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Protein Bioinformatics

Volume 1558 of the series Methods in Molecular Biology pp 271-301

Date:

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

  • Rudolf T. PillichAffiliated withUC San Diego Center for Computational Biology and Bioinformatics (MC 0681), University of California San Diego Email author 
  • , Jing ChenAffiliated withUC San Diego Center for Computational Biology and Bioinformatics (MC 0681), University of California San Diego
  • , Vladimir RynkovAffiliated withUC San Diego Center for Computational Biology and Bioinformatics (MC 0681), University of California San Diego
  • , David WelkerAffiliated withUC San Diego Center for Computational Biology and Bioinformatics (MC 0681), University of California San Diego
  • , Dexter PrattAffiliated withUC San Diego Center for Computational Biology and Bioinformatics (MC 0681), University of California San Diego

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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