[Fwd: FW: suggestions for 'POC' methods]
Pankaj Jaiswal
pj37 at cornell.edu
Mon Mar 25 10:04:09 EST 2002
Hi Sue,
I guess quite a number of issues did get resolved in the last week and things
are certainly moving ahead.
My reply to your queries follows..
Sue Rhee wrote:
>
> 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.
I agree and that's the way it should be. So this is no more an issue now.
(Resolved)
> 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.
>
I agree, it is no more an issue because now everyone is going to use the PO
identifiers using the allotted number spaces.
Thanks
Pankaj
> > 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.
> -----------------------------------------------------------------------------
--
******************************************
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
******************************************
More information about the Gramene
mailing list