Collect with Onyx

What is Onyx?

Onyx is a web-based application that manages participant baseline interviews at assessment centres or clinics. As depicted in the figure below, an interview is represented as a set of interdependent stages that participants have to go through in order to complete their visit (consent form signature, health questionnaire, biosample collection, and so on). Onyx stores the data collected during the stages centrally and makes it available to all workstations.

Onyx controls both the order and availability of the interview stages (for example, no stages are available prior to the informed consent is signed) and captures many administrative parameters such as the starting and ending times of each stage. Onyx also manages a participant appointment list and reception of participants, as well as data filtering and encryption prior to export to a central study database (see Opal).

What Onyx Can Do for You

Onyx is designed to ensure that data is collected in an automated, efficient and secure way in order to minimize human errors and interview length. Onyx can optimize the workflow of your baseline interviews by:

  • Managing appointment lists and walk-ins.
  • Controlling stage availability and dependencies (examples: requiring consent before an interview can proceed; dependent measurements).
  • Capturing administrative parameters such as starting and ending times of each stage.
  • Managing participant consents (electronic and handwritten).
  • Administering health questionnaires electronically.
  • Facilitating collection of biosamples (barcode scanning).
  • Automating physical measurements.
  • Producing personalized reports for participants.
  • Exporting encrypted data to multiple destinations.

A Highly Customizable Software Solution

Onyx is modular as shown in the figure below. The Onyx engine is a backbone to which independent data collection components can be connected in order to manage the various interview stages. Studies can configure Onyx for their own specific stages and data collection software.

To learn how Onyx could be adapted to your needs, read the documentation or write to us at


Onyx consists of an application engine and a series of stage-specific data collection modules.

Onyx Engine

The Onyx engine supplies this main functionality:

  • Manages appointment lists and walk-ins,
  • Can connect to external participant registries to fetch identifiable information at reception,
  • Manages the flow of interviews,
  • Controls stage availability and dependency,
  • Encrypts data before exporting it to the study central database,
  • Can filter data on export to protect participant privacy,
  • Supports multiple languages,
  • Printing interview reports and handouts (PDF),
  • Workstation management (environmental conditions, assigned instruments).

Consent Module

The Onyx Consent Module collects the participant’s consent to partake in the assessment center interview. The module displays customizable consent forms onscreen.

The Consent Module's special features include:

  • Capture of electronic signatures,
  • Support for manual signatures,
  • Capture of any kind of consent form in any language.

Electronic signatures are embedded in the document making it impossible to modify the document once it has been signed. Signed consent forms are saved as PDF files.

Questionnaire Module

The Onyx Questionnaire Module administers custom questionnaires to participants It displays questions on screen, and captures and validates answers.

The Questionnaire Module's advanced features include:

  • Multiple language versions of the same questionnaire,
  • Support for many question/answer formats, such as open text, single-selection, multiple selection, dropdown lists, tables, and so on.
  • Questions can be grouped into sections,
  • Time-stamping permits evaluation of the efficiency of various sections,
  • Answer validation based on rules, such as valid ranges and data format,
  • Answer validation based on answers to previous questions. Example: Participant could not have started smoking at 50 if he is only 40 years old.
  • Answer validation using an arbitrary script (JavaScript),
  • Skip patterns. Example: Smoking section is only displayed for smokers,
  • Complex, scripted (JavaScript) skip patterns,
  • Questionnaire can be completed in multiple sittings—after a pause, questionnaire resumes at the last question answered.
  • Comment can be added for participant's answer to each question,
  • Display images, play audio or videos as instructions (for example) to the participant,
  • Audio recording: record participant as they answer question using a microphone,
  • A comprehensive and user-friendly web interface to create and edit questionnaires.

The questionnaire module supports two forms of survey administration: assisted (interviewer asks questions and enters participant's answers); and self-administered (participant answers the survey questions independently).

Both versions of the interface were developed in consultation with a professional software ergonomist ensuring that a variety of value-added features are available. For example, the nurse-assisted interface can take advantage of different question formats.

The self-administered interface takes into account the diverse needs of participants. It can be presented on a user-friendly touch screen that allows participants who have few or no computer skills, to navigate the questionnaire. A broad range of features has also been built in—from simple progress bars to accommodation for color blindness.

This rich set of features makes the Onyx Questionnaire Module an excellent questionnaire administration tool for different biobank studies.

Physical Measurement Module

Onyx’s Physical Measurement Module captures data from manual and electronic instruments used for physical measurements such as blood pressure, bone density, hip/waist circumference, and so on. This module prevents completion of a particular stage if there are any contraindications either in the contraindication questionnaire stage (previously administered using the questionnaire module) or immediately before the measurement. Interfaces are available to enter measurements made using manual instruments, or electronic data can be imported or exported between proprietary software and the database.

The Physical Measurement Module offers the following features:

  • Manages proprietary software from instrument vendors,
  • Can connect directly to instruments to capture measurements,
  • Automatically provides input to instruments when available (age, gender, height, weight, and so on),
  • Multiple and conditional measurements from the same instrument,
  • Manages contraindications,
  • Pre-populates a printable form with data collected during each physical measurement stage of the interview.

Calibration and Experimental Condition Logs

Instrument calibration data and experimental conditions (such as room temperature and humidity) can be entered in logs configured to the study's requirements. This data can be exported along with participant data to ensure that all relevant information is available for future analysis.

Supported Instruments

The Physical Measurement Module can support any number of instruments. Below is a non exhaustive list of instrument's models that have already been implemented:

Instrument Type Vendor Model
Blood Pressure VSM MedTech BPM-200 or BPM-300
Bioimpedance Tanita TBF-310
Bioimpedance Tanita BC-418
Spirometry MIR Minispir
Spirometry ndd Medical Technologies Easy on-PC
Arterial stiffness AtCor Medical SphygmoCor SCOR-Px
Arterial stiffness Summit Doppler Vantage ABI
Osteodensity (ultrasound) GE Healthcare Lunar Achilles Express
Osteodensity (DXA) Hologic Discovery
Grip Strength JTECH Medical Tracker Freedom Grip
ECG GE Healthcare Cardiosoft
Audiogram Tremetrics RA-300

Sample Collection Module

Onyx's Sample Collection Module collects and validates the bar codes on sample tubes. Like the Physical Measurement Module, the Sample Collection Module monitors for contraindications to ensure that samples are not collected if contraindications exist.

The Sample Collection Module can be configured via a number of attributes including:

  • Number of tubes containing the primary samples expected,
  • Bar code structure, length and format (smart or random),
  • Elements making up the bar code (participant code, additive code, or random numbers).



Onyx is a Java-based application, so it should run on any platform for which a Java Virtual Machine is provided.

Onyx is a web application that requires to be deployed in web server container such as Tomcat or Jetty .


For a quick start, we provide a Onyx Demo template project, which can be built and immediately tested. The build instructions can be found in the project's README file.

Onyx Demo (latest .zip)

Once the web archive (.war) file of your Onyx-based application has been built, detailed installation instructions can be found in Onyx Installation Guide .


Before you can use Onyx for your own purposes, it needs extensive configuration to fit your specific needs. Doing so requires reading the Onyx Customization & Configuration Guide and editing several files. This can be a complex operation that is done over several days depending on the features that need to be configured.

Try Onyx

We've prepared a demo configuration of Onyx that allows you to try out some of the features. Keep in mind that most parts of Onyx are configurable, thus what you see in this demo can be completely different if required by your use-cases.

To have a closer look at Onyx try our demo site :

  • username: administrator
  • password: password