The Network Data Exchange - a Network Commons for Biologists

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THE NETWORK DATA EXCHANGE – A NETWORK COMMONS FOR BIOLOGISTS PROJECT SUMMARY Knowledge of biological networks has been critical to the analysis of big biomedical datasets, including interpretation of the molecular heterogeneity seen within and across tumors. NDEx, the Network Data Exchange (ndexbio.org), is an online commons where scientists find, share, and publicly distribute biological networks. With a previous grant from the Informatics Technology for Cancer Research program (ITCR U24 CA184427), we created the NDEx open-source database platform along with its public website and query system. Further, we enabled interoperability with the Python and R data science platforms and built NDEx seamlessly into the Cytoscape network analysis and visualization ecosystem. NDEx presently serves a large base of users and network content, with approximately 3285 accounts linked to >180,000 networks, of which approximately 6500 are publicly accessible. NDEx is the approved network repository for articles published in the Springer Nature and Public Library of Science (PLoS) families of journals. We are requesting sustained ITCR funding for the NDEx project to maintain, scale, and enhance the NDEx system, meeting the evolving needs of the biomedical research community via the following five Specific Aims: 1. Maintain and scale NDEx and its services to support a large and growing community of users. Regular software releases of NDEx will continue to extend its capabilities. Targeted server hardware upgrades will increase capacity and performance to match the growing use of NDEx. 2. Extend the NDEx corpus of cancer pathway networks. We will continue to maintain and extend the NDEx Cancer Collection (NCC) corpus of networks via outreach, collaborations, and automated text and image analysis methods to capture cancer networks from literature. 3. Enable the use of networks in next-generation cancer genome analysis. We will enhance the use of networks in existing 'omics analysis tools used by the cancer research community and develop and maintain analysis tools that leverage NDEx functionality and data. 4. Enable publishing of interactive networks. Building on our success in enabling publications to link to NDEx networks, we will add new capabilities for authors and readers to enhance the dissemination of interactive networks and their use in publications. 5. Provide support and training, track usage, and gather feedback. The NDEx Project is committed to user engagement and development driven by the needs of cancer researchers and their user feedback. Through these aims, the NDEx project will transition from system-building to sustaining and enabling network biology for the NCI-supported cancer community.