Developed by at The Children's Hospital of Philadelphia Research Institute

About

What is The Biorepository Portal Toolkit?

The Biorepository Portal (BRP) is a federated web application originally designed to support longitudinal biospecimen collection activities. Using HTTP protocols, it interfaces with downstream data systems, including REDCap and Thermo Fisher Scientific's Nautilus LIMS, to provide a single unified interface for data collection and update activities. An electronic honest broker (eHB) ensures longitudinal data collection is performed in a manner compliant with NCI Best Practices for Biospecimen Resources.


The Children’s Hospital of Philadelphia (CHOP) Department of Biomedical and Health Informatics (DBHi) developed an open-source informatics infrastructure to support data-intensive longitudinal biorepository studies.


Benefits of using the BRP Toolkit include:

  • De-identification and re-identification of subjects on-the-fly
  • Creation and addition of records in multiple research systems to ensure patient privacy.
  • A longitudinally updated specimen and data resource that enables more flexible non-human subjects research.

  • Read more from the 2015 AMIA Peer-Guided Workshop Abstract

    History

    The Department of Biomedical and Health Informatics at The Children’s Hospital of Philadelphia developed an honest brokered modular tool-kit for biorepositories and biobank management. This tool-kit was developed to facilitate biorepository workflows that are asynchronous and longitudinal. The design needed to:

  • Protect subject privacy;
  • Utilize disparate research and clinical systems;
  • Allow for complex workflows in research and specimen coordination;
  • Facilitate cohort analysis and scientific discovery through a de-identified, non-human subjects resource
  • Future proof the data and specimens at the most granular level to allow for supplemental annotation as the science advances.
  • The enterprise application development team at the Department of Biomedical and Health Informatics (DBHi) developed this toolkit to replace an paper recording process for two projects; the Children’s Brain Tumor Tissue Consortium (CBBTC) and the Center for Childhood Cancer Research (CCCR) general accrual biorepository.

    Architecture

    The design of this integrated application set serves a two-fold process: integrating data on the way in and on the way out. Therefore, the applications support study management/operations AND data query/scientific data integration. The toolkit integrates fully with REDCap and our enterprise LIMS for study data management. For data discovery, it integrates the Harvest Data Discovery Platform where the Portal and Honest Broker components of the toolkit broker data needs across systems and use cases.

    Components

    • electronic Honest Broker (eHB)

      ehb-client
      ehb-service
    • eHB Datasources

      ehb-datasources
      REDCap Client

      A client to REDCap. Allowing study coordinators to associate multiple REDCap projects with a single honest-broker subject, and view or enter data de-identified into the forms on those projects.

      LIMS Client

      A custom client to our enterprise LIMS system. Please contact us to discuss the details of this project.

    • Query

      For all researcher-facing projects we utilize the open-source Harvest data exploration platform to display de-identified specimen, clinical and genomic data on a project-by-project basis.

    • Data Integration and ETL

      For each project we build a custom set of scripts to pull data into a relational form that allows for domain specific research questions, quality assurance and analysis. In the case of the Biorepository use case, we utilize the ehb-serviceand biorepo-portalAPI to create a base set of data.

      REDCap data can be queried via the traditional API or open source software like PyCap and the newly developed GO-cap (a REDCap Client and CLI written in Go).

      Two of our data load processes are available on our public git repository:
      Bio Repository Portal Data Demo
      CBTTC Data

    Putting it all together...

    Study Operations

    Scientific Data Integration

    Technically Speaking...

    We took a modular, entity-based, best-of-breed integrated systems approach to facilitate this variable set of specimen acquisition and data collection events. The first entity is the subject. The subject entity is moved to the honest broker and stored in a master patient index (MPI). Each external research record in the data management tool or research system, in this case REDCap, can have different entity relationship-type relations with the subject entity. We built a research portal, dubbed the Biorepository Portal (BRP), which can access subject records in the eHB and subsequent external research records through token-based authorization from that client system. The BRP reproduces the REDCap eCRFs based on records stored in the eHB with a custom REDCap client utilizing the REDCap API in real-time, producing a complete form for that subject at time of access. It displays the subject information and identifiers at the top of the screen at all times during form data entry and while shifting from form to form. The section of this paper, “REDCap client”, describes and illustrates this feature. A research coordinator or data manager can enter any temporal research data based on their protocol subject list at anytime or in any order, asynchronously while maintaining the continuous de-identification and re-identification of research data automatically.

    At the Children’s Hospital of Philadelphia, its Biorepository Core Facility utilizes ThermoFisher Nautilus as its Laboratory Information Management System (LIMS). We also built a client to this LIMS that allows for association of LIMS records with a subject record. This also is collected longitudinally. Data and specimen coordinators have the ability to associate sets of specimens with a subject or event and annotate that specimen on the fly in one front-facing system. For downstream integration, we use the same eHB software service to perform our Extract Transform Load (ETL) processes that are tailored to each project. The result is a fluid, nightly updating non-human subject research database that allows for seamless queries across research and clinical systems. We allow collaborators to access specific sets of data via the data exploration tool, Harvest, customized for each project11. What follows is a description of each component of the modular tool kit

    Is the Biorepository Portal Toolkit for me?

    The Modular Application Approach

    This modular set of tools allows for one subject to have multiple de-identified research records in multiple best- of-breed systems.

    Simply A REDCap Supplement

    During development we've found the simple ability to extract a subject entity away from research systems is not only helpful for biorepository honest broker processes, but also in a REDCap enviornment where a project or project record could represent data with multiple/variable relations to the research subject.

    • electronic Honest Broker (eHB)

      ehb-client
      ehb-service
    • eHB Datasources

      ehb-datasources
      REDCap Client

      A client to REDCap. Allowing study coordinators to associate multiple REDCap projects with a single honest-broker subject, and view or enter data de-identified into the forms on those projects.

      LIMS Client

      A custom client to our enterprise LIMS system. Please contact us to discuss the details of this project.

    • Query

      Harvest:For all researcher-facing projects we utilize the open-source Harvestdata exploration platform to display de-identified specimen, clinical and genomic data on a project-by-project basis.