GO Vs Traits

[Pankaj Jaiswal]

Dear Michael,

As you know at Gramene I am presently curating the terms for the traits. While
curating, the traits i figured out that GO has similar/same terms for the
various stress related factors, under biological process. I am having a problem
right now about how to relate the two terms we will be having (one from GO and
one from
us). I know that different types of stresses e.g water stress (drought or
flooding or dessication)/herbicide or antibiotic
stress/light/temperature/nutrients/etc. are all types of 
physical/physiological/chemical/environmental stress an organism
experiences in various lab/natural environments and the people record the
responses against these factors in the form of a phenotype, which is nothing but
trait and not a biological process. Interestingly these responses can be defined
as either resistant/susceptible/intermediate/others i.e the scale (for which we
have yet to figure out how to represent that). My point here is that, a response
to any stress can be defined in the form of a scale ie resistant-tolerant eg.
drought tolerance/resistance. Now this is not a biological process, instead a
whole lot of biochemical/physiological/environmental factors represent this
term. Lets say if we have this term under traits then it works, because
everytime (i beleive) this term will be used it will be for the expression
profiling of the associated genes, eg.  gene"X" is expressed specifically in
roots (organ)/ it is localized in certain cellular component of a "Y" cell type
of a tissue, when a particular organism was exposed to "drought stress" (which
is not a bilogical process), and the response (resistance/susceptibility)
reflected by the organism, is actually the recording of the trait, which is
again not the biological process. There are several biological processes related
with the response, where "response" is merely an "act". 

I am quoting the examples after the following questions.

Two main questions arise out of these arguments:
1       Should some of the responses be categorised as traits and not under
biological
processes.
2       If not then is there a way to relate the trait terms with the GO terms.

example for "drought tolerance" in Gene ontology:(for real)

Gene_Ontology (GO:0003673) 
        [p] biological_process (GO:0008150) 
           [i] cell communication (GO:0007154) 
              [i] response to external stimulus (GO:0009605) 
                  [i] response to abiotic stimulus (GO:0009628) 
                     [i] water response (GO:0009415) 
                        [i] drought response (GO:0009414) 
                            [i] drought tolerance (GO:0009633) 
           [i] cell growth and/or maintenance (GO:0008151) 
              [i] stress response (GO:0006950) 
                  [i] drought response (GO:0009414) 
                     [i] drought tolerance (GO:0009633) 

Example from Trait ontology at Gramene: (GO IDs are arbitrary)
 
$Trait_Ontology ; GO:1000000
  %genetic trait ; GO:1000002
   %plant genetic trait ; GO:1100013
    %agronomic trait ; GO:1100014
     %stress response or crop damage traits ; GO:0302110
      %abiotic stress resistance ; GO:0302105
       %physicochemical stress ; GO:0301797
        %chemical stress ; GO:0301774
        %physiological stress ; GO:0301775
         %deepwater stress ; GO:0302189 ; synonym:flooding
          %elongation ; GO:0302188 ; ICIS:1209 ; synonym:Elon
          %kneeing ability ; GO:0302185 ; ICIS:1212 ; synonym:KnA
          %submergence tolerance ; GO:0302187 ; ICIS:1215 ; synonym:Sub
         %drought stress ; GO:0302193
          %drought recovery ; GO:0302190 ; synonym:DRR
          %drought sensitivity ; GO:0302192 ; synonym:DRS
          %drought tolerance ; GO:0302191
         %light stress ; GO:0301777
          %photoperiod sensitivity ; GO:0301776
         %temperature stress ; GO:0302206
          %cold tolerance ; GO:0302204 ; synonym:CTol
          %heat tolerance ; GO:0302194 ; ICIS:1210 ; synonym:HTol




Your feedback will be highly appreciated

Pankaj

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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   http://ars-genome.cornell.edu/rice
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