title: Combining clinical and genomics queries using i2b2 - Three methods.
abstract: We are fortunate to be living in an era of twin biomedical data surges: a burgeoning representation of human phenotypes in the medical records of our healthcare systems, and high-throughput sequencing making rapid technological advances. The difficulty representing genomic data and its annotations has almost by itself led to the recognition of a biomedical "Big Data" challenge, and the complexity of healthcare data only compounds the problem to the point that coherent representation of both systems on the same platform seems insuperably difficult. We investigated the capability for complex, integrative genomic and clinical queries to be supported in the Informatics for Integrating Biology and the Bedside (i2b2) translational software package. Three different data integration approaches were developed: The first is based on Sequence Ontology, the second is based on the tranSMART engine, and the third on CouchDB. These novel methods for representing and querying complex genomic and clinical data on the i2b2 platform are available today for advancing precision medicine.
authors.affiliation: Research IS and Computing, Partners HealthCare, Charlestown, Massachusetts, United States of America.|Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America.|Laboratory of Computer Science, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
authors.forename: Shawn N
authors.initials: SN
authors.lastname: Murphy
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America.|Children's Hospital Informatics Program, Boston Children's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Paul
authors.initials: P
authors.lastname: Avillach
authors.affiliation: Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.|IRCCS Fondazione S. Maugeri, Pavia, Italy.|Centre for Health Technologies, University of Pavia, Pavia, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Bellazzi
authors.affiliation: Research IS and Computing, Partners HealthCare, Charlestown, Massachusetts, United States of America.
authors.forename: Lori
authors.initials: L
authors.lastname: Phillips
authors.affiliation: Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.|Biomeris s.r.l, Via Ferrata, Pavia, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Gabetta
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America.|Children's Hospital Informatics Program, Boston Children's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Alal
authors.initials: A
authors.lastname: Eran
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America.|Children's Hospital Informatics Program, Boston Children's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Michael T
authors.initials: MT
authors.lastname: McDuffie
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America.|Children's Hospital Informatics Program, Boston Children's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
mesh_terms: D023281:Genomics; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011381:Programming Languages; D012984:Software; D018511:Systems Integration