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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.

Collection Protocol Fields.

Note: There is no support for importing main CP fields

...

Field Name

...

Data type

...

Mandatory

...

Description

...

Validations

...

Sites

...

From v9.0. OpenSpecimen supports Add and Update of CPs using the CSV import. From v10.3, we have made significant changes to the CSV template with an option to export and import CPs similar to other biospecimen data.

Below is the template:

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. It is mandatory for updating the CP. 

Unique within the system

Title

String

Yes

The

Collection protocol long title

of the research study

Unique within the system

Short Title

String

Yes

Short title to identify the study from the CP list pageShould be unique Should be unique

Collection protocol short title

Unique within the system

Code

String

No

'CP code' that can be used to generate the participant IDs

Collection protocol code

Unique within the system

Principal Investigator

PI#PI Email

String

Email

Yes

The user who leads the studyProtocol CoordinatorStringNo

A specialized a researcher who supports the management and coordination of clinical research studies. There can be multiple coordinators selected.

DateIntegerNoStart and End date of the study. Some clinical trials are for a specific duration.Ethics Approval ID/IRB IDIntegerNoThe 'approval ID' given by the Ethics committee to conduct the study TypeStringNoIf the study collects participant's information, then select 'Participant centric' else 'Specimen centric' for specimen biobanks.

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

The

A number

of participants that

of participants will be registered in the Collection protocol.


PPID Format

String

No

Participant Protocol ID format to

the protocol. (The number of actual registrations can exceed)SOP Document URLStringNo

Link to the SOP document uploaded on the university web portal

SOP Document FileNoDuring CP creation, the user can also upload the study-related standard operating procedure document files. The users can access the SOPs that have been set at the CP level during data entry. This helps them perform any procedure consistently.Store SPRs?NoThe visit page will show the SPR tab if enabled.Extract Text from SPR PDF Docs?NoThe text from the uploaded SPR file is shown in the 'Surgical Pathology Reports' section when enabled. (If the SPR contains scanned images, then there is no text extracted)

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:

View file
namecp_create_202204200312000 (1).csv

Steps to Import:

  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 import CP event and specimen requirements. From v10.3 it is possible to export-import events/SRs across multiple/all collection protocols. This allows users to copy events/SRs from one env to another/ update existing setup.

Refer to the below pages for details.