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

[Heikki Lehvaslaiho]

Bioperlers,

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 

	http://industry.ebi.ac.uk/openBQS/


	-Heikki

-------- 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

Jason,
   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
styles/policies.

> 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.
> 
   Yes.
   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
bioperl.

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

   Martin

-- 
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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