GO Vs Traits
Midori Harris
midori at ebi.ac.uk
Fri Sep 7 06:03:47 EDT 2001
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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