[Fwd: FW: suggestions for 'POC' methods]
Sue Rhee
rhee at acoma.Stanford.EDU
Fri Mar 22 15:41:45 EST 2002
Pankaj,
Great. I'm happy to stick to Plant Anatomy and Developmental Stage
Ontology accessions to be used with the PO prefix. And we are also good
with leaving out trait ontolgies as a part of PO for now, particularly
because there may be a more general trait ontology developing and it may
be more desirable to minimize the number of Accessions for the same term.
If we agree on the 7 digit integer, we would like to use up
1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR temporal or
0000001-0002000 and 0002001-0003000, respectively if you want a leading
zero, since we already have these accessions associated to the terms we
have.
I'm not sure what you mean below when you say you will provide PO IDs from
the database for TAIR terms and use TAIR IDs as synonyms. Since we agree
on the namespace, there will be one and only one accession for the TAIR
anatomy and temporal terms. We will have internal identifiers but these
won't need to be used externally.
> Lastly but not the least, since we are designating the number space to every
> group, I am not hesitant in using the TAIR IDs as either DBXref/synonyms. Next
> time when we update the DB I will provide the PO ID for the anatomy/development
> term, and will use the TAIR ID as either the synonym or DBXref, if you agree.
> Could you please tell me if you have already incorporated these terms/IDs in
> your curation or still in the process of using them. It will help us at Gramene
> in setting up the tables and browser. Even though I am suggesting all these view
> points you will agree that it takes a certain amount of resources and time and
> everyone of us is limited within the scope and mandate, we will try our best.
>
> Thanks
>
> Pankaj
>
> Sue Rhee wrote:
> >
> > 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
> > > ******************************************
> > >
> >
> > -----------------------------------------------------------------------------
> > 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.
> > -----------------------------------------------------------------------------
>
> --
>
> ******************************************
> 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
> ******************************************
>
-----------------------------------------------------------------------------
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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