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

  • Rudolf T. Pillich
  • Jing Chen
  • Vladimir Rynkov
  • David Welker
  • Dexter Pratt
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1558)

Abstract

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.

Key words

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

Notes

Acknowledgments

The NDEx Project is a joint effort of the Cytoscape Consortium and the Ideker Lab at the UC San Diego School of Medicine.

Primary financial support for The NDEx Project is from the National Cancer Institute (U24 CA-184427), F. Hoffmann-La Roche Ltd., Janssen Research and Development, LLC, and Pfizer, Inc.

NDEx is also supported by the National Resource for Network Biology (P41 GM103504).

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Rudolf T. Pillich
    • 1
  • Jing Chen
    • 1
  • Vladimir Rynkov
    • 1
  • David Welker
    • 1
  • Dexter Pratt
    • 1
  1. 1.UC San Diego Center for Computational Biology and Bioinformatics (MC 0681)University of California San DiegoLa JollaUSA

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