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Bio::Graph::IO::psi_xml.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Graph::IO::psi_xml - access and manipulate PSI XML graphsSYNOPSIS
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
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