R Engine Cell: integrating R into the i2b2 software infrastructure
- Daniele Segagni1,
- Fulvia Ferrazzi1,2,
- Cristiana Larizza2,
- Valentina Tibollo1,
- Carlo Napolitano1,3,
- Silvia G Priori1,3,4,
- Riccardo Bellazzi1,2
- 1IRCCS Fondazione S. Maugeri, Pavia, Italy
- 2Dipartimento di Informatica e Sistemistica, Università di Pavia, Pavia, Italy
- 3New York University School of Medicine, New York, USA
- 4Department of Cardiology, Università di Pavia, Pavia, Italy
- Correspondence to Dr Riccardo Bellazzi, Dipartimento di Informatica e Sistemistica, University of Pavia, Via Ferrata, 1, 27100 Pavia, Italy;
- Received 14 August 2010
- Accepted 10 December 2010
- Published Online First 24 January 2011
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, the authors 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, the authors have first concentrated on making Kaplan–Meier analyses available within the i2b2 web interface. To this aim, the authors developed a web-client 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.
Funding This work has been supported by IRCCS Fondazione S Maugeri and by FIRB project ITALBIONET ‘Rete Nazionale di Bioinformatica’ funded by the Italian Ministry of Education and Research.
Competing interests None.
Provenance and peer review Not commissioned; externally peer reviewed.