Biomedical researchers often confront large quantities of information that may be amassed in many forms: vital signs, blood cell counts, lengthy DNA sequences, bar graphs, MRIs, patient demographics, and so much more. How do researchers assemble, access and analyze all that data without having to become specialized database technicians themselves?

A team of informatics experts and biomedical researchers at The Children’s Hospital of Philadelphia (CHOP) offers a new software toolkit to help researchers wrangle data. Their open-source, highly interactive framework called Harvest (http://harvest.research.chop.edu) is designed to let users to navigate quickly among different types and levels of data.

“We want to help researchers explore their data, not their database,” said Byron Ruth, lead developer of Harvest at CHOP’s Center for Biomedical Informatics (CBMi). Ruth is one of the co-authors of a paper introducing CBMi’s Harvest framework, appearing online Oct. 16 in the Journal of the American Medical Informatics Association.

Co-author Michael J. Italia added, “Research institutions typically work through their information technology staff to provide a single data warehouse that may be too general-purpose for all its projects, or develop one-off solutions on a case-by-case basis for each project.”

“Our approach in Harvest is different,” said Italia, the CBMi’s manager of Applications Research. “We decided to focus on end-users, generalizing the toolkit for application to any biomedical study with multiple collaborators, but also allowing individual software developers and data managers to customize the software for specific projects.”

Harvest, said Italia, “isn’t just shrink-wrapped, ready-to-go software.” He estimates that Harvest typically provides 80 percent of the work, leaving it to any institution’s software developer to adapt the framework to a project’s needs, in collaboration with each project’s principal investigator. Harvest is open-source, so users are free to see bug reports, check software patches, and share fixes and customizations with a wider community of users.

A key feature of Harvest is the ability to maneuver smoothly among various levels of data, from individual patient records to aggregated reports of all patients in a database, and to subpopulations in between. Users can construct queries to slice and dice data—grouping subjects, for instance, by age or ethnicity, calling up individual blood test results or MRIs, or including or excluding specific diagnoses.

One advantage of Harvest is that it provides transparency and visibility to data in a manner that is familiar to a researcher who is invested in a particular disease or project. “Harvest adopts convenient and clear interfaces to view and explore data that are increasingly used in other industries, such as social media,” said senior author and CBMi director Peter S. White, Ph.D. “We have found that this often helps users to quickly familiarize themselves with data they are seeing, which increases the likelihood that they will trust the resource, and even be incentivized to contribute to the project as it develops.”

CHOP offers new software toolkit to help researchers wrangle data http://www.officestorejp.com/

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