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Collection Protocol CSV

From v9.0. OpenSpecimen supports creating the participant and specimen-centric CPs using the CSV import. In order to use that user has to fill the below template and follow the steps to import the CPs in bulk.


Field NameData TypeMandatoryDescriptionValidation
TitleStringYesCollection protocol long titleUnique within the system
Short TitleStringYesCollection protocol short titleUnique within the system
CodeStringNoCollection protocol codeUnique within the system
Start DateDateNoCollection protocol start date-
End DateDateNoCollection protocol end date-
Specimen CentricBooleanNoCollection 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-
IRB IDStringNoIRB protocol number that was assigned to your study by the Institutional Review Board-
Anticipated Participants CountIntegerNoA number of participants will be registered in the Collection protocol.
PPID Format

String

NoParticipant Protocol ID format to generate the PPIDs by OpenSpecimen. Refer to this for more details.
Visit Name FormatStringNoVisit Name format to generate the Visits by OpenSpecimen. Refer to this for more details.
Label FormatStringNoPrimary specimen label format, refer to this wiki for more details
Derivative Label FormatStringNoDerived specimen label format, refer to this wiki for more details
Aliquot Label FormatStringNoAliquot specimen label format, refer to this wiki for more details
User inputs PPIDStringNoValues are Yes/No; if Yes, OpenSpecimen allows the user to input the PPID
User inputs Visit NameStringNoValues are Yes/No; if Yes, OpenSpecimen allows the user to input the Visit Name
User inputs Specimen LabelStringNoValues are Yes/No; if Yes, OpenSpecimen allows the user to input the specimen labels
Label Pre-print ModeBooleanNoPre-printing the label format. Refer wiki a page for more details.
Description URLStringNoCollection Protocol additional details
Activity StatusStringNoActive/Disabled, By default, it's Active.
Sites#1#NameStringYesCollection Protocol Site Name
Sites#1#CodeStringNoSite Code
Sites#2#NameStringNoCollection Protocol Site Name
Sites#2#CodeStringNoSite Code
PI#PI EmailEmailYesPrinciple Investigator of the collection protocol. Users need to provide the email ID in this field
Coordinator#1#Coordinator EmailEmailNoCollection Protocol coordinator. Users need to provide the email ID in this field


Example Collection Protocol Bulk Import Template:


Steps to Import Collection Protocol CSV:

  1. Download the above template and fill in all the required details
  2. Follow the steps on this wiki (Section - Rules for the import file naming) page to give the specific naming convention to the filled template.
  3. Once the file is ready, Go to Extras → Import Records
  4. Upload the CSV file you created (You can upload the CSV or ZIP, which includes the CSV)
  5. Check the import status


Import CP Events and Specimen Requirement:

From v7.1, it is possible to bulk import CP event and specimen requirements. This is useful for bulk importing legacy data, managing large CPs, or interfacing with external apps.

Refer to the below pages for details.


Got feedback or spotted a mistake?

Leave a comment at the end of this page or email contact@krishagni.com