[Bioperl-l] [Fwd: [Biohackathon] Re: bibliography stuff in perl]

Heikki Lehvaslaiho heikki@ebi.ac.uk
Thu, 07 Feb 2002 11:55:19 +0000


The bibliographic classes, java code and a SOAP server were described by
Martin Senger at the Tucson Biohachathon. I started writing Bio::Biblio
classes according to Martin's schema while at Hackthon. Next, Martin will
write parsers to read Medline XML data in to objects.

Learn more about Martin's work on bibliographies at 



-------- Original Message --------
Subject: [Biohackathon] Re: bibliography stuff in perl
Date: Wed, 6 Feb 2002 15:15:35 +0000 (GMT)
From: Martin Senger <senger@ebi.ac.uk>
Reply-To: biohackathon@egenetics.com
To: Jason Stajich <jason@cgt.mc.duke.edu>
CC: biohackathon@egenetics.com

   I have discussed the plan with Heikke and thenks to him I seem now to
understand the way how it should be done to be compliant with the bioperl

> The Medline XML
> parser would be excellent - I imagined that a Bio::Biblio::IO factory
> would create a Bio::Biblio::IO::medlinexml parser.  This would build and
> populate the appropriate Bibilo objects just as we do in SeqIO and
> SearchIO.
   An object Bio::Biblio::IO will instantiate and use an instance of
Bio::Biblio::IO::medlinexml if '-format=>'medlinexml' is given. It reads
XML MEDLINE file with one or more citations and convert them into the
Heikke's objects of type Bio::Biblio::RefI (actually its sub-classes). I
do not expect to implement also a 'write' method to converting back
Heikke's objects to the XML MEDLINE format.
   The class Bio::Biblio::IO will be a subclass of Bio::SeqIO.
   Is this correct vision?

   Additionally to that I plan to write a Bio::Factory::Biblio module
which instantiates and uses - again depending on the 'format' parameter
(or 'protocol' in this case?) - module Bio::Factory::Biblio::soap. It
implements query methods (similar as they are defined now for Java in
BibRefQuery and BibRefSupport interfaces) in order to get citations using
SOAP protocol. Note that this is _not_ repository-dependent - it can
deliver MEDLINE citations as well as citations from other bibliographic
repository (the difference is in the contents of the XML file - but this
module knows only that it is a string).
   Does it still fit with your vision?

   And, finally, I need also to provide the bibligraphy web service based
on SOAP, here at EBI, but it is a different question, not related only to

   Regarding the XML parser, I have not decided which one to use. I will
play with them a bit.


Martin Senger

EMBL Outstation - Hinxton                Senger@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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