Protein Bioinformatics pp 271-301

Part of the Methods in Molecular Biology book series (MIMB, volume 1558)

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

  • Rudolf T. Pillich
  • Jing Chen
  • Vladimir Rynkov
  • David Welker
  • Dexter Pratt
Protocol

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 

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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