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
>> **************************************************************
>>
>>
--
======================================================================
Doreen Ware
Cold Spring Harbor Laboratory voice: (516) 367-6979
Freeman Bldg. fax: (516) 367-8389
1 Bungtown Rd. email: ware at cshl.org
Cold Spring Harbor, NY. 11724 url: www.gramene.org
======================================================================
More information about the Gramene
mailing list