NAME

Bio::Graph::IO::psi_xml - access and manipulate PSI XML graphs

SYNOPSIS

Do not use this module directly, use Bio::Graph::IO, for example:

  my $graph_io = Bio::Graph::IO->new(-format => 'psi_xml',
                                     -file   => 'data.xml');

DESCRIPTION

PSI XML is a format to describe protein-protein interactions and interaction networks. The following databases support PSI XML:

BIND

http://www.bind.ca

DIP

http://dip.doe-mbi.ucla.edu/

HPRD

http://www.hprd.org

IntAct

http://www.ebi.ac.uk/intact

MINT

http://cbm.bio.uniroma2.it/mint/

Notes on PSI XML from various databases can be found in the Bioperl Wiki at http://bioperl.org/wiki/Module:Bio::Graph::IO::psi_xml

Documentation for PSI XML can be found at http://psidev.sourceforge.net.

METHODS

The naming system is analagous to the SeqIO system, although usually next_network() will be called only once per file.

next_network

 name       : next_network
 purpose    : to construct a protein interaction graph from xml data
 usage      : my $gr = $io->next_network();
 arguments  : void
 returns    : A Bio::Graph::ProteinGraph object

_proteinInteractor

 name      : _proteinInteractor
 purpose   : parses protein information into Bio::Seq::RichSeq objects
 returns   : void
 usage     : internally called by next_network(), 
 arguments : none.

add_edge

 name     : _addEdge
 purpose  : adds a new edge to a graph
 usage    : do not call, called by next_network
 returns  : void