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Beyond Single-Selects – Managing Long Lists in OpenClinica

Here at the VU Medical Center Amsterdam, we’re implementing OpenClinica (OC) for CTMM TRACER. TRACER aims at improving diagnosis, prognosis and therapy selection for rheumatoid arthritis. A series of eCRFs are being developed, ranging from questionnaires to joint scoring and DAS-score calculations.

One of our most recent CRFs is concerned with a patient’s medication. In this CRF one of the items of interest is the medication the patient is currently on. The code system employed for medication is the Anatomical Therapeutic Chemical (ATC) Classification System, which contains over 500 entries. Initially, we intended to create a single-select field containing the ATC codes and their description. Unfortunately, the number of characters involved is way more than the maximum of 4000 allowed by OC. The easy alternative would have been to define a free text field, but it is generally best to avoid those, as the data in these fields tends to pollute easily.

The solution we created employs JavaScript and JQuery. Without getting into the technical details (you can get them here), the approach is to create a (read-only) text field in OC and let a non-OC single-select item write data to this field. This ensures that the values written to OC are limited to those specified in the list, without having to store the complete list in OC. The list entries themselves are stored in an external XML file, which is stored on the OC server. If at some point the ATC-codes need to be updated, we can simply update the XML file and the updates will be available for the users.

Whereas our problem was concerned with a long list of ATC-codes, the solution can be applied to any list which is longer than OC’s maximum number of characters. All you have to do is create an XML file, which describes the list, make some minor changes to the example code provided on the wiki page and upload two files to your OC server.

Sander de Ridder (MSc Computer Science, MSc Bioinformatics)

OpenClinica Web Services Tutorial Videos

OpenClinica’s web services layer provides a powerful mechanism for programmatic data interchange between OpenClinica and other systems. Below are the first two videos in a series of tutorials on working with web services. The videos are created by Hiro Honshuku, including the background music! Thanks Hiro!





The OpenClinica Platform – Developer Round Table Discussions

OpenClinica is a clinical trial software platform that aims to provide data capture, data management, and operations management functionality to support human subjects-based research. It can be used for traditional clinical trials as well as a wide variety of other types of human subjects-based research.

Our vision for the product is to provide data capture, data management, and operations management functionality out-of-the-box, in an easily configurable, usable, and highly reliable manner. The underlying platform should be interoperable, modular, extensible, and familiar – so users can solve specific problems, in a generalizable way.

This past spring, the development team here at OpenClinica, LLC held a series of round table discussions about how this vision is reflected in the product. Our goals were to learn critical standards and information models needed for our technology to truly reflect this vision, to develop a consistent, shared vocabulary for the problem domain and the OpenClinica technology, and identify the most urgent opportunities to put these lessons into practice in the product and the community. In particular, we spent a lot of the time in these discussions about how OpenClinica’s use of the CDISC Operational Data Model helps enable this vision.

The discussions were invigorating and thought-provoking. We’ve recorded them to share with the greater community of OpenClinica developers, integrators, and others who want to better understand how the technology works, the design philosophy behind it, and where we’re going in the future. The videos are embedded below.

But before getting to the videos, here’s a bit more background on how we think about OpenClinica as a product and a platform.

First, OpenClinica functionality should be ready out-of-the-box, easily configurable and highly usable. Some of the most important features include:

  • Data definition and instrument/form design with no or minimal programming
  • Sophisticated data structures such as repeating items and item groups
  • Support for a wide variety of response types and data types (single select, multiple choice, free text, image)
  • Data management and review capabilities (including discrepancy management and clinical monitoring) with flexible workflows
  • ALCOA-compliant controls and audit history over all data and metadata, including electronic signature capabilities
  • Patient visit calendar design with management of multiple patient encounters and multi-form support
  • Reporting and data extract to a wide variety of formats (tab, SPSS, CDISC ODM)
  • Ability to combine electronic patient reported outcome (ePRO) data with clinically reported data using common form definitions (write once, run anywhere)
  • Deployment via multiple media, mobile or standard web browser

Many of these things have already been implemented, and more are under development.

The core concept around which OpenClinica is organized is the electronic case report form (CRF). In OpenClinica, a CRF is a resource that is essentially a bunch of metadata modeled in CDISC ODM with OpenClinica extensions. It doesn’t (necessarily) have to correspond to a physical or virtual form; it may represent a lab data set or something similar. An OpenClinica Event CRF is that same bunch of metadata populated with actual data about a particular study participant. Thus, it combines the metadata with the corresponding item (field) data, with references to the study subject, event definition, CRF version, and event ordinal that it pertains to. In this conceptual view of the world, CRFs (as well as CRF items, studies, study events, etc.) are resources with core, intrinsic properties and then some other metadata that has to do with how they are presented in a particular representation. Built around these core resources are all the workflow, reporting, API, security, and other mechanisms that allow OpenClinica to actually save you time and increase accuracy in your research.

Second, OpenClinica should be interoperable. The ultimate measure of interoperability is having shared, machine readable study protocol definitions, and robust, real-time, ALCOA-compliant exchange of clinical data and metadata that aligns with user’s business processes. It should be easy to plug in and pull out or mix-and-match different features, such as forms, rules, study definitions, report/export formats, and modules, to transport them across OpenClinica instances or interact with other applications. Establishing well defined methods and approaches for integration into existing health data environments is a key goal of interoperability.

Third, OpenClinica should be modular and extensible. OpenClinica already provides some of the most common data capture and data management components and aims to have a very broad selection of input types, rules, reports, data extracts, and workflows. However OpenClinica developers should also have the freedom to come up with their own twist on a workflow, module, or data review workflow and have it work easily and relatively seamlessly with the rest of OpenClinica. User identification, authentication, and authorization should be highly configurable and support commonly used general purpose technologies for user credentialing and single-sign-on (such as LDAP & OAuth).

The CRF-centric model allows us a great deal of flexibility and extensibility. We can support multiple modalities, with different representation metadata for rendering the same form, or perhaps the shared representation metadata but applied in a different way (i.e. web browser vs. mobile vs. import job). We can address any part of the CRF in an atomic, computable manner. This approach has been successfully applied in the Rule Designer, which takes the ODM study metadata and allows browsing of the study CRFs and items, with the ability to drag and drop those resources to form rule expressions. Features such as rules and report/export formats are represented as XML documents. These documents define how the features behave in standardized ways so that one rule can, say, be easily replaced with another rule without having to modify all the code that makes use of the rule.

Finally, OpenClinica aims to be familiar in the sense of allowing data managers, developers, statisticians to work in a design/configuration/programming environment that they already know. Programmers don’t all have the same experience, and it would be somewhat limiting to force OpenClinica developers to all use the same language (Java) that OpenClinica was written in. We are constantly looking at ways to make it possible (not to mention reliable and easy!) for users and developers to interact with and extend OpenClinica in a programmatic way. This can mean anything from data loading to more meaningful integrations of applications common to the clinical research environment. As proponents of open, standards-based interoperability, our starting point is always to develop interfaces for these interactions based on the most successful, open, and proven methods in the history of technology – namely the protocols that power the World Wide Web (such as HTTP, SSL, XML, OAuth 2.0). They are relatively simple, extensively documented, widely understood, and well-supported out of the box in a large number of programming and IT environments. On top of this foundation, we rely heavily on the wonderful work of CDISC and the CDISC ODM to model and represent the clinical research protocol and clinical data.

Session 1:  from 30-March-2012 (start at the 5 min 20 sec mark)

Session 2:  from 06-April-2012 (start at the 1 min 25 sec mark)

Session 2a:  from 20-April-2012

Session 3:  from 27-April-2012

Session 4:  from 11-May-2012

OpenClinica Exhibiting at DIA China Conference (May 20-23, Shanghai)

OpenClinica is exhibiting at the Drug Information Association’s 4th Annual China Meeting, May 20-23 at the Shanghai International Convention Center.

The environment for clinical research is rapidly evolving in China. This theme of this year’s event is “collaboration and innovation in China.” Sessions features numerous topics related to China and global pharmaceuticals.

Stop by the OpenClinica booth to learn about how OpenClinica is leading the way for modern, more effective clinical research in China.

OpenClinica at Society for Clinical Trials Annual Meeting (May 20-23, Miami)

OpenClinica will be both exhibiting and presenting at this year’s Society for Clinical Trials Annual Meeting, May 20-23 in Miami. Come by the OpenClinica booth to introduce yourself and learn about the many exciting things happening within the OpenClinica software and community! On Wednesday, May 23, OpenClinica’s, CEO, Cal Collins, will lead a presentation showcasing an innovative new OpenClinica mobile data capture technology. The session is titled “Electronic Patient Reported Data for Risk Screening in Primary Care Clinics using OpenClinica and CDISC ODM.”

OpenClinica Conference Showcases Innovation

Innovation in the OpenClinica community occurs on many different levels and in many places around the world. The 2012 OpenClinica Conference earlier this week brought together a diverse group of clinical and IT professionals to share first-hand a lot of the innovative, cutting-edge work being done within our community. Mobile, compliance, best practices, SAS, were all key themes at this year’s event. I was very encouraged by the growing enthusiasm for OpenClinica, and came a way more excited than ever about our collective ability to positively transform clinical research.

Here are some photos on Facebook: http://www.facebook.com/pages/2012-OpenClinica-Conference/228070113945322

Thanks to everyone for helping to make the 2012 OpenClinica Conference the best yet!

- Ben Baumann

Community OpenClinica Meetup in Vienna April 17th!

In the time leading up to the OpenClinica Global Conference, we are able to organize some small events outside of the USA.

We’d like to hold an informal meetup for all interested users of OpenClinica in Vienna Austria, April 17th 2012, 7pm-9pm, at the Starbucks Bräunerstraße. For a full address and map, please click here.

The agenda is currently open – we’d like for everyone to come with their own ideas, opinions and stories and be ready to share. From the OpenClinica LLC side, Tom Hickerson will be organizing the event, and if you have any questions or suggestions, please get in touch with him through thickerson -at- openclinica.com. You can also leave a comment below, or at our LinkedIn page!

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