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The NIH BD2K center for big data in translational genomics

Paten, Benedict and Diekhans, Mark and Druker, Brian J. and Friend, Stephen and Guinney, Justin and Gassner, Nadine and Guttman, Mitchell and Kent, W. James and Mantey, Patrick and Margolin, Adam A. and Massie, Matt and Novak, Adam M. and Nothaft, Frank and Pachter, Lior and Patterson, David and Smuga-Otto, Maciej and Stuart, Joshua M. and Van’t Veer, Laura and Wold, Barbara and Haussler, David (2015) The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association, 22 (6). pp. 1143-1147. ISSN 1067-5027. PMCID PMC5009913. https://resolver.caltech.edu/CaltechAUTHORS:20150721-085701041

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1093/jamia/ocv047DOIArticle
http://jamia.oxfordjournals.org/content/22/6/1143PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009913/PubMed CentralArticle
ORCID:
AuthorORCID
Guttman, Mitchell0000-0003-4748-9352
Pachter, Lior0000-0002-9164-6231
Wold, Barbara0000-0003-3235-8130
Additional Information:© 2015 The Author. Published by Oxford University Press on behalf of the American Medical Informatics Association. First published online: 14 July 2015. We would like to thank the reviewers for their helpful comments and suggestions. Funding: This work was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U54HG007990. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Contributors: BP and DH wrote the manuscript with assistance from other authors. FN and MS created the figures. All the authors edited the manuscript.
Funders:
Funding AgencyGrant Number
National Human Genome Research InstituteU54HG007990
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Issue or Number:6
PubMed Central ID:PMC5009913
Record Number:CaltechAUTHORS:20150721-085701041
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20150721-085701041
Official Citation:The NIH BD2K center for big data in translational genomics Benedict Paten, Mark Diekhans, Brian J. Druker, Stephen Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W James Kent, Patrick Mantey, Adam A 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 Journal of the American Medical Informatics Association 1143-1147 First published online: 13 July 2015 DOI: 10.1093/jamia/ocv047
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:58956
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Jul 2015 20:49
Last Modified:24 Feb 2020 10:30

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