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.

Similarly, visit related data can be downloaded using visit name and specimen related data using the specimen label. To download consent and SPR 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 be exported from within the CP too from the participants list page. The only difference would be it will only download the records for that CP.

Go inside the Collection Protocol: Participant List Page → More – Export
You can find many options to Export: Participant, Visits, and Specimen etc
Select appropriate object, provide the list and export

Export Biospecimen Data

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Introduction

Export data for all CPs

Export data for specific CP