| Literature DB >> 26174866 |
Benedict Paten1, Mark Diekhans2, Brian J Druker3, Stephen Friend4, Justin Guinney4, Nadine Gassner2, Mitchell Guttman5, W James Kent2, Patrick Mantey6, Adam A Margolin7, Matt Massie8, Adam M Novak2, Frank Nothaft8, Lior Pachter9, David Patterson8, Maciej Smuga-Otto2, Joshua M Stuart2, Laura Van't Veer10, Barbara Wold11, David Haussler12.
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
Mesh:
Year: 2015 PMID: 26174866 PMCID: PMC5009913 DOI: 10.1093/jamia/ocv047
Source DB: PubMed Journal: J Am Med Inform Assoc ISSN: 1067-5027 Impact factor: 4.497