i2b2 - tranSMART

Overview

The i2b2 – tranSMART platform is an open-source, community-driven knowledge management platform for translational research and personalized medicine. It is a project that is being collaboratively developed by more than 100 computer scientists and medical scientists from more than 20 organizations from around the world. Managed by the i2b2 – tranSMART Foundation, a non-profit organization enabling technological and scientific collaboration to drive translational biomedical research, the i2b2 – tranSMART platform is a single, integrated analytics and data-sharing platform for clinical and translational research. Open to every scientist globally, it can enable pre-competitive and private data sharing and foster collaboration within an organization or with partners and contractors around the world.

Capabilities

The i2b2 – tranSMART platform provides tools for loading a variety of high-content data types, chemical, biological and ‘omic’ research and clinical data, from a range of sources. The platform enables scientists to discover and refine hypotheses by investigating the relationships between genetic and phenotypic data for cohorts of patients, and to assess their analytic results in the context of published literature and their internal work. It is designed to meet the needs of basic scientists, clinician-scientists, pharmacologists, toxicologists, and others involved in therapeutics and diagnostics discovery and development of new therapies for patients.

The i2b2 -⇒ tranSMART platform implements a set of data models, shared datasets, data transformation utilities, and analytical web applications all centered on the patient, to accelerate discoveries by creating a standardized and semantically integrated data warehouse of research results linked to reusable and scalable self-service analytics.

An API has been added to the tranSMART platform that allows connection to external packages for extended data viewing (Genome Browser, etc.), statistical analysis (R) and visualization and analytics (Spotfire). These may be part of the distributed open source platform or distributed privately by vendors who are using the open API.

Applications

The i2b2 – tranSMART platform organizes clinical and research data on a per patient basis. This enables scientists to perform the following types of research activities, with the goal of improving their understanding of healthy and disease processes in the discovery of new treatment and diagnostic tools and products for patients.

  • Compare data from proteomics, metabolomics and other “omics” studies
  • Contrast patterns of gene expression in healthy and diseased individuals and in human tissue samples
  • Investigate correlations between genotype and phenotype in clinical trial data
  • Mine pre-clinical data for insights into the biology of human disease
  • Study genetic and environmental factors involved in human disease
  • Display data visually using a graphical interface
  • Stratify clinical data into molecular subtypes of a specific disease
  • Collaborate across academic, government and corporate research sectors

For more information about tranSMART please visit: http://transmartfoundation.org