# $Id$

bioperl-network README

1. Installation
2. PSI Formats
3. Overview
4. Status
5. History


1. Installation

See the accompanying INSTALL file for details on installing
bioperl-network.


2. PSI Formats

Different databases offer different variants of the PSI 2.5
format. Some of these files cannot be parsed by this package. Please see:

http://www.bioperl.org/wiki/Module:Bio::Graph::IO::psi_xml


3. Overview

A ProteinNet is a representation of a protein-protein interaction network.
Its functionality derives from the Graph module of Perl and from BioPerl.
These sorts of networks, or graphs, can be modeled as nodes, or
vertices, connected by edges.

A node is one or more BioPerl sequence objects, a Bio::Seq or 
Bio::Seq::RichSeq object. Since a node can contain more than one
Sequence object it can represent protein complexes as well as proteins.
Essentially the node can be any Bioperl object that implements the
Bio::AnnotatableI and Bio::IdentifiableI interfaces. This is relevant since the 
identities of nodes are determined by their identifiers.

The bioperl-network modules use Perl's Graph::Undirected 
module and inherit its formal model as well. An edge corresponds to a 
pair of nodes, and there is only one edge per pair. An interaction is an 
attribute of an edge, and there can be 1 or more interactions per edge.
An interaction can be thought of as one experiment or one experimental 
observation. 

The formats that can be parsed are DIP (tab-delimited) and PSI MI
(XML), either version 1 or version 2.5. Capabilities include the
ability to merge networks, select nodes and interactions by
identifier, add and delete components (nodes, interactions, and
edges), count all components of a certain type, get all components of
a certain type, and get subgraphs. Then you have all the functionality
of Perl's Graph in addition such as traversal using different
algorithms, getting interior and exterior nodes, and getting all  
connected subgraphs. Graph is quite rich in functionality, this list
is only a small subset of available methods, see the documentation 
for Graph for more detail (http://search.cpan.org/~jhi/Graph/lib/Graph.pod).

For more detailed documentation also see the
Bio::Network::ProteinNet module.


4. Status

This package should be considered a preliminary piece of
work. Although the code is tested and stable it lacks functionality. Not
all fields in the PSI MI standard are parsed into a network, for example.
The BioPAX format is not parsed, arguably as important a format as
PSI MI. In addition useful functions such as searching by sequence or 
ontology term aren't yet implemented. If you are interested in contributing
please contact Brian Osborne at bioperl-l@bioperl.org.


5. History

Modules similar to these were first released as part of the core BioPerl package
and were called Bio::Graph*. Bio::Graph was copied to a separate package,
bioperl-network, and renamed Bio::Network. All of the modules were
revised and a new module, Interaction.pm, was added. The
functionality of the PSI MI 1.0 parser was enhanced and a version
2.5 parser was added.

Graph manipulation in the predecessor Bio::Graph was based on the 
Bio::Graph::SimpleGraph module by Nat Goodman. The first release as a
separate package, bioperl-network, replaced SimpleGraph with the Perl
Graph package. Other API changes were also made, partly to keep
nomenclature consistent with BioPerl, partly to use the terms used by
the public protein interaction databases, and partly to accommodate the
differences between Graph and Bio::Graph::SimpleGraph.

The advantages to using Graph are that Bioperl developers are not
responsible for maintaining the code that actually handles graph
manipulation and there is more functionality in Graph than in SimpleGraph.
You must install version .86 of Graph, or greater.
