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Hi Folks,
<br>There is some more from Robin.
<p>-Pankaj
<br>
<br>
<p>-------- Original Message --------
<table BORDER=0 CELLSPACING=0 CELLPADDING=0 >
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>From: </th>
<td>Robin Winter <rwinter@ich.ucl.ac.uk></td>
</tr>
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>Subject: </th>
<td>Re: Environment Ontology</td>
</tr>
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>To: </th>
<td>Pankaj Jaiswal <pj37@cornell.edu></td>
</tr>
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>CC: </th>
<td>pj37@cornell.edu, rd120@gen.cam.ac.uk</td>
</tr>
</table>
<p>Dear Pankaj,
<p>Looking at your scheme
<br>a) The term 'genetic environment' is a bit confusing (unless you are
trying to bring in maternal effects etc.). Why not just 'genotype'
<p>I think the two examples you give just reflect how the phenotype descriptors
(built into phenotypes) can be used.
<br>Thus
<br>
<blockquote type=cite class=cite cite>Pankaj - 1-In most of your cases
that a physician records one may not know the genetic
<br>component
<br>So it will follow the path of A-B-F</blockquote>
<p><br>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)
<br>
<br>
<blockquote type=cite class=cite cite>Pankaj - 2-In cases, where the genetic
component is known then the path would depend on
<br>how a person proceeds. A-(C+B)-E or D-E.</blockquote>
<p><br>Robin - In this case the clinicician will be saying 'the effect
of genotype Q in environment X is phenoype A'
<p>We are just giving people the controlled vocabularies (phenotype descriptor/environment/genotype)
to build these statements
<br>Robin
<br>
<p>-------- Original Message --------
<br>
<p>Hi Everyone,
<p>For the last couple of days Robin, Pete, Rachel and myself were
discussing some of the phenotype ontology details.
<br>Please see the attached file phenotype_robin.txt, where Robin has tried
to outline some of his thoughts on phenotype ontology.
<br>
<p>The text from our discussions is as follows....
<p>Cheers
<p>-Pankaj
<p>-------- Original Message --------
<table BORDER=0 CELLSPACING=0 CELLPADDING=0 >
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>From: </th>
<td>Robin Winter <rwinter@ich.ucl.ac.uk></td>
</tr>
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>Subject: </th>
<td>Re: Environment Ontology</td>
</tr>
<tr>
<th ALIGN=RIGHT VALIGN=BASELINE NOWRAP>To: </th>
<td>Pankaj Jaiswal <pj37@cornell.edu></td>
</tr>
</table>
<p>Thanks for this,
<br>I am glad I have started some debate !
<br>Give me a bit of time to digest this and I will get back to you.
<br>Robin
<br>
<p>At 13:17 16/12/02 -0500, you wrote:
<blockquote type=cite class=cite cite>Thanks Robin and Pete,
<p>If you remember, I presented the same upcoming strategy from Gramene,
that a
<br>phenotype description is a collection of descriptors with its own attributes
and
<br>values, instead of a one single phenotype term.
<br>Here is how we started curating the rice phenotypes associated to various
genes
<br>and their alleles
<br><a href="http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-present.png" eudora="autourl">http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-present.png</a>
<p>But as we progressed, the strategies got modified based on the complexity
and
<br>type of data that we were curating. This resulted in a modified approach,
which
<br>we presented at the TIGR meeting.
<br><a href="http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-new.png" eudora="autourl">http://ascus.plbr.cornell.edu/~gramene/phenotype/Gramene-new.png</a>
<br>In this scheme you will see that there are 2 types of phenotypes, simple
and
<br>complex, which is the same as you have in your databases. Simple ones
with only
<br>one descriptor where as the complex ones with one to many descriptors
and a
<br>possible one-many gene interaction in a given set of genetic
and physical
<br>environments.
<p>Based on these modifications we can certainly create a multi dimensional
or
<br>dynamic matrix comprising of
<br><x-tab></x-tab>-type of interaction among
<br><x-tab></x-tab><x-tab></x-tab>-genetic to genetic components AND/OR
<br><x-tab></x-tab><x-tab></x-tab>- genetic to environment components
<br><x-tab></x-tab>-the observable features
<br><x-tab></x-tab><x-tab></x-tab>-Anatomy
<br><x-tab></x-tab><x-tab></x-tab>-growth stage/ontogeny/developmental
time line
<br><x-tab></x-tab><x-tab></x-tab>-Biochemical profiles (mol function/process/cellular
component)
<br><x-tab></x-tab><x-tab></x-tab><x-tab></x-tab>
<br>Both of them will have their own attributes, values and scores, which
determines
<br>the net observations for a phenotype.
<p>In that way you are right, we don't need a phenotype ontology. In order
to build
<br>the various dynamic phenotype relationships every, database should
have an
<br>anatomy to describe the organism on which it presents the data, the
growth
<br>stages, various physical (biotic/abiotic) environments under which
the
<br>responses/behavior/diseases for instance are recorded. The biochemical
<br>components will come from Gene Ontology. After identifying these components
the
<br>question is how do we assess them, i.e. the attributes associated with
them.
<p>e.g. for an enzyme, it could be its
<br>enzymatic activity/ Km
<br>inhibition/ Ki
<br>activation/ Ka
<br>structure (molecules structural integrity)
<br>sequence (modified sequence)
<br>etc.
<p>These attributes will have values of high/low/more/less on a comparative
scale
<br>or on absolute scale of mM (milli molar) numerical values for Km etc.
Similar to
<br>one records in biochemical analyses of Blood serum, urine samples.
If I am not
<br>wrong, what we want is a uniform vocabulary of attributes and values
that we
<br>want to associate to an observable feature.
<p>such as
<p>function and appearance
<p>Given this background here is the strategy, that I can think of
<p><a href="http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype.png" eudora="autourl">http://ascus.plbr.cornell.edu/~gramene/phenotype/phenotype.png</a>
<p>1-In most of your cases that a physician records one may not know the
genetic
<br>component
<br>So it will follow the path of A-B-F
<p>2-In cases, where the genetic component is known then the path would
depend on
<br>how a person proceeds. A-(C+B)-E or D-E.
<p>I think the situation #1 will solve the problem you suggested in meeting,
about
<br>phalanges etc. Whereas in cases of syndrome you suggested, the situation
#2
<br>should work.
<p>In plants #2 is certainly the case. #1 will appear only in cases where
a
<br>randomly mutagenized population of individuals is present.
<p>By going through your notes it seems that you need to put up a controlled
<br>vocabulary of diseases and syndromes. The vocabulary already exists,
all you may
<br>need is to put it in a DAG
<br>(<a href="http://www.geneontology.org/doc/GO.usage.html#General" eudora="autourl">http://www.geneontology.org/doc/GO.usage.html#General</a>)
to show multiple
<br>relationships for a complex disease.
<p>Best regards
<br>Pankaj
<p>Robin Winter wrote:
<br>>
<br>> Thanks,
<br>> I am not sure if people got the attached musings on syndromes/diseases
etc.
<br>> Robin
<br>>
<br>> At 17:03 13/12/02 -0500, you wrote:
<br>>
<br>> > Hello Everyone,
<br>> >
<br>> > As we discussed at last weekend's phenotype ontology meeting at
TIGR,
<br>> > Gramene
<br>> > Environment Ontology (GEO) is now available via GOBO site at
<br>> >
<a href="http://www.geneontology.org/doc/gobo.html" eudora="autourl">http://www.geneontology.org/doc/gobo.html</a>
<br>> > Pl. see the section on Environment.
<br>> >
<br>> > The GEO is in the developing stage, thus it needs your feedback.
<br>> >
<br>> > Cheers
<br>> > Pankaj
<br>> >
<br>> > ******************************************
<br>> > Pankaj Jaiswal, Ph.D.
<br>> > Dept. of Plant Breeding
<br>> > Cornell University
<br>> > Ithaca, NY-14853, USA
<br>> >
<br>> > Tel:+1-607-255-3103 / Fax:+1-607-255-6683
<br>> > E mail: pj37@cornell.edu
<br>> >
<a href="http://www.gramene.org/" eudora="autourl">http://www.gramene.org</a>
<br>> > ******************************************
<br>>
<br>> Prof. RM Winter
<br>> Dept Clinical and Molecular Genetics
<br>> Institute of Child Health
<br>> 30 Guilford Street
<br>> London WC1N 1EH
<br>> Tel: 0207 242 9789 ext. 2108
<br>> Fax: 0207 813 8141
<br>> Email: Rwinter@ich.ucl.ac.uk
<br>>
<br>>
Name: Phenotypes.doc
<br>> Phenotypes.doc Type: Microsoft
Word Document (application/msword)
<br>>
Encoding: base64
<p>--
<br>
<br> </blockquote>
<x-sigsep>
<p></x-sigsep><b>Prof. RM Winter</b>
<br><b>Dept Clinical and Molecular Genetics</b>
<br><b>Institute of Child Health</b>
<br><b>30 Guilford Street</b>
<br><b>London WC1N 1EH</b>
<br><b>Tel: 0207 242 9789 ext. 2108</b>
<br><b>Fax: 0207 813 8141</b>
<br><b>Email: Rwinter@ich.ucl.ac.uk</b></html>