[Bioperl-l] Browsing the NCBI PubMed database

[Elia Stupka]

> may I use Bioperl to browse the PubMed database ? What I would do is
> to run a perl script, give it the keywords and retrieves all the
> article related without accessing to the NCBI PubMed site.

You should have a look at the documentation of Bio::Biblio, a module that
was written to handle this type of query. It is quite easy to use, and you
can even do what you are saying with a one-liner perl like this:

perl -MBio::Biblio -e 'print join ("\n", @{ new
Bio::Biblio->find("brazma")->get_all_ids })

which would return you all ids for articles matching Brazma

You should also check the http://industry.ebi.ac.uk/openBQS/ which
maintains the development of the repositories.

Elia

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