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Additional Data Entry Modes (RDE/SDE)

Owned by Poornima Govindrao
Last updated: Aug 26, 2024 by Amol Gayakwad
154 min read

Rapid Data Entry (RDE)

RDE and SDE plugins are removed from v11 onwards. For multiple participant registrations, you need to setup a custom workflow.

Introduction

The RDE plugin is designed for clinical study based collections where the type of specimens and collection schedule is well-defined. It is dependent on well-defined label formats for participants, visits and specimens, which can be preprinted either from OpenSpecimen or generated outside.

The RDE plugin allows you to do the following:

  1. Specimen collection based on barcode scanning

  2. Process multiple participants in one-go

  3. Process aliquots in bulk

It is meant for high-throughput clinical studies or trials where 5–10 patients visit the clinic every day.

Workflow Configuration

The typical workflow of clinical studies is: A participant visits a clinic where the primary specimens are collected (e.g. whole blood, tissue, urine, etc.) based on the event time point (e.g. day 0 - screening, day 30 - pre-op, etc.). These primary specimens are then sent to the lab for further processing like DNA, RNA, and/or aliquoting. 

RDE can be configured to mimic this workflow. Once RDE is configured, the 'Rapid Collection' button is visible on the CP's 'View Participants' list page.

Steps to register the multiple participants in one go along with specimens

Step 1: Register participants

Data fields required for this step is configurable. Multiple participants can be registered at once. Existing participants can be entered in this step to add specimens for follow-up visits.

Step 2: Select visit under which the specimens needs to be accessioned

The visit selected can be different per participant. If existing participants are entered in the first step, the matching participants are populated in this step.

Step 3: Enter details about primary samples collected

Based on the protocol definition, the primary samples to be collected is shown for each participant and visit. You can select the ones that are collected and mark the ones that are missed.

Step 4 (Option 1): Scan aliquots in the box view- this is useful if a box scanner is used and the order of scanning the aliquots is fixed

Different box layouts can be defined per type, CP, etc. The order of scanning the aliquots is determined by order of requirements defined in the CP. If some samples are not processed as per CP, those slots can be left empty. 

Example JSON

Step 4 (Option 2): Processing aliquots: Scan aliquots directly in actual container boxes

The system will show a list of available storage boxes. You can select specific boxes and scan labels or barcodes. This will mark the aliquots as collected and store them in specific boxes.

For this option to work, the CP should have pre-defined label formats and pre-print options checked so that the labels are auto-generated for pending aliquots.

Example JSON

Step 5: Configurable to add additional details about the aliquots- any fields like frozen time, spun time etc. can be entered for all aliquots on this page

This is an optional step and can be configured to show specific fields per aliquot.

Add visit name on participant and visit registration in RDE

Previously on the RDE visit screen, the only visit field was 'Event name'. The system used to autogenerate the visit names according to the default format or the one provided by the user. Now the visit name can be taken as user input and used as a part of the specimen labels.

Add the below-mentioned code block in the section 'regFields' of the JSON to add the visit name field on the 'Collect Visit Details' page. Refer to page Configuring RDE for details on JSON configuration.

{ "name": "visit.name", "caption": "Requisition ID", "type": "text", "regVisit": true }

The 'Collect Visit Details' page would look like the screenshot mentioned below, where the field 'Requisition ID' is the visit name

Enable standard tree-view/nth-step specimen collection within RD

This feature allows you to:

  1. Show the tree-view/nth step collection page. 

  2. Collection of specimens for multiple patients one after another in a loop

  3. Data entry screens look similar to single entry mode

  4. Skip the RDE configuration: If "collectionWorkflow": "standard", it shows the standard collection page

Code snippet
... { "name": "rde", "data": { ... "collectionWorkflow": "standard" ... } } ...
Example JSON

 

Here the example of JSON file where we enabled nth step specimen collection within RD.

Steps with Screenshots

Screenshots:

  1. Add multiple patients with event time points → Proceed to Collect Specimens.

    2. Patient-1 (RDE-TST-001): Shows standard specimen collection page based on the above JSON configuration, and it skips the RDE layout.

3. Shows nth steps if present in the JSON workflow as below, 

4. Once submitted, it navigates to the collection page for the second patient (RDE-TST-002)

 

Configuration to use the existing visit

To reuse the existing visit for the timepoint selected during RDE data entry instead of creating a new visit, the following attribute should be added to the RDE section of the workflow JSON:

Code snippet

Use-cases: During RDE data entry, if the above flag (lookup Visit) is set to true, below are different use cases of how it will work when a time point is selected, and you can proceed to collect specimens:

Sr No.

Test Case

Results

Sr No.

Test Case

Results

1

Only one visit exist for the time point selected

Uses the same visit and show all the pending specimen to collect

2

No visit exists

Create new visit

3

More than one complete visit exists - with different visit dates

Choose the latest visit for collection

4

One complete and one pending visit exists

Uses the Pending visit

5

One complete and one missed visit exists

Uses the complete visit to collect the pending specimens

6

Only 1 missed visit exists

Create new visit

7

Visit exist with few specimens collected

Throw error saying, No pending specimens to collect in this visit. 

Example JSON

Simple Data Entry (SDE)

Create planned specimens using SDE

SDE deposit mode allows the user to create multiple specimens in one go. This can even be across patients and visits. For creating planned specimens (as per requirements defined in collection protocol), you must include the 'Requirement Code' within the deposit screen. This will allow the system to map the specimen being created to the requirement in the CP.

Define the requirement code in the dictionary as below, which will be displayed as a dropdown of existing codes within that event of the CP:

The below example shows how the requirement code can be used within the deposit table of SDE. The fields defined in the requirement can be skipped here so that the value has defaulted from the requirement. For example, the specimen type is not included in the below example so that the system will take it from the corresponding requirement.

 

Screenshot:

Create container along with specimen

In the screen where specimens are collected, you have an option to create containers like boxes too. This is useful for a workflow where a lab receives a box of specimens, and they want to store the box as is in their freezers. This workflow reduces the step of creating the empty box first.

 

Got feedback or spotted a mistake?

Leave a comment at the end of this page or email contact@krishagni.com