GO Vs Traits

Doreen Ware ware at phage.cshl.org
Fri Sep 7 10:02:50 EDT 2001


Pankaj,

I think Midori has a point.  If you remove these processes can you 
still have the dag for the trait.

doreen



>Hi Pankaj,
>
>Let me see if I can clarify things a bit.
>
>A stress is not a biological process; nor is it a trait. It's a condition
>(or set of conditions) or event that an organism may encounter.
>
>A stress response is what an organism does when it is subjected to stress,
>and therefore is unquestionably a biological process.
>
>Whether an organism is susceptible or resistant to a given stress is a
>phenotype or trait. It can depend on whether a stress response is
>functioning normally or is impaired.
>
>I would actually recommend removing these terms from the trait ontology
>because they name different kinds of stress rather than traits:
>
>       %physicochemical stress ; GO:0301797
>       %chemical stress ; GO:0301774
>       %physiological stress ; GO:0301775
>       %deepwater stress ; GO:0302189 ; synonym:flooding
>       %drought stress ; GO:0302193
>       %light stress ; GO:0301777
>       %temperature stress ; GO:0302206
>
>These terms do describe traits, so they should stay:
>
>       %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
>       %kneeing ability ; GO:0302185 ; ICIS:1212 ; synonym:KnA
>       %submergence tolerance ; GO:0302187 ; ICIS:1215 ; synonym:Sub
>       %drought sensitivity ; GO:0302192 ; synonym:DRS
>       %drought tolerance ; GO:0302191
>       %photoperiod sensitivity ; GO:0301776
>       %cold tolerance ; GO:0302204 ; synonym:CTol
>       %heat tolerance ; GO:0302194 ; ICIS:1210 ; synonym:HTol
>
>I'm not sure about these; they could be processes:
>
>           %elongation ; GO:0302188 ; ICIS:1209 ; synonym:Elon
>           %drought recovery ; GO:0302190 ; synonym:DRR
>
>Cheers,
>Midori
>
>On Thu, 6 Sep 2001, Pankaj Jaiswal wrote:
>
>>
>>  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
>>
>>  **************************************************************
>>  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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Doreen Ware
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