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J Am Med Inform Assoc doi:10.1136/amiajnl-2013-001825
  • Case report

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications

Open Access
  1. Peter S White1,4,5
  1. 1Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  2. 2Center for Childhood Communication, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  3. 3Department of Otorhinolaryngology: Head and Neck Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
  4. 4Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  5. 5Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
  1. Correspondence to Peter S White, Children's Hospital of Philadelphia, 34th St and Civic Center Blvd, Rm 1024 CHOP North, Philadelphia, PA 19104-4318, USA; whitep{at}email.chop.edu
  • Received 20 March 2013
  • Revised 4 September 2013
  • Accepted 28 September 2013
  • Published Online First 16 October 2013

Abstract

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu

This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/3.0/

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