tranSMART

tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work.

The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART's specific applications include:

• Revalidating previous hypotheses
• Testing and refining novel hypotheses
• Conducting cross-study meta-analysis
• Searching across multiple data sources to find associations of concepts, such as a gene's involvement in biological processes or experimental results
• Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas

Data Repository

The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates:

• Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events
• High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data
• Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers
• Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc.
• Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART

Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research.

External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups.

Dataset Explorer

tranSMART's Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools.

Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART's capabilities.

tranSMART's design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal.

Data Security

The tranSMART system also incorporates role-based security protections to enable use of the platform across large organizations. User authentication for tranSMART can be integrated into an organization's existing infrastructure to simplify user management.

The tranSMART security model allows an organization to control data access and use in accordance with internal policies governing the use of research data, as well as HIPAA, IRB, FDA, EMEA, and other regulatory requirements.

Licensing & Availability

A growing number of biopharmaceutical companies, academic medical centers, and other research-oriented organizations are joining the tranSMART community, affirming the 2010 Bio-IT World Best Practices and CIO 100 awards granted for the platform's innovation and potential to advance translational research. For more information, visit the Licensing section of the project wiki.