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Ruben Verborgh

Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop

Kathleen Jagodnik, Simon Koplev, Lucila Ohno-Machado, Benedict Paten, Stephan Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil McKenna, Ravi Madduri, Ajay Pillai, and Avi Ma’ayan

The volume and diversity of data in biomedical research has been rapidly increasing in recent years. While such data hold significant promise for accelerating discovery, their use entails many challenges including: the need for adequate computational infrastructure, secure processes for data sharing and access, tools that allow researchers to find and integrate diverse datasets, and standardized methods of analysis. These are just some elements of a complex ecosystem that needs to be built to support the rapid accumulation of these data. The NIH Big Data to Knowledge (BD2K) initiative aims to facilitate digitally enabled biomedical research. Within the BD2K framework, the Commons initiative is intended to establish a virtual environment that will facilitate the use, interoperability, and discoverability of shared digital objects used for research. The BD2K Commons Framework Pilots Working Group (CFPWG) was established to clarify goals and work on pilot projects that would address existing gaps toward realizing the vision of the BD2K Commons. This report reviews highlights from a two-day meeting involving the BD2K CFPWG to provide insights on trends and considerations in advancing Big Data science for biomedical research in the United States.

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Published in 2017 in Journal of Biomedical Semantics.

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@article{maayan_jbi_2017,
  title = {Developing a Framework for Digital Objects in the {Big Data to Knowledge (BD2K) Commons:} Report from the {Commons} Framework Pilots Workshop},
  author = {Jagodnik, Kathleen and Koplev, Simon and Ohno-Machado, Lucila and Paten, Benedict and Sch\"urer, Stephan and Dumontier, Michel and Verborgh, Ruben and Bui, Alex and Ping, Peipei and McKenna, Neil and Madduri, Ravi and Pillai, Ajay and Ma'ayan, Avi},
  journal = {Journal of Biomedical Semantics},
  year = 2017,
  volume = 71,
  month = jul,
  pages = {49--57},
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2017.05.006},
  url = {http://www.sciencedirect.com/science/article/pii/S1532046417301016},
}

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ACM
Kathleen Jagodnik, Simon Koplev, Lucila Ohno-Machado, Benedict Paten, Stephan Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil McKenna, Ravi Madduri, Ajay Pillai, and Avi Ma’ayan. 2017. Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Semantics 71, (July 2017), 49–57.
APA
Jagodnik, K., Koplev, S., Ohno-Machado, L., Paten, B., Schürer, S., Dumontier, M., Verborgh, R., Bui, A., Ping, P., McKenna, N., Madduri, R., Pillai, A., & Ma’ayan, A. (2017). Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Semantics, 71, 49–57.
IEEE
K. Jagodnik et al., “Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop,” Journal of Biomedical Semantics, vol. 71, pp. 49–57, Jul. 2017.
LNCS
Jagodnik, K., Koplev, S., Ohno-Machado, L., Paten, B., Schürer, S., Dumontier, M., Verborgh, R., Bui, A., Ping, P., McKenna, N., Madduri, R., Pillai, A., Ma’ayan, A.: Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Semantics. 71, 49–57 (2017).
MLA
Jagodnik, Kathleen, et al. “Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop.” Journal of Biomedical Semantics, vol. 71, Elsevier, July 2017, pp. 49–57.

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