NAME
Bio::Network::IO::psi25
SYNOPSIS
Do not use this module directly, use Bio::Network::IO:
my $io = Bio::Network::IO->new(-format => 'psi25',
-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. This module parses version 2.5 of PSI MI.
Databases
The following databases provide their data as PSI MI XML:
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" whereas PSI MI from IntAct or MINT has the "xml" suffix.
Documentation for PSI XML can be found at http://www.psidev.info.
Version
This module supports a subset of the fields described in PSI MI version 2.5. (http://www.psidev.info/index.php?q=node/60). The DATA IN THE NODE section below describes which fields are currently parsed into ProteinNet networks.
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.
DATA IN THE NODE
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/fullName
Annotation::SimpleValue
interactor/xref/primaryRef
Annotation::DBLink
interactor/xref/secondaryRef
Annotation::DBLink
Bio::Species object
interactor/organism/names/alias
Bio::Species object
interactor/organism/names/fullName
Bio::Species object
interactor/organism/names/shortLabel
Bio::Species object
DATA NOT YET AVAILABLE
The following are subclasses of interactor whose values are currently not accessible through the Node object.
interactor/names/alias
Annotation::SimpleValue
interactor/sequence
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/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 NOT yet 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 listsReporting 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
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_addInteractor
Name : _addInteractor
Purpose : Parses protein information into Bio::Seq::RichSeq objects
Returns :
Usage : Internally called by next_network()
Arguments : None
Notes : Interactors without organism data get their Bio::Species
fields set to -1_addInteraction
Name : _addInteraction
Purpose : Adds a new Interaction to a graph
Usage : Do not call, called internally by next_network()
Returns :
Notes : All interactions are made of 2 nodes - if there are more
or less than 2 then no Interaction object is created