This article is written based on our implementation experience at the University of New South Wales biorepository.

To ensure data privacy and minimize data vulnerability, Krishagni provides an option to encrypt the OpenSpecimen MySQL database “at rest”, which will ensure that if anyone with malicious intent gets access to the server will not decrypt the data.

Below is a typical network diagram of OpenSpecimen deployment. Usually, on-premise deployments are safer than on-cloud deployments since the database is deployed within the institute’s VPN. However, when the database is on the cloud, it is vulnerable to attacks.

There are two types of data encryption:

At rest: In the database, all the patient’s data is stored in files. The attacker can retrieve sensitive data if they get direct access to these files. To avoid this, we can encrypt these data files in such a way that even if someone gains access to the data files, they cannot access the data.

In transit: When data transfers through a network, it can be intercepted before it reaches the target system. It is also known as “Man In The Middle” attack. To prevent this, the data during transit is encrypted using SSL encryption.

MySQL Database Encryption

The MySQL database can be encrypted using the “Keyring Plugin” provided by MySQL.

MySQL provides the keyring plugin to encrypt the table data files. To encrypt and decrypt database keyring files is used. This file should be kept outside of the database server file system, i.e., on any external hard drive or remote server for more security.

While this article is written for MySQL, the same can be achieved with other databases like Oracle. Post encryption, we have not experienced any performance (speed) drop in the OpenSpecimen application. 

Written by: Krishna Waidande. Krishna is a System Administrator at OpenSpecimen and manages product deployments, databases and configuration.

For more details email contact@krishagni.com

SpecimenCatalog helps with sharing biospecimen data with researchers.

It provides an easy-to-use interface for researchers to look for specimens of interest and submit requests. Catalogs can be created based on various conditions such as specimen type, pathological conditions, clinical diagnosis, etc.

The researchers can access each Catalog using its URL. The researchers can choose the desired specimens using various filters, add them to the cart, and place specimen requests. The Request Admins receive notifications for new Requests and can further process them.

The SpecimenCatalog module not only saves time and efforts of both biobank and researchers, but it also takes care of the specimen disposal process after distribution.

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SpecimenCatalog Highlights

• Create multiple Catalogs – based on diseases and research needs
• Control access to the Catalog through the login
• Manage/Track specimen requests by various researchers
• Download reports for the specimen requests
• Can be shared with researchers who do not have OpenSpecimen

Request Workflow

A researcher can shortlist the specimens using the “easy to use” catalog user interface and add these specimens to a Cart. Once ready, the research can fill in a “request form” customized for this Catalog.

The Request Admins can review the Request and approve/reject them.

Uploading Data

Multiple groups/labs can upload data into the Catalog using the CSV Import feature – even from groups not using OpenSpecimen.

It is also possible to configure the dataset dictionary with SpecimenCatalog based on the disease and research needs of the institute.

Demo and More Details

Email: contact@krishagni.com

From v4.3, you can change the order of data entry forms through collection protocol settings.

To reorder:

Go to Collection Protocol -> Settings -> Forms and drag and drop the forms to reorder them.

“Save and Next” button:

Further to make the data entry simpler, the ‘Save and Next’ button on the forms page takes the user to the next form in the list.

For more details refer: https://openspecimen.atlassian.net/wiki/x/IYD0Dw

Ability to search forms by additional filters: 

Earlier the forms were searchable only by name. It was difficult to find out which CP or level the forms were attached to. From v6.2, two new search filters are added:

1. Collection Protocol title
2. Attachment level

Better UI to attach forms: 

Initially, the forms attachment levels were primarily CP driven. However, the UI to attach forms was confusing since we now support many non-CP related levels (e.g. Container, Site, DPs, etc). 

This is resolved in v6.2 with a much cleaner UI to attach forms.

Ability to edit the multi-record option: 

Sometimes there might be protocol changes and the user might need to switch from single to multiple record collection or vice versa. Earlier it was not possible to edit the multi-record option. From v6.2, the user can edit it just by checking/unchecking the checkbox next to the multi-record option. 

For more details refer: https://openspecimen.atlassian.net/wiki/x/AQD1Dw

• Who transferred the container
• Date and time of transfer
• Reason for transfer
• Generate reports of such transfers
• See the transfer details in the specimen level

Starting from v6.2, the containers can be transferred by clicking the “Transfer” button present on the container overview page. Once the transfer is done the system will log a “transfer event” at the container level as well as for the specimens stored in that container.

Transfer Event at container level:

Container Transfer Event at specimen level:

For more details refer: https://openspecimen.atlassian.net/wiki/x/54DIBg

OpenSpecimen has introduced a new default role “Clinician” for such users. Clinician users can only perform participant registration, ship specimens, and accession primary specimens.

To know more details: https://openspecimen.atlassian.net/wiki/x/X4CB

1. Not able to query across multiple CPs using custom forms
2. Cumbersome to manage updates to JSON workflows in multiple CPs

From v6.2, OpenSpecimen allows creating “Collection Protocol Groups (CPG)” for easy maintenance of such protocols. This feature allows the user to-

• Have the same JSON configuration for all the collection protocols in a CPG
• Add custom forms or custom fields to all the collection protocols in a CPG in one-go
• Query custom form data from multiple protocols within a CPG

For more information refer: https://openspecimen.atlassian.net/wiki/x/X4CB

OpenSpecimen can be integrated with REDCap (or other EDCs like OpenClinica) to eliminate manual data entry and query data across the two systems. The plugin is currently used by many customers including Washington University, Columbia University, Telethon Kids (Perth), and University of British Columbia (Vancouver). 

The plugin performs the one-way data synchronization from REDCap to OpenSpecimen. The data pulled includes all the instrument information (i.e. CRFs) into OpenSpecimen Forms. This data can be used to populate participants, visits, and any other clinical data.