Harvest Framework

The Harvest framework integrates data from multiple clinical and research-focused sources to generate a cohesive view of a patient relative to a therapeutic area. Designed by and for biomedical researchers, Harvest is an open source toolkit for building web applications for integrating, discovering, and reporting data that addresses the unique needs of biomedical researchers.

Researchers require tools that scale with this increase without added complexity. To address this need we have developed Harvest, an open source framework for rapid development of purpose-built data discovery web applications.

Read the paper published online October 16, 2013 in the Journal of the American Medical Informatics Association.

Through our experience developing many data-intensive biomedical applications, our team at The Children’s Hospital of Philadelphia (CHOP) has been researching ways to lower the barriers for researchers and clinicians to explore their data. The result of our efforts is an open source framework called Harvest. Harvest is designed to alleviate complex (and often opaque) data models and enable interactive visual exploration of large data sets. It is composed of three primary components: Avocado, a dynamic query engine built on top of Django’s object relational mapper (ORM), Serrano, a REST API which exposes endpoints for clients, and Cilantro, a web application written in JavaScript using HTML5 and CSS3 technologies to enable interactive query and display of data.

Harvest was designed to alleviate the opaqueness of complex data models and large data sets and assists researchers with:

  • Integration of genomic, imaging, research, and clinical endpoints
  • Dynamic querying engine with visualizations
  • Hypothesis-driven exploration of data

Harvest implements an HTML5 web interface supported by a collection of discoverable REST APIs.

Nationally Funded Harvest Deployments

National Human Genome Research Institute – Longitudinal Pediatric Data Resource

National Institute on Deafness and Other Communication Disorders- AudGenDB

National Heart, Lung and Blood Institute. – Pediatric Cardiac Genomics Consortium Data Hub



0 items