Johns Hopkins’ OpenSpecimen adoption over the years

The Johns Hopkins University School of Medicine has adopted OpenSpecimen as a scalable solution for biospecimen information management. Key features possible in OpenSpecimen that led to its adoption include:

  • Annotation of research and clinical data
  • Interfaces with clinical and research systems
  • Query capability
  • Open Source with strong user community
  • Security
  • Specimen and Derivative Tracking

OpenSpecimen v2.5 was adopted in December of 2016. Faculty and IT staff meet monthly in the OpenSpecimen Steering Committee to discuss OpenSpecimen support and future development.  A dedicated IT team at Johns Hopkins provides onsite support which is augmented by a service contract with Krishagni. The Johns Hopkins OpenSpecimen team is active in both the public forums and the user meetings, thus supporting new adopters and assisting in the creation of a strong user community.

Krishagni team with Johns Hopkins’ OpenSpecimen implementation team

As OpenSpecimen is open-source, meaningful modifications have been made to the application to better serve the needs of the Johns Hopkins research community. These modifications include a web-service interface with surgical pathology reports, which allows study team members to view surgical pathology reports for specimens belonging to Johns Hopkins study participants. Other projects that further extend the OpenSpecimen application are either ongoing or being planned, including the development of a plugin to match OpenSpecimen participants to patient records in Epic, the use and/or creation of a REDCap interface, and the creation of an enterprise login via Shibboleth. Some details of these projects are discussed in more detail below.


Prior to OpenSpecimen, caTissue was piloted by Johns Hopkins beginning in 2008. In September 2011, an evaluation of caTissue v1.2 was led by the Hopkins Conte Digestive Disease Center, which then helped to educate and train users from other Divisions and Departments. In July 2013, an upgrade to caTissue Plus v3.0 was performed, which was followed by the adoption of OpenSpecimen v1.0 in early 2015. An upgrade to OpenSpecimen v2.5 was performed in early 2016 and Johns Hopkins is currently in the process of upgrading to OpenSpecimen v3.3.

Overview of current usage
OpenSpecimen is used at Johns Hopkins University School of Medicine. A variety of specimen collection workflows is supported depending on the needs of the study teams. Study teams initially meet with the Johns Hopkins OpenSpecimen team to discuss the nature of specimen collection (I.e. prospective or legacy), and to determine how to best configure the application based on research needs. The application is presented to study teams through an initial demonstration, after which time study team members are granted access to an internal Test server instance of OpenSpecimen to become oriented to the application and to evaluate draft collection protocols. Recording of legacy specimen collections in OpenSpecimen is facilitated by a data-checker template that was developed internally, which validates the format of legacy data for upload to OpenSpecimen.

Implementation details

Implementations and upgrades are performed internally by the Johns Hopkins OpenSpecimen team.  The source code is pulled from GitHub, and the application is built from the code for each upgrade. Currently, three environments are used to help implement and test OpenSpecimen: Dev, Test, and Prod. Key functionality is tested using a regression test plan. Release notes are developed and distributed internally, which highlight key functionality relevant to the Johns Hopkins research community.

Integration with pathology database

OpenSpecimen is integrated with our pathology database to display the surgical pathology reports for research participants. As user permissions in OpenSpecimen are role-based, study team members with appropriate user privileges can view the surgical pathology reports for their study participants who have registered with valid Hopkins medical record numbers. This allows the study team to view surgical pathology results relevant to specimens collected, which can be annotated in OpenSpecimen with custom forms.

Integration with EPIC (in progress)

Research participants are often registered within the application by manual data entry, which can introduce data entry errors.To mitigate these errors and to support matching OpenSpecimen data with clinical data, we are creating an interface to validate participant data entry into OpenSpecimen against Epic. This will be a real time link between OpenSpecimen and EPIC wherein when a MRN or eMPI is entered in OpenSpecimen, it will make a web service call to EPIC to fetch the demographic data. This data is stored in OpenSpecimen in a “locked” manner to prevent editing in OpenSpecimen.