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J Am Med Inform Assoc. 2014 Mar-Apr;21(2):379-83. doi: 10.1136/amiajnl-2013-001825. Epub 2013 Oct 16.

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

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Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.


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


application development; data discovery; data visualization; database; open-source

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