View the latest version of the Onyx User Guide in PDF format.

Contents of this Guide

• Introduction
• Getting Started
• Viewing Participants
• Managing an Interview
• Obtaining Participant Consent
• Completing Questionnaires
• Collecting Physical Measurements
• Collecting Biospecimens
• Managing Your Onyx User Profile
• Managing an Onyx Workstation
• Topics for Participant Managers
• Topics for System Administrators

Introduction

If you are new to Onyx and would like a gentle introduction, this chapter is for you.

If you are already familiar with Onyx and need specific information about how to do something, skip this chapter and find the topic you need by scanning the table of contents or by searching for some key words that describe what you are looking for.

This chapter covers these topics:

• What Onyx is
• Key concepts related to the way Onyx works
• What Onyx does
• Who makes Onyx
• Onyx documentation
• Onyx user support

What is Onyx?

Onyx is a web-based application used to manage participant baseline interviews by assessment centres and clinics that are collecting data for research. Typically, the data is being collected for biobanks or large-scale population studies. this figure shows the typical assessment centre activities that Onyx supports. As shown in the figure, Onyx is installed on a server in the assessment centre and can be accessed from workstations via the assessment centre's intranet. An assessment centre may have one or more workstations dedicated to collecting data using Onyx.

A Highly Customizable Software Solution

Onyx is modular as shown in this figure. The Onyx engine is a backbone into which independent data collection components are inserted. Onyx is configurable which means certain stages may or may not be included in your version of Onyx. For example, your study may not accept volunteer participants. And if a stage is included, it can be fine-tuned to meet the requirements of your study. For example, for your study Onyx may be configured to only accept electronic signatures for consent forms, whereas for another study Onyx may accept electronic or handwritten signatures. Onyx is also customizable which means certain stages are tailor-made for each research study. For example, each study develops its own questionnaires, and each study defines which physical measurements will be collected and in which order.

Key Concepts

Participant

A participant is a person who has come to the assessment centre in order to participate in the research study. Assessment centre staff collect data from participants by asking questions, collecting biospecimens, and taking physical measurements.

Each research study determines how they will recruit participants. Typically, participants are either invited or volunteers. Onyx can be customized to accept volunteer participants or not. Whether or not this functionality appears in Onyx at your assessment centre depends on how Onyx was configured for your study. See Receiving vs. Enrolling Participants.

Invited Participant

A participant who was selected by the study and given an appointment time for their interview.

Volunteer Participant

A volunteer participant (also known as a "walk-in" Walk-in participants) arrives at the assessment centre without an appointment. They heard about the study in some way and decided that they would like to participate.

Interview

Onyx treats an interview as a set of interdependent stages that a participant goes through in order to complete their visit to the assessment centre. See this figure. An interview starts when a staff member receives the participant and enters registration information for the participant in Onyx. The participant then passes through some or all the stages that have been defined for the study. The interview ends when a staff member clicks the Close interview button in Onyx.

Interview Stages

An interview stage is one of the interdependent parts of an interview during which a particular type of data is collected from the participant. Each research study defines the stages it requires to obtain the necessary data, as well as the sequence in which the stages appear in Onyx. Typical interview stages include:

• Signing a consent form
• Questionnaires (one or more)
• Physical measurements (one or more)
• Collection of biospecimens (one or more)
• Conclusion of the interview (may include printing a report for the participant that includes information considered appropriate by the research study)

Each research study defines its own stages, creates its own questionnaires, and decides which physical measurements and biospecimens must be collected. Onyx stores the data collected during the stages centrally and makes it available to all workstations.

Who Uses Onyx

Onyx is used by the staff of an assessment center or a clinic that is collecting data from participants in a biobank study.

Onyx supports four roles for users. An individual user can be assigned one or several of these roles:

• Data Collectors
• Participant Managers
• Questionnaire Editors
• System Administrators

Data Collectors

These Onyx users are responsible for one or more of these tasks:

• interviewing participants
• collecting biospecimens
• taking physical measurements

Onyx data collectors are typically nurses and technologists.

Participant Managers

These Onyx users coordinate the activities of data collectors. Participant managers can do the tasks of a data collector, and in addition, they can do these tasks :

• receiving participants
• enrolling volunteer participants (if your study permits this)
• updating the appointment list
• unlocking a locked interview

Questionnaire Editors

These Onyx users create and edit the questionnaires that form part of an Onyx interview. Typically, they would be researchers involved in the design of the study, but not in interviewing participants. This role only gives a user the permission to create and edit questionnaires.

System Administrators

These Onyx users are typically Information Technology Managers (IT Managers) who handle the technical tasks required to set up and maintain Onyx. This role gives a user the permission to manage users and data.

What Onyx Does

Onyx facilitates the work of the staff members by allowing them to collect data electronically:

• obtain participant consent with the help of an electronic signature pad (if your assessment centre does not have a signature pad or the pad is not available, you record the fact that the patient signed a printed consent form in Onyx)
• complete onscreen questionnaires with participants
• set up participants to answer self-administered questionnaires on a touchscreen or a workstation
• record the collection of biospecimens (using a barcode scanner to identify the sample or entering a sample number manually)
• register physical measurements—such as height, weight, bone density, and any other measurements that the study may require

Onyx provides researchers with tools that allow them to optimize the workflow of baseline interviews:

• control stage availability and dependencies between stages (some examples: require that consent was obtained before an interview can proceed; prevent staff from taking measurements or samples that are contraindicated; ensure that dependent measurements are done in the correct order)
• capture administrative parameters such as start and end times of each stage
• automate the calibration of electronic instruments used to take physical measurements
• produce personalized reports for participants
• export encrypted data to multiple destinations

Some things Onyx does not do

While Onyx includes many features and functions that an assessment centre needs, it does not include the following functionality:

• Onyx does not allow you to schedule participant appointments. The appointment list must be imported into Onyx.
• Onyx does not arbitrarily decide when and whether you can proceed with a certain stage of an interview. Onyx is highly configurable and customizable. Each research study defines its own questionnaires, the physical measurments and biospecimens to be collected, the order of interview stages, and the conditions for passing from one stage to another. Based on how your research study configured Onyx, Onyx may inform you that a stage is contraindicated or prompt you about what to do during a certain stage. For example because of the participant's answers to certain questions, Onyx might prompt you about how to measure the participan'ts blood pressure: Use the participant's right arm to take blood pressure
• Onyx does not allow you to analyze the data collected from participants. It can export the data to other destinations where the analysis can be done.
• Onyx is not a Laboratory Information Management System (LIMS). It does not track processing of biospecimens.

Who Makes Onyx

Onyx is developed by OBiBa, a collaborative international project whose mission is to build high-quality open source software for biobanks. To learn more about OBiBa, please have a look at our website.

Onyx Documentation

In addition to this PDF version of the Onyx User Guide, an Online Help version of this guide is being prepared.

Information about configuring Onyx can be found in the Onyx Configuration Guide.

Version of Onyx Covered by this Guide

This version of the Onyx User Guide describes Onyx 1.8.0, in particular, version 1.8.0 of Onyx.

How this Guide is Organized

Since most Onyx users are data collectors, most of this guide explains how to use Onyx to collect participant data. This guide also includes chapters for Participant Managers, Questionnaire Editors, and for System Administrators.

This guide consists of the following chapters:

• Chapter 1: Introduction. Presents Onyx. Includes key concepts that will help you understand Onyx's approach to baseline interviews. For new Onyx users.
• Chapter 2: Getting Started. Presents the Onyx Home page. Explains how to log in to Onyx and the simplest way to start an interview. For new Onyx users.
• Chapter 3: Viewing Participants. Presents the Participants page and key concepts related to viewing participants. Explains the ways you can search for a participant in Onyx. For new Onyx users.
• Chapter 4: Managing an Interview. Presents the Interview page and key concepts related to navigating through an interview. Covers various ways to access and exit the stages of an interview: starting, stopping, pausing, resuming, and so on. Of most interest to Onyx data collectors and participant managers.
• Chapter 5: Obtaining Participant Consent. Presents Onyx's way of handling participant consent. Covers electronic consent forms and registering paper consent. Of most interest to Onyx data collectors and participant managers.
• Chapter 6: Completing Questionnaires. Presents key concepts related to the way questionnaires are handled in Onyx—such as assisted versus self-administered questionnaires. Since each study designs its custom questionnaires, the chapter explains the types of questions and answers users will see, rather than how to answer the particular questions in your study's questionnaires. Of most interest to Onyx data collectors and participant managers.
• Chapter 7: Collecting Physical Measurements. Presents key concepts related to physical measurement stages. Since each study determines the physical measurements it requires, the chapter explains the general workflow of a physical measurement stage and demonstrates the workflow with an example stage. Of most interest to Onyx data collectors and participant managers.
• Chapter 8: Collecting Biospecimens. Presents key concepts related to stages used to record the collection of biospecimens. Since each study determines the biospecimens it requires, the chapter provides an example biospecimen collection stage. Of most interest to Onyx data collectors and participant managers.
• Chapter 9: Managing Your Onyx User Profile. Explains how to do a few tasks that customize Onyx for you: changing your password and changing the language of the Onyx user interface (English or French are currently available). For all Onyx users.
• Chapter 10: Managing an Onyx Workstation. Presents the Workstation page and key concepts related to storing data about a workstation. Explains how to register and calibrate instruments used for physical measurements, and how to maintain logs of experimental conditions. Of most interest to Onyx users who will register and calibrate instruments, and log experimental conditions.
• Chapter 11: Creating and Editing Questionnaires. Explains how to create and edit questionnaires that can be included as stages of an Onyx interview. This work is typically done by researchers involved in design of the study. Of interest to users with the role of questionnaire editor.
• Chapter 12: Topics for Participant Managers. Explains certain tasks that only participant managers can do—such as receiving and enrolling participants. Of most interest to participant managers.
• Chapter 13: Topics for System Administrators. Explains certain tasks that only system administrators can do—such as managing Onyx users, and exporting and purging data. Of most interest to system administrators.

Icons Used in this Guide

Key Concept: This icon appears beside explanations of key concepts. In most chapters of this guide, you will find explanations of key concepts relevant to the chapter.

Customizable: This icon appears besides notes that explain a feature of Onyx that can be customized. Since each study customizes Onyx for its needs, these sections explain why you may not see a certain feature in your version of Onyx.

Procedure: This icon appears beside procedures—step-by-step instructions for performing a task in Onyx.

Pointer: This icon appears beside suggestions that could make your work in Onyx a little easier.

Onyx Support

• You can reach Onyx customer support by email at: support@obiba.org
• You can join the OBiBa users group. New releases of Onyx are announced through this group. You can use this forum to make comments, to ask questions, and to share ideas with other users of OBiBa software.
• You can visit the OBiBa website where you will find:
  • News stories and presentations about Onyx and other OBiBa products
  • JIRA, an issue-tracking system that allows you to enter bug reports, request new features, and suggest ways to improve Onyx

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