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

Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, Dexter Pratt
2017 Msphere  
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
more » ... 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. researchers can be stored, shared, discussed, reviewed, and used. This chapter describes NDEx, the Network Data Exchange, an online commons where scientists can store, share and publicly distribute biological networks as dynamic actionable data, and develop applications using them [8] . One of the goals of the NDEx Project is to create a home for network models that are currently available only as figures, tables, or supplementary information, such as networks produced via systematic mining and integration of largescale molecular data. In doing this, the NDEx project does not compete with existing pathway and interaction databases, such as KEGG or Reactome; instead, NDEx provides a novel, common distribution channel for these efforts, preserving their identity and attribution rather than subsuming them. By providing a flexible computable medium for biological knowledge, networks are also becoming a critical element for new models of scientific publication, in which data and its derivatives are as important as text [9] . The NDEx platform is intended to enable experimentation with novel forms of scientific review and discourse. NDEx networks are assigned stable, globally unique URIs and can be referenced by publications, by other networks, and by analytic applications. NDEx aims to become the main hub for the development of new, lightweight applications and scripts capable of accessing and manipulating networks via the NDEx API, making it easy for scientists to develop novel network-based analyses. An example is CyNDEx, the NDEx Cytoscape App: CyNDEx enables users to access an NDEx server directly from Cytoscape and engage its full range of tools to analyze and transform any networks stored on NDEx. The NDEx project fosters the creation of new utilities and analytic tools that use NDEx via code examples, client libraries in multiple languages, developer documentation, and a strong social media outreach campaign to drive community awareness and engagement.
doi:10.1007/978-1-4939-6783-4_13 pmid:28150243 fatcat:g7o7npnizjgingotcpqmsgkpc4