Is there a niche for open source tools in Clinical Data Management. Till date, this field has been monopolised by the likes of Oracle and Phase Forward or custom software. With stringent regulatory framework, and a highly closed industry, there are very few open source packages which have made any kind of inroads into this domain. We have implemented a few solutions and have found that most products give us comparable or sometimes better user acceptance, always cost-effective and almost always better speed of deployment.
In this post, i will review OpenClinica which i think has the potential to lead the way for OSS clinical data management.
From their site

OpenClinica is a web-based software platform developed by Akaza Research for managing multi-site clinical research studies. It facilitates protocol configuration, design of case report forms, electronic data capture, retrieval, and management. OpenClinica supports HIPAA guidelines, and is designed as a standards-based extensible, modular, and open source platform.

I found the following from the UConn website

Akaza Research, the team behind OpenClinica initially developed Pheno, as it was initially called, in conjunction with investigators at the Psychiatric and Neurodevelopmental Genetics Unit at Massachusetts General Hospital (MGH) and the Broad Institute (formerly the Whitehead Institute/MIT Center for Genome Research). OpenClinica dynamically generates web-based interfaces for the clinical instruments defined within a project, while implementing the validation logic specified. It provides investigators with intuitive web-based workflows to submit, query and export datasets, manage multi-site projects and administer project-specific user roles and privileges. OpenClinica serves as a centralized data repository for all GCRC studies. Each investigator can setup his/her own research projects, define custom clinical assessment instruments, and manage policies for his/her own studies in diverse clinical research domains. OpenClinica implements a robust security model, advanced data integrity, and comprehensive auditing. It fosters interoperability and cooperation among investigators by facilitating data exchange using standardized formats.
Key Features:

  • Centralized clinical data repository to securely manage data while providing distributed web-based access for collaborative research.
  • Organization and management of clinical research along multiple hierarchical studies, each with its own set of authorized users, protocols, patient cohorts, CRFs, and saved queries; the system supports sharing resources across projects in a secure and transparent manner.
  • Dynamic generation of web-based case report forms (CRFS) for clinical assessment instruments from user-defined clinical parameters, protocols and validation logic.
  • Double Data Entry capabilities for clinical data to ensure accuracy when transcribing data from paper forms.
  • Intuitive workflows and user interfaces integrated within the context of a familiar web-based environment; this improves access and minimizes the need for dedicated training.
  • Extensive interfaces for data query and retrieval across projects, individuals and phenotypic parameters, with export of datasets in standardized formats for statistical analysis in SAS/SPSS.
  • Compliance with HIPAA privacy and security guidelines including use of hierarchical user roles and privileges within projects, SSL web access, de-identification and encryption of Protected Health Information (PHI), and auditing of data updates/access.
  • Runs on the Java J2EE and Struts framework, with an Oracle or PostgreSQL RDBMS (relational database management system) and data import/export tools. This architecture provides a secure, robust and extensible system for managing multiple clinical research studies within a centralized repository. Clinical data can be securely accessed within a GCRC intranet or across research sites distributed worldwide.
  • The single most important advantage with OpenClinica is the user interface. The workflow is highly intuitive, with user cues all along. Another great feature is the ability to design protocols, studies and create CRFs with no programming knowledge. I always felt that involving a programmer in creating the CRF is an unncessary step as this invariably leads to delays.
    OpenClinica currently runs on Windows/Linux platform with Postgres Database and i am hoping that new platforms will be in out soon. (
    While digging up data on OpenClinica, i also found a due-dilligence done by Northwestern University in June 2005, and here are the main areas of concern, according to them.

    Lack of sufficient functionality, including absent or inadequate features in ALL of these areas:
    Study calendar
    Billing / Financial information
    Auditing and Security / 21 CFR Part 11 compliance
    Inability to interoperate with existing systems
    Limited or no data export functionality
    No real programmatic access to CTMS functionality
    HL7 message processing
    Workflow control

    Pro: Great Installation guide
    Con: Need NTFS system on your machine, so have to format one part of your disk.
    When we tried to install openClinica using the windows installer, we could not get to the front page, and our feeling was that we were not able to connect to the database.
    Our application, JDK and tomcat were installed on C Drive and the database on E Drive.
    Doing a fresh install on E Drive solved the problem, we were able to do a fresh install, including installing postgres, tomcat and openclinica in less than one hour.
    Creating Studies and CRFs
    Absolutely smooth.
    We were able to set up a study and start the work on the CRF within an hour of installation. The key advantage is the ability to design CRFs using Microsoft Excel template, which everyone is comfortable with and then uploading it to create a new CRF.
    Overall, a great application. Will be posting bugs as we test drive it. Please contact us if you need help in installation or using.


      • Raghav

      • 17 years ago

      Hi Ashwin,
      I tried installing PostgreSQL, but it needed that the file system should be NTFS. Is that you converted your E drive to NTFS and then installed PostgreSQL, OpenClinica, Java and Tomcat on the same (E drive). Please let me know. How much space you need for an overall installation including (Openclinica, Java, PostgreSQL and Tomcat) cause I am trying to partition my E drive.
      Will be waiting for your response.
      Thanks in advance

    1. I am also very curious as to how much space I need for an overall installation including Openclinica, Java, PostgreSQL and Tomcat. Thanks CMR

      • Rahul Arya

      • 13 years ago

      Hello Loraine,
      The installation does not needs huge amount of space. The installation can be completed in 200 MB of space including Postgres, Tomcat, JAVA. However, I would recommend 2 GB of free space for test purpose and if you are going for production, much higher space would be needed depending upon the amount of data that will be stored in the database.
      Rahul Arya

    Leave a Reply

    Your email address will not be published. Required fields are marked *