HELP!: GO Term Error
Polacco, Mary L.
polaccom at missouri.edu
Fri Aug 16 14:45:05 EDT 2002
Both term parsimony, and GO harmony are served if we stop at amino acid reserve, with the location not being included in the function. Leaf proteins may also have a nutrient reserve role, so you wouldn't have to invent a new term
for those guys.
-mary; curator MaizeDB
-----Original Message-----
From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
Sent: Thu 8/15/2002 1:31 PM
To: Pankaj Jaiswal
Cc: Midori Harris; Suparna Mundodi; Tanya Berardini; GO MAILING LIST; TAIR curators; brie
Subject: Re: HELP!: GO Term Error
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
> ******************************************
>
-----------------------------------------------------------------------------
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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