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. 2015 Nov;22(6):1143-7.
doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13.

The NIH BD2K Center for Big Data in Translational Genomics

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Free PMC article

The NIH BD2K Center for Big Data in Translational Genomics

Benedict Paten et al. J Am Med Inform Assoc. .
Free PMC article

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.

Keywords: APIs; big data; computational genomics; genome informatics; genomics.

Figures

Figure 1:
Figure 1:
Through the development of standard APIs and the deployment of container technologies, the CBDTG aims to facilitate the move from the status quo (A) to a state in which interoperability and data sharing is the norm (B).
Figure 2:
Figure 2:
ADAM’s stack decouples “under-the-hood” implementation details from the abstractions used to implement genomic analyses. Thus, ADAM provides bioinformaticians with a wide variety of fast programming abstractions and can be deployed flexibly across a variety of systems, including a single machine, a Hadoop cluster, an HPC grid, or a cloud. The explicit use of a simple, small, yet efficient, data schema is the “narrow waist” of the stack.

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