[Bioperl-l] PMC and EUtilities, was bioperl::db

Chris Fields cjfields at uiuc.edu
Sun Apr 29 20:31:15 EDT 2007


There may be a way to limit the initial query to full text docs from  
esearch, then use the history to retrieve only the XML docs you  
want.  Is that what you mean?

BioPerl-based access to PMC is limited at best.  Bio::DB::EUtilities  
only returns raw PMC XML with no post-processing of raw data (for  
good reason, as EUtilities is meant to be an intermediate step).   
Allen Day's Bio::DB::Biblio::eutils module supposedly allows PMC  
queries.  I'm also pretty sure that PubMedXML != PMC XML, in other  
words the Bio::Biblio XML format parsers may not work on PMC XML.

chris

On Apr 29, 2007, at 5:57 PM, Bernd Mueller wrote:

> Hello list,
>
> I figured out my problem. Actually it was because of problems in the
> versioning of bioperl. It is described to figure out the available
> versions of bioperl in CPAN but afterwards it is described to  
> install a
> much higher version wich is not listed as distribution in CPAN. So it
> works fine now. Thanks anyway. Proficiency in reading results in  
> success ;-)
>
> But I have another question: Does anyone know how to retrieve free
> fulltext documents with EUtilities from Pubmed Central? All my queries
> result in a corpora of free and non-free articles.
>
> Thanks and regards,
>
> Bernd
>
>
> Bernd Mueller wrote:
>> Hi,
>>
>> I followed those instructions on bioperl.org for installing  
>> bioperl via
>> cpan. But actually it is impossible for me to install the bioperl::db
>> module.
>>
>> How does this work?
>>
>> Moreover none of these Birney distribution are installable on my  
>> system.
>> After typing cpan> install BIRNEY/bioperl-x.x.x.x, the tests always
>> fail. So I have to install the CRAFFI bundle but it does not seem  
>> that
>> Bio::DB module is included in this bundle because my programs  
>> using that
>> module do not work.
>>
>> Help would be appreciated :)
>>
>> Cheers,
>> Bernd
>>
>> Appendix:
>>
>> cpan[6]> d /bioperl/
>> Distribution    BIRNEY/bioperl-1.2.1.tar.gz
>> Distribution    BIRNEY/bioperl-1.2.2.tar.gz
>> Distribution    BIRNEY/bioperl-1.2.3.tar.gz
>> Distribution    BIRNEY/bioperl-1.2.tar.gz
>> Distribution    BIRNEY/bioperl-1.4.tar.gz
>> Distribution    BIRNEY/bioperl-db-0.1.tar.gz
>> Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
>> Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
>> Distribution    BIRNEY/bioperl-run-1.2.2.tar.gz
>> Distribution    BIRNEY/bioperl-run-1.4.tar.gz
>> Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
>> Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
>> 12 items found
>>
>>
>
> -- 
> Dipl.-Inform.(FH)
> Bernd Mueller
> phone: +49 179 2336692
> email: bernd at kirx.de
>
> _______________________________________________
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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