Knowledge of the hallmark networks of cancer has been key to interpreting the molecular heterogeneity seen within and across tumors. NDEx, the Network Data Exchange (, is an online commons where scientists can upload, share, and publicly distribute molecular networks and pathway models. We are currently two years into a three-year grant from the National Cancer Institute (U24 CA184427A), during which time we have created the NDEx open-source platform; released NDEx as a public website; and begun to link NDEx to applications such as Cytoscape. Having built this initial system, our goals for the next funding period are to rapidly develop NDEx network content and communities and the means by which these resources impact cancer research and treatment. In particular, we will (1) Connect NDEx networks to next-generation cancer genome analysis; (2) Enable the direct publishing of interactive networks on journal websites; (3) Develop hallmark cancer pathway content via social organization and automation; and (4) Scale the NDEx framework to support a growing community of users and analysis tools. Through these aims, the emphasis of the NDEx Project transitions from core infrastructure to genome analysis workflows, cancer-relevant network content, publishing, and community building. These developments address a strong and immediate need in cancer research for a cyberinfrastructure that can analyze genome-scale information in the context of molecular networks.

Public Health Relevance

NDEx ( is an online commons in which biological networks can be shared, published and used by cancer researchers. Informatics applications for analysis and visualization can use NDEx as a hub to exchange networks, facilitating modular workflows. NDEx is a step towards new forms of scientific publication and collaboration in which networks bearing data, hypotheses, and findings flow easily between scientists.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Resource-Related Research Projects--Cooperative Agreements (U24)
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Special Emphasis Panel (ZCA1)
Program Officer
Li, Jerry
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University of California, San Diego
Internal Medicine/Medicine
Schools of Medicine
La Jolla
United States
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Zhang, Wei; Ma, Jianzhu; Ideker, Trey (2018) Classifying tumors by supervised network propagation. Bioinformatics 34:i484-i493
Auer, Florian; Hammoud, Zaynab; Ishkin, Alexandr et al. (2018) ndexr-an R package to interface with the network data exchange. Bioinformatics 34:716-717
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