[Fwd: FW: suggestions for 'POC' methods]

[Bruskiewich, Richard]

Hello,

Sorry I missed the conference call. Confusion at my end given a barrage of
other distractions.

I need to clarify something: are we sharing a single 7 digit identifier
space with all other (GO database schema based) ontologies? 7 digits == big
number... should be feasible.
If so, could we set aside the most significant (leading) two digits to
subpartition the space into up to 99 distinct subspaces, of 5 digits
(100,000 term entries each) for each specialized ontology? Some smaller
ontologies could be combined into one subspace if need be. Each group/lab
assigned prefix (GO, TAIR, etc.) could be assigned to a specific subspace. 

Is this feasible/desirable? Or, do I misunderstand the problem?

Cheers
Richard

-----Original Message-----
From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
Sent: Thursday, March 21, 2002 5:42 AM
To: Pankaj Jaiswal
Cc: Vincent Leszek; Ed Coe; Polacco, M; Curator TAIR; Leonor Reiser;
Richard Bruskiewich; Tanya; Lincoln Stein; Susan McCouch; Doreen Ware;
brie
Subject: Re: [Fwd: FW: suggestions for 'POC' methods]


Hi, Pankaj,

I don't see that Michael is suggesting one versus the other in what I can
make out of the message below. The important issue about the identifier is
that we divide up the numberspaces among the three groups such that we do
not use the same number (accession). We reached an agreement on this
yesterday, yes?

We have been designating a seven digit number and if this is suitable for
everyone, each group can take 10,000 numbers to start with (We've used up
~200 in Anatomy).

In terms of the prefix, the reason I see for using a prefix to this number
accession is to distinguish the shared plant anatomy ontology from
different ontologies (e.g. GO, and inevitabley more ontologies to follow).
Since we agreed on making a shared plant anatomy ontology, using PA as the
prefix sounds ok to me so long as it is limited to 'Plant Anatomy
Ontology' and that we stick to the numberspaces for the numbers (so that
we don't create yet another accession for anatomy for Arabidopsis, for
example).

PO sounds a bit too general for this ontology. If we agree on making a
combined plant ontology for Developmental Stages (or temporal), we can
perhaps designate a different prefix. At this point, it is not clear to me
that we can develop a combined temporal ontology for plants, but it is
certainly worth a try if you are willing/interested. It is likely that the
development of Trait and other types of ontologies would occur as a
collaboration of more than plant groups, and may end up with a differnt
prefix.

Sue

On Wed, 20 Mar 2002, Pankaj Jaiswal wrote:

> Dear Everyone,
>
> I am forwarding you an e mail from Michael, Some of you must have seen it
> earlier also. There he has tried to resolve the issue of identifiers
(agenda no.
> 2 from yesterday's conference call) and suggested to use PA "Plant
Anatomy"
> which is a more generic identifier. I am strongly seconding his suggestion
and
> would recommend using "PO" Plant Ontology instead of the PA or the
identifiers
> from respective databases. I would invite everyone to discuss pros and
cons of
> it while building up the database. It is infact has turned out to be a
major
> issue and should be resolved ASAP.
>
> Thanks
>
> Pankaj
>
>
> "Michael Ashburner (Genetics)" wrote:
> >
> > Curious what emails cross one's desk !
> >
> > If I may express a view, it for option 1. BUT John Richter
> > should be consulted how DAGedit will cope with mixed if prefixes.
> > The thing is for option 1 is that should any one want an ontology
> > just for Arabidopsis then the Zea etc specific terms could be stripped
> > in a thrice with an editor.
> >
> > The other way is to have a generic prefix for these terms, eg. PA
> > for "Plant Anatomoy" and either use these in your individual databases
> > or have your own id's as synonyms.
> >
> > Two points, one minor.
> > Not
> >              adult leaf sensu Arabidopsis thaliana TAIR:
> > but
> >              adult leaf (sensu Arabidopsis thaliana) TAIR:
> >
> > Two, I am no botanist but could these not be made a bit broader
> > eg
> > (sensu Brassicae)
> > (sensu Graminae)
> >
> > (???or sensu dicots, senu monocots) and then only go to a more
> > specific sense if the biology so demands ?
> >
> > Hope I am not butting in when inappropriate.
> >
> > Michael
>
> --
>
> ******************************************
> 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
> ******************************************
>

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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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