Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
Pankaj Jaiswal
pj37 at cornell.edu
Mon Mar 25 09:38:43 EST 2002
Hi Sue,
You are right, the PO will represent Plant Anatomy and developmental(Growth)
stages. I know development is the GO domain and having it there is fine and will
be duly represented on the POC site and the ontology browser. I am making PO, GO
and TO all three available as part of ontology database at POC. They will also
carry the associations as well like Gene product associations/phenotypes. Users
will have the option to search in a particular ontology type.
I think that should clear up any confusions on Plant Development Process (GO).
Thanks
Pankaj
Sue Rhee wrote:
>
> Vincent,
>
> THis sounds great. We will update our ontology files accordingly in
> gorgonzola. One minor point in that I think there are only two ontologies
> that we are collaborating as a part of PO currently: Plant Anatomy and
> Plant Temporal. I think development is part of GO process onology that
> should be modified to suit plant needs within GO. Please let me know if
> this is not what is going on..
>
> Sue
>
> On Fri, 22 Mar 2002, Vincent, Leszek wrote:
>
> > Hi Colleagues
> >
> > Lots of good email 'dialogue' has been taking place during the past few days, predominantly regarding the questions of number space & prefix.
> >
> > Based on what's been offered here's my synthesis / proposal.
> >
> > Number Space: Allocation of groups of 5,000 numbers from within the 7 digit number space as follows:
> >
> > 0000001 - 0005000 TAIR
> > 0005001 - 0010000 GRAMENE
> > 0010001 - 0015000 IRRI
> > 0015001 - 0020000 MAIZEDB
> >
> > This would seem to provide ample number space for each group's development of ontologies. It also provides lots of room for further number space allocations to be made to new plant ontologists.
> >
> > Prefix: PO is to be used as the prefix for all the ontologies originating from the various collaborating groups of the POC. Anatomy, development, temporal etc. ontologies will all be included under the PO umbrella prefix (this parallels the GO paradigm). The same applies to Trait ontologies (TO), however it is represented.
> >
> > May I suggest that we consider acknowledging the source of the relevant CV terms by inserting our database 'acronym' and perhaps the initials of the curator in the Dbxref field adjacent to the term definition field in DAG-Edit (e.g. MAIZEDB:pldv, GRAMENE:pj, TAIR:lr etc.). This would be in addition to the relevant Dbxref info. provided for the term being defined. Leonore did this for some of the terms in her anatomy ontology & I think it provides a useful link to the origins of the term - perhaps especially important with us working in a multi-species arena. It seems like the browser would need to be tweaked so that this Dbxref field is displayed. In any case I think it is very important that the Dbxref info. for the term definition be displayed as it's an important component of the definition. So also including the database abbreviation & curator initials from this Dbxref field should be feasible. Comments on this??
> >
> > The conference call stimulated considerable thought about matters raised during the call and it has been great reading the constructive dialogue that has followed. Thanks for working to reach consensus.
> >
> > I'll copy the recent emails to Victor Ulat, Richard's DB colleague at IRRI - add his email to your list (V.ULAT at CGIAR.ORG).
> >
> > If you think I've misrepresented something please don't hesitate to point this out to me - we're learning together.
> >
> > Sincerely,
> > - 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: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > Sent: Friday, March 22, 2002 2:42 PM
> > > To: Pankaj Jaiswal
> > > Cc: Vincent, Leszek; Coe, Edward H.; Polacco, Mary L.; Curator TAIR;
> > > Leonor Reiser; Richard Bruskiewich; Tanya; Lincoln Stein;
> > > Susan McCouch;
> > > Doreen Ware; brie
> > > Subject: Re: [Fwd: FW: suggestions for 'POC' methods]
> > >
> > >
> > > 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.
> > > --------------------------------------------------------------
> > > ---------------
> > >
> > >
> > >
> >
>
> -----------------------------------------------------------------------------
> 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
******************************************
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