[BioSQL-l] Pubmed-ID's from SwissPort

[Richard HOLLAND]

This may sound a bit obvious, but I think BioPerl stores the PUBMED
references with a dbname of 'PubMed' not 'PUBMED'. Have you tried
searching with the correct use of case, or is your PostgreSQL
case-insensitive?

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biosql-l-bounces at portal.open-bio.org 
> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> Silke Trissl
> Sent: Friday, October 07, 2005 11:53 PM
> To: Hilmar Lapp
> Cc: Biosql
> Subject: Re: [BioSQL-l] Pubmed-ID's from SwissPort
> 
> 
> Hi Hilmar,
> 
> thank you for your very fast answer, but I still have problems with
> PubMed-IDs. I simply don't get them at all.
> 
> Hilmar Lapp wrote:
> > The annotation is taken from what's in the source record, so I'm
> > assuming you're referring to those references that have a 
> PubMed as well
> > as a MEDLINE ID annotated in the SwissProt record.
> 
> Yes, these are the one's I am looking for, but there are some 
> with only
> the PubMed-ID or Medline-ID alone. But in any case, I am interested in
> PubMed-IDs.
> > 
> > If only one ID is provided, that ID will be stored in the database
> > (using a foreign key in the Reference table to Dbxref), so if the
> > MEDLINE ID is absent the PubMed ID will substitute for it if it was
> > present in the source entry. 
> 
> I hoped so, but I don't even get one PubMed-ID, although I produced a
> swissprot file where some entries only have a PubMed-ID. But in my
> database there is no entry in the dbxref-table that has 
> 'PUBMED' as dbname.
> 
> I attached a small swissprot-file, where I deleted some references to
> Medline. If it is working for you, i.e. you get the 
> PubMed-ID's, please
> tell me which versions of BioPerl and BioSQL you use. I work with perl
> and fill a PostgreSQL database.
> 
> Regards,
> 
> 	Silke Trissl
>