GO accession numbers
Pankaj Jaiswal
pj37 at cornell.edu
Thu Jul 5 13:05:29 EDT 2001
Even I agree on this as I was expecting a similar feedback). Yes ! we have to be
more generic. Continuing with the CV/O identifier prefixes, I recommend TO
(trait ontology), PO (plant ontology)/OO (organismal ontology, where the
animals(AO if required) will also be represented and does not need PO/AO then).
Do you think of any other way to represent Anatomy ? any suggestions for
Identifiers if necessary?
pankaj
Leonore Reiser wrote:
>
> 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.
> > ========================================================================
> >
>
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------
--
**************************************************************
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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