[Bioperl-l] protein networks
boris.steipe at utoronto.ca
Thu Mar 11 10:42:36 EST 2004
Thanks for this initiative !
I might suggest including "interaction" in the package name rather than
"protein" since this is what you are graphing. Also there are
Protein-DNA and DNA-DNA interactions (and there will be many more)
which are being stored by some.
In terms of IO, I would like to suggest supporting the HUPO-PSI
standard (which DIP supports) for consideration, and naming the module
after the format, not the database.
In terms of methods: again, I am not sure you *want* to restrict
yourself to protein only. MolecularInteraction.pm would suggest itself.
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics
> You may want to reconsider the name "ProteinGraphIO::xml.pm" since
> 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
> 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.
> 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
> 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
> 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
> 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
> EH4 2XU
> Tel: 44 131 651 1084
> richard.adams at ed.ac.uk
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