[Bioperl-l] pubmed article download and storing in object
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.
EMBL Outstation - Hinxton Senger at EBI.ac.uk
European Bioinformatics Institute Phone: (+44) 1223 494636
Wellcome Trust Genome Campus (Switchboard: 494444)
Hinxton Fax : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom http://industry.ebi.ac.uk/~senger
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