Feedback on POC

[Shuly Avraham]

Dear Georgi,

Thank you for your feedback.

The references and dbxref URLs are not coming from the database, but  
from the software source code (this is the way it was originally  
implemented by the GO)
When you're using AmiGO to connect to the database, the module  
NameMunger.pm holds the URL for each database. We have customized the  
module for the PO purpose. If you would like I can send you our version  
of the code.

So, for the dbxrefs URLs, we are using these for each datasource symbol:

'tair'=>'TAIR',
'tair_id' => 'TAIR',
'gr' => 'Gramene',
'maizegdb' => 'MaizeGDB',
'nasc' => 'NASC',

"gro"=>"http://www.gramene.org/db/ontology/search_term?id=GRO:$acc_no",
"tair"=>"http://arabidopsis.org/servlets/TairObject? 
accession=Keyword:$acc_no",
"maizegdb"=>"http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=$acc_no",
  "nasc"=>"http://arabidopsis.info/StockInfo?NASC_id=$acc_no",
   
"go"=>"http://www.godatabase.org/cgi-bin/amigo/go.cgi? 
view=details&search_constraint=terms&depth=0&query=$acc_no"

For the associations URLs:

  "gr"=>"http://www.gramene.org/db/genes/search_gene?acc=$acc_no",
"maizegdb"=>"http://www.maizegdb.org/cgi-bin/id_search.cgi?id=$acc_no",
"tair"=>"http://arabidopsis.org/servlets/TairObject?accession=$acc_no",
"nasc"=>"http://arabidopsis.info/StockInfo?NASC_id=$acc_no",

For the references URLs

"gr"=>"http://www.gramene.org/perl/pub_search?ref_id=$acc_no",
"gr_ref"=>"http://www.gramene.org/perl/pub_search?ref_id=$acc_no",
"tair"=>"http://arabidopsis.org/servlets/TairObject?accession=$acc_no",
"nasc"=>"http://arabidopsis.info/StockInfo?NASC_id=$acc_no",
"maizegdb"=>"http://www.maizegdb.org/cgi-bin/id_search.cgi?id=$acc_no",

I hope this helps.

Shuly.

On Sep 26, 2006, at 8:03 AM, feedback_submission at filetta.cshl.edu wrote:

>     *** Feedback from Plant Ontology Live Site ***
>
> refer_to_url: http://www.plantontology.org/index.html
>
> comments: Dear PO team,
>
>
> First of all I would like to thank you for excellent plant resource. I  
> found it useful and decided to have it in the house. Unfortunately I  
> had problem to connect gene products (symbols) from the table  
> “gene_products” to ncbi pubmed paper ids, it should come from the  
> table “dbxref”? The same as in the final result of your entries and a  
> category called “Gene Product Associations to Term and its Children”  
> column “Reference”. Please note that I am using the provided on the  
> web site MySql dump and I am using all the provided tables and  
> provided corresponding data.
>
> Thank you in advance, and wish you favorable working day
> GG
>
>
> name: georgi georgiev
>
> email: ggeca at bas.bg
>
> organization: bulgarian academy of science
>
> send_feedback: Send your feedback
>