Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
Pankaj Jaiswal
pj37 at cornell.edu
Mon Mar 25 09:52:49 EST 2002
Hi Richard
My comments are as follows
"Bruskiewich, Richard" wrote:
>
> Hi Leszek,
>
> Thank you for your thoughtful leadership on all fronts.
> One quick change: IRRI => IRIS (International Rice Information System) for
> dbxref (i.e. all the other designations are databases, not places ;-))
The DBXref you are suggesting will be represented in POC DBXref as
abbreviation: PO
definition:Plant Ontology Consortium
example:PO
generic_url:http://www.plantontology.org
url_syntax:
abbreviation: GR
definition:Gramene-A Comparative mapping Resource
example:GR
generic_url:http://www.gramene.org
url_syntax:
abbreviation: ICIS
definition:International Crop Information System
example:ICIS
generic_url:http://www.cgiar.org/icis/
url_syntax:
abbreviation: IRIS
definition:International Rice Information System
example:IRIS
generic_url:http://www.iris.irri.org/
url_syntax:
MaizeDB and TAIR are already represented in the GO DBXrefs and we don't need to
change that since we are building up the PO database as an integration into
GO-DB for POC. Nothing different except for some new term relationship types
that will be adopted/integrated from anatomy and cross products.
> Has some thought been given to keeping the other (international) attendees
> of the PAMG-X workshop in the discussion loop? I am cc:'ing to the
> sprig-CVO_dev at bioinformatics.org list for this purpose. Most of you will
> thus get two emails (hint, hint!). Some of those groups may wish to actively
> contribute plant ontology terms to the database.
This will certainly help us a lot and we as POC members welcome any number of
constructive suggestions. Ontology term contributions can be made using the web
based submission forms.
Thanks
Pankaj
> I like the curator attribution idea for dbxref. Might help experts target
> their constructive suggestions about particular terms to the persons who
> defined them.
>
> Richard
>
> -----Original Message-----
> From: Vincent, Leszek [mailto:Leszek at missouri.edu]
> Sent: Saturday, March 23, 2002 7:39 AM
> To: Curators At TAIR (E-mail); Doreen Ware (E-mail); Ed Coe (E-mail);
> Gramene developers; Leonore Reiser (E-mail); Lincoln Stein (E-mail);
> Mary Polacco (E-mail); Pankaj Jaiswal (E-mail); Richard Bruskiewich
> (E-mail); Susan McCouch (E-mail); Tanya Berardini; Victor Ulat (E-mail)
> Subject: Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
>
> 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.
> > --------------------------------------------------------------
> > ---------------
> >
> >
> >
--
******************************************
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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