GO Vs Traits
Vincent, Leszek
Leszek at missouri.edu
Fri Sep 7 17:42:05 EDT 2001
Hi Pankaj, Jun Jian & others
This wrestling with affiliating 'things' with biological process vs traits
is philosophically & biologically interesting & pragmatically important.
>From the Systematics perspective (be that plant or animal systematics) the
concept of the term 'trait' can be alternatively described as a
distinguishing quality or characteristic - clearly a relatively generic
concept. In systematics the term trait is synonymous with the term
'Character' (and the various phenotypes of a trait are similarly referred to
as character states - just f.y.i.). Implicit in the term trait can be a
range of biotic- & abiotic-related phenomena e.g. biological processes (some
being responses to abiotic/environmental factors). Why am I thinking aloud
like this with you? Well, Pankaj raised the point about "the contradiction
between the Molecular biologist/Biochemist and the plant breeder/Geneticist,
on how he percieves the response. Whether as a trait or as a Bilogical
process ??" I suggest that this perceptual difference is going to remain
with us so am left wondering about how we will provide ontologies that are
biologically accurate & appropriate for the molecular etc. biologist as well
as being useful to a user of generic trait terms e.g. plant
breeder/geneticist. Photoperiod sensitivity is clearly a trait to a
geneticist (with a range of taxon-specific phenotypes) while at the same
time it is clearly based on an underlying biological process. The same
argument applies to 'Elongation'. It is likely that a breeder or geneticist
may not recognize a trait 'buried' within a biological process ontology. So,
I'm wondering if any thought has been given by the GO folk to the possible
inclusion of XML metatags within the ontologies so that ontology browsers
will be able to locate trait-related terms within the ontologies. The
purpose of this approach being to maintain the integrity of the ontologies,
w.r.t. the organizing principles, but at the same time provide embedded tags
to the generic labels which, for example, breeders & geneticists would
probably be more familiar with. This approach could overcome the need to
resolve the conflict between ascribing something to biological process vs a
trait - the trait info. would be embedded, via the metatags, in the
biologically sound relevant ontology.
Enjoy a thoughtful & fun weekend!
- Leszek
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P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
884-3716 (Agronomy), Fax:(573) 884-7850;
Ph/Fax (Home): (573) 441-1228;
Email: Leszek at missouri.edu
Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
(http://www.cafnr.missouri.edu/mmp/ and http://www.agron.missouri.edu/)
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Friday, September 07, 2001 2:24 PM
> To: gramene at brie.cshl.org
> Cc: ma11 at gen.cam.ac.uk; go at geneontology.org;
> monocot-cv at cgnet.com; Susan
> McCouch
> Subject: Re: GO Vs Traits
>
>
> Ni,
>
> I have the comments as follows:###
>
> Jun Jian Ni wrote:
> >
> > Hi,
> >
> > I have three points.
> >
> > 1. photoperiod sensitivity is not light stress related
> trait. It is related with
> > maturity and also called as "environmental related trait".
> However, it is not related
> > stress.
>
> ### I will call it a light related since it represents the
> affect on plant due
> to Day length period. Now this change in day length period,
> is one of the
> component which affect the maturity of plant in terms of "Days to
> heading/flowering /maturity" i.e either there is a delay
> /early flowering.
>
> > 2. Kneeling ability and submergence tolerance and
> elongation ability are traits. So, no
> > need put "trait" after those again and again.
> >
>
> ### Accepted, but have a look at Michael's e mail , he
> suggests that elongation
> is a biological process.
>
> > 3. I suggest to remove "physicochemical stress ", "
> chemical stress " and
> > "physiological stress". We can directly use "response to
> water stress" "response to
> > temperature stress", etc.
>
> ### Again try to resolve, response is a process/trait. I have
> changed the above
> terms as broad trait categories.
>
>
> ### Here comes the contradiction between the Molecular
> biologist/Biochemist and
> the plant breeder/Geneticist, on how he percieves the
> response. Whether as a
> trait or as a Bilogical process ??
>
> pankaj
>
> >
> > Ni
> >
> > Pankaj Jaiswal wrote:
> >
> > > Wait wait,
> > >
> > > let me rephrase the things here. What actually Michael
> did here and I can do the
> > > same too. (i apologise for not doing it earlier).....
> > > in trait ontologies, instead of framing the term as
> "deep water stress" , which
> > > is rightly pointed out by Midori and Micheal as
> physiological stress type.
> > > Michael reframed it as "response to deep water" which
> then becomes the
> > > biological process. Now what? if I reframe it as
> > >
> > > "deep water related trait"
> > >
> > > then will it fit the traits ontology. This is to curate a
> group of defined
> > > classes of trait factors (on a higher note) which the
> people will be looking in
> > > for. They later become the parent for
> X-tolerance/X-resistance type of trait,
> > > otherwise the higher nodes of biotic/abiotic stress
> related traits will have a
> > > long list of children.
> > >
> > > > These, as Midori says, are environmental conditions:
> > > >
> > > > %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
> > >
> > > I change them to :
> > >
> > >
> > > > %physicochemical stress related trait ; GO:0301797
> > > > %chemical stress related trait; GO:0301774
> > > > %physiological stress related trait; GO:0301775
> > > > %deepwater stress related trait; GO:0302189 ;
> synonym:flooding related trait
> > > %kneeling ability trait ; GO:0302185 ; ICIS:1212
> ; synonym:KnA
> > > %submergence tolerance trait; GO:0302187 ;
> ICIS:1215 ; synonym:Sub
> > > %elongation trait; GO:0302188 ; ICIS:1209 ; synonym:Elon
> > > > %drought stress related trait; GO:0302193
> > > %drought sensitivity ; GO:0302192 ; synonym:DRS
> > > %drought tolerance ; GO:0302191
> > > %drought recovery ; GO:0302190 ; synonym:DRR
> > > > %light stress related trait; GO:0301777
> > > %photoperiod sensitivity ; GO:0301776
> > > > %temperature stress related trait; GO:0302206
> > > %cold tolerance ; GO:0302204 ; synonym:CTol
> > > %heat tolerance ; GO:0302194 ; ICIS:1210 ; synonym:HTol
> > >
> > >
> > > pankaj
> > >
> > > Lincoln Stein wrote:
> > > >
> > > > > %response to deepwater stress ; GO:0302189 ;
> synonym:flooding
> > > >
> > > > "synonym: response to flooding" no?
> > > >
> > > > Lincoln
> > > >
> > > > --
> > > -
>
> --
>
> **************************************************************
> 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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