DBXrefs

Fri Apr 16 15:11:36 EDT 2004

Just to add:

In our first ontology draft, most of the definitions were taken from  
APWeb glossary (that's OK).  But when we used definitions that Gramene,  
TAIR or MayzeGDB had (either from  ISBN XXXXX or not) we just used  
GR:pj, TAIR:lr and Mayze:lv and we did not make explicit reference to  
the ISBN used in those ontologies.

F

On Apr 16, 2004, at 1:04 PM, Leonore Reiser wrote:

>
> 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
> ----------------------------------------------------------------------- 
> --------
>
>
~~~~~~
Felipe Zapata
University of Missouri St. Louis
Department of Biology
8001 Natural Bridge Rd.
St. Louis, MO 63121
314 516-6200