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For mapping, the REDCap variables can be obtained from the ‘data dictionary’ available under ‘Project Home and Design’.
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Configure REDCap Server
Before configuring the REDCap project to a specific Collection Protocol in OpenSpecimen, you must 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:
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Data Dictionary for Server Configuration
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Add REDCap Project
To add a new REDCap project to your desired collection protocol, you can follow the below steps:
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Data Dictionary for Project details
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Mapping Participants and Visits
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List of Participant Fields and Variables
Field Name | Variable Name |
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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.<custom_field_name> For example: if the field name is 'redcap_age' in the custom form the use: participant.extensionDetail.attrsMap.redcap_age |
Event and Visit Level Mapping
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List of Visit Fields and Variables
Fields Name | Variable Name |
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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 |
Custom Field | extensionDetail.attrsMap.<custom_field_name> For example: if the field name is 'visit_number' in the custom form the use: extensionDetail.attrsMap.visit_number |
Advance Features
Add the list of forms/fields separated by comma, tab, or newline.
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Like ‘Forms Exclusion List’, the user can also define the list of fields to either include or exclude for synchronization. The user can’t define both the parameters at once.
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’.
To include or exclude a form/field use the variable name of the form/field from REDCap.
Data Dictionary for Fields and Events Mapping
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Field Name | Mandatory? | Supported study type | Description |
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Participant Fields Mapping | No | Classical/Longitudinal | Specifies the list of OpenSpecimen participant fields that are mapped to their respective REDCap fields. For example, rcRecordId=ppid,dob=participant.birthDate |
Visit Fields Mapping | No | Classical/Longitudinal | Specifies the list of OpenSpecimen visit fields which are mapped to their respective REDCap fields. For example, visit_label=eventLable,visit_site=site,visit_date=visitDate |
Records Inclusion Rule | No | Classical/Longitudinal | Defines condition/s to synchronize specific REDCap records to OpenSpecimen. The expression is formed using REDCap variables obtained from the 'data dictionary'. For example, to fetch the records of female participants who are 18 years old or older we can use following expression: #sex == 'Female' and #yearBetween(#dob, #regDate) >= 18 |
Form Exclusion List | No | Classical/Longitudinal | Defines the list of forms to be excluded for synchronization irrespective of being mapped to participant or visit field. For examples, Follow_up_year_1,Follow_up_year_2 |
Fields Inclusion List | No | Classical/Longitudinal | Defines the list of fields to be included for synchronization. For examples, enrollment_date, consent_date |
Fields Exclusion List | No | Classical/Longitudinal | Defines the list of fields to be excluded for synchronization irrespective of being mapped to participant or visit field. |
Events Mapping | No | Longitudinal | Specifies the list of OpenSpecimen events which are mapped to their respective REDCap events. |
Ignore Unmapped Events | No | Longitudinal | Checkbox fields that can be ‘ticked’ to ignore the unmapped events of the REDCap. This prevents the creation of unwanted, unplanned events in OpenSpecimen. |
Integration Points
REDCap | OpenSpecimen | Description |
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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:
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