DBXrefs

Fri Apr 16 14:04:12 EDT 2004

Im just curious about when these DBXrefs are being used and for what
purpose.
So when I included say TAIR:lr in a reference for a definition, I did to
to  mean
1) I wrote this definition myself from my own head OR
2) When used with another citation (eg. ISBN:XXXXXX) it means the
definition has been paraphrased or modified from its original text.

I never used it to say-- these terms came from TAIR or whereever. Thats
why we all have numberspaces... like the GO... and we track who added the
terms in CVS...

Do I understand the usage of these dbxrefs correctly?
Leonore

On Fri, 16 Apr 2004, Felipe Zapata wrote:

> If I'm not wrong I think I have used little letters
> F
> On Apr 16, 2004, at 11:47 AM, Pankaj Jaiswal wrote:
>
> >
> >
> > Katica Ilic wrote:
> >> Hi Pankaj,
> >> I thought we agreed to use PO as the database name, so that every
> >> definition 'created' by POC ontology developers would have PO as
> >> database name. Term ID (which also has PO as prefix) would indicate
> >> where
> >> the term came from (by the number range). Is there any reason for
> >> doing it
> >> otherwise?
> > Personally, I don't recall this conversation, though, there was a
> > discussion on how are we going to put the DBXrefs for the definition,
> > if they are coming from people in Monsanto for example. The reason was
> > Monsanto do not want anyone to know if this term is tracing back to
> > their ontologies.
> >
> > Therefore the agreement was that such cases where we do not want to
> > disclose the identity, the database name will be "Poc" not "PO"and the
> > database id will be "curators". In rest of the instances developers
> > will use their own initials and the respective database id. Atleast
> > this is also followed at GO. Every developer is not from GO for
> > instance.
> >
> > You may want to cross check, following DBXrefs are already using the
> > consistent style.
> > definition_reference: Poc:curators
> > definition_reference: TAIR:lr
> > definition_reference: GR:pj
> > definition_reference: MaizeDB:lv
> >
> >
> >> By the way, I did not know about the lower case initials. I have it
> >> all in
> >> capital letters (and I also told Leszek to follow the same). Any
> >> particular reason for this? I ma just curious, of course we can
> >> always easily change
> >> it, but it seems that most of us have used capital letters so far
> >> (though
> >> I am not sure about Felipe).
> > My suggestion was based on precedence and following it with a
> > consistent style. Infact it maintains the consistency when we are
> > pulling out DBXrefs from species specific ontologies.
> >
> > Pankaj
> >
> >
> > PS: I forgot to add the generic POC DBXref. Here it is
> >
> > database name : Poc
> > database id: curators
> > description: The Plant Ontology Consortium
> >
> >
> >> Katica
> >> On Fri, 16 Apr 2004, Pankaj Jaiswal wrote:
> >>>
> >>> Hi Everyone,
> >>>
> >>> Here are the my suggestions for DBxrefs. Please use the consistent
> >>> style
> >>> by configuring the DBXrefs in your DAG-Edit DBXref library. Try to
> >>> use
> >>> lower case letters for your initials. Unless you have modified the
> >>> definition available from another source do not add your id in
> >>> addition to
> >>> the source DBXref. If the definition is completely given by the
> >>> developer
> >>> based on his/her understanding, then the use of dveloper id DBXref is
> >>> valid.
> >>>
> >>> I hope this will clear up some of the inconsistencies.
> >>>
> >>> Pankaj
> >>>
> >>>
> >>> database name : TAIR
> >>> database id: kl --->for Katica
> >>> description: The Arabidopsis Information resource
> >>>
> >>> Similarly create ids for any other developer from TAIR
> >>>
> >>> database name : MaizeGDB
> >>> database id: lv --->for Leszek
> >>> description: maize Genetics and Genomics Database
> >>>
> >>> create ids for any other developer from MaizeGDB, e.g. mary (mp)
> >>>
> >>> database name : UMSL
> >>> database id: fz --->for Felipe
> >>> description: University of Missouri, St. Louis
> >>>
> >>> create ids for Toby (tk) and Peter (ps)
> >>>
> >>> database name : GR
> >>> database id: pj --->for Pankaj
> >>> description: Gramene Database
> >>>
> >>> database name : ISBN
> >>> database id: 0080374913-->for Plant Anatomy by Fahn A
> >>> description: International Standard Book Numbering
> >>>
> >>> similarly create any other ISBN ids for Essau's etc.
> >>>
> >>>
> >>> database name : AP web Glosssary
> >>> database id:
> >>> http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html
> >>> description: Angiosperm Phylogeny Website
> >>>
> >>>
> >>>
> >>> database name : Web
> >>> database id: URL --->for any other web resource
> >>> description: Website
> >>>
> >>>
> >>>
> >> ----------------------------------------------------------------------
> >> ----
> >> Katica Ilic             		katica at acoma.stanford.edu
> >> The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
> >> Carnegie Institution of Washington 	FAX: (650) 325-6857
> >> Department of Plant Biology 		URL: http://arabidopsis.org/
> >> 260 Panama St.
> >> Stanford, CA 94305
> >> U.S.A.
> >> ----------------------------------------------------------------------
> >> ----
> >
> > --
> > ******************************
> > Pankaj Jaiswal, PhD
> > Gramene Database
> > Department of Plant Breeding
> > G-15 Bradfield Hall
> > Cornell University
> > Ithaca, NY-14853
> >
> > tel: +1-607-255-3103
> > fax: +1-607-255-6683
> > web: http://www.gramene.org
> > *****************************
> >
> >
> >
> ~~~~~~
> Felipe Zapata
> University of Missouri St. Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis, MO 63121
> 314 516-6200
>

-------------------------------------------------------------------------------
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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