[Bioperl-l] pubmed article download and storing in object

Martin Senger senger at ebi.ac.uk
Sun Jul 3 08:50:17 EDT 2005

   My few cents regarding the Bio::Biblio module:

   1) You are right that the doumentation of the created Perl objects is
poor. I will try to improve it.

   2) The modules in Bio::Biblio are of two categories: the first ones get
you XML from MEDLINE/Pubmed (by default it gets it from the EBI using
SOAP). And the second ones convert it - either to nothing, so you still
have an XML, or to Perl biblio objects (that are poorly documented, as
mentioned above; blam me), or to a simple hash (with similar names of keys
as used in the Perl objects). I agree that it would be nice to have more
outputs (like a printed versions of various level of details).

   3) The best way to see how the Bio::Biblio modules work is to check the
script bioperl-live/scripts/biblio/biblio.PLS (try with -h first). It uses
all the methods - so you can directly use it, or to copy&paste the code
into your own programs.

   With regards,

Martin Senger

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