Bio::Graph::IO::psi_xml.3pm

Langue: en

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

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