HELP!: GO Term Error
Sue Rhee
rhee at acoma.Stanford.EDU
Thu Aug 15 14:31:36 EDT 2002
how about:
nutrient reserve
amino acid reserve
amino acid reserve in seed syn: seed storage protein
or is this something already in place?
sue
On Thu, 15 Aug 2002, Pankaj Jaiswal wrote:
> Well I disagree with Midori !
> Reason at some point in an organism's life if one looks logically, each and
> every one of the gene product can be called as a nutrient reserve in some form
> or the other. All the proteins can be broken down in its components for example
> into peptides ->amino acids->C/H/N/O/P/S/. This is what actually happens when
> an organism undergoes a situation where it becomes its necessity to survive by
> recycling its own organization units i.e. at the time of "aging". Proteins is
> just one example, same is true for nucleotides and carbohydrates and lipids.
>
> Therefore I still feel that this term "storage protein of seed" should be
> brought back. Another reason that these proteins in "Monocot plants" also have
> an additional function of "serine protease inhibitor". There are several
> instances of such proteins as Tanya already mentioned about them in her first
> mail at the start of this debate.(cited below)
>
> http://www.geneontology.org/email/go-arc/go-2002/2028.html
>
> "Midori: There are many different seed storage proteins: vicilin-type
> globulin, albumin, glutenin/gliadin, C hordein, etc. "
>
> From my perspective 'nutrient reserve' is a very broad term and we will mislead
> the community by annotating any such term.
>
> Pankaj
>
>
> Midori Harris wrote:
> >
> > Hi,
> >
> > We will stick with 'nutrient reserve'. "Storage protein of seed" has
> > exactly the same problems as "seed storage protein": 'seed' is a
> > localization and 'protein' is a gene product, not an activity.
> >
> > I'll put 'nutrient reserve' in the SourceForge list so we don't forget to
> > actually add it.
> >
> > Midori
> >
> > On Wed, 14 Aug 2002, Suparna Mundodi wrote:
> >
> > > Hi Midori,
> > >
> > > What has happened to the "seed storage protein" term. Recently there was a
> > > request from Pankaj to include the "storage protein of seed" and I think
> > > he makes a valid point here. Are we going to stick with the "nutreint
> > > reserve" term or "Storage protein of seed"?
> > >
> > > I have attached Pankaj's email below.
> > >
> > > Suparna
> > >
> > >
> > >
> > > Date: Tue, 13 Aug 2002 16:11:02 -0400
> > > From: Pankaj Jaiswal <pj37 at cornell.edu>
> > > To: Tanya Berardini <tberardi at acoma.Stanford.EDU>
> > > Subject: Re: seed storage protein
> > >
> > > Hi Tanya,
> > >
> > > I really did not know about this debate. Why can't we have a term instead
> > > "storage protein of seed", just to convince the concept. Doesn't matter if
> > > there
> > > is a compartmentalization aspect here "anatomy term=seed". If GO can have
> > > fat
> > > body/lipid storage body/protein storage vacuole(!!!), then this is a valid
> > > reframed term that defines a function, that its a storage protein
> > > providing
> > > nutritional buffer to the embryo, when it undergoes germination.
> > >
> > > Now the situation is how should we annotate "alpha-globulin", the function
> > > is
> > > seed storage protein. The other model organisms don't have this seed
> > > storage
> > > protein example is
> > > http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/blink?pid=1783206&tax=0&org=0&pdb=0&sort=1&cut=100&all=0
> > >
> > > there are 75 such entries from plants but none from others. I was even
> > > going to
> > > ask a new term request for "alpha-globulin", which is an instance of
> > > storage
> > > protein of seed by functional definition.
> > > _________________________
> > >
> > > Same way GO has different terms for "response" "susceptibility" &
> > > "resistance".
> > > I think resistance and susceptibility is a score/attribute of determining
> > > the
> > > level of "response". The "Response" is biological in origin but the
> > > "resistance"
> > > / "susceptible" are phenotype terms and one needs to avoid this. We have
> > > had a
> > > considerable discussion on this before when Leonore was there and she
> > > reframed
> > > the phenotypic terms to responses, but they have reappeared.
> > >
> > >
> > > Pankaj
> > >
> > >
> > >
> > >
> > >
> > > On Wed, 31 Jul 2002, Midori Harris wrote:
> > >
> > > > Of course I like 'nutrient reserve' -- it was my idea. ;)
> > > >
> > > > If no one complains (and soon) we will put 'nutrient reserve' in, with a
> > > > comment that it can be used for gene products formerly annotated to any of
> > > > the 'storage protein' terms.
> > > >
> > > > Midori
> > > >
> > > > On Wed, 31 Jul 2002, Suparna Mundodi wrote:
> > > >
> > > > > Midori: If we are making "seed storage protein" obsolete, then have we
> > > > > come to a consensus on the term this is going to replace "seed storage protein"
> > > > > ? I vote on the use of "nutrient reserve" and "amino acid reserve" as you
> > > > > suggested earlier.
> > > > >
> > > > > Suparna
> > > > >
> > > > >
> > > > > On Mon, 29
> > > > > Jul 2002, Tanya Berardini wrote:
> > > > >
> > > > > > Thanks for the note, Harold.
> > > > > >
> > > > > > Midori: There are many different seed storage proteins: vicilin-type
> > > > > > globulin, albumin, glutenin/gliadin, C hordein, etc.
> > > > > >
> > > > > > Please bring back "seed storage protein" from the dead!!! Oddly enough,
> > > > > > the other term that I added the same day GO:0009914 is still alive
> > > > > > and well.
> > > > > >
> > > > > > Advice on what to do??
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Tanya
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Mon, 29 Jul 2002, Midori Harris wrote:
> > > > > >
> > > > > > > sounds like it ought to be obsolete -- gene product-y
> > > > > > >
> > > > > > > m
> > > > > > >
> > > > > > > On Mon, 29 Jul 2002, Harold Drabkin wrote:
> > > > > > >
> > > > > > > > Thought someone in TAIR or GRAMANE would want to know:
> > > > > > > >
> > > > > > > > While we were doing our nightly load of GO, we noticed that
> > > > > > > >
> > > > > > > > GO:0009915 (seed storage protein) exists in current our GO vocabulary from
> > > > > > > > the previous load, but it is not in
> > > > > > > > the recent input file.
> > > > > > > >
> > > > > > > > It's not in the obsolete nodes either.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > -------------------------------------------------------------------------------
> > > > > > Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu
> > > > > > The Arabidopsis Information Resource FAX: (650) 325-6857
> > > > > > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325
> > > > > > Department of Plant Biology URL: http://arabidopsis.org/
> > > > > > 260 Panama St.
> > > > > > Stanford, CA 94305
> > > > > > -------------------------------------------------------------------------------
> > > > > >
> > > > >
> > > > > ****************************************************************************
> > > > > Suparna Mundodi, Ph.D. email:smundodi at acoma.stanford.edu
> > > > > Curator, Tel:650-325-1521 x342
> > > > > The Arabidopsis Information Resources Fax:650-325-6857
> > > > > Carnegie Institution of Washington URL:http://arabidopsis.org/
> > > > > Department of Plant Biology
> > > > > 260 Panama St.
> > > > > Stanford, CA 94305
> > > > > ****************************************************************************
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > ****************************************************************************
> > > Suparna Mundodi, Ph.D. email:smundodi at acoma.stanford.edu
> > > Curator, Tel:650-325-1521 x342
> > > The Arabidopsis Information Resources Fax:650-325-6857
> > > Carnegie Institution of Washington URL:http://arabidopsis.org/
> > > Department of Plant Biology
> > > 260 Panama St.
> > > Stanford, CA 94305
> > > ****************************************************************************
> > >
> > >
> > >
>
> --
>
> ******************************************
> 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
> ******************************************
>
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Sue Rhee rhee at acoma.stanford.edu
The Arabidopsis Information Resource URL: www.arabidopsis.org
Carnegie Institution of Washington FAX: +1-650-325-6857
Department of Plant Biology Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
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