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

[Silke Trissl]

Richard HOLLAND wrote:
> 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?

Well I did get no PubMed-Id - either spelling or case.

By now I found out what was the problem with the PubMed-Ids. Every time
I only had a PubMed-ID given in a SwissProt file this ID was not taken
and parsed into the database. I thought it is a problem with BioSQL, but
it was a problem with BioPERL, where the swissprot parser has a problem.
I reported the bug and it should be fixed in a forthcoming release.

Therefore no problem with BioSQL, but BioPerl and sorry that I have
bothered the list.

Regards,

      Silke Trißl


> 
> 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
>>
> 
> 


-- 
________________________________________________________________________

Silke Trißl, MSc
Wissensmanagement in der Bioinformatik          Raum IV.104
                                                Rudower Chaussee 25
Institut für Informatik                         12489 Berlin, GERMANY
Humboldt-Universität zu Berlin
                                                Tel: ++49 30 2093 3904
www.informatik.hu-berlin.de/~trissl             Fax: ++49 30 2093 5484