NDEx

NDEx, the Network Data Exchange, is a web-based repository and cloud platform for storing, sharing, searching, and publishing biological network models of essentially any type and size. It is developed and maintained by the Ideker Lab at UC San Diego together with the Cytoscape Consortium, with copyright held by the Regents of the University of California, and it has been supported by pharmaceutical partners including Pfizer, Janssen, and Roche. NDEx is recognized as a recommended repository by Nature Scientific Data and can mint DOIs so that networks become citable research artifacts. Registered users receive free cloud storage, and networks can be kept private, shared with collaborators, or made public.

NDEx is one of the two pillars of the Cytoscape ecosystem, complementing the desktop application Cytoscape and the browser-based Cytoscape.js used for rendering. Its native interchange format is Cytoscape Exchange (CX), an aspect-oriented JSON format in which different classes of information—nodes, edges, node and edge attributes, network attributes, and visual/layout properties (Cyto­scape visual styles)—are separated into independent modules called aspects. Because aspect elements can be fragmented and transmitted in any order, CX is designed to be streamed as a REST message payload rather than optimized for long-term storage or in-application computation. The original CX specification appeared in 2015 (Cytoscape CX); the current revision CX2 (Cytoscape CX2) simplifies the data model, reduces memory footprint, and improves streaming and transfer efficiency, and it is the recommended target for new applications while legacy CX remains supported. A hierarchical variant, HCX (HCX), encodes nested/hierarchical models on top of CX2.

Programmatic access is provided through a documented REST API and the ndex2 Python client (with its NiceCXNetwork abstraction), plus the RCX R package, enabling upload, download by network UUID, retrieval of single aspects, neighborhood queries, and management of network sets. Because CX is graph-agnostic—imposing minimal structural constraints and treating edges as directed unless annotated otherwise—NDEx serves as a hub where networks flow between Cytoscape, analysis pipelines, and downstream tools rather than as a converter to unrelated graph formats.

In practice NDEx is most valuable for network-biology workflows: curating pathway and interaction networks, disseminating supplementary networks for publications, and driving tools such as the iQuery gene-set analysis service. Its principal limitations are scope and lock-in: it is oriented toward the biological CX/CX2 model and the Cytoscape ecosystem, so it is not a general-purpose graph database or a broad format-conversion engine, and consuming its data outside that ecosystem generally requires translating CX into more common graph representations.