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Export Biospecimen Data
Video
Introduction
OpenSpecimen allows users to export data in bulk for all or specific records using unique identifiers like label, name, etc.
If an export takes longer than expected, OpenSpecimen sends the export file to the user via email. To receive these emails, the user's ‘Disabled Notifications’ setting must be “No.”
It can be used to download data for:
Participants
Consents
Visits
Specimens
Events
Custom forms (at any level)
The data is exported in CSV format, which is similar to the bulk import template. This is useful when we want to import the exported records into another instance of OpenSpecimen.
We can do this in 2 ways:
Outside the CP (from CP list view)
Inside a CP (from the Participant list view of a CP)
How to export all records vs specific records?
In the text area field, if you do not enter any identifiers (like PPID, label, visit name, etc), all records will be exported.
To export records for specific fields, enter the object-specific ID in the text area (separated by comma, tab, new line, etc.)
Participant: PPID
Visit: Visit name
Specimen: Label or barcode
Export data for all CPs
Note: When exporting data from the CP list view, OpenSpecimen does not have the context of a CP. This impact in the following way:
Positive: Can export data for multiple CPs.
Negative: The exported data does not include CP-specific custom fields or forms. Only system-level forms and fields are included.
Step 1: Go to the ‘Collection Protocol’ page and click on the export button.
Step 2: Select the record type from the ‘Record Type’ dropdown and click on the “Export” button.
Export data for a specific CP
Positive: Includes CP-specific custom fields and forms when the correct record type is selected.
Negative: Export is limited to only one CP at a time, which may require multiple exports for multi-CP analysis.
Note: Custom fields only appear if you select the appropriate record type (e.g., you must select "Specimen" to export specimen custom fields).
Step 1: Go to the ‘Participant List View’ page and click on the export button.
Step 2: Select the record type from the ‘Record Type’ dropdown and click on the “Export” button.