NDEx: A Community Resource for Sharing and Publishing of Biological Networks

Methods Mol Biol. 2017;1558:271-301. doi: 10.1007/978-1-4939-6783-4_13.


Networks are a powerful and flexible paradigm that facilitate communication and computation about interactions of any type, whether social, economic, or biological. NDEx, the Network Data Exchange, is an online commons to enable new modes of collaboration and publication using biological networks. NDEx creates an access point and interface to a broad range of networks, whether they express molecular interactions, curated relationships from literature, or the outputs of systematic analysis of big data. Research organizations can use NDEx as a distribution channel for networks they generate or curate. Developers of bioinformatic applications can store and query NDEx networks via a common programmatic interface. NDEx can also facilitate the integration of networks as data in electronic publications, thus making a step toward an ecosystem in which networks bearing data, hypotheses, and findings flow seamlessly between scientists.

Keywords: Big data; BioPAX3; Biological networks; Cyberinfrastructure; Cytoscape; Java; Open source; OpenBEL; Pathway analysis; Provenance; Python; REST API.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods*
  • Databases, Genetic*
  • Gene Regulatory Networks
  • Information Dissemination / methods*
  • Metabolic Networks and Pathways
  • Protein Interaction Maps
  • Publications
  • Publishing*
  • Search Engine
  • Signal Transduction
  • Software*
  • User-Computer Interface*
  • Web Browser*