Users can create/update multiple CPs at once using the 'CP CSV import' feature of OpenSpecimen.
To update any field of the collection protocol, it's important to ensure that all columns and their existing values are maintained during the update process. If any fields are left blank, those fields will be overwritten with empty values, potentially causing data loss or incorrect updates.
Below are the fields in the template:
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Field Name | Data Type | Mandatory | Description | Validation |
|---|
SitesX#Name | String | Yes | Sites for the CP. You can create multiple columns replacing 'X' with number. E.g., Sites#1#Name, Sites#2#Name, etc. | Site name should be present in OpenSpecimen. |
SitesX#Code | String | No | Site codes for the CP. You can create multiple columns replacing 'X' with number. E.g., Sites#1#Code, Sites#2#Code, etc. | Site code should be present and associated to the site in OpenSpecimen. |
Identifier | Integer | No | The CP Identifier. Mandatory: when updating Short Title. | Unique within the system |
Title | String | Yes | Collection protocol long title | Unique within the system |
Short Title | String | Yes | Collection protocol short title. Mandatory: when updating CP Details. | Unique within the system |
Code | String | No | Collection protocol code | Unique within the system |
PI#PI Email | Email | Yes | Principle Investigator of the collection protocol. Users need to provide the email ID in this field | |
Coordinator#1#Coordinator Email | Email | No | Collection Protocol coordinator. Users need to provide the email ID in this field | |
Start Date | Date | No | Collection protocol start date | - |
End Date | Date | No | Collection protocol end date | - |
IRB ID | String | No | IRB protocol number that was assigned to your study by the Institutional Review Board | Unique across the system |
Specimen Centric | Boolean | No | Collection Protocol Type: If value = TRUE/YES, it will create the Specimen Centric CP. Else, it will create the participant centric by default if you have not provided any option. For FALSE/NO, it will create the participant-centric CP | - |
Anticipated Participants Count | Integer | No | A number of participants will be registered in the Collection protocol. | |
PPID Format | String | No | Participant Protocol ID format to generate the PPIDs by OpenSpecimen. Refer to this for more details. | |
Visit Name Format | String | No | Visit Name format to generate the Visits by OpenSpecimen. Refer to this for more details. | |
Label Format | String | No | Primary specimen label format, refer to this wiki for more details | |
Derivative Label Format | String | No | Derived specimen label format, refer to this wiki for more details | |
Aliquot Label Format | String | No | Aliquot specimen label format, refer to this wiki for more details | |
User inputs PPID | String | No | Values are Yes/No; if Yes, OpenSpecimen allows the user to input the PPID | |
User inputs Visit Name | String | No | Values are Yes/No; if Yes, OpenSpecimen allows the user to input the Visit Name | |
User inputs Specimen Label | String | No | Values are Yes/No; if Yes, OpenSpecimen allows the user to input the specimen labels | |
Label Pre-print Mode | Boolean | No | Pre-printing the label format. Refer wiki a page for more details. | |
Description URL | String | No | Collection Protocol additional details | |
Activity Status | String | No | Active/Disabled, By default, it's Active. | |
Example Collection Protocol Bulk Import Template:
.csv?version=1&modificationDate=1659877814031&cacheVersion=1&api=v2&viewType=fileMacro)
Steps to Import:
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Download the above template and fill in all the required details
Follow the steps on this wiki (Section - Rules for the import file naming) page to give the specific naming convention to the filled template.
Once the file is ready, Go to Extras → Import Records
Upload the CSV file you created (You can upload the CSV or ZIP, which includes the CSV)
Check the import status
Steps to Update:
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Export the CP details by navigating to CP List Page → More → Export → Collection Protocol.
Update values for required column, and save the CSV file.
Navigate to CP List Page → Import Biospecimen Data → Select Collection Protocol → Choose the above saved CSV file → Import.