DBXrefs

[Pankaj Jaiswal]

Hi Mary

Mary Polacco wrote:

> Hi Pankaj,
> 
> 
> The NCBI listing for MaizeDB has yet to be updated, although Plant Genome
> section is now linking to MaizeGDB. I will contact NCBI on this, but in the
> meantime, the list as it stands now is incorrect and the corrrection is
> provided below.
> 
> Also, to make the list useful for Phenotype XREF, not just locus, I've added
> url_syntax for the phenotype objects in MaizeGDB that will be directly
> linked to POC terms. Does the group think this might be useful?
> 
Strategy would be that each DB builds their own set of mappings to the POC terms 
and contributes them to POC. The POC DB will act as a central repository to give 
a summary of all the associations to an ontology term based on a passport info 
it will store. For further info the associated object will direct a link to the 
reference db.



> Another question, what is the purpose of the list?

the objective is to have a list of standardized Xrefs in POC Db. These xrefs are 
used by the
#1 Ontology developers as xrefs to the
	-definitions of the terms
	-synonyms to the terms
	-any generic xrefs
#2 In the near future when we start having the associations, from contributing 
DBs, then in the Ontology DB, we require these Xrefs to link back to the objects 
(proteins/genes/phenotypes/etc) to their source DB by using the standardized 
list of Xrefs and formats.

#3 This is something in common with the GO application. Also its a better way of 
assigning the unique identifiers/abbreviations to the DBs and objects.

> 
> -mary
> 
> On 11/4/03 4:51 PM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
> 
> 
>>abbreviation: MaizeDB
>>database: Maize Genome Database.
>>object: Canonical name of gene.
>>example: MaizeDB:apb1
>>generic_url: http://www.agron.missouri.edu/
>>url_syntax:
>>
>>abbreviation: MaizeDBID
>>database: Maize Genome Database.
>>object: Identifier.
>>example: MaizeDBID:12008
>>generic_url: http://www.agron.missouri.edu/
>>url_syntax:
> 
> 
> 
> abbreviation: MaizeGDB
> database: Maize Genetics and Genome Database.
> object: Canonical name of gene.
> example: MaizeGDB:apb1
> generic_url: http://www.maizegdb.org/
> url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=
> object: Phenotype of gene variant
> example: MaizeGDB:liguleless
> url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term=
>  
> abbreviation: MaizeGDBID
> database: Maize Genome Database.
> object: locus Identifier.
> example: MaizeGDBID:12008
> generic_url: http://www.maizegdb.org/
> url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=
> object: phenotype identifier
> example:MaizeGDBID:61504
> url_syntax:http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id=
> 
>