02. Creating RCX from scratch

Florian J. Auer1*

1Augsburg of University

*Florian.Auer@informatik.uni-augsburg.de

Contents

1 The Cytoscape Exchange (CX) Format

CX is an “aspect-oriented” data structure, which means that the network is divided into several independent modules (“aspects”). Each aspect has its own schema for its contained information, and links between aspects are realized by referencing the unique internal IDs of other aspects.

The CX format comes with some pre-defined aspects, which are divided in three groups:

• core aspects, with which the most properties of the network can be defined
  • nodes
  • edges
  • nodeAttributes
  • edgeAttributes
  • networkAttributes
  • cartesianLayout
• cytoscape aspects, which provide additional information to visualize the networks with Cytoscape
  • cyGroups
  • cyVisualProperties
  • cyHiddenAttributes
  • cyNetworkRelations
  • cySubnetworks
  • cyTableColumn
• meta aspects, which are necessary for data transmission
  • metaData
  • status

RCX data structure