[Bioperl-l] Not picking up Dbxrefs EMBL records

Hilmar Lapp hlapp at gnf.org
Mon Aug 8 16:04:08 EDT 2005

Are you referring to references and their PMID? These you would find in 
the Reference table, which has a foreign key to dbxref, which would 
only store the PUBMED or MEDLINE ID (not both at this time). Can you 
given an example accession that's giving you grief?


On Aug 8, 2005, at 1:17 AM, SG Edwards wrote:

> Hi folks,
> I have a BioSQL database (PostgreSQL 7.4.3, BioPerl 1.4, bioperl-db 
> 1.2) set up
> containing protein and gene data. However, when I load gene sequence 
> records
> (EMBL or Genbank) using:
> perl load_seqdatabase.pl -driver Pg -safe -lookup -dbname milk -dbuser 
> s0460205
> -dbpass password -format embl /home/s0460205/file_name.txt
> from bioperl-db it does not pick up any dbxrefs i.e. there is no 
> dbxref_id for
> MEDLINE etc.
> Has anyone else come across this rpoblem and is ther a fix?
> Cheers,
> Stephen
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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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