Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
Leonore Reiser
lreiser at acoma.Stanford.EDU
Tue Apr 16 15:04:35 EDT 2002
It could be the curator or maybe better the database that is the source of
the term....
Leonore
On Tue, 16 Apr 2002, Pankaj Jaiswal wrote:
> Hi Leonore,
>
> Now, since you have cleared my doubts about getting rid of previous TAIR IDs
> altogether. It becomes easy for me to integrate the terms from your files. This
> also means that we are not going to store TAIR IDs as DBXref in the PO database
> which we will have for POC, instead the terms coming from TAIR files will be
> identified by their number space and the curator who submitted the term (as
> DBXref for definition of a term).
>
> For GOBO, PO will definitely be a new submission. We will see when that happens,
> when we submit.
>
> Pankaj
>
> Leonore Reiser wrote:
> >
> > Pankaj,
> >
> > I think there should not be a problem. When I talked with Tanya and Sue we
> > all concurred that the agreement from the phone conference and subsequent
> > emails was that we at TAIR were OK with changing the numberspace as the
> > inculded email from Leszek indicates- that we would remove the leading
> > zeros and not worry about the previously assigned numbers. Also, that
> > since the prefix would be assigned based upon the term type (e.g. anatomy
> > and
> > development as Plant Ontology terms-get a PO prefix)so that actually
> > changing the prefix in
> > the files was not necessary (ie. that it was a display issue where
> > anatomy/development terms were given a PO prefix). It seemed that the
> > important thing was that we used the assigned numberspace. This is an easy
> > remidy (a simple replace ) if need be.
> >
> > Based upon what you sent it looks like we have assigned same
> > numberspace- just
> > different prefixes- is that your assessment?
> >
> > We plan to change the files in our FTP and include that changes in the
> > readme file so people who have been using this understand that only the
> > leading numbers have changed.
> >
> > For GOBO-wont PO be a new submission with its own prefixes?
> >
> > I am also including the content of Sues email from March 25 for reference.
> >
> > Leonore and Tanya
> >
> > >From Sue:
> > 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.
> >
> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > On Tue, 16 Apr 2002, Pankaj Jaiswal wrote:
> >
> > > Hi Leonore ,
> > >
> > > I saw the changes you made at GOBO on GOCVS. It is like
> > >
> > > !autogenerated-by: DAG-Edit version 1.311
> > > !saved-by: lreiser
> > > !date: Mon Apr 15 18:32:37 PDT 2002
> > > !version: $Revision: 1.2 $
> > > !editors: Leonore Reiser, Jonathan Clarke
> > > $TAIR_ontology_of_arabidopsis ; TAIR:0000001
> > > %TAIR_anatomy_of_Arabidopsis ; TAIR:0000111
> > > %whole organism ; TAIR:0000304
> > > <cell type ; TAIR:0000298
> > > %aerenchyma cell ; TAIR:0000294
> > > %antipodal cell ; TAIR:0000192 < megagametophyte ; TAIR:0000188
> > > %atrichoblast ; TAIR:0000263 ; synonym:non-hair cell < elongation zone ;
> > > TAIR:0000324 < root epidermis ; TAIR:0000361
> > > %cambial initial ; TAIR:0000295
> > > %central cell ; TAIR:0000194 < megagametophyte ; TAIR:0000188
> > > <polar nucleus ; TAIR:0000196
> > >
> > > I am still surprised to see the identifiers that we agreed not to have, although
> > > it does make sense to have them, since it is representing Arabidopsis. In the
> > > past we agreed to have a PO identifier and an assigned number space similar to
> > > GO. However, what I could recollect from the conference call and some other e
> > > mails is that Sue (TAIR) did not want to create another accession and virtually
> > > agreed to use the PO identifier for the terms coming from anatomy and
> > > developmental stages. We also agreed and the same was again followed up when I
> > > had a talk with Tanya last week, that its fine. The reason, since TAIR has
> > > already released the arabidopsis anatomy and temporal ontology to the public
> > > which the people might have started using them. Given the situation its wise for
> > > us to use the terms with PO identifiers to make it generic for others to use
> > > (attributing the PO terms, with the original TAIR ID:1111xxx as a DBXref.) and
> > > identify it by the number space showing it was contributed by TAIR.
> > >
> > > Following our conversations on e mail, I am adopting the same strategy, while
> > > integrating the TAIR terms in a test release of PO.
> > >
> > > Here is an example of my flat file, (the example, helps me in integrating the
> > > TAIR terms in PO since it allows me to use DAG edit tool to drag and drop the
> > > DBXref field, that's why you see TAIR written twice once as DBXref and another
> > > as synonym). I will clean the flat file once I am done with the complete
> > > integration.
> > >
> > >
> > > $Plant ontology ; PO:0006561
> > > %plant anatomy ; PO:0005025
> > > %whole organism ; PO:0000304 ; TAIR:1111304 ; synonym:TAIR\:1111304
> > > <cell type ; PO:0000298 ; TAIR:1111298 ; synonym:TAIR\:1111298
> > > %aerenchyma cell ; PO:0000294 ; TAIR:1111294 ; synonym:TAIR\:1111294
> > > %antipodal cell ; PO:0000192 ; TAIR:1111192 ; synonym:TAIR\:1111192 <
> > > megagametophyte ; PO:0000188
> > >
> > > I am in the process of compiling the integrated version and putting it up on the
> > > web (test version) for everyone from POC to look at it. At the moment my
> > > suggestion would be of not changing anything on our respective databases untill,
> > > the integration is complete. I wish we would be able to integrate the PO very
> > > soon.
> > >
> > > I will be happy to share my flat files, once I am satisfied with the draft
> > > version.
> > >
> > > With kind regards
> > >
> > > Pankaj
> > >
> > >
> > > Leonore Reiser wrote:
> > > >
> > > > I finally got around to changing the numberspace- I removed the leading
> > > > zeros so now TAIR terms start from 0000001-
> > > >
> > > > since I only changed the 1111 to 0000 the last 3 digits should be the
> > > > same.
> > > > I have updated this in gobo on GO cvs and will update files in TAIR's ftp
> > > > site and literature curation database tomrrow.
> > > >
> > > > Leonore
> > > >
> > > > 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.
> > > > > > --------------------------------------------------------------
> > > > > > ---------------
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > > -------------------------------------------------------------------------------
> > > > Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
> > > > The Arabidopsis Information Resource FAX: (650) 325-6857
> > > > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
> > > > Department of Plant Biology URL: http://arabidopsis.org/
> > > > 260 Panama St.
> > > > Stanford, CA 94305
> > > > -------------------------------------------------------------------------------
> > >
> > > --
> > >
> > > ******************************************
> > > 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
> > > ******************************************
> > >
> >
> > -------------------------------------------------------------------------------
> > Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource FAX: (650) 325-6857
> > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------------
>
> --
>
> ******************************************
> 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
> ******************************************
>
-------------------------------------------------------------------------------
Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
The Arabidopsis Information Resource FAX: (650) 325-6857
Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
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