Introduction
REDCap does not have fixed instruments for participants and visits. Therefore, you need to map the REDCap Instruments with OpenSpecimen Participant and Visit fields.
For mapping, the REDCap variables can be obtained from the ‘data dictionary’ available under ‘Project Home and Design’.
Add REDCap Server
Before configuring the REDCap project to a specific Collection Protocol in OpenSpecimen, you need to establish a link between your desired REDCap and OpenSpecimen servers. This will helps the OpenSpecimen to pull the data from the REDCap projects associated with the REDCap server using API tokens. Furthermore, once the server is configured you can reuse the saved configuration multiple times for adding the projects. You can add the REDCap Server in the following steps:
Go to the CP Overview Page and click on the 'Settings' tab on the left sidebar.
Select ‘REDCap Project Configuration' and click on the 'Add Project’ button.
Click on the ‘Add New’, provide details on server name, host base URL, plugin path, and time zone, and click on the ‘save’ button.
Data Dictionary for Server Configuration
Please note that the PHP plugin can be placed anywhere on the REDCap server as long as the PHP file is executable by the web server and the functioning of the plugin PHP is not compromised.
Field Name | Mandatory? | Description |
|---|---|---|
Server Name | Yes | Free text to enter a name for the REDCap server. For example, OpenSpecimen REDCap QA server |
Host URL | Yes | The base URL for the REDCap server. For example, https://www.project-redcap.org |
Plugin Path | No | The relative path for the PHP plugin installed on the REDCap server. To check the all the plugins installed on the REDCap server, add ‘/plugins’ at the end of your REDCap base URL. For example, https://www.project-redcap.org/plugins |
Time Zone | No | The timezone of the REDCap server. |
Add Project
To add a new REDCap project to your desired collection protocol, you can follow the below steps:
Go to the CP Overview Page and click on the 'Settings' tab on the left sidebar.
Select ‘REDCap Project Configuration' and click on the 'Add Project’ button.
Provide information on the project name, server name, API token, site, PHI data, snapshot download page size, and users.
Data Dictionary for Project Configuration
Field Name | Mandatory? | Description |
|---|---|---|
Name | Yes | Free text to enter a name for the REDCap Project. For example, Testing_RC |
Server Name | Yes | Name for the REDCap server where your REDCap server is configured. For example, OpenSpecimen REDCap QA server |
API Token | Yes | User specific API token generated for the project. For example, A411D356AXYRC0C8A2742EBC366778HD |
Site | No | Site linked with your collection protocol. |
Save PHI Data | Yes | ‘Enable' or 'Disable’ option to allow or pervent the collection of Personal Health Information (PHI) of the participant respectively. |
Snapshot Download Page Size | No | Specifies the maximum number of records that will be pulled from the REDCap at each interval. This is repeated ‘N' numbers of times until all records are pulled. It helps to minimize the overload to the OpenSpecimen server. For example, if there are 10,000 records in REDCap project, and you have set the 'Snapshot Download Page Size' value to 5000, then OpenSpecimen will take 2 turns to pull all 10,000 records from the REDCap. The default value is '1000’. |
Notify Users on Errors | No | Specifies the name of the users who will be notified when there are any error during REDCap synchronization process. |
Mapping Participants and Visits
Mapping can be done at two levels:
Participant (Both classical and longitutinal studies)
Visit (Logngitutinal study)
Participant Level Mapping
The steps for mapping the participant fields are as follow:
Add the list of RC-OS variable pairs separated by comma, tab, or newline.
After configuring study level mapping, you can move to the ‘Fields and Events Mapping’ page by clicking on the 'Next button.
Map REDCap variables (on the right) obtained from the 'data dictionary' to OpenSpecimen (on the left) as shown below.
List of Participant Fields and Variables
Field Name | Variable Name | |
|---|---|---|
PPID | ppid | |
Registration Date | registrationDate | |
External Subject ID | externalSubjectId | |
Registration Site | site | |
First Name | participant.firstName | |
Last Name | participant.lastName | |
Middle Name | participant.middleName | |
Birth Date | participant.birthDate | |
Death Date | participant.deathDate | |
Gender | participant.gender | |
Races | participant.races | |
Vital Status | participant.vitalStatus | |
Ethnicity | participant.ethnicities | |
eMPI | participant.empi | |
National ID / SSN | participant.uid | |
MRN Site | participant.pmis.siteName | |
MRN | participant.pmis.mrn | |
Custom field | participant.extensionDetail.attrsMap.ST2 |
Event and Visit Level Mapping
It is exclusively for longitudinal studies.
Like 'Participant Level Mapping', map visits fields for the REDCap project as shown below in the red box.
Additionally, you can map events for the REDCap project, as shown below.
Those events from REDCap which are not mapped can create unwanted, unplanned events in OpenSpecimen. To avoid this, click on the 'Ignore Unmapped Events’ checkbox.
List of Visit Fields and Variables
Fields Name | Variable Name |
|---|---|
Event Label | eventLabel |
Visit Date | visitDate |
Clinical Diagnosis | clinicalDiagnoses |
Visit Site | site |
Clinical Status | clinicalStatus |
Path. Report Number | surgicalPathologyNumber |
Cohort | cohort |
Comments | comments |
Collection Status | status |
Advance Features
Add the list of forms/fields separated by comma, tab or newline.
Records Inclusion Rule
The user can define certain conditions (as shown below in the red box) to synchronize specific REDCap records to OpenSpecimen. Once applied, the system will ignore all other records that don’t satisfy the criteria irrespective of being mapped to the participant or visit field.
The expression is formed using REDCap variables as shown above.
The example shown in the red box below will only fetch the records of female participants from REDCap who are 18 years old or older.
Forms Exclusion List
The user can define the list of forms to exclude for synchronization irrespective of being mapped to participant or visit field.
If the user provides the list to the ‘Forms Exclusion list’ text box, then all the forms will be synchronized except the forms mentioned on the list.
Fields Exclusion/Inclusion List
Like ‘Forms Exclusion List’, the user can also define the list of fields to either include or exclude for synchronization.
If the user provides the list to the ‘Field Exclusion list’ text box, then all the fields will be synchronized except the fields mentioned on the list. On the other hand, only specified fields will be synchronized if the user provides the list to the ‘Field Inclusion list’.
Integration Points
REDCap | OpenSpecimen | Description |
|---|---|---|
Project | Collection Protocol | The RC project can be synchronized with a particular CP in OS. |
Instruments/Forms | Forms | The instruments from RC can be synchronized with forms linked with a particular CP in OS. |
Records | Participant | The records from RC can be synchronized with participants linked with a particular CP in OS. |
Visits/Events | Visits/Events | The visits/events from RC can be synchronized with visits/events linked with a particular CP in OS. |
Adding more project
To add more than one REDCap project to your collection protocol in OpenSpecimen, you can follow below steps:
Go to the REDCap configuration page for your collection protocol of choice.
Click on the ‘More' option and select ‘+Add Another’.
Configure the new project as shown above.
