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Overview

In longitudinal collections, specific time points for collection, specimen requirements, and processing details are defined at the start of the study. The planned collection workflow of OpenSpecimen allows you to define study calendars and SOP for the study.

While these specimens are ‘expected’ to be collected for each participant in some cases, there might be ‘deviations’ that can be handled during specimen collection.

The participant missed the whole event
Repeat visit for the same visit
Some specimens are not collected
Some specimens are partially collected
Additional specimens are collected

Prerequisites

Refer to https://openspecimen.atlassian.net/wiki/x/EgB9 page for details on configuring the longitudinal collection protocol.

Collecting planned specimens

You can collect specimens of a visit based on the specimen requirements defined in the collection protocol. The specimen collection button is available in many places to minimize the number of clicks.

When you Create visits | From Registration Page or Create visits | From Participant Overview Page, the next step in the workflow is to collect the specimens.
If the labels are autogenerated, then the user is not allowed to enter the label format
If there is no label format set, then the user can add labels for the specimens.
In the screenshot below, the user is not allowed to add labels for primary and derived specimens but can add aliquot labels
If there is a nth step configured in the JSON, then the fields will be visible in the next step.

Collecting pending specimens

Example scenarios:

The visit may be created on the previous day of the surgery and the specimens are collected post-surgery. The user will add a visit first and collect the pending specimens later.
The collection site sent 2 tubes on day 1 and the other 2 tubes on day 2. In this case, the user will collect the first 2 tubes first and collect the pending specimens later

From the participant overview page, click on the dotted menu of the occurred visit->Collect Pending Specimen
You will be navigated to the ‘Collect Pending Specimens’ workflow

Deviations

You can change the number of aliquots, specimen status, specimen quantity, etc. at the time of specimen collection.

Change the number of aliquots:

Click on the dotted menu to change the number of aliquots and click 'Ok.'
Once done you can scan the labels in the text box above
The labels will be assigned to individual rows as below

Change the status of the specimen:

Click on 'Status' drop-down to change the status (Collected/Missed/Pending) of the specimen

Change the quantity per aliquot:

Click on the ‘Quantity’ field and update the value
Click on ‘Submit’ once the values are entered
The ‘Available Quantity’ for the parent specimen will be updated based on the total quantity of direct aliquots created under it.

Missed Visits or Specimens

If a specimen is not collected, you can create specimens with the status ‘missed’ for audit/reporting purposes. E.g., give a list of all missed specimens.

If a visit is marked as ‘Missed Collection’ then all the specimens under that visit are marked as missed. Refer to Create visits | Create missed visit for more details
If you want to mark a few specimens as missed, you can change the specimen status in the collect specimen step.

Collecting Additional specimens

You can create additional specimens that are not defined in the protocol. Refer to Unplanned Specimens for more details.

Longitudinal Specimen Collection