Cytoscape CX2

CX2 (Cytoscape Exchange Format, Version 2) is a JSON-based, aspect-oriented format for representing networks together with their attributes and visual styling. It was developed jointly by the Cytoscape and NDEx (Network Data Exchange) teams as the successor to the original CX format (Cytoscape CX), designed to be more compact, more streaming-friendly, and simpler to parse. It is the native transport format used to move networks between Cytoscape Desktop, Cytoscape Web, and the NDEx repository.

A CX2 document is a single JSON array. Its first element is a required CX descriptor declaring the version; the final element is a required status object confirming successful generation. Between them sit optional pre/post metadata blocks and a sequence of "aspect" data blocks, each an independently schema'd fragment of the network. Core aspects include attributeDeclarations (which types every attribute and defines defaults and aliases, and must precede any aspect that references those attributes), nodes, edges, networkAttributes, and visualProperties, plus nodeBypasses/edgeBypasses for per-element style overrides and visualEditorProperties for viewport and table UI state. Nodes carry a unique id, optional x/y/z coordinates, and an attribute object "v"; edges carry a unique id, source ("s"), target ("t"), and their own "v" object. Supported attribute types include string, long, integer, double, boolean and their list variants.

The most visible change from CX1 is that node coordinates are embedded directly on node elements rather than held in a separate cartesianLayout aspect; the two mechanisms must not be mixed. CX2 also leans on Cytoscape Portable Graphic Styles so that discrete, continuous, and passthrough visual mappings travel with the network across tools.

CX2's strengths are lossless round-tripping of Cytoscape networks (topology, typed attributes, and full visual styling), an aspect model that lets consumers ingest or filter incrementally while streaming, and a compact web-oriented encoding. Its limitations are that it is tightly coupled to the Cytoscape/NDEx ecosystem rather than a neutral interchange format; non-portable styles must be relegated to opaque aspects; special float values such as NaN and Infinity collapse to null; and coordinates are all-or-nothing across nodes. For lighter Cytoscape.js consumption, the simpler Cytoscape JSON is often used instead, and HCX layers hierarchical semantics on top of CX2.