[BioSQL-l] bioseq swissprot Medline links

[Hilmar Lapp]

What was the query that you issued? Note that the references (RN lines 
and friends) in swissprot end up as rows in the table reference, with 
bioentry_reference being the association table with bioentry. The 
reference table does have a foreign key to dbxref for the actual pubmed 
or medline id. So, in order to just get bioentries and pubmed/medline 
ids in the query you still need to join through bioentry_reference and 
reference.

BTW there were certain problems with swissprot reference parsing in 
certain versions of bioperl. You may want to read the respective email 
to the bioperl-l list if you haven't yet: 
http://bioperl.org/pipermail/bioperl-l/2004-December/017649.html

	-hilmar

On Friday, December 17, 2004, at 07:21  AM, Gihan wrote:

> Hi all,
>
> We installed swissprot as the first database in the bioseqdb scheme 
> (using load_seqdatabase.pl) and apparently it looked succesful (using 
> --safe). However, when we tried to join the bioentry table to the 
> dbxref
> through bioentry_dbxref to get the MEDLINE refrences it seems like 
> these link doesnt exist for MEDLINE but for PDB for example  .
>
> Any idea how to get those links working??
>
> Cheers,
> Gihan Dawelbait
> PhD student,
> BioTec Dresden
>
>
>
>
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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