NAME

Bio::Das::ProServer::SourceAdaptor::Transport::sif

VERSION

$LastChangedRevision: 453 $

SYNOPSIS

my $hInteractions = $oTransport->query('interactorA'); my $hInteractions = $oTransport->query('interactorA', 'interactorB');

DESCRIPTION

A data transport exposing interactions stored in a SIF file, along with attributes stored in Cytoscape attribute files. Access is via the 'query' method.

FILE FORMAT

Each line of a Simple Interaction Format (SIF) file describes one or more binary interactions, and takes the form: nodeA lineType nodeB [nodeC ...]

This example describes a protein-protein interaction between interactorA and interactorB: interactorA pp interactorB

This example describes three separate interactions, each involving interactorA: interactorA pp interactorB interactorC interactor D

Node attribute files may be used to add DAS 'detail' elements to interactors: description interactorA = An example interactor interactorB = Another example of an interactor ...

Edge attribute files may be used to add DAS 'detail' elements to interactions: score interactorA pp interactorB = 2.43 interactorX pp interactorY = 5.1 ...

CONFIGURATION AND ENVIRONMENT

Configured as part of each source's ProServer 2 INI file:

[mysif]
... source configuration ...
transport  = sif
filename   = /data/interactions.sif
attributes = /data/node-attribute.noa ; /data/edge-attributes.eda

SUBROUTINES/METHODS

query : Retrieves interactions for one or two interactors

Retrieves interactions involving interactorA:
$hInteractions = $oTransport->query('interactorA');

Retrieves an interaction involving both interactorA and interactorB:
$hInteractions = $oTransport->query('interactorA', 'interactorB');

The returned hash is of the structure expected by ProServer.

DESTROY : object destructor - disconnect filehandles

Generally not directly invoked, but if you really want to:

$transport->DESTROY();

DIAGNOSTICS

Run ProServer with the -debug flag.

SEE ALSO

http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_Formats Cytoscape - SIF

http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Attributes Cytoscape - Attributes

DEPENDENCIES

Carp

Bio::Das::ProServer::SourceAdaptor::Transport::file

BUGS AND LIMITATIONS

The Simple Interaction Format is very simple, and therefore only supports a limited range of DAS annotation details. It also only handles binary interactions (i.e. those with exactly two interactors).

INCOMPATIBILITIES

None reported.

AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

LICENSE AND COPYRIGHT

Copyright (c) 2008 EMBL-EBI

cpanm Bio::Das::ProServer

perl -MCPAN -e shell
install Bio::Das::ProServer