Publications by authors named "Atul Kaushal"

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caTissue Suite to OpenSpecimen: Developing an extensible, open source, web-based biobanking management system.

J Biomed Inform 2015 Oct 29;57:456-64. Epub 2015 Aug 29.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.

The National Cancer Institute (NCI) Cancer Biomedical Informatics GridĀ® (caBIGĀ®) program established standards and best practices for biorepository data management by creating an infrastructure to propagate biospecimen resource sharing while maintaining data integrity and security. caTissue Suite, a biospecimen data management software tool, has evolved from this effort. More recently, the caTissue Suite continues to evolve as an open source initiative known as OpenSpecimen. The essential functionality of OpenSpecimen includes the capture and representation of highly granular, hierarchically-structured data for biospecimen processing, quality assurance, tracking, and annotation. Ideal for multi-user and multi-site biorepository environments, OpenSpecimen permits role-based access to specific sets of data operations through a user-interface designed to accommodate varying workflows and unique user needs. The software is interoperable, both syntactically and semantically, with an array of other bioinformatics tools given its integration of standard vocabularies thus enabling research involving biospecimens. End-users are encouraged to share their day-to-day experiences in working with the application, thus providing to the community board insight into the needs and limitations which need be addressed. Users are also requested to review and validate new features through group testing environments and mock screens. Through this user interaction, application flexibility and interoperability have been recognized as necessary developmental focuses essential for accommodating diverse adoption scenarios and biobanking workflows to catalyze advances in biomedical research and operations. Given the diversity of biobanking practices and workforce roles, efforts have been made consistently to maintain robust data granularity while aiding user accessibility, data discoverability, and security within and across applications by providing a lower learning curve in using OpenSpecimen. Iterative development and testing cycles provide continuous maintenance and up-to-date capabilities for this freely available, open-access, web-based software application that is globally-adopted at over 25 institutions.
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http://dx.doi.org/10.1016/j.jbi.2015.08.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772150PMC
October 2015