[Bioperl-l] Not picking up Dbxrefs EMBL records

[SG Edwards]

Hi,

My installation does not pick up ANY dbxrefs for gene records e.g. Pubmed,
MEDLINE(either EMBL or Genbank formats). When I load them into the database
they go in fine but no dbxref_ids are mapped to the bioentry_id in the
bioentry_dbxref table. Therefore, nothing appears in the dbxref table either!

The system works fine for UniProt protein entries into the database. I am
currently installing BioPerl v 1.5 to see if this resolves the problem.

An example: NM_214434 from Genbank which has the dbxrefs:

Pubmed 1503277
Taxon  9823
GeneID 404088

Quoting Hilmar Lapp <hlapp at gnf.org>:

> 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?
>
> 	-hilmar
>
> 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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> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>