/ 
bioperl-network-1.5.2_005-RC
/ Bio::Network::IO::psi

NAME

Bio::Network::IO::psi

SYNOPSIS

Do not use this module directly, use Bio::Network::IO:

my $io = Bio::Network::IO->new(-format => 'psi',
                               -file   => 'data.xml');

my $network = $io->next_network;

DESCRIPTION

PSI MI (Protein Standards Initiative Molecular Interaction) XML is a format to describe protein-protein interactions and interaction networks.

Databases

The following databases provide their data as PSI MI 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/

Each of these databases will call PSI format by some different name. For example, PSI MI from DIP comes in files with the suffix "mif".

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

Version

This module supports PSI MI version 2.5, described at http://psidev.sourceforge.net/mi/rel25/.

Notes

See the Bio::Network::IO::psi_xml page in the Bioperl Wiki (http://bioperl.open-bio.org/wiki/Bio::Network::IO::psi_xml) for notes on PSI XML from various databases.

When using this parser recall that some PSI MI fields, or classes, are populated by values taken from an ontology created for the PSI MI format. This ontology is an OBO ontology and can be browsed at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI.

METHODS

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

NODE DATA

The Node (protein or protein complex) is roughly equivalent to the PSI MI interactor (entrySet/entry/interactorList/interactor). The following are subclasses of interactor whose values are accessible through the Node object.

interactor/names/shortLabel

Annotation::SimpleValue

interactor/names/alias

Annotation::SimpleValue

interactor/names/fullName

Annotation::SimpleValue

interactor/sequence

Sequence object

interactor/interactorType/names

Controlled vocabulary maintained by PSI MI http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI. Example: "protein".

OntologyTerm

interactor/interactorType/xref

Annotation::DBLink

interactor/xref/primaryRef

Annotation::DBLink

interactor/xref/secondaryRef

Annotation::DBLink

interactor/organism/names/shortLabel

Bio::Species object

interactor/organism/names/alias

Bio::Species object

interactor/organism/names/fullName

Bio::Species object

interactor/organism/cellType

Annotation::OntologyTerm

interactor/organism/compartment

Annotation::OntologyTerm

interactor/organism/tissue

Annotation::OntologyTerm

INTERACTION DATA

The Interaction object is roughly equivalent to the PSI MI interaction (entrySet/entry/interactionList/interaction) and experimentDescription (entrySet/entry/experimentList/experimentDescription). The following are subclasses of interaction and experimentDescription whose values are accessible through the Interaction object.

interaction/xref/primaryRef

Annotation::DBLink

interaction/xref/secondaryRef

Annotation::DBLink

interaction/organism/names/shortLabel

Bio::Species object

interaction/organism/names/alias

Bio::Species object

interaction/organism/names/fullName

Bio::Species object

interaction/modelled

Annotation::SimpleValue

interaction/intraMolecular

Annotation::SimpleValue

interaction/negative

Annotation::SimpleValue

interaction/interactionType

Controlled vocabulary maintained by PSI MI http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI. Example: "phosphorylation reaction".

OntologyTerm

interaction/confidenceList

Annotation::SimpleValue

experimentDescription/confidenceList

Annotation::SimpleValue

experimentDescription/interactionDetectionMethod

Controlled vocabulary maintained by PSI MI http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI. Example: "two hybrid array".

Annotation::OntologyTerm

featureElementType/featureType

Controlled vocabulary maintained by PSI MI http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI. The featureType includes data on post-translational modification. Example: "phospho-histidine".

Annotation::OntologyTerm

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHORS

Richard Adams richard.adams@ed.ac.uk Brian Osborne bosborne at alum.mit.edu

next_network

Name       : next_network
Purpose    : Constructs a protein interaction graph from PSI XML data
Usage      : my $net = $io->next_network()
Arguments  :
Returns    : A Bio::Network::ProteinNet object

_proteinInteractor

Name      : _proteinInteractor
Purpose   : Parses protein information into Bio::Seq::RichSeq objects
Returns   :
Usage     : Internally called by next_network()
Arguments : None

_addInteraction

Name     : _addInteraction
Purpose  : Adds a new Interaction to a graph
Usage    : Do not call, called internally by next_network()
Returns  :