NAME

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

VERSION

$LastChangedRevision: 688 $

SYNOPSIS

  Interactions involving 001:
  <host>/das/<source>/interaction?interactor=001
  
  Interactions between 001 and 002
  <host>/das/<source>/interaction?interactor=001;interactor=002

DESCRIPTION

Serves up interaction DAS responses from 'Simple Interaction Format' (SIF) files. See http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_Formats http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_Formats for details of the file format.

CONFIGURATION AND ENVIRONMENT

  [mysif]
  adaptor                  = sif
  state                    = on
  transport                = sif
  ; the main SIF file:
  filename                 = /data/interactions.sif
  ; zero or more attribute files:
  attributes               = /data/node-attribute.noa ; /data/edge-attributes.eda
  ; coordinates will be used as 'dbCoordSys':
  coordinates              = MyCoordSys -> 001
  ; static parameters:
  interaction.dbSource     = MyInteractionDB
  interaction.dbSourceCvId = MIDB
  interaction.dbVersion    = 12
  interactor.dbSource      = MyProteinDB
  interactor.dbSourceCvId  = MPDB
  interactor.dbVersion     = 23

DIAGNOSTICS

Run ProServer with the -debug flag.

SUBROUTINES/METHODS

build_interaction - Builds the DAS response

See documentation in superclass.

capabilities - Provides details of the adaptor's capabilities

This adaptor supports the 'interaction' command only.

SEE ALSO

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

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