XForms and OpenClinica

Here at Geneuity, we do a lot of contract research work for sponsors of clinical trials.  That sometimes means developing and validating custom assays that aren’t available off the shelf. And this, in turn, often means developing special interfaces for data capture that can’t be configured inside OpenClinica (as yet).

Does that mean we jettison OpenClinica?

No, absolutely not!

Since OpenClinica is open source and dedicated to interoperability, it can be easily extended.  This article describes the specifics of one such case involving XForms.

A while back, Geneuity was developing an ELISA to measure the abundance of a specific protein in plasma.  We needed a single web form with a spreadsheet-like feel and functionality in which lab technicians could enter data, interpolate unknowns, send the resulting interpolated values for insertion into OpenClinica and then perform source data verification.  Additionally, the form needed to be pre-populated with the accession numbers of specimens requiring testing.  The form had to work on any browser and not be dependent on any browser plugins.  And we had to have it fast.

Impossible? No, not with XForms and the open source XForms renderer betterFORM.

XForms have several advantages.  First of all, you author the forms in relatively simple XML while the complicated AJAX that makes the spreadsheet-like feel and functionality is rendered by the renderer and presented to the client browser for you.  Secondly, XForms allows you to easily call upon webservices to populate data items in the form.  In our case, we developed three such services: one to return a list of accession numbers corresponding to specimens yet to be tested along with corresponding hyperlinks directed inside OpenClinica for rapid source data verification (SDV); another to calculate and graph a standard curve and to interpolate the specimen unknowns; and still another to insert the interpolated values into OpenClinica.  The data flow is diagrammed in Figure 1.  Although a great deal is going on behind the scenes, the user experience is seamless as a single form is being used while data retrieval and refreshment are being done without interrupting the display (thanks to AJAX as automatically implemented by betterFORM). The form itself is pictured in Figure 2.

And there you have it.  The bottom-line: no matter how complicated your data capture requirements are, you can count of the interoperability of OpenClinica.

Figure 1. First, the lab tech initially summons the XForm which calls upon OpenClinica via a webservice for the list of specimens for which there are no test results. The tech enters the data and clicks on the appropriate button to call for data interpolation and calculation. After review of the results, the tech then submits the data for insertion into OpenClinica (for more on this see here). Finally, the tech performs source data verification using the hyperlinks populated in the XForm as the result of step 1.
Figure 2. This is a snapshot of the XForm as it exists after interpolation and calculation. Only two specimens are shown, but usually there are many more in a batch.

OpenClinica 3.0 Features Preview – Part II

Welcome to Part II of the OpenClinica 3.0 features! I previously wrote about three of the main features for 3.0, Source Data Verification, new User Interface for navigation in the system, and a new Home Page for each user.

This post is about three additional features: (i) the new Build Study module, (ii) setting the length and significant digits of items, and (iii) the improved performance of the Subject Matrix.

In 3.0,  all the study build tools will accessed from one main page following a task-based approach. There are five tasks available to the user at the outset. Once the user finishes these first five tasks, two more tasks will become available (see image). This allows the complete study from CRFs to event definitions to sites to assignment of users be done all from a single page. There is also a checklist to let the user easily see how many tasks have been completed so they know how much more configuration is needed before the study is ready to start enrolling subjects.

Build Study Page in OpenClinica

OpenClinica 3.0 also allows the creator of CRFs to set the allowable length of  text fields including the number of decimal places a REAL number should be rounded to. This parameter is set in the OpenClinica CRF Template in a new field called Width_Decimal. The user will specify the width and decimal for a particular field which will force the user to enter the most precise data as possible in a CRF. No longer will the system round to the 4th decimal place at all times and allow up to 255 characters in the field if the CRF creator does not want them to. For example, the creator could specify that a field should have no more than 5 digits total with a maximum of 1 decimal place by entering 5(1) in the Width_Decimal column of the OpenClinica template. If the data entry person tried to enter 3.4444 or 678913 they would told the value is invalid.

By providing this functionality, OpenClinica will help the users get their data into SAS and SPSS more easily.

One of the most important and information-rich pages in OpenClinica is Subject Matrix page, and OpenClinica 3.0 provides significant performance enhancements on this page for studies with large numbers of of subjects.  From the Subject Matrix page users can see a snapshot of where the subjects are in the study, schedule a new event, view a subject record, view a subject event, enter data in a CRF and sign a subject’s record without having to navigate to different pages in this system. A number of users were reporting sluggish performance with the Subject Matrix when they had 5000 or more subjects enrolled in a study.

OpenClinica 3.0 utilizes a new table structure that allows users to load the Subject Matrix containing over 10,000 subjects and 15 event definitions in fewer than 5 seconds (this process could take upwards of a minute in previous releases of OpenClinica).

Please feel free to download the Beta version of OpenClinica 3.0 at http://svn.akazaresearch.com/OpenClinica-3.0-distros/.

OpenClinica 3.0 Features Preview – Part I

We have been working hard on OpenClinica 3.0 for the last 9 months and are getting closer and closer to a production release ready for use in live clinical studies. In the meantime, I wanted to talk about some of the new features over the next few weeks to let folks know what is coming.

OpenClinica 3.0 is sure to bring a lot of excitement to all users of the rapidly growing open source electronic data capture system. A lot of focus in this release has been put on the way trial sponsors use an EDC system and I’d like to point out some of the new features that should enhance their user experiences.

OpenClinica 3.0 will provide a new home page to study-level users providing key information about the progress of a study. These users will be able to see a summary of the subjects enrolled at each site compared to their expected total enrollment as well as the overall subject enrollment for the complete study. Also, these study-level users will be shown a count of the number of study events that are in a particular status. A summary for the number of subject statuses will be displayed so the study-level user can easily see how many subjects are signed, source data verified etc.

OpenClinica 3.0 will provide monitors a workspace to source data verify subjects and their data. The workspace will allow users to source data verify information collected at each visit one-by-one, or verify the information in a bulk process. These two options allow the monitors to perform remote source data verification daily for subjects in the study. Or, if the monitor has to be on site to review and verify information, he/she can go back to their hotel room and check-off verification for many subjects and events at once so they do not have to go one-by-one through every subject and event CRF.

The top-level navigation in OpenClinica 3.0 has been streamlined so site users of the application understand exactly what they have to do after they login. A new home page for investigators and clinical research coordinator users will show the number of queries assigned to them with a link to see every Query assigned them. The home page will show the 5 most recent queries to give the user an idea of what they need to respond to that day.

The new navigation points to the 3 main actions the site users should take. The “Subject Matrix” link will bring them to the new and improved subject matrix in OpenClinica. This matrix will allow users to easily add subjects, schedule events and even enter data from a single, powerful screen. The “Add Subject” link will bring them to a page where they can add a new subject to the study. “Notes & Discrepancies” will bring them to a page where they can see all the queries for their site and allow them to provide a response.

Above is just a small sample of the new features in OpenClinica 3.0. Like I said, I will plan on posting additional features once a week so be sure to check back often. In the meantime, please feel free to download the alpha2 at http://svn.akazaresearch.com/OpenClinica-3.0-distros/.

– Paul Galvin