R Engine Cell: integrating R into the i2b2 software infrastructure

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Informatics for Integrating Biology and the Bedside (i2b2) is an initiative funded by the NIH that aims at building an informatics infrastructure to support biomedical research. The University of Pavia has recently integrated i2b2 infrastructure with a registry of inherited arrhythmogenic diseases. Within this project, we created a novel i2b2 cell, named R Engine Cell, which allows the communication between i2b2  and the R statistical software. As survival analyses are routinely performed by cardiology researchers, we have first concentrated on making Kaplan Meier analyses available within i2b2 web interface. To this aim we developed a plug-in to select the patient set on which to perform the analysis and to display the results in a graphical, intuitive way. R Engine Cell has been designed to easily support the integration of other R-based statistical analyses into i2b2.

Authors

Daniele Segagni
Riccardo Bellazzi

Associated Institutions

IRCCS Fondazione S. Maugeri Pavia Italy
Dipartimento di Informatica e Sistemistica Università di Pavia Italy

Application Domains
  • Clinical records
Other Resource Type
Software Subtype
  • Algorithm implementation
  • Query tools/business intelligence
Programming Languages
  • Java
Operating Systems
Included Components
  • Plug-in to other software
Dataset Subtype
Data Model Subtype
Online Resource Subtype
Knowledge Base Subtype
Intended User Types
  • Clinical researcher
Citations
  • Murphy SN, Mendis M, Hackett K, et al. Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside. AMIA Annu Symp Proc. 2007:548-52
  • Mendis M, Wattanasin N, Kuttan R, et al. Integration of Hive and cell software in the i2b2 architecture. AMIA Annu Symp Proc. 2007:1048
  • R Development Core Team. The R Project for Statistical Computing (v. 2.8.1). http://www.r-project.org/
  • JRI - Java/R Interface. http://www.rforge.net/JRI/
Available Documentation
  • API
  • Web page/HTML documentation
Licensing Type
LGPL
Date of Latest Version