[Bioperl-l] protein networks

Brian Osborne brian_osborne at cognia.com
Thu Mar 11 08:16:43 EST 2004


You may want to reconsider the name "ProteinGraphIO::xml.pm" since other
pathway databases (BIND certainly, KEGG perhaps) also export to XML.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Richard Adams
Sent: Monday, March 08, 2004 4:31 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] protein networks

I've been writing some modules to apply Nathan Goodman's
"SimpleGraph.pm" module to protein interaction networks. He has
written this as a replacement for the the broken CPAN graph modules. The
aim of these modules is

1. To convert protein interaction data between differentet formats
2. To be able to link protein interaction data to protein sequence data.
3. To be able to read in interaction data from separate sources, and
make a merged graph with duplicate interactions flagged or removed.

Could some core person give some idea for namespace to put these in CVS?

The modules are :
1. Nathan's modules
SimpleGraph.pm                   - a generic graph  module with methods
to build and represent a graph
SimpleGraph::Traversal.pm - generic methods to navigate a graph.

2. My modules

a. An I/O system analagous to SeqIO that lazyloads the correct modules
for a particular format
     ProteinGraphIO.pm      - with next_graph, write_graph methods
       ProteinGraphIO::dip.pm    - parser for DIP format interactions
         - to read in PSI_XML formatted records
(still being worked on).

b.   Modules to represent a protein network:
    PrimaryProteinGraph.pm - subclass of SimpleGraph.pm. This will be
made from a dip record, analagous to PrimarySeq
    FullProteinGraph .pm       - subclas of SimpleGraph.pm,  contains
PrimaryProteinGraph and metadata of graph, will be made from an XML
file, analagous to RichSeq.

c.  Classes to represent nodes/ edges.
   NodeI.pm    - interface describing methods that all nodes should have
        ProteinNode.pm - implements NodeI, currently has methods
primary_id(), seq(), secondary_id()
         InteractionI.pm    - interface describing methods all edges
should have
        ProteinInteraction.pm - implements InteractionI, currently has
methods weight(), interactors(), id().

Cheers Richard

Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK

Tel: 44 131 651 1084
richard.adams at ed.ac.uk

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