Export all data

Exporting all data from a Collection Protocol (CP) or exporting data within a CP can be extremely time-consuming, especially if the system contains thousands or millions of records. This operation has the potential to slow down or even bring down the system.

To avoid performance issues, it is recommended to export data for specific participants, visits, or specimens within the CPs, rather than attempting to export all data at once.

Introduction

OpenSpecimen allows users to export data in bulk for all or specific records using unique identifiers like label, name etc.

It can be used to download data for:

Participants
Consents, including consent files
Visits including surgical pathology reports
Specimens including events
Custom forms data 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
Inside the CP

Export data for all CPs

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 “Export” button.

Note:

Export all records: If no “Participant Protocol IDs” are specified and export is clicked, it will download a CSV file which contains all participant records from all CPs.
Export data for specific records: You can also specify specific PPIDs in the “Participant Protocol IDs” separated by the comma(‘,’), tab, or new-line. This will download data for only those participants.

Visit-related data can be downloaded using the visit name, while specimen-related data can be accessed through the specimen label. For instructions on downloading consent and SPR files, please refer to the wiki page: Download SPR/Consent files in bulk.

Note: Data is exported for the CPs to which the user has access.

Export data for specific CP

Data can also be exported from the participants list page within the CP. The key distinction is that this export will only include the records specific to that CP.

To export data for custom fields, such as Specimen Custom Fields, you must select "Specimen" as the record type. This selection applies to participants, visits, and other related entries.

Navigate to the Collection Protocol: Participant List Page and select More → Export.
You will see several export options available, including Participant, Visits, and Specimen, among others.
Choose the relevant object, input the required list, and proceed with the export.

OpenSpecimen

Export Biospecimen Data

Introduction

Export data for all CPs

Export data for specific CP

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