OC Study Setup

1 Project Mapping
2 Site Mapping
3 Exclude and Include CRFs
4 Participant Mapping
5 Visit Mapping
- 5.1 Conditional Mapping
6 Specimen Mapping

Project Mapping

One or more OC Projects can be linked to an OS CP.

From the CP settings menu, click on ‘OpenClinica Study Configuration’
Users can use the ‘Add Study’ feature or 'Import Study' displayed on the page.
1. If the user uses the ‘Add Study’ feature user will need to enter the details on UI

b. If the user uses the ‘Import Study (JSON)’ feature, the user will need to upload the JSON file.

3. Enter all the valid details by referring to the table

Field Name	Description

Field Name	Description
Name	Name of the OC study
Server	Dropdown with the list of servers configured.
Dataset	Name of the dataset from OC
Import CRFs	Options: All, Completed Denotes whether to fetch data for all or only completed CRFs
Notification Recipients	The email address of users who will be notified of the OC job success/failure

Site Mapping

Site mapping is needed to map the OC sites to the sites in OS. These sites are used as the registration and visit sites when adding participants and visits, respectively. Ensure that these sites are created and added to the protocol in OS before adding the mapping.

The OIDs for the sites can be found on the study overview page in OC. Refer to the screenshot below.

The mapping needs to be done like below, where the study OIDs are on the left side, and the sites are displayed in the CP site dropdown.

Exclude and Include CRFs

It is possible to exclude the CRFs (Case report forms in OC) from being synced into OpenSpecimen by uploading a list of the OC_CRF_OID names. Or the user can include only specific CRFs and fields from CRFs to be synced into OpenSpecimen.

From v10.2 onwards, if only the CRF include list is created in OID mapping, all the other CRFs will be excluded and will not be synced.

Click on the ‘More’ button → ‘Import OIDs Mapping’ option.
Upload the CSV file on the below page and click ‘Submit.’
Once the file is imported, the ‘OIDs Mapping’ section will be populated with the OIDs uploaded like below.

Field	Description
OC_CRF_OID	The OID of the CRF that needs to be synced from OpenClinica
OC_GROUP_OID	The group OIDs of the fields that need to be synced in OpenSpecimen
OC_ITEM_OID	The field OIDs from the CRFs that should be synced
OS_INCLUDED	Add Yes to include the CRF/field.
OS_EXCLUDED	Add Yes to exclude the CRF/field. No need to add the CRFs that needs to be excluded from v10.2.

Usecases to build the CSV based on the requirement:

Use case	Description
Adding only CRF OID	Will sync the whole CRF data from OpenClinica to OpenSpecimen
Adding only the CRF OID and Group OID	Will sync all the fields under the group OID to OpenSpecimen
Adding specific fields and their Group OIDs	Only the mentioned fields of the form will sync in OpenSpecimen.
Adding only CRF OID and exclude 'Yes'	Excludes whole CRF from sync

Example file

Participant Mapping

The participants will be created in the OS when the user runs the ‘Data Imported’ job. If the user needs to map fields from CRFs to OpenSpecimen fields, the user must add mapping in the participant fields section. Users can map both OS (gender, DOB, name, etc.) and custom fields in the section.

An example code is added below, in which the field ‘Patient Initials’ is mapped to the custom field ‘ST2.’

{
  "F_SPECIMENFORM": [
    {
      "crfOid": null,
      "fieldsMap": {
        "I_PATIE_SEX": {
          "name": "cpr.participant.gender",
          "type": null,
          "valueMapping": {
            "Female": "Female",
            "Male": "Male",
            "Prefer not to disclose": "Unknown"
          }
        },
        "I_SPECI_PATIENT_INITIALS": {
          "name": "cpr.participant.extensionDetail.attrsMap.ST2",
          "type": null,
          "valueMapping": {}
        }
      }
    }
  ]
}

Add the mapping in the ‘Participants Fields’ section.

Visit Mapping

Depending on which events the specimens have collected, the user can add the mapping of OC to OS events. It will help if the user creates those events in OpenSpecimen before adding the mapping so that the events are populated in the CP event dropdown. A visit will be created in the OS whenever an event is added in OC.

Specimen Mapping

To add PV mapping, the user needs to add the ‘valueMapping’ section to list OS values to be mapped to OC values.

Users can add a "when" condition to pull the specific type of specimens from CRF; the specimens will be identified based on the condition. UsersUsers can use the "default values" section to specify the specimen class and type values.

Refer to the specimen status code block below for mapping.