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

[Silke Trissl]

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
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