some individual phenotype descriptors can be phenotypes in themselves.  
Thus, a cataract can be a phenotype descriptor, but can also be used on its own to define a phenotype.
The effect of some alleles on specific genetic backgrounds in mammals can be an isolated cataract (ie: cataract on its own with no other problems).  In this case the phenotype is ?isolated cataract? and it is made up of the single phenotype descriptor ?cataract?
On the other hand there may be a syndrome (eg: Winter Syndrome) which includes cataracts and deafness which is caused a mutant allele. In this case the phenotype is ?Winter syndrome? and this is defined by the phenotype descriptors ?cataract? and ?deafness?

If we accept that phenotypes are made up of one or more phenotype descriptor, then we don?t need controlled vocabularies for phenotypes (or diseases or syndromes), we just need controlled vocabularies for phenotype descriptors.  
Note that some diseases are phenotypes (i.e. collections of phenotype descriptors), and some not).  Marfan syndrome is a disease and a phenotype, because it is the effect of a single allele causing the combination of descriptors long fingers, dislocation of the lens, heart valve abnormalities etc.

Malaria is not a phenotype, because it is not the consequence of an allele or alleles.  On the other hand, susceptibility to malaria is a phenotype (as described by the phenotype descriptors for various antigen responses).

The consequence of all this is that we do not need the concept of complex or compound phenotypes (a phenotype is defined as a combination of one or more phenotype descriptors).  We also do not need a controlled vocabulary for diseases or syndromes, as if these are phenotypes, they are just made up of combinations of phenotype descriptors from a controlled vocabulary.  

It also means that the controlled vocabulary for phenotypes does not need to include terms to describe the environment.  Terms to describe the environment need their own controlled vocabulary.  The phenotype descriptors will however include terms for response to environment.  In the example of ?response to malaria?, the environmental descriptor might be ?antigen challenge? whereas the phenotype descriptor is ?response to antigen challenge?.

Does this make sense ? 

From pj37 at cornell.edu  Tue Dec 17 10:20:12 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 17 Dec 2002 10:20:12 -0500
Subject: [Fwd: Re: Environment Ontology]
Message-ID: <3DFF40AC.83E7E538@cornell.edu>

Hi Everyone,

For the last couple of days Robin, Pete, Rachel  and myself were discussing some
of the phenotype ontology details.
Please see the attached file phenotype_robin.txt, where Robin has tried to
outline some of his thoughts on phenotype ontology.


The text from our discussions is as follows....

Cheers

-Pankaj

-------- Original Message --------
   From: Robin Winter <rwinter at ich.ucl.ac.uk>
Subject: Re: Environment Ontology
     To: Pankaj Jaiswal <pj37 at cornell.edu>

Thanks for this,
I am glad I have started some debate !
Give me a bit of time to digest this and I will get back to you.
Robin


At 13:17 16/12/02 -0500, you wrote:

> Thanks Robin and Pete,
>
> If you remember, I presented the same upcoming strategy from Gramene, that a
> phenotype description is a collection of descriptors with its own attributes
> and
> values, instead of a one single phenotype term.
> Here is how we started curating the rice phenotypes associated to various
> genes
> and their alleles
> http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-present.png
>
> But as we progressed, the strategies got modified based on the complexity and
> type of data that we were curating. This resulted in a modified approach,
> which
> we presented at the TIGR meeting.
> http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-new.png
> In this scheme you will see that there are 2 types of phenotypes, simple and
> complex, which is the same as you have in your databases. Simple ones with
> only
> one descriptor where as the complex ones with one to many descriptors and a
> possible one-many gene interaction in a  given set of genetic and physical
> environments.
>
> Based on these modifications we can certainly create a multi dimensional or
> dynamic matrix comprising of
> -type of interaction among
> -genetic to genetic components AND/OR
> - genetic to environment components
> -the observable features
> -Anatomy
> -growth stage/ontogeny/developmental time line
> -Biochemical profiles (mol function/process/cellular component)
>
> Both of them will have their own attributes, values and scores, which
> determines
> the net observations for a phenotype.
>
> In that way you are right, we don't need a phenotype ontology. In order to
> build
> the various dynamic phenotype relationships every, database should have an
> anatomy to describe the organism on which it presents the data, the growth
> stages, various physical (biotic/abiotic) environments under which the
> responses/behavior/diseases for instance are recorded. The biochemical
> components will come from Gene Ontology. After identifying these components
> the
> question is how do we assess them, i.e. the attributes associated with them.
>
> e.g. for an enzyme, it could be its
> enzymatic activity/ Km
> inhibition/ Ki
> activation/ Ka
> structure (molecules structural integrity)
> sequence (modified sequence)
> etc.
>
> These attributes will have values of high/low/more/less on a comparative scale
>
> or on absolute scale of mM (milli molar) numerical values for Km etc. Similar
> to
> one records in biochemical analyses of Blood serum, urine samples. If I am not
>
> wrong, what we want is a uniform vocabulary of attributes and values that we
> want to associate to an observable feature.
>
> such as
>
> function and appearance
>
> Given this background here is the strategy, that I can think of
>
> http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype.png
>
> 1-In most of your cases that a physician records one may not know the genetic
> component
> So it will follow the path of A-B-F
>
> 2-In cases, where the genetic component is known then the path would depend on
>
> how a person proceeds. A-(C+B)-E or D-E.
>
> I think the situation #1 will solve the problem you suggested in meeting,
> about
> phalanges etc. Whereas in cases of syndrome you suggested, the situation #2
> should work.
>
> In plants #2 is certainly the case. #1 will appear only in cases where a
> randomly mutagenized population of individuals is present.
>
> By going through your notes it seems that you need to put up a controlled
> vocabulary of diseases and syndromes. The vocabulary already exists, all you
> may
> need is to put it in a DAG
> (http://www.geneontology.org/doc/GO.usage.html#General) to show multiple
> relationships for a complex disease.
>
> Best regards
> Pankaj
>
> Robin Winter wrote:
> >
> > Thanks,
> > I am not sure if people got the attached musings on syndromes/diseases etc.
> > Robin
> >
> > At 17:03 13/12/02 -0500, you wrote:
> >
> > > Hello Everyone,
> > >
> > > As we discussed at last weekend's phenotype ontology meeting at TIGR,
> > > Gramene
> > > Environment Ontology (GEO) is now available via GOBO site at
> > > http://www.geneontology.org/doc/gobo.html
> > > Pl. see the section on Environment.
> > >
> > > The GEO is in the developing stage, thus it needs your feedback.
> > >
> > > Cheers
> > > Pankaj
> > >
> > > ******************************************
> > > Pankaj Jaiswal, Ph.D.
> > > 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
> > > ******************************************
> >
> > Prof. RM Winter
> > Dept Clinical and Molecular Genetics
> > Institute of Child Health
> > 30 Guilford Street
> > London WC1N  1EH
> > Tel: 0207 242 9789 ext. 2108
> > Fax: 0207 813 8141
> > Email: Rwinter at ich.ucl.ac.uk
> >
> >                      Name: Phenotypes.doc
> >    Phenotypes.doc    Type: Microsoft Word Document (application/msword)
> >                  Encoding: base64
>
> --
>
>

Prof. RM Winter
Dept Clinical and Molecular Genetics
Institute of Child Health
30 Guilford Street
London WC1N  1EH
Tel: 0207 242 9789 ext. 2108
Fax: 0207 813 8141
Email: Rwinter at ich.ucl.ac.uk
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!From Robin White. 
!Email: Rwinter at ich.ucl.ac.uk
!Copied from his original file sent to Pankaj on Saturday, 12/13/2002
____________________________________________________


Some thoughts on Phenotypes/Diseases/Syndromes etc.   

I was thinking about compound/complex phenotypes and don?t think we need these terms.

Presumably we would agree that the definition of a phenotype should be something like ?the effect on an organism of an allele, or group of alleles, given a specific genetic background, and a specific environment?.

However, what we were actually trying to construct controlled vocabularies for are phenotype descriptors.  
These are individual units that can be put together to make up a phenotype.  
A phenotype is made up of one or more phenotype descriptor.
Different groups call phenotype descriptors different things (traits, symptoms, signs etc.). Confusion arises because some individual phenotype descriptors can be phenotypes in themselves.  
Thus, a cataract can be a phenotype descriptor, but can also be used on its own to define a phenotype.
The effect of some alleles on specific genetic backgrounds in mammals can be an isolated cataract (ie: cataract on its own with no other problems).  In this case the phenotype is ?isolated cataract? and it is made up of the single phenotype descriptor ?cataract?
On the other hand there may be a syndrome (eg: Winter Syndrome) which includes cataracts and deafness which is caused a mutant allele. In this case the phenotype is ?Winter syndrome? and this is defined by the phenotype descriptors ?cataract? and ?deafness?

If we accept that phenotypes are made up of one or more phenotype descriptor, then we don?t need controlled vocabularies for phenotypes (or diseases or syndromes), we just need controlled vocabularies for phenotype descriptors.  
Note that some diseases are phenotypes (i.e. collections of phenotype descriptors), and some not).  Marfan syndrome is a disease and a phenotype, because it is the effect of a single allele causing the combination of descriptors long fingers, dislocation of the lens, heart valve abnormalities etc.

Malaria is not a phenotype, because it is not the consequence of an allele or alleles.  On the other hand, susceptibility to malaria is a phenotype (as described by the phenotype descriptors for various antigen responses).

The consequence of all this is that we do not need the concept of complex or compound phenotypes (a phenotype is defined as a combination of one or more phenotype descriptors).  We also do not need a controlled vocabulary for diseases or syndromes, as if these are phenotypes, they are just made up of combinations of phenotype descriptors from a controlled vocabulary.  

It also means that the controlled vocabulary for phenotypes does not need to include terms to describe the environment.  Terms to describe the environment need their own controlled vocabulary.  The phenotype descriptors will however include terms for response to environment.  In the example of ?response to malaria?, the environmental descriptor might be ?antigen challenge? whereas the phenotype descriptor is ?response to antigen challenge?.

Does this make sense ? 

From pj37 at cornell.edu  Tue Dec 17 14:11:31 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 17 Dec 2002 14:11:31 -0500
Subject: Environment Ontology
References: <E18GO0A-0004vR-00@ma11>
	 <5.2.0.9.0.20021214115735.02fb9310@pop-smtp.ich.ucl.ac.uk> <5.2.0.9.0.20021217121554.02da2d90@pop-smtp.ich.ucl.ac.uk>
Message-ID: <3DFF76E3.D63C62FB@cornell.edu>

Here are my comments...
-Pankaj

Robin Winter wrote:
> 
> Dear Pankaj,
> 
> Looking at your scheme
> a) The term 'genetic environment' is a bit confusing (unless you are trying to
> bring in maternal effects etc.). Why not just 'genotype'
> 
Pankaj: Maternal effects will certainly be there, as in plants we have a well
defined set of cytoplasm. So lets put this Genotype in the front. This means, an
individual/genotype/accession, definitely has a genetic component (synonym:
genetic environment). I will take out the genetic environment out of the
Environment Ontology, so that it contains only the physical components of biotic
and abiotic. 

Have a look at
http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype-new.png

> I think the two examples you give just reflect how the phenotype descriptors
> (built into phenotypes) can be used.
> Thus
> 
> > Pankaj - 1-In most of your cases that a physician records one may not know
> > the genetic
> > component
> > So it will follow the path of A-B-F
> 
> Robin - This is the situation where a clinician is asking 'I wonder if
> phenotype A in environment X has a genetic component ? ' (ie: it is a
> hypothetical phenotype - the clinician needs to prove there is a genetic
> component)
> 

Pankaj: Exactly. The clinician can hypothetically assess the genetic component
of this individual/accession/genotype. If he happens to know the exact genetic
component then its fine, if not the genetic component as everyone knows, is
always associated to an individual. So its an open option, it may or may not be
defined. As suggsted at 
http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype-new.png

> > Pankaj - 2-In cases, where the genetic component is known then the path
> > would depend on
> > how a person proceeds. A-(C+B)-E or D-E.
> 
> Robin - In this case the clinicician will be saying 'the effect of genotype Q
> in environment X is phenoype A'
> 

Pankaj: Exactly !
at http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype-new.png

it suggests, that an individual for which we may or may not know the genetic
constitution, if placed in a given set of environment(s), this interaction in 
association of certain observable features, which have the attriubutes of so and
so forth. 
Also a Disease or a behavior is  a gross phenotypic effect which can be
associated to a number of possible observable features, which can be atributed
to an individual, but will certainly have a component of environment in it.

> We are just giving people the controlled vocabularies (phenotype
> descriptor/environment/genotype) to build these statements
> Robin
> 

Pankaj: Certainly that's the idea. 

Pankaj: Here are 2 examples from Plants. TO in these statements mean the Gramene
Trait Ontology (TO), a controlled vocabulary we developed initially to represent
all the traits in rice and other plants. This TO will eventually dissolve in our
new approach. But still having it in some place helps in building a matrix to
find out what anatomy, growth stage and environments are associated with a
particular trait. Its like defining the various components of an assay.
Classically in plants, the traits have actually been used as phenotypes, whereas
logically they should be the assays/descriptors.

1       Phenotype: ACC insensitive

existing-----Trait Ontology(TO) term: ACC sensitivity | score_ absent

suggested----GO Process_Response to ACC | score_insensitive

2       Phenotype: very long hypocotyl; bright green rosette; asymmetric leaves. 
        (this will have mutiple associations)

existing-----TO term: hypocotyl length | score very long
suggested----Anatomy_hypocotyl | attribute_length | score_very long  
        

existing-----TO term: rosette color | score_bright green
suggested----Anatomy_rosette | attribute_color_green | score_bright
        

existing-----TO term: leaf symmetry | score_asymmetric
suggested----Anatomy_leaf | attribute_symmetry | score_asymmetric

-Pankaj

>  ? At 13:17 16/12/02 -0500, you wrote:
> 
> > Thanks Robin and Pete,
> >
> > If you remember, I presented the same upcoming strategy from Gramene, that a
> > phenotype description is a collection of descriptors with its own attributes
> > and
> > values, instead of a one single phenotype term.
> > Here is how we started curating the rice phenotypes associated to various
> > genes
> > and their alleles
> > http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-present.png
> >
> > But as we progressed, the strategies got modified based on the complexity
> > and
> > type of data that we were curating. This resulted in a modified approach,
> > which
> > we presented at the TIGR meeting.
> > http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-new.png
> > In this scheme you will see that there are 2 types of phenotypes, simple and
> > complex, which is the same as you have in your databases. Simple ones with
> > only
> > one descriptor where as the complex ones with one to many descriptors and a
> > possible one-many gene interaction in a  given set of genetic and physical
> > environments.
> >
> > Based on these modifications we can certainly create a multi dimensional or
> > dynamic matrix comprising of
> >         -type of interaction among
> >                 -genetic to genetic components AND/OR
> >                 - genetic to environment components
> >         -the observable features
> >                 -Anatomy
> >                 -growth stage/ontogeny/developmental time line
> >                 -Biochemical profiles (mol function/process/cellular
> > component)
> >
> > Both of them will have their own attributes, values and scores, which
> > determines
> > the net observations for a phenotype.
> >
> > In that way you are right, we don't need a phenotype ontology. In order to
> > build
> > the various dynamic phenotype relationships every, database should have an
> > anatomy to describe the organism on which it presents the data, the growth
> > stages, various physical (biotic/abiotic) environments under which the
> > responses/behavior/diseases for instance are recorded. The biochemical
> > components will come from Gene Ontology. After identifying these components
> > the
> > question is how do we assess them, i.e. the attributes associated with them.
> >
> > e.g. for an enzyme, it could be its
> > enzymatic activity/ Km
> > inhibition/ Ki
> > activation/ Ka
> > structure (molecules structural integrity)
> > sequence (modified sequence)
> > etc.
> >
> > These attributes will have values of high/low/more/less on a comparative
> > scale
> > or on absolute scale of mM (milli molar) numerical values for Km etc.
> > Similar to
> > one records in biochemical analyses of Blood serum, urine samples. If I am
> > not
> > wrong, what we want is a uniform vocabulary of attributes and values that we
> > want to associate to an observable feature.
> >
> > such as
> >
> > function and appearance
> >
> > Given this background here is the strategy, that I can think of
> >
> > http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype.png
> >
> > 1-In most of your cases that a physician records one may not know the
> > genetic
> > component
> > So it will follow the path of A-B-F
> >
> > 2-In cases, where the genetic component is known then the path would depend
> > on
> > how a person proceeds. A-(C+B)-E or D-E.
> >
> > I think the situation #1 will solve the problem you suggested in meeting,
> > about
> > phalanges etc. Whereas in cases of syndrome you suggested, the situation #2
> > should work.
> >
> > In plants #2 is certainly the case. #1 will appear only in cases where a
> > randomly mutagenized population of individuals is present.
> >
> > By going through your notes it seems that you need to put up a controlled
> > vocabulary of diseases and syndromes. The vocabulary already exists, all you
> > may
> > need is to put it in a DAG
> > (http://www.geneontology.org/doc/GO.usage.html#General) to show multiple
> > relationships for a complex disease.
> >
> > Best regards
> > Pankaj
> >
> > Robin Winter wrote:
> > >
> > > Thanks,
> > > I am not sure if people got the attached musings on syndromes/diseases
> > etc.
> > > Robin
> > >
> > > At 17:03 13/12/02 -0500, you wrote:
> > >
> > > > Hello Everyone,
> > > >
> > > > As we discussed at last weekend's phenotype ontology meeting at TIGR,
> > > > Gramene
> > > > Environment Ontology (GEO) is now available via GOBO site at
> > > > http://www.geneontology.org/doc/gobo.html
> > > > Pl. see the section on Environment.
> > > >
> > > > The GEO is in the developing stage, thus it needs your feedback.
> > > >
> > > > Cheers
> > > > Pankaj
> > > >
> > > > ******************************************
> > > > Pankaj Jaiswal, Ph.D.
> > > > 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
> > > > ******************************************
> > >
> > > Prof. RM Winter
> > > Dept Clinical and Molecular Genetics
> > > Institute of Child Health
> > > 30 Guilford Street
> > > London WC1N  1EH
> > > Tel: 0207 242 9789 ext. 2108
> > > Fax: 0207 813 8141
> > > Email: Rwinter at ich.ucl.ac.uk
> > >
> > >                      Name: Phenotypes.doc
> > >    Phenotypes.doc    Type: Microsoft Word Document (application/msword)
> > >                  Encoding: base64
> >
> > --
> >
> > ******************************************
> > 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
> > ******************************************
> 
> Prof. RM Winter
> Dept Clinical and Molecular Genetics
> Institute of Child Health
> 30 Guilford Street
> London WC1N  1EH
> Tel: 0207 242 9789 ext. 2108
> Fax: 0207 813 8141
> Email: Rwinter at ich.ucl.ac.uk

-- 

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




From pj37 at cornell.edu  Tue Dec 17 14:11:31 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 17 Dec 2002 14:11:31 -0500
Subject: Environment Ontology
References: <E18GO0A-0004vR-00@ma11>
	 <5.2.0.9.0.20021214115735.02fb9310@pop-smtp.ich.ucl.ac.uk> <5.2.0.9.0.20021217121554.02da2d90@pop-smtp.ich.ucl.ac.uk>
Message-ID: <3DFF76E3.D63C62FB@cornell.edu>

Here are my comments...
-Pankaj

Robin Winter wrote:
> 
> Dear Pankaj,
> 
> Looking at your scheme
> a) The term 'genetic environment' is a bit confusing (unless you are trying to
> bring in maternal effects etc.). Why not just 'genotype'
> 
Pankaj: Maternal effects will certainly be there, as in plants we have a well
defined set of cytoplasm. So lets put this Genotype in the front. This means, an
individual/genotype/accession, definitely has a genetic component (synonym:
genetic environment). I will take out the genetic environment out of the
Environment Ontology, so that it contains only the physical components of biotic
and abiotic. 

Have a look at
http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype-new.png

> I think the two examples you give just reflect how the phenotype descriptors
> (built into phenotypes) can be used.
> Thus
> 
> > Pankaj - 1-In most of your cases that a physician records one may not know
> > the genetic
> > component
> > So it will follow the path of A-B-F
> 
> Robin - This is the situation where a clinician is asking 'I wonder if
> phenotype A in environment X has a genetic component ? ' (ie: it is a
> hypothetical phenotype - the clinician needs to prove there is a genetic
> component)
> 

Pankaj: Exactly. The clinician can hypothetically assess the genetic component
of this individual/accession/genotype. If he happens to know the exact genetic
component then its fine, if not the genetic component as everyone knows, is
always associated to an individual. So its an open option, it may or may not be
defined. As suggsted at 
http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype-new.png

> > Pankaj - 2-In cases, where the genetic component is known then the path
> > would depend on
> > how a person proceeds. A-(C+B)-E or D-E.
> 
> Robin - In this case the clinicician will be saying 'the effect of genotype Q
> in environment X is phenoype A'
> 

Pankaj: Exactly !
at http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype-new.png

it suggests, that an individual for which we may or may not know the genetic
constitution, if placed in a given set of environment(s), this interaction in 
association of certain observable features, which have the attriubutes of so and
so forth. 
Also a Disease or a behavior is  a gross phenotypic effect which can be
associated to a number of possible observable features, which can be atributed
to an individual, but will certainly have a component of environment in it.

> We are just giving people the controlled vocabularies (phenotype
> descriptor/environment/genotype) to build these statements
> Robin
> 

Pankaj: Certainly that's the idea. 

Pankaj: Here are 2 examples from Plants. TO in these statements mean the Gramene
Trait Ontology (TO), a controlled vocabulary we developed initially to represent
all the traits in rice and other plants. This TO will eventually dissolve in our
new approach. But still having it in some place helps in building a matrix to
find out what anatomy, growth stage and environments are associated with a
particular trait. Its like defining the various components of an assay.
Classically in plants, the traits have actually been used as phenotypes, whereas
logically they should be the assays/descriptors.

1       Phenotype: ACC insensitive

existing-----Trait Ontology(TO) term: ACC sensitivity | score_ absent

suggested----GO Process_Response to ACC | score_insensitive

2       Phenotype: very long hypocotyl; bright green rosette; asymmetric leaves. 
        (this will have mutiple associations)

existing-----TO term: hypocotyl length | score very long
suggested----Anatomy_hypocotyl | attribute_length | score_very long  
        

existing-----TO term: rosette color | score_bright green
suggested----Anatomy_rosette | attribute_color_green | score_bright
        

existing-----TO term: leaf symmetry | score_asymmetric
suggested----Anatomy_leaf | attribute_symmetry | score_asymmetric

-Pankaj

>  ? At 13:17 16/12/02 -0500, you wrote:
> 
> > Thanks Robin and Pete,
> >
> > If you remember, I presented the same upcoming strategy from Gramene, that a
> > phenotype description is a collection of descriptors with its own attributes
> > and
> > values, instead of a one single phenotype term.
> > Here is how we started curating the rice phenotypes associated to various
> > genes
> > and their alleles
> > http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-present.png
> >
> > But as we progressed, the strategies got modified based on the complexity
> > and
> > type of data that we were curating. This resulted in a modified approach,
> > which
> > we presented at the TIGR meeting.
> > http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-new.png
> > In this scheme you will see that there are 2 types of phenotypes, simple and
> > complex, which is the same as you have in your databases. Simple ones with
> > only
> > one descriptor where as the complex ones with one to many descriptors and a
> > possible one-many gene interaction in a  given set of genetic and physical
> > environments.
> >
> > Based on these modifications we can certainly create a multi dimensional or
> > dynamic matrix comprising of
> >         -type of interaction among
> >                 -genetic to genetic components AND/OR
> >                 - genetic to environment components
> >         -the observable features
> >                 -Anatomy
> >                 -growth stage/ontogeny/developmental time line
> >                 -Biochemical profiles (mol function/process/cellular
> > component)
> >
> > Both of them will have their own attributes, values and scores, which
> > determines
> > the net observations for a phenotype.
> >
> > In that way you are right, we don't need a phenotype ontology. In order to
> > build
> > the various dynamic phenotype relationships every, database should have an
> > anatomy to describe the organism on which it presents the data, the growth
> > stages, various physical (biotic/abiotic) environments under which the
> > responses/behavior/diseases for instance are recorded. The biochemical
> > components will come from Gene Ontology. After identifying these components
> > the
> > question is how do we assess them, i.e. the attributes associated with them.
> >
> > e.g. for an enzyme, it could be its
> > enzymatic activity/ Km
> > inhibition/ Ki
> > activation/ Ka
> > structure (molecules structural integrity)
> > sequence (modified sequence)
> > etc.
> >
> > These attributes will have values of high/low/more/less on a comparative
> > scale
> > or on absolute scale of mM (milli molar) numerical values for Km etc.
> > Similar to
> > one records in biochemical analyses of Blood serum, urine samples. If I am
> > not
> > wrong, what we want is a uniform vocabulary of attributes and values that we
> > want to associate to an observable feature.
> >
> > such as
> >
> > function and appearance
> >
> > Given this background here is the strategy, that I can think of
> >
> > http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype.png
> >
> > 1-In most of your cases that a physician records one may not know the
> > genetic
> > component
> > So it will follow the path of A-B-F
> >
> > 2-In cases, where the genetic component is known then the path would depend
> > on
> > how a person proceeds. A-(C+B)-E or D-E.
> >
> > I think the situation #1 will solve the problem you suggested in meeting,
> > about
> > phalanges etc. Whereas in cases of syndrome you suggested, the situation #2
> > should work.
> >
> > In plants #2 is certainly the case. #1 will appear only in cases where a
> > randomly mutagenized population of individuals is present.
> >
> > By going through your notes it seems that you need to put up a controlled
> > vocabulary of diseases and syndromes. The vocabulary already exists, all you
> > may
> > need is to put it in a DAG
> > (http://www.geneontology.org/doc/GO.usage.html#General) to show multiple
> > relationships for a complex disease.
> >
> > Best regards
> > Pankaj
> >
> > Robin Winter wrote:
> > >
> > > Thanks,
> > > I am not sure if people got the attached musings on syndromes/diseases
> > etc.
> > > Robin
> > >
> > > At 17:03 13/12/02 -0500, you wrote:
> > >
> > > > Hello Everyone,
> > > >
> > > > As we discussed at last weekend's phenotype ontology meeting at TIGR,
> > > > Gramene
> > > > Environment Ontology (GEO) is now available via GOBO site at
> > > > http://www.geneontology.org/doc/gobo.html
> > > > Pl. see the section on Environment.
> > > >
> > > > The GEO is in the developing stage, thus it needs your feedback.
> > > >
> > > > Cheers
> > > > Pankaj
> > > >
> > > > ******************************************
> > > > Pankaj Jaiswal, Ph.D.
> > > > 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
> > > > ******************************************
> > >
> > > Prof. RM Winter
> > > Dept Clinical and Molecular Genetics
> > > Institute of Child Health
> > > 30 Guilford Street
> > > London WC1N  1EH
> > > Tel: 0207 242 9789 ext. 2108
> > > Fax: 0207 813 8141
> > > Email: Rwinter at ich.ucl.ac.uk
> > >
> > >                      Name: Phenotypes.doc
> > >    Phenotypes.doc    Type: Microsoft Word Document (application/msword)
> > >                  Encoding: base64
> >
> > --
> >
> > ******************************************
> > 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
> > ******************************************
> 
> Prof. RM Winter
> Dept Clinical and Molecular Genetics
> Institute of Child Health
> 30 Guilford Street
> London WC1N  1EH
> Tel: 0207 242 9789 ext. 2108
> Fax: 0207 813 8141
> Email: Rwinter at ich.ucl.ac.uk

-- 

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


From guizotia at yahoo.com  Sat Dec 21 08:26:57 2002
From: guizotia at yahoo.com (aneesh nair)
Date: Sat, 21 Dec 2002 05:26:57 -0800 (PST)
Subject: request
Message-ID: <20021221132657.32734.qmail@web10808.mail.yahoo.com>

respected sir,
i had gone through the very interesting paper of yours
entitled "Classification of rice germplasm from Iran
through isozyme analysis". kindly send a reprint of
the same.
i will be highly obliged for you help.
thanking you, yours faithfully,
aneesh kumar k c,
p g research centre, dept. of botany, modern college,
pune-411005, MS, INDIA
e-mail: aneeshknair at hotmail.com
waiting anxiously for your reply
with regards
aneesh

__________________________________________________
Do you Yahoo!?
Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
http://mailplus.yahoo.com


From w.haiyan at warkaa.net  Fri Dec 20 15:42:09 2002
From: w.haiyan at warkaa.net (haiyan)
Date: Fri, 20 Dec 2002 23:42:09 +0300
Subject: message from Iraq
Message-ID: <001b01c2a872$bf78d360$020a040a@haiyan>

      I am a postgraduated student from the university of Al-Mustansireah - Baghdad . My field work is 
" the production of salt tolerance plantlets of rice using tissue culture technique ". 
     I would appreciate receiving from you the PDF about "Salt tolerance of rice callus clones" by Koh-Ichi MORI and Toshiro KINOSHITA and any reprints concerning and related to my subject and adresses or web site of any useful scientific place or person . 
I am waiting for your answer as soon as possible .

Thank you for your courtesy .


Sincerely yours
Arwa Abdul-Kareem Tawfiq

E-mail : haiyan at warkaa.net 
home address :IRAQ - BAGHDAD
                      Al-khadraa area
                      quarter  641
                      street  15
                      home no.  27 
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From pj37 at cornell.edu  Mon Dec 23 14:08:48 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 23 Dec 2002 14:08:48 -0500
Subject: request
References: <20021221132657.32734.qmail@web10808.mail.yahoo.com>
Message-ID: <3E075F40.E200E4C@cornell.edu>

Dear Aneesh,

We are sorry to provide any reprints you requested. Please follow the Gramene
Policy by going through the message at
http://www.gramene.org/mailarch/0418.html
Anyhow the publication you cited is available at 
http://www.gramene.org/newsletters/rice_genetics/rgn10/vXI9.htm

This is not an abstract, but a full report published by the authors in RGN.

Sincerely,

Pankaj
www.gramene.org

aneesh nair wrote:
> 
> respected sir,
> i had gone through the very interesting paper of yours
> entitled "Classification of rice germplasm from Iran
> through isozyme analysis". kindly send a reprint of
> the same.
> i will be highly obliged for you help.
> thanking you, yours faithfully,
> aneesh kumar k c,
> p g research centre, dept. of botany, modern college,
> pune-411005, MS, INDIA
> e-mail: aneeshknair at hotmail.com
> waiting anxiously for your reply
> with regards
> aneesh
> 
> __________________________________________________
> Do you Yahoo!?
> Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
> http://mailplus.yahoo.com

--


From w.haiyan at warkaa.net  Fri Dec 27 14:03:12 2002
From: w.haiyan at warkaa.net (haiyan)
Date: Fri, 27 Dec 2002 22:03:12 +0300
Subject: message from Iraq
Message-ID: <001701c2addf$49c5b080$130a040a@haiyan>

      I am a postgraduated student from the university of Al-Mustansireah - Baghdad . My field work is 
" the production of salt tolerance plantlets of rise using tissue culture technique ". 
     I would appreciate receiving from you any reprints and PDF concerning and related to my subject and adresses or web site of any useful scientific place or person . 
I am waiting for your answer as soon as possible .

Thank you for your courtesy .

Sincerely yours
Arwa Abdul-Kareem Tawfiq
E- mail : haiyan at warkaa.net
home address : Iraq-Baghdad 
                       Al- khadraa Area 
                       Quarter     641 
                        Street      15     
                       Home       27
                                     
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From zhaow at cshl.edu  Tue Dec 31 20:19:25 2002
From: zhaow at cshl.edu (Wei Zhao)
Date: Tue, 31 Dec 2002 20:19:25 -0500 (EST)
Subject: Gramene User Survey
Message-ID: <Pine.GSO.4.05.10212311549350.27344-100000@phage.cshl.org>


Hi everyone,

We have put up a user survey at our website (www.gramene.org). Your
feedback will greatly help us to better serve the community, so please
fill in and submit the user survey at
http://www.gramene.org/survey/survey.html
(all answers will be held strictly confidential).

Thanks and Happy New Year!






