GO accession numbers

[Pankaj Jaiswal]

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
**************************************************************