1 Introductory Video
2 Defining Timepoints
- 2.1 Adding Events
3 Adding Specimen Requirements (SR)
- 3.1 How to set the Default value for the custom field at the individual SR level?
- 3.2 Adding Derivatives and Aliquots
4 Defining Consents

In a longitudinal Collection Protocol, subjects are followed over time with continuous or repeated timepoints to collect biospecimens. The list of biospecimens to be collected per timepoint and their processing details are predefined.

Introductory Video

In OpenSpecimen, you can create a CP with basic details for your study.

Select 'Collection Protocols' from the left side menu or home screen
Click the 'Create' button from the protocol's list page.
Enter the required information according to your study and click the 'Create' button
Example: Creating a CP for the 'Lung cancer research study.'

Details for all the fields on the CP overview page,

Note:

The CP level PI and Coordinators will not be assigned roles automatically or by default.
After creating the CP, the admin has to manually assign specific roles to all the users who need to access the CP.
The CP Start and End Date:
1. These dates denote the CP's validity; PIs are sent reminders when a CP is approaching its expiry.
2. Users can update the Start/End Date of CP
3. The dates do not have any functional effects on the CP and its operations.

Defining Timepoints

For longitudinal collections, you have the ability to configure event points and specify specimen requirements. By predefining more CP events, you can significantly reduce the amount of daily data entry needed. The system is equipped to manage various types of deviations, such as instances where the collected quantity is less than planned, during the collection process.

Adding Events

An event represents one collection time point in which one or more specimens are collected. E.g. Day 0, Day 30, Cycle 1 etc.

Click the 'Events' tab on the left-hand side of the CP details page.
Click 'Add Event' and enter the required information.

Field	Mandatory?	Description

Field	Mandatory?	Description
Event code	No	It's a shortcode for an event that can be used for specimen barcoding or auto label generation.
Event Point (number)	No	Timepoint within the study calendar on which the specimen collection or registration is due. It decides the order of events displayed on the CP and participant overview page. You can edit the event point to change the order of events.
Event Point Unit (new in v4.3)	No	Timepoint units like Days, Weeks, Months, and Years.
Event Point Label	Yes	A unique name within the CP for this time point. For example, Pre-Surgery, Surgery, 90-day follow-up, Relapse, etc.
Default Site	No	You can select the default site for the event timepoint.

For an unplanned CP, it is not required to predefine event time points. However, it is mandatory to have at least one event defined in the current version.

Adding Specimen Requirements (SR)

Specimen requirement defines what specimens are expected to be collected and how they should be processed at each time point. E.g., Collect two whole blood specimens, process one into plasma, and the other into serum.

Click 'Add Specimen Requirements' and enter the required information.

Field Title	Mandatory?	Description

Field Title	Mandatory?	Description
Name	No	The user-friendly name for the requirement. (Used for display and query. E.g., Pre-op blood.)
Code	No	A short unique code that is used for auto-labeling specimens. e.g., WBEDTA stands for whole blood in EDTA
Stored in the repository?	No	Whether the specimen would be fully utilized in processing or stored in the repository, E.g., 'Whole blood' will be stored in aliquots. For setting up auto container allocation, refer to https://openspecimen.atlassian.net/wiki/x/KABLB
Sort Order (Number)	No	This field is used to decide the order of the specimen requirement(SR). By default, SRs appear in the order they were added by you. If you wish to reorder the sequence of SRs to accurately mimic the collection process, edit the SR, and assign new values to the sort order.
Collection Container	No	Type of container used for specimen collection.
Pre-barcoded Tube	No	Pre-barcoded Tube option indicates whether the tube/vial to store the anticipated specimen will be pre-barcoded or not. When the pre-barcoded tube option is enabled, barcodes will not be auto-generated. Users will have to manually specify the specimen barcode where the barcode format is set or not.
Default Custom field Values (v11.2)	No	Allows you to default specimen custom field values at the individual specimen requirement level.

How to set the Default value for the custom field at the individual SR level?

In many studies, certain specimen custom fields often have default values that sometimes/never change, for example, Additive = EDTA for Whole Blood.

These impacts data entry in 2 ways:

Forcing users to create custom workflows/ configure the Nth step
Create multiple custom workflows/ add complex logic for defaulting values in individual steps

Defaulting values in Specimen Requirements (SRs) automatically update these values without showing fields during data entry in System Workflows. These values are shown as default values in custom workflow steps. This feature helps end users with easier maintenance, a less complex workflow setup

Navigate to Collection Protocol → Events → Specimen Requirement → Edit the SR-> Add the JSON code in the 'Custom Field Default Values' field.

Syntax to be used:

{
“Form_field_variable_name1”: “Value to be defaulted”,
“Form_field_Variable_name2”: “Value to be defaulted”
}

Example Code

{
  "another_additive": "Glycerol",
  "collection_approved": "Yes",
  "req_reference_id": "GAS28712",
  "analysis_type": "Genomics",
  "tube_type": "Matrix 0.5ml tube with screw caps",
  "additional_comments": "Confirmed Cancer samples by lab",
  "media_volume": "1",
  "processing_type": [
    "Plasma Extraction"
  ],
  "equipment_used": [
    "Janus G3 Expanded"
  ],
  "cold_ischemia_by": "current_user",
  "cold_ischemia_start_time": "current_date",
  "cold_ischemia_at": "Saurav_Biobank"
}

Note: The default values won’t be visible in the system workflows while doing data entry. However, it will be visible for custom workflows

Adding Derivatives and Aliquots

A derivative is the parent specimen's processed outcome (e.g., plasma or serum from blood), whereas an aliquot is the smaller portion of the parent specimen.

Click the dotted menu of the specimen and click 'Create Derivatives'
Enter the required information and click on Create Derivative
To add aliquots, follow the same steps and select 'Create Aliquots'

To create aliquot with 0 quantity, you need to ask the super admin to enable "Mandatory Aliquot Quantity" under the "Settings" card.

You can default values of custom fields for individual derivative and aliquot using code same as Longitudinal Collection Protocol | Adding Specimen Requirements (SR)

Defining Consents

Consent statements are created at the system level by super admins and institute admins. Once created, the User can use it in multiple CPs. Refer 'Coded consents' for more details.

Go to the CP in which you want to add the consents.
Click the 'Consents' tab from the left-side menu.
Click 'Add Statement'. A drop-down list of existing consent statements will appear.
Search for the required consent statement using its code or the statement itself and click 'Add.'

If you are not planning to use a consent feature for your CP, select 'Consent Waived?' as 'Yes.' This will hide the consent tab from the participant-level page.