GO accession numbers
Leonore Reiser
lreiser at acoma.Stanford.EDU
Thu Jul 5 12:54:06 EDT 2001
I agree with Lincoln. Mouse and fly have excellent anatomy CVs already.
One of the projects David Hill at MGI is working on is stripping away
species terms from the GO so that cross products can be used between more
generic terms to be more specific. So even less anatomy will be
represented in the GO ontologies.
Regards
Leonore
On Thu, 5 Jul 2001, Lincoln Stein wrote:
> I really don't think it appropriate for Plants to have a top-level
> ontology for the anatomy. The Gene Ontology is careful to be as
> generic as possible, and to make species-specific caveats wherever
> necessary (using sensu terms).
>
> I would prefer for there to be an Anatomy Ontology node, followed by
> specific anatomies for plants and animals. This is much the same as
> what you did with the TO.
>
> Lincoln
>
> Pankaj Jaiswal writes:
> > Hi everyone,
> >
> > Please have a look at the follwoing scheme text: I am suggesting this
> > format. This way we can remain more generic, by
> > not being too strict with the individual plant categories. for the
> > anatomical and morphological terms, as everyone
> > knows that we have a choice of having plant anatomy/anatomy, as a more
> > generic one or if one really prefers
> > can be more specific. However the difference is not much. Eventually we
> > will come across similar child-parent
> > relationships. I am open to that category, which ever way one wants. the
> > terms will not be that many in number
> > that we can't fit everything under PO IDs with 0-9999999. traits TO i
> > would like them once again to be more
> > generic and can go under TO. no need to extrapolate into PTO etc. you
> > will notice chemical (CO and clinical KO
> > ontology thing in the picture. well this is just for the future because
> > at some point chemists and clinician(already
> > there with human genone) would be interested in joining. For teh fly i
> > would even suggest that
> > theer should be one Animal_ontology AO and fly should be there under the
> > phyla representing the insects (and
> > not as FB). Well i should not to say much about animals, but as far as
> > possible i intend to be more generic for
> > plants atleast and stick to the classical way of presenting the terms
> > rather than experimenting in a new way
> > (sometimes its good also). What do you guys say?
> >
> > -thanks
> > pankaj
> >
> > ps:For the gramene project people, This is not the final word. the
> > matter is still under discussion!
> >
> > here is the scheme:
> >
> > $Ontology ;
> > %Chemical_ontology (CO) ;
> > %elements ;
> > %molecules ;
> > %inorganic ;
> > %organic ;
> > %Clinical_ontology (KO) ;
> > %Gene 0ntology (GO) ;
> > %Biological function ;
> > %cellular component ;
> > %molecular function ;
> > %Plant ontology (PO) ;
> > %algal_ontology ;
> > %angiosperms_ontology ;
> > %Dicot_ontology ;
> > %dicot_anatomy ;
> > %root ;
> > %shoot ;
> > %dicot_morphology ;
> > %root ;
> > %shoot ;
> > %Monocot_ontology ;
> > %monocot_anatomy ;
> > %root ;
> > %shoot ;
> > %monocot_morphology ;
> > %root ;
> > %shoot ;
> > %bryophyte_ontology ;
> > %Fungal_ontology ;
> > %Gymnosperm_ontology ;
> > %Pteridophyte_ontology ;
> > %Trait_ontology (TO) ;
> > %genetic trait_ontology ;
> > %plant genetic trait_ontology ;
> > %agronomic traits_ontology ;
> > %Plant Morphological traits_ontology ;
> >
> >
> >
> >
> >
> > "Vincent, Leszek" wrote:
> >
> > "Vincent, Leszek" <Leszek at missouri.edu>,Leonor Reiser
> > <lreiser at acoma.stanford.edu>
> > Subject: RE: [Fwd: Re: GO accession numbers]
> > Date: Fri, 22 Jun 2001 09:50:26 -0500
> > MIME-Version: 1.0
> > X-Mailer: Internet Mail Service (5.5.2653.19)
> > Content-Type: text/plain;
> > charset="iso-8859-1"
> >
> > Hi folk
> >
> > Here's my briefly considered suggestion. I think it would be useful
> > for us
> > to have a prefix which includes an identifier for the relevant taxon
> > (monocot & dicot) & another identifier for the specific domain that
> > the
> > prefix encompases.
> >
> > For the taxon identifier I suggest we use M for monocot & D for Dicot
> > (not
> > very original but botanically pretty useful) (If/when we get to
> > include
> > gymnosperm, pteridophyte folk etc. I think there will be room even
> > then to
> > use a single letter identifier e.g. G for gymnosperm, P for
> > pteridophytes -
> > but that's looking way ahead perhaps).
> >
> > For the domain identifier - here's the list that I think is relevant
> > (hopefully I haven't left out one): Developmental, Anatomy,
> > Morphology,
> > Phenotype, Trait. If we use the 1st letter of each & combine it with
> > the
> > taxon identifier we would get the following:
> >
> > MD - monocot developmental
> > MA - monocot anatomy
> > MM - monocot morphology
> > MT - monocot trait
> > MP - monocot phenotype
> >
> > DD - dicot developmental
> > DA - dicot anatomy
> > DM - dicot morphology
> > DT - dicot trait
> > DP - dicot phenotype
> >
> > I think the taxon identifiers & domain identifiers will ring good
> > 'bells'
> > with non-ontologists interested in our activities/joining in. I think
> > they're reasonably understandable & carry enough info. to enable one
> > to
> > understand the coverage of each prefix. These are just my thoughts &
> > I'm not
> > wanting to be presciptive. Let's see what the rest of us suggest
> > before we
> > get back to Suzie & Lincoln. (PS I was thinking of discussing this at
> > the
> > Bar Harbor meeting but there's no time like the present).
> >
> > - Leszek
> >
> >
> >
> > Lincoln Stein wrote:
> >
> > Hi Folks,
> >
> > The GO consortium thinks we should make up a prefix for the phenotype
> > terms and let them know. So please send Suzi Lewis the prefix(es)
> > when you've chosen them.
> >
> > Lincoln
> >
> > Suzanna Lewis writes:
> > > >
> > > > My monocot database group is happily creating ontologies for
> > plant
> > > > traits and anatomies. Your group has been great at helping us
> > get the
> > > > ontology editor up and running.
> > > >
> > > > A question: when we create these parallel ontologies, what prefix
> > > > should we use for the accession numbers? Should we make one up
> > and
> > > > tell you what it is later?
> > > >
> > >
> > > I think that is best. Pavel Tomancak here in Berkeley is doing
> > > something similar for the fly anatomy and developmental stages.
> > For
> > > these we are using the FB identifiers and I think this situation is
> > > analogous.
> > >
> > > -S
> >
> > --
> >
> > ========================================================================
> > Lincoln D. Stein Cold Spring Harbor
> > Laboratory
> > lstein at cshl.org Cold Spring Harbor,
> > NY
> >
> > NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS.
> > PLEASE WRITE FOR DETAILS.
> >
> > ========================================================================
> >
> >
> >
> > --
> >
> > **************************************************************
> > 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
> > **************************************************************
>
> --
> ========================================================================
> Lincoln D. Stein Cold Spring Harbor Laboratory
> lstein at cshl.org Cold Spring Harbor, NY
>
> NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS.
> PLEASE WRITE FOR DETAILS.
> ========================================================================
>
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Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
The Arabidopsis Information Resource FAX: (650) 325-6857
Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
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