Environment Ontology
Pankaj Jaiswal
pj37 at cornell.edu
Tue Dec 17 14:11:31 EST 2002
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
******************************************
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