The NIH BD2K center for big data in translational genomics

Benedict Paten, Mark Diekhans, Brian Druker, Stephen Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W. James Kent, Patrick Mantey, Adam Margolin, Matt Massie, Adam M. Novak, Frank Nothaft, Lior Pachter, David Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura Van't Veer, Barbara Wold, David Haussler

Research output: Contribution to journalArticle

28 Scopus citations

Abstract

The world's genomics data will never be stored in a single repository - rather, it will be distributed among many sites in many countries. No one site will have enough data to explain genotype to phenotype relationships in rare diseases; therefore, sites must share data. To accomplish this, the genetics community must forge common standards and protocols to make sharing and computing data among many sites a seamless activity. Through the Global Alliance for Genomics and Health, we are pioneering the development of shared application programming interfaces (APIs) to connect the world's genome repositories. In parallel, we are developing an open source software stack (ADAM) that uses these APIs. This combination will create a cohesive genome informatics ecosystem. Using containers, we are facilitating the deployment of this software in a diverse array of environments. Through benchmarking efforts and big data driver projects, we are ensuring ADAM's performance and utility.

Original languageEnglish (US)
Pages (from-to)1143-1147
Number of pages5
JournalJournal of the American Medical Informatics Association
Volume22
Issue number6
DOIs
StatePublished - 2015

Keywords

  • APIs
  • Big data
  • Computational genomics
  • Genome informatics
  • Genomics

ASJC Scopus subject areas

  • Health Informatics

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  • Cite this

    Paten, B., Diekhans, M., Druker, B., Friend, S., Guinney, J., Gassner, N., Guttman, M., James Kent, W., Mantey, P., Margolin, A., Massie, M., Novak, A. M., Nothaft, F., Pachter, L., Patterson, D., Smuga-Otto, M., Stuart, J. M., Van't Veer, L., Wold, B., & Haussler, D. (2015). The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association, 22(6), 1143-1147. https://doi.org/10.1093/jamia/ocv047