OCCAMS: An Open Source Clinical Content Analysis and Management System and Its Application to HIV Primary Infection Research
Jason Young*1, D Mote1, M Martinez1, J Mueller1, S Weaver1, D Smith1,2, D Richman1,2, S Little1, and S Kosakovsky Pond1
1Univ of California, San Diego, La Jolla, US and 2VA San Diego Hlthcare System, CA, US
Background: Modern clinical research requires flexible software tools for the management of complex data types, rapid testing of hypotheses, and easy access and sharing of information between institutions via the web. In recent years, open source software solutions have matured to the point where they now match the power, performance, and security of closed and costly propriety systems.
Methods: We have developed a robust, extensible, secure, and free Open source Clinical Content Analysis and Management System (OCCAMS). Developed within the open source web-based content management system Plone, OCCAMS provides at its core all functionality needed for HIV study data management. This includes methods for visit schedule and form creation; specimen storage and tracking; form and data versioning; integrated quality control logic and workflows; real-time web reporting of data accrual; data export; and granular permission controls. Most importantly, the modularized design and open source nature of OCCAMS encourages community development of plug-ins that provide new functionality to address the specific needs of any particular area of research.
Results: For over a year, OCCAMS has been used to manage data of ~6500 individuals enrolled on 10 longitudinal HIV primary infection research studies at the UCSD Anti-Viral Research Center and collaborating sites. Data types range from demographic, behavioral, sexual partner information, and drug history, to laboratory results, specimen records, and both Sanger and ultra-deep sequences. To address specific needs of our HIV primary infection cohort, we developed several HIV-specific plug-ins to calculate the estimated date of infection, infer the structure of molecular transmission networks, and visualize their dynamics, and a sequence analysis suite for drug resistance and subtype determination. Whereas previously complex analyses such as these required custom offline scripting, within OCCAMS, access to these data and analysis tools is standardized and made available directly to researchers through an intuitive and permission controlled web portal.
Conclusions: OCCAMS is a flexible, powerful, and cost-effective software framework for managing clinical research that can be easily extended to meet a variety of research data needs. When applied to HIV primary infection research, it has greatly facilitated the ease of data collection, quality control, scientific analysis, and information sharing, all at a low overall cost.