The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics

Objective

Integrating and harmonizing disparate patient data sources into one consolidated data portal enables researchers to conduct analysis efficiently and effectively.

Materials and Methods

We describe an implementation of Informatics for Integrating Biology and the Bedside (i2b2) to create the Mass General Brigham (MGB) Biobank Portal data repository. The repository integrates data from primary and curated data sources and is updated weekly. The data are made readily available to investigators in a data portal where they can easily construct and export customized datasets for analysis.

Results

As of July 2021, there are 125 645 consented patients enrolled in the MGB Biobank. 88 527 (70.5%) have a biospecimen, 55 121 (43.9%) have completed the health information survey, 43 552 (34.7%) have genomic data and 124 760 (99.3%) have EHR data. Twenty machine learning computed phenotypes are calculated on a weekly basis. There are currently 1220 active investigators who have run 58 793 patient queries and exported 10 257 analysis files.

Discussion

The Biobank Portal allows noninformatics researchers to conduct study feasibility by querying across many data sources and then extract data that are most useful to them for clinical studies. While institutions require substantial informatics resources to establish and maintain integrated data repositories, they yield significant research value to a wide range of investigators.

Conclusion

The Biobank Portal and other patient data portals that integrate complex and simple datasets enable diverse research use cases. i2b2 tools to implement these registries and make the data interoperable are open source and freely available.

Web services for data warehouses: OMOP and PCORnet on i2b2

Objective

Healthcare organizations use research data models supported by projects and tools that interest them, which often means organizations must support the same data in multiple models. The healthcare research ecosystem would benefit if tools and projects could be adopted independently from the underlying data model. Here, we introduce the concept of a reusable application programming interface (API) for healthcare and show that the i2b2 API can be adapted to support diverse patient-centric data models.

Materials and Methods

We develop methodology for extending i2b2’s pre-existing API to query additional data models, using i2b2’s recent “multi-fact-table querying” feature. Our method involves developing data-model-specific i2b2 ontologies and mapping these to query non-standard table structure.

Results

We implement this methodology to query OMOP and PCORnet models, which we validate with the i2b2 query tool. We implement the entire PCORnet data model and a five-domain subset of the OMOP model. We also demonstrate that additional, ancillary data model columns can be modeled and queried as i2b2 “modifiers.”

Discussion

i2b2’s REST API can be used to query multiple healthcare data models, enabling shared tooling to have a choice of backend data stores. This enables separation between data model and software tooling for some of the more popular open analytic data models in healthcare.

Conclusion

This methodology immediately allows querying OMOP and PCORnet using the i2b2 API. It is released as an open-source set of Docker images, and also on the i2b2 community wiki.

High throughput tools to access images from clinical archives for research

Historically, medical images collected in the course of clinical care have been difficult to access for secondary research studies. While there is a tremendous potential value in the large volume of studies contained in clinical image archives, Picture Archiving and Communication Systems (PACS) are designed to optimize clinical operations and workflow. Search capabilities in PACS are basic, limiting their use for population studies, and duplication of archives for research is costly. To address this need, we augment the Informatics for Integrating Biology and the Bedside (i2b2) open source software, providing investigators with the tools necessary to query and integrate medical record and clinical research data. Over 100 healthcare institutions have installed this suite of software tools that allows investigators to search medical record metadata including images for specific types of patients. In this report, we describe a new Medical Imaging Informatics Bench to Bedside (mi2b2) module (www.mi2b2.org), available now as an open source addition to the i2b2 software platform that allows medical imaging examinations collected during routine clinical care to be made available to translational investigators directly from their institution’s clinical PACS for research and educational use in compliance with the Health Insurance Portability and Accountability Act (HIPAA) Omnibus Rule. Access governance within the mi2b2 module is customizable per institution and PACS minimizing impact on clinical systems. Currently in active use at our institutions, this new technology has already been used to facilitate access to thousands of clinical MRI brain studies representing specific patient phenotypes for use in research.

Mining for associations between categorical data items in a clinical data repository

We present here our preliminary work in using simple two-way categorical tests to discover associations between categorical items in a clinical data repository. Initial results using the chi square test yielded diagnosis code associations that seemed plausible as well as several that did not. This may be due in part to the effect of sample size. Tests more resistant to the effects of sample size may yield a higher fraction of plausible diagnosis code associations.

IL-4 promotes airway eosinophilia by suppressing IFN-gamma production: defining a novel role for IFN-gamma in the regulation of allergic airway inflammation

Airway eosinophilia in asthma is dependent on cytokines secreted by Th2 cells, including IL-5 and IL-4. In these studies we investigated why the absence of IL-4 led to a reduction in airway, but not lung tissue, eosinophils. Using adoptively transferred, in vitro-generated TCR-transgenic Th2 cells deficient in IL-4, we show that this effect is independent of IL-5 and Th2 cell generation. Airway eosinophilia was no longer inhibited when IL-4(-/-) Th2 cells were transferred into IFN-gammaR(-/-) mice, indicating that IFN-gamma was responsible for reducing airway eosinophils in the absence of IL-4. Intranasal administration of IFN-gamma to mice after IL-4(+/+) Th2 cell transfer also caused a reduction in airway, but not lung parenchymal, eosinophils. These studies show that IL-4 indirectly promotes airway eosinophilia by suppressing the production of IFN-gamma. IFN-gamma reduces airway eosinophils by engaging its receptor on hemopoietic cells, possibly the eosinophil itself. These studies capitalize on the complex counterregulatory effects of Th1 and Th2 cytokines in vivo and clarify how IL-4 influences lung eosinophilia. We define a new regulatory role for IFN-gamma, demonstrating that eosinophilic inflammation is differentially regulated at distinct sites within the respiratory tract.

Mental disorders and syndromes found among Asians residing in the United States

The Asian population in the United States is the fastest growing minority; consequently it behooves psychiatric nurses and other mental health professionals to be aware of symptom presentation of emotional problems that may differ from those of other population groups. Specific syndromes, psychiatric disorders, and symptoms that commonly present as physical disorders are discussed. Recommended adaptations of psychiatric interventions, including medications and other therapies, are offered to enable mental health professionals to provide culturally sensitive care. Mental health care that is culturally competent may improve access to care for Asians residing in the United States.

The dynamic interplay of malignant and benign T cells in cutaneous T-cell lymphoma

Cutaneous T-cell lymphoma is a malignancy of functional, tissue-specific T cells. Many characteristics of the disease can be explained by virtue of the ability of the malignant cell population to actively participate in the host's immunologic network. Various aspects of this dynamic interplay between malignant and benign T cells are discussed, including impact on diagnosis, staging, and therapy.

Peer review in a shared governance model

Peer review is a process by which professional nurses measure the quality of nursing practice in relation to established standards of practice. Shared governance provides a framework in which professional nurses self-regulate practice in their domain. Quality of nursing care is assessed through the peer review process in a shared governance model. This article describes the development, implementation, and evaluation of a peer review process and tool designed for postanesthesia nursing practice.