GO accession numbers
Vincent, Leszek
Leszek at missouri.edu
Fri Jun 22 17:46:20 EDT 2001
Hi all,
I like Pankaj's approach, specifically the Plant ontology (PO) and Trait
ontology (TO) components, because it is generic enough to encompass so many
domains. I think I was trying to be too specific by suggesting the prefixes
for the specific domains within PO. But clearly that's unnecessary (in fact
probably very undesirable!). Having a browser similar to that at FlyBase for
browsing the PO will enable folk to locate their area of interest without
having a myriad of prefixes to comprehend.
I'm having some difficulty accommodating Fungal ontology within Plant
ontology (raises taxonomic questions! & it may be 'politically incorrect?).
The algal ontology too might need looking further. I need to review the
current perspectives on Kingdoms etc.
I was wondering if the Trait ontology (TO) format would be adequate for the
traits of all possible taxa - but pondering this further I think it would
work.
So, according to Pankaj's scheme we would recommend just two prefixes - PO &
TO - am I understanding this correctly??
I'll stew on this over the w/end but I think it will work.
I look forward to 'hearing' what others think.
Regards,
- Leszek
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
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, June 22, 2001 1:41 PM
> To: gramene at brie.cshl.org; Vincent Leszek; Richard Bruskiewich; Leonor
> Reiser
> Subject: Re: GO accession numbers
>
>
> 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
> **************************************************************
>
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