Tools and Tips

This page describes helpful tools, add-ons, and tips for OpenClinica contributed by members of the OpenClinica community. Anyone can add to or edit the information here. You’ll have to register for a wiki account first.

Category Description Contributor Link to tool
Documentation In addition to the official OpenClinica documentation, there is a very helpful voluntary work done by OpenClinica users hosted at wikibooks.org Various OpenClinica Wikibook
Forums OpenClinica has two email forums: one for users (users@openclinica.org) and the other for software developers (developers@openclinica.org). Various Forum Archives
Data Extract A utility that provides simplicity of use by data management staff (not and end user tool). It is invoked from the command line, creates an XML ‘dump’ of all critical study data, and is fast – not encumbered by a user interface or web based delivery. It outputs XML readable directly via the SAS Libname engine (requires minimal coding to import the data into SAS), generates XML output directly from the PostgreSQL database, and leverages existing study metadata to generate SAS labels and format catalog. The tool translates response options to SAS formats/informats and translates OpenClinica null values to SAS special missing values. Rick Watts, University of Alberta WCHRI OpenClinica Export
Data Extract A SQL script to get a full dataset for a particular study, and the steps in constructing it. According to the author: “It seems to work but I can’t claim much testing. As the document says it almost certainly needs refinement to take into account the statuses of the various entities, but that will take some further work. This is shared as-is, on the chance that others might want to do / already have done a similar thing. If you find any errors I’d be very happy to receive the details.” Steven Canham Data Extract SQL Script
Data Extract for STATA Converts OpenClinica SPSS output to STATA. More information. Luke Stevens, Murdoch Childrens in Melbourne, Australia Convert an OpenClinica SPSS Export to Stata Format
Data Import OpenClinica supports CDISC ODM XML based data import. Data in this format can be loaded via the user interface, from a defined file location via the Job Scheduler, or via Web Services. Getting data into ODM XML can be a challenge. There are multiple tools and approaches you can take to map your data file for import if it is not already in ODM XML (such as if it is in Excel, tab, or HL7). Various You can read about these options here
caBIG® Clinical Connector Web Services caBIG® (sponsored by the U.S. National Cancer Institute) is a collaborative information network intended on accelerating the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer. The open source caBIG Clinical Trials Suite is an integrated set of open-source standards-based tools that facilitate electronic management of clinical trials and associated data, and enable comprehensive sharing and integration of clinical research information. The OpenClinica caBIG Web Services package were created specifically to be used with caBIG® Clinical Trials Suite and are conformant to the caBIG® Clinical Connector specifications. This package (which is separate from the standard web services package) communicates with the caBIG Clinical Connector accepts Study and Site Creation, Subject Registration, and lab data API calls. Find out more about how it works here OpenClinica, LLC and Ekagra Inc. Download
Translations Tranlsations of OpenClinica into various languages. Various OpenClinica Internationalization Project
Codelist lookup Use a 3rd party application to lookup/search for a code or term from an OpenClinica CRF via a popup window, and send the term back to the CRF field. Implemented using HTML5 PostMessage() Tom Hickerson Cross-site messaging and Controlled Vocabularies
Rule Design Tool Microsoft Access based rules designer for OpenClinica. Quickly and easily define rules, have the database generate the relevant XML and upload the XML to OpenClinica. (Works perfectly for “within form” rules and I’ll tweak it for cross form / cross event rules when I have time.) Clemens Masesa https://www.sugarsync.com/pf/D6631089_7069449_993441
Metadata Listings Generate printable metadata listings for an OpenClinica study using OpenClinica’s ODM 1.2 extract format and CDISC’s define.xml Cal Collins Instructions and example
Using OpenClinica in “Offline” mode An interface to have OC working in offline mode, automated through python scripts. Use Dropbox to make site data sharing faster and safer. Michael Ochieng and Raymond Omollo Python Scripts Documentation

Related Projects

  • The Connecticut Health Information Network is a partnership between the University of Connecticut, OpenClinica LLC, and Connecticut’s state agencies to develop a federated computer network linking diverse databases across agencies. This innovative network complies with stringent security and privacy standards, and offers unprecedented opportunities to integrate and analyze public health data to inform program development and policy decisions. More information about CHIN and the underlying technology is available by emailing contact@openclinica.com.

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