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Essaid S, Andre J, Brooks IM, Hohman KH, Hull M, Jackson SL, Kahn MG, Kraus EM, Mandadi N, Martinez AK, Mui JY, Zambarano B, Soares A. MENDS-on-FHIR: leveraging the OMOP common data model and FHIR standards for national chronic disease surveillance. JAMIA Open 2024; 7:ooae045. [PMID: 38818114 PMCID: PMC11137321 DOI: 10.1093/jamiaopen/ooae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/20/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
Objectives The Multi-State EHR-Based Network for Disease Surveillance (MENDS) is a population-based chronic disease surveillance distributed data network that uses institution-specific extraction-transformation-load (ETL) routines. MENDS-on-FHIR examined using Health Language Seven's Fast Healthcare Interoperability Resources (HL7® FHIR®) and US Core Implementation Guide (US Core IG) compliant resources derived from the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to create a standards-based ETL pipeline. Materials and Methods The input data source was a research data warehouse containing clinical and administrative data in OMOP CDM Version 5.3 format. OMOP-to-FHIR transformations, using a unique JavaScript Object Notation (JSON)-to-JSON transformation language called Whistle, created FHIR R4 V4.0.1/US Core IG V4.0.0 conformant resources that were stored in a local FHIR server. A REST-based Bulk FHIR $export request extracted FHIR resources to populate a local MENDS database. Results Eleven OMOP tables were used to create 10 FHIR/US Core compliant resource types. A total of 1.13 trillion resources were extracted and inserted into the MENDS repository. A very low rate of non-compliant resources was observed. Discussion OMOP-to-FHIR transformation results passed validation with less than a 1% non-compliance rate. These standards-compliant FHIR resources provided standardized data elements required by the MENDS surveillance use case. The Bulk FHIR application programming interface (API) enabled population-level data exchange using interoperable FHIR resources. The OMOP-to-FHIR transformation pipeline creates a FHIR interface for accessing OMOP data. Conclusion MENDS-on-FHIR successfully replaced custom ETL with standards-based interoperable FHIR resources using Bulk FHIR. The OMOP-to-FHIR transformations provide an alternative mechanism for sharing OMOP data.
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Affiliation(s)
- Shahim Essaid
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
| | - Jeff Andre
- Commonwealth Informatics Inc, Waltham, MA 02451, United States
| | - Ian M Brooks
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
| | - Katherine H Hohman
- National Association of Chronic Disease Directors (NACDD), Decatur, GA 30030, United States
| | - Madelyne Hull
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
| | - Sandra L Jackson
- National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, United States
| | - Michael G Kahn
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
| | - Emily M Kraus
- Kraushold Consulting, Denver, CO 80120, United States
- Public Health Informatics Institute, Decatur, GA 30030, United States
| | - Neha Mandadi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
| | - Amanda K Martinez
- National Association of Chronic Disease Directors (NACDD), Decatur, GA 30030, United States
| | - Joyce Y Mui
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
| | - Bob Zambarano
- Commonwealth Informatics Inc, Waltham, MA 02451, United States
| | - Andrey Soares
- Department of Medicine, University of Colorado Anschutz Medical Campus, Denver, CO 80045, United States
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2
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Palojoki S, Lehtonen L, Vuokko R. Semantic Interoperability of Electronic Health Records: Systematic Review of Alternative Approaches for Enhancing Patient Information Availability. JMIR Med Inform 2024; 12:e53535. [PMID: 38686541 PMCID: PMC11066539 DOI: 10.2196/53535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/02/2024] Open
Abstract
Background Semantic interoperability facilitates the exchange of and access to health data that are being documented in electronic health records (EHRs) with various semantic features. The main goals of semantic interoperability development entail patient data availability and use in diverse EHRs without a loss of meaning. Internationally, current initiatives aim to enhance semantic development of EHR data and, consequently, the availability of patient data. Interoperability between health information systems is among the core goals of the European Health Data Space regulation proposal and the World Health Organization's Global Strategy on Digital Health 2020-2025. Objective To achieve integrated health data ecosystems, stakeholders need to overcome challenges of implementing semantic interoperability elements. To research the available scientific evidence on semantic interoperability development, we defined the following research questions: What are the key elements of and approaches for building semantic interoperability integrated in EHRs? What kinds of goals are driving the development? and What kinds of clinical benefits are perceived following this development? Methods Our research questions focused on key aspects and approaches for semantic interoperability and on possible clinical and semantic benefits of these choices in the context of EHRs. Therefore, we performed a systematic literature review in PubMed by defining our study framework based on previous research. Results Our analysis consisted of 14 studies where data models, ontologies, terminologies, classifications, and standards were applied for building interoperability. All articles reported clinical benefits of the selected approach to enhancing semantic interoperability. We identified 3 main categories: increasing the availability of data for clinicians (n=6, 43%), increasing the quality of care (n=4, 29%), and enhancing clinical data use and reuse for varied purposes (n=4, 29%). Regarding semantic development goals, data harmonization and developing semantic interoperability between different EHRs was the largest category (n=8, 57%). Enhancing health data quality through standardization (n=5, 36%) and developing EHR-integrated tools based on interoperable data (n=1, 7%) were the other identified categories. The results were closely coupled with the need to build usable and computable data out of heterogeneous medical information that is accessible through various EHRs and databases (eg, registers). Conclusions When heading toward semantic harmonization of clinical data, more experiences and analyses are needed to assess how applicable the chosen solutions are for semantic interoperability of health care data. Instead of promoting a single approach, semantic interoperability should be assessed through several levels of semantic requirements A dual model or multimodel approach is possibly usable to address different semantic interoperability issues during development. The objectives of semantic interoperability are to be achieved in diffuse and disconnected clinical care environments. Therefore, approaches for enhancing clinical data availability should be well prepared, thought out, and justified to meet economically sustainable and long-term outcomes.
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Affiliation(s)
- Sari Palojoki
- Department of Steering of Healthcare and Social Welfare, Ministry of Social Affairs and Health, Helsinki, Finland
| | - Lasse Lehtonen
- Diagnostic Center, Helsinki University Hospital District, Helsinki, Finland
| | - Riikka Vuokko
- Department of Steering of Healthcare and Social Welfare, Ministry of Social Affairs and Health, Helsinki, Finland
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3
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Khnaisser C, Looten V, Lavoie L, Burgun A, Ethier JF. Building ontology-based temporal databases for data reuse: An applied example on hospital organizational structures. Health Informatics J 2024; 30:14604582241259336. [PMID: 38848696 DOI: 10.1177/14604582241259336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Keeping track of data semantics and data changes in the databases is essential to support retrospective studies and the reproducibility of longitudinal clinical analysis by preventing false conclusions from being drawn from outdated data. A knowledge model combined with a temporal model plays an essential role in organizing the data and improving query expressiveness across time and multiple institutions. This paper presents a modelling framework for temporal relational databases using an ontology to derive a shareable and interoperable data model. The framework is based on: OntoRela an ontology-driven database modelling approach and Unified Historicization Framework a temporal database modelling approach. The method was applied to hospital organizational structures to show the impact of tracking organizational changes on data quality assessment, healthcare activities and data access rights. The paper demonstrated the usefulness of an ontology to provide a formal, interoperable, and reusable definition of entities and their relationships, as well as the adequacy of the temporal database to store, trace, and query data over time.
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Affiliation(s)
| | - Vincent Looten
- Association des Centres Médicaux et Sociaux (ACMS), Suresnes, France
| | - Luc Lavoie
- Université de Sherbrooke, Département d'informatique, Sherbrooke, QC, Canada
| | - Anita Burgun
- Université de Sherbrooke, Sherbrooke, QC, Canada; Université Paris Cité, Paris, France; Hôpital Européen Georges-Pompidou, Paris, France
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Amar F, April A, Abran A. Electronic Health Record and Semantic Issues Using Fast Healthcare Interoperability Resources: Systematic Mapping Review. J Med Internet Res 2024; 26:e45209. [PMID: 38289660 PMCID: PMC10865191 DOI: 10.2196/45209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/07/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND The increasing use of electronic health records and the Internet of Things has led to interoperability issues at different levels (structural and semantic). Standards are important not only for successfully exchanging data but also for appropriately interpreting them (semantic interoperability). Thus, to facilitate the semantic interoperability of data exchanged in health care, considerable resources have been deployed to improve the quality of shared clinical data by structuring and mapping them to the Fast Healthcare Interoperability Resources (FHIR) standard. OBJECTIVE The aims of this study are 2-fold: to inventory the studies on FHIR semantic interoperability resources and terminologies and to identify and classify the approaches and contributions proposed in these studies. METHODS A systematic mapping review (SMR) was conducted using 10 electronic databases as sources of information for inventory and review studies published during 2012 to 2022 on the development and improvement of semantic interoperability using the FHIR standard. RESULTS A total of 70 FHIR studies were selected and analyzed to identify FHIR resource types and terminologies from a semantic perspective. The proposed semantic approaches were classified into 6 categories, namely mapping (31/126, 24.6%), terminology services (18/126, 14.3%), resource description framework or web ontology language-based proposals (24/126, 19%), annotation proposals (18/126, 14.3%), machine learning (ML) and natural language processing (NLP) proposals (20/126, 15.9%), and ontology-based proposals (15/126, 11.9%). From 2012 to 2022, there has been continued research in 6 categories of approaches as well as in new and emerging annotations and ML and NLP proposals. This SMR also classifies the contributions of the selected studies into 5 categories: framework or architecture proposals, model proposals, technique proposals, comparison services, and tool proposals. The most frequent type of contribution is the proposal of a framework or architecture to enable semantic interoperability. CONCLUSIONS This SMR provides a classification of the different solutions proposed to address semantic interoperability using FHIR at different levels: collecting, extracting and annotating data, modeling electronic health record data from legacy systems, and applying transformation and mapping to FHIR models and terminologies. The use of ML and NLP for unstructured data is promising and has been applied to specific use case scenarios. In addition, terminology services are needed to accelerate their use and adoption; furthermore, techniques and tools to automate annotation and ontology comparison should help reduce human interaction.
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Affiliation(s)
- Fouzia Amar
- École de technologie supérieure - ETS, Montreal, QC, Canada
| | - Alain April
- École de technologie supérieure - ETS, Montreal, QC, Canada
| | - Alain Abran
- École de technologie supérieure - ETS, Montreal, QC, Canada
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5
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Fernandez ME, Martinez-Romero J, Aon MA, Bernier M, Price NL, de Cabo R. How is Big Data reshaping preclinical aging research? Lab Anim (NY) 2023; 52:289-314. [PMID: 38017182 DOI: 10.1038/s41684-023-01286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
The exponential scientific and technological progress during the past 30 years has favored the comprehensive characterization of aging processes with their multivariate nature, leading to the advent of Big Data in preclinical aging research. Spanning from molecular omics to organism-level deep phenotyping, Big Data demands large computational resources for storage and analysis, as well as new analytical tools and conceptual frameworks to gain novel insights leading to discovery. Systems biology has emerged as a paradigm that utilizes Big Data to gain insightful information enabling a better understanding of living organisms, visualized as multilayered networks of interacting molecules, cells, tissues and organs at different spatiotemporal scales. In this framework, where aging, health and disease represent emergent states from an evolving dynamic complex system, context given by, for example, strain, sex and feeding times, becomes paramount for defining the biological trajectory of an organism. Using bioinformatics and artificial intelligence, the systems biology approach is leading to remarkable advances in our understanding of the underlying mechanism of aging biology and assisting in creative experimental study designs in animal models. Future in-depth knowledge acquisition will depend on the ability to fully integrate information from different spatiotemporal scales in organisms, which will probably require the adoption of theories and methods from the field of complex systems. Here we review state-of-the-art approaches in preclinical research, with a focus on rodent models, that are leading to conceptual and/or technical advances in leveraging Big Data to understand basic aging biology and its full translational potential.
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Affiliation(s)
- Maria Emilia Fernandez
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jorge Martinez-Romero
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Miguel A Aon
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Michel Bernier
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nathan L Price
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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6
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Essaid S, Andre J, Brooks IM, Hohman KH, Hull M, Jackson SL, Kahn MG, Kraus EM, Mandadi N, Martinez AK, Mui JY, Zambarano B, Soares A. MENDS-on-FHIR: Leveraging the OMOP common data model and FHIR standards for national chronic disease surveillance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.09.23293900. [PMID: 38045364 PMCID: PMC10690355 DOI: 10.1101/2023.08.09.23293900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Objective The Multi-State EHR-Based Network for Disease Surveillance (MENDS) is a population-based chronic disease surveillance distributed data network that uses institution-specific extraction-transformation-load (ETL) routines. MENDS-on-FHIR examined using Health Language Seven's Fast Healthcare Interoperability Resources (HL7® FHIR®) and US Core Implementation Guide (US Core IG) compliant resources derived from the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to create a standards-based ETL pipeline. Materials and Methods The input data source was a research data warehouse containing clinical and administrative data in OMOP CDM Version 5.3 format. OMOP-to-FHIR transformations, using a unique JavaScript Object Notation (JSON)-to-JSON transformation language called Whistle, created FHIR R4 V4.0.1/US Core IG V4.0.0 conformant resources that were stored in a local FHIR server. A REST-based Bulk FHIR $export request extracted FHIR resources to populate a local MENDS database. Results Eleven OMOP tables were used to create 10 FHIR/US Core compliant resource types. A total of 1.13 trillion resources were extracted and inserted into the MENDS repository. A very low rate of non-compliant resources was observed. Discussion OMOP-to-FHIR transformation results passed validation with less than a 1% non-compliance rate. These standards-compliant FHIR resources provided standardized data elements required by the MENDS surveillance use case. The Bulk FHIR application programming interface (API) enabled population-level data exchange using interoperable FHIR resources. The OMOP-to-FHIR transformation pipeline creates a FHIR interface for accessing OMOP data. Conclusion MENDS-on-FHIR successfully replaced custom ETL with standards-based interoperable FHIR resources using Bulk FHIR. The OMOP-to-FHIR transformations provide an alternative mechanism for sharing OMOP data.
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Affiliation(s)
- Shahim Essaid
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver CO
| | - Jeff Andre
- Commonwealth Informatics Inc, Waltham MA
| | - Ian M Brooks
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver CO
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver CO
| | | | - Madelyne Hull
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver CO
| | - Sandra L Jackson
- National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention (CDC), Atlanta GA
| | - Michael G Kahn
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver CO
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver CO
| | - Emily M Kraus
- Kraushold Consulting, Denver CO
- Public Health Informatics Institute, Decatur, GA
| | - Neha Mandadi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver CO
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver CO
| | - Amanda K Martinez
- National Association of Chronic Disease Directors (NACDD), Decatur GA
| | - Joyce Y Mui
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Denver CO
- Health Data Compass, University of Colorado Anschutz Medical Campus, Denver CO
| | | | - Andrey Soares
- Department of Medicine, University of Colorado Anschutz Medical Campus, Denver CO
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7
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Nan J, Xu LQ. Designing Interoperable Health Care Services Based on Fast Healthcare Interoperability Resources: Literature Review. JMIR Med Inform 2023; 11:e44842. [PMID: 37603388 PMCID: PMC10477925 DOI: 10.2196/44842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND With the advent of the digital economy and the aging population, the demand for diversified health care services and innovative care delivery models has been overwhelming. This trend has accelerated the urgency to implement effective and efficient data exchange and service interoperability, which underpins coordinated care services among tiered health care institutions, improves the quality of oversight of regulators, and provides vast and comprehensive data collection to support clinical medicine and health economics research, thus improving the overall service quality and patient satisfaction. To meet this demand and facilitate the interoperability of IT systems of stakeholders, after years of preparation, Health Level 7 formally introduced, in 2014, the Fast Healthcare Interoperability Resources (FHIR) standard. It has since continued to evolve. FHIR depends on the Implementation Guide (IG) to ensure feasibility and consistency while developing an interoperable health care service. The IG defines rules with associated documentation on how FHIR resources are used to tackle a particular problem. However, a gap remains between IGs and the process of building actual services because IGs are rules without specifying concrete methods, procedures, or tools. Thus, stakeholders may feel it nontrivial to participate in the ecosystem, giving rise to the need for a more actionable practice guideline (PG) for promoting FHIR's fast adoption. OBJECTIVE This study aimed to propose a general FHIR PG to facilitate stakeholders in the health care ecosystem to understand FHIR and quickly develop interoperable health care services. METHODS We selected a collection of FHIR-related papers about the latest studies or use cases on designing and building FHIR-based interoperable health care services and tagged each use case as belonging to 1 of the 3 dominant innovation feature groups that are also associated with practice stages, that is, data standardization, data management, and data integration. Next, we reviewed each group's detailed process and key techniques to build respective care services and collate a complete FHIR PG. Finally, as an example, we arbitrarily selected a use case outside the scope of the reviewed papers and mapped it back to the FHIR PG to demonstrate the effectiveness and generalizability of the PG. RESULTS The FHIR PG includes 2 core elements: one is a practice design that defines the responsibilities of stakeholders and outlines the complete procedure from data to services, and the other is a development architecture for practice design, which lists the available tools for each practice step and provides direct and actionable recommendations. CONCLUSIONS The FHIR PG can bridge the gap between IGs and the process of building actual services by proposing actionable methods, procedures, and tools. It assists stakeholders in identifying participants' roles, managing the scope of responsibilities, and developing relevant modules, thus helping promote FHIR-based interoperable health care services.
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Affiliation(s)
- Jingwen Nan
- Health IT Research, China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Li-Qun Xu
- Health IT Research, China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
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8
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Soares A, Afshar M, Moesel C, Grasso MA, Pan E, Solomonides A, Richardson JE, Barone E, Lomotan EA, Schilling LM. Playing in the clinical decision support sandbox: tools and training for all. JAMIA Open 2023; 6:ooad038. [PMID: 37351012 PMCID: PMC10283349 DOI: 10.1093/jamiaopen/ooad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 01/09/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
Objectives Introduce the CDS-Sandbox, a cloud-based virtual machine created to facilitate Clinical Decision Support (CDS) developers and implementers in the use of FHIR- and CQL-based open-source tools and technologies for building and testing CDS artifacts. Materials and Methods The CDS-Sandbox includes components that enable workflows for authoring and testing CDS artifacts. Two workshops at the 2020 and 2021 AMIA Annual Symposia were conducted to demonstrate the use of the open-source CDS tools. Results The CDS-Sandbox successfully integrated the use of open-source CDS tools. Both workshops were well attended. Participants demonstrated use and understanding of the workshop materials and provided positive feedback after the workshops. Discussion The CDS-Sandbox and publicly available tutorial materials facilitated an understanding of the leading-edge open-source CDS infrastructure components. Conclusion The CDS-Sandbox supports integrated use of the key CDS open-source tools that may be used to introduce CDS concepts and practice to the clinical informatics community.
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Affiliation(s)
- Andrey Soares
- Corresponding Author: Andrey Soares, PhD, Division of General Internal Medicine and the Data Science to Patient Value Initiative, School of Medicine, University of Colorado Anschutz Medical Campus, Anschutz Health Sciences Building, Mailstop F443, 1890 N. Revere Court, Aurora, CO 80045, USA;
| | - Majid Afshar
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - Chris Moesel
- Open Health Solutions Department, The MITRE Corporation, Bedford, Massachusetts, USA
| | - Michael A Grasso
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eric Pan
- Westat Inc, Center for Healthcare Delivery Research and Evaluation, Rockville, Maryland, USA
| | - Anthony Solomonides
- Outcomes Research Network, Research Institute, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Joshua E Richardson
- Center for Health Informatics and Evidence Synthesis, RTI International, Chicago, Illinois, USA
| | - Eleanor Barone
- Office of Health Informatics/Clinical Informatics and Data Management Organization, Veteran’s Affairs, Fayetteville, North Carolina, USA
| | - Edwin A Lomotan
- Center for Evidence and Practice Improvement, Agency for Healthcare Research and Quality, Rockville, Maryland, USA
| | - Lisa M Schilling
- Division of General Internal Medicine, Department of Medicine, and the Data Science to Patient Value Initiative, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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9
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Baron JM. Artificial Intelligence in the Clinical Laboratory: An Overview with Frequently Asked Questions. Clin Lab Med 2023; 43:1-16. [PMID: 36764803 DOI: 10.1016/j.cll.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This article provides an overview of machine learning fundamentals and some applications of machine learning to clinical laboratory diagnostics and patient management. A key goal of this article is to provide a basic foundation in clinical machine learning for readers with clinical laboratory experience that will set them up for more in-depth study of the topic and/or to become a better collaborator with computational colleagues in the development and deployment of machine learning-based solutions.
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Affiliation(s)
- Jason M Baron
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114-2696, USA.
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10
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Duda SN, Kennedy N, Conway D, Cheng AC, Nguyen V, Zayas-Cabán T, Harris PA. HL7 FHIR-based tools and initiatives to support clinical research: a scoping review. J Am Med Inform Assoc 2022; 29:1642-1653. [PMID: 35818340 DOI: 10.1093/jamia/ocac105] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The HL7® fast healthcare interoperability resources (FHIR®) specification has emerged as the leading interoperability standard for the exchange of healthcare data. We conducted a scoping review to identify trends and gaps in the use of FHIR for clinical research. MATERIALS AND METHODS We reviewed published literature, federally funded project databases, application websites, and other sources to discover FHIR-based papers, projects, and tools (collectively, "FHIR projects") available to support clinical research activities. RESULTS Our search identified 203 different FHIR projects applicable to clinical research. Most were associated with preparations to conduct research, such as data mapping to and from FHIR formats (n = 66, 32.5%) and managing ontologies with FHIR (n = 30, 14.8%), or post-study data activities, such as sharing data using repositories or registries (n = 24, 11.8%), general research data sharing (n = 23, 11.3%), and management of genomic data (n = 21, 10.3%). With the exception of phenotyping (n = 19, 9.4%), fewer FHIR-based projects focused on needs within the clinical research process itself. DISCUSSION Funding and usage of FHIR-enabled solutions for research are expanding, but most projects appear focused on establishing data pipelines and linking clinical systems such as electronic health records, patient-facing data systems, and registries, possibly due to the relative newness of FHIR and the incentives for FHIR integration in health information systems. Fewer FHIR projects were associated with research-only activities. CONCLUSION The FHIR standard is becoming an essential component of the clinical research enterprise. To develop FHIR's full potential for clinical research, funding and operational stakeholders should address gaps in FHIR-based research tools and methods.
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Affiliation(s)
- Stephany N Duda
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Douglas Conway
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alex C Cheng
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Viet Nguyen
- Stratametrics LLC, Salt Lake City, Utah, USA.,HL7 Da Vinci Project, Ann Arbor, Michigan, USA
| | - Teresa Zayas-Cabán
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Harris
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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Urbanowicz RJ, Holmes JH, Appleby D, Narasimhan V, Durborow S, Al-Naamani N, Fernando M, Kawut SM. A Semi-Automated Term Harmonization Pipeline Applied to Pulmonary Arterial Hypertension Clinical Trials. Methods Inf Med 2022; 61:3-10. [PMID: 34820791 PMCID: PMC9978994 DOI: 10.1055/s-0041-1739361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Data harmonization is essential to integrate individual participant data from multiple sites, time periods, and trials for meta-analysis. The process of mapping terms and phrases to an ontology is complicated by typographic errors, abbreviations, truncation, and plurality. We sought to harmonize medical history (MH) and adverse events (AE) term records across 21 randomized clinical trials in pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension. METHODS We developed and applied a semi-automated harmonization pipeline for use with domain-expert annotators to resolve ambiguous term mappings using exact and fuzzy matching. We summarized MH and AE term mapping success, including map quality measures, and imputation of a generalizing term hierarchy as defined by the applied Medical Dictionary for Regulatory Activities (MedDRA) ontology standard. RESULTS Over 99.6% of both MH (N = 37,105) and AE (N = 58,170) records were successfully mapped to MedDRA low-level terms. Automated exact matching accounted for 74.9% of MH and 85.5% of AE mappings. Term recommendations from fuzzy matching in the pipeline facilitated annotator mapping of the remaining 24.9% of MH and 13.8% of AE records. Imputation of the generalized MedDRA term hierarchy was unambiguous in 85.2% of high-level terms, 99.4% of high-level group terms, and 99.5% of system organ class in MH, and 75% of high-level terms, 98.3% of high-level group terms, and 98.4% of system organ class in AE. CONCLUSION This pipeline dramatically reduced the burden of manual annotation for MH and AE term harmonization and could be adapted to other data integration efforts.
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Affiliation(s)
- Ryan J. Urbanowicz
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - John H. Holmes
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Dina Appleby
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Vanamala Narasimhan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Stephen Durborow
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Nadine Al-Naamani
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Melissa Fernando
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Steven M. Kawut
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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12
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A Privacy-Preserving and Standard-Based Architecture for Secondary Use of Clinical Data. INFORMATION 2022. [DOI: 10.3390/info13020087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The heterogeneity of the formats and standards of clinical data, which includes both structured, semi-structured, and unstructured data, in addition to the sensitive information contained in them, require the definition of specific approaches that are able to implement methodologies that can permit the extraction of valuable information buried under such data. Although many challenges and issues that have not been fully addressed still exist when this information must be processed and used for further purposes, the most recent techniques based on machine learning and big data analytics can support the information extraction process for the secondary use of clinical data. In particular, these techniques can facilitate the transformation of heterogeneous data into a common standard format. Moreover, they can also be exploited to define anonymization or pseudonymization approaches, respecting the privacy requirements stated in the General Data Protection Regulation, Health Insurance Portability and Accountability Act and other national and regional laws. In fact, compliance with these laws requires that only de-identified clinical and personal data can be processed for secondary analyses, in particular when data is shared or exchanged across different institutions. This work proposes a modular architecture capable of collecting clinical data from heterogeneous sources and transforming them into useful data for secondary uses, such as research, governance, and medical education purposes. The proposed architecture is able to exploit appropriate modules and algorithms, carry out transformations (pseudonymization and standardization) required to use data for the second purposes, as well as provide efficient tools to facilitate the retrieval and analysis processes. Preliminary experimental tests show good accuracy in terms of quantitative evaluations.
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13
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Rosenau L, Majeed RW, Ingenerf J, Kiel A, Kroll B, Köhler T, Prokosch HU, Gruendner J. Generation of a Fast Healthcare Interoperability Resources (FHIR)-based Ontology for federated Feasibility Queries in the context of COVID-19: An automated approach (Preprint). JMIR Med Inform 2021; 10:e35789. [PMID: 35380548 PMCID: PMC9049646 DOI: 10.2196/35789] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/27/2022] [Accepted: 02/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background The COVID-19 pandemic highlighted the importance of making research data from all German hospitals available to scientists to respond to current and future pandemics promptly. The heterogeneous data originating from proprietary systems at hospitals' sites must be harmonized and accessible. The German Corona Consensus Dataset (GECCO) specifies how data for COVID-19 patients will be standardized in Fast Healthcare Interoperability Resources (FHIR) profiles across German hospitals. However, given the complexity of the FHIR standard, the data harmonization is not sufficient to make the data accessible. A simplified visual representation is needed to reduce the technical burden, while allowing feasibility queries. Objective This study investigates how a search ontology can be automatically generated using FHIR profiles and a terminology server. Furthermore, it describes how this ontology can be used in a user interface (UI) and how a mapping and a terminology tree created together with the ontology can translate user input into FHIR queries. Methods We used the FHIR profiles from the GECCO data set combined with a terminology server to generate an ontology and the required mapping files for the translation. We analyzed the profiles and identified search criteria for the visual representation. In this process, we reduced the complex profiles to code value pairs for improved usability. We enriched our ontology with the necessary information to display it in a UI. We also developed an intermediate query language to transform the queries from the UI to federated FHIR requests. Separation of concerns resulted in discrepancies between the criteria used in the intermediate query format and the target query language. Therefore, a mapping was created to reintroduce all information relevant for creating the query in its target language. Further, we generated a tree representation of the ontology hierarchy, which allows resolving child concepts in the process. Results In the scope of this project, 82 (99%) of 83 elements defined in the GECCO profile were successfully implemented. We verified our solution based on an independently developed test patient. A discrepancy between the test data and the criteria was found in 6 cases due to different versions used to generate the test data and the UI profiles, the support for specific code systems, and the evaluation of postcoordinated Systematized Nomenclature of Medicine (SNOMED) codes. Our results highlight the need for governance mechanisms for version changes, concept mapping between values from different code systems encoding the same concept, and support for different unit dimensions. Conclusions We developed an automatic process to generate ontology and mapping files for FHIR-formatted data. Our tests found that this process works for most of our chosen FHIR profile criteria. The process established here works directly with FHIR profiles and a terminology server, making it extendable to other FHIR profiles and demonstrating that automatic ontology generation on FHIR profiles is feasible.
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Affiliation(s)
| | - Raphael W Majeed
- Institute for Medical Informatics, University Clinic Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | | | - Alexander Kiel
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Björn Kroll
- IT Center for Clinical Research, Lübeck, Germany
| | - Thomas Köhler
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
- Complex Data Processing in Medical Informatics, Medical Faculty Mannheim, Mannheim, Germany
| | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Julian Gruendner
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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14
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Shi Y, Amill-Rosario A, Rudin RS, Fischer SH, Shekelle P, Scanlon DP, Damberg CL. Barriers to using clinical decision support in ambulatory care: Do clinics in health systems fare better? J Am Med Inform Assoc 2021; 28:1667-1675. [PMID: 33895828 DOI: 10.1093/jamia/ocab064] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/14/2021] [Accepted: 03/24/2021] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE We quantify the use of clinical decision support (CDS) and the specific barriers reported by ambulatory clinics and examine whether CDS utilization and barriers differed based on clinics' affiliation with health systems, providing a benchmark for future empirical research and policies related to this topic. MATERIALS AND METHODS Despite much discussion at the theoretic level, the existing literature provides little empirical understanding of barriers to using CDS in ambulatory care. We analyze data from 821 clinics in 117 medical groups, based on in Minnesota Community Measurement's annual Health Information Technology Survey (2014-2016). We examine clinics' use of 7 CDS tools, along with 7 barriers in 3 areas (resource, user acceptance, and technology). Employing linear probability models, we examine factors associated with CDS barriers. RESULTS Clinics in health systems used more CDS tools than did clinics not in systems (24 percentage points higher in automated reminders), but they also reported more barriers related to resources and user acceptance (26 percentage points higher in barriers to implementation and 33 points higher in disruptive alarms). Barriers related to workflow redesign increased in clinics affiliated with health systems (33 points higher). Rural clinics were more likely to report barriers to training. CONCLUSIONS CDS barriers related to resources and user acceptance remained substantial. Health systems, while being effective in promoting CDS tools, may need to provide further assistance to their affiliated ambulatory clinics to overcome barriers, especially the requirement to redesign workflow. Rural clinics may need more resources for training.
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Affiliation(s)
- Yunfeng Shi
- Department of Health Policy and Administration, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Alejandro Amill-Rosario
- Department of Health Policy and Administration, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | | | - Dennis P Scanlon
- Department of Health Policy and Administration, The Pennsylvania State University, University Park, Pennsylvania, USA
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15
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Abstract
Given the ever-growing body of knowledge, healthcare improvement hinges more than ever on efficient knowledge transfer to clinicians and patients. Promoted initially by the Institute of Medicine, the Learning Health System (LHS) framework emerged in the early 2000s. It places focus on learning cycles where care delivery is tightly coupled with research activities, which in turn is closely tied to knowledge transfer, ultimately injecting solid improvements into medical practice. Sensitive health data access across multiple organisations is therefore paramount to support LHSs. While the LHS vision is well established, security requirements to support them are not. Health data exchange approaches have been implemented (e.g., HL7 FHIR) or proposed (e.g., blockchain-based methods), but none cover the entire LHS requirement spectrum. To address this, the Sensitive Data Access Model (SDAM) is proposed. Using a representation of agents and processes of data access systems, specific security requirements are presented and the SDAM layer architecture is described, with an emphasis on its mix-network dynamic topology approach. A clinical application benefiting from the model is subsequently presented and an analysis evaluates the security properties and vulnerability mitigation strategies offered by a protocol suite following SDAM and in parallel, by FHIR.
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16
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Experience in Developing an FHIR Medical Data Management Platform to Provide Clinical Decision Support. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 17:ijerph17010073. [PMID: 31861851 PMCID: PMC6981801 DOI: 10.3390/ijerph17010073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/13/2019] [Accepted: 12/10/2019] [Indexed: 01/17/2023]
Abstract
This paper is an extension of work originally presented to pHealth 2019—16th International Conference on Wearable, Micro and Nano Technologies for Personalized Health. To provide an efficient decision support, it is necessary to integrate clinical decision support systems (CDSSs) in information systems routinely operated by healthcare professionals, such as hospital information systems (HISs), or by patients deploying their personal health records (PHR). CDSSs should be able to use the semantics and the clinical context of the data imported from other systems and data repositories. A CDSS platform was developed as a set of separate microservices. In this context, we implemented the core components of a CDSS platform, namely its communication services and logical inference components. A fast healthcare interoperability resources (FHIR)-based CDSS platform addresses the ease of access to clinical decision support services by providing standard-based interfaces and workflows. This type of CDSS may be able to improve the quality of care for doctors who are using HIS without CDSS features. The HL7 FHIR interoperability standards provide a platform usable by all HISs that are FHIR enabled. The platform has been implemented and is now productive, with a rule-based engine processing around 50,000 transactions a day with more than 400 decision support models and a Bayes Engine processing around 2000 transactions a day with 128 Bayesian diagnostics models.
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17
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Pfaff ER, Champion J, Bradford RL, Clark M, Xu H, Fecho K, Krishnamurthy A, Cox S, Chute CG, Overby Taylor C, Ahalt S. Fast Healthcare Interoperability Resources (FHIR) as a Meta Model to Integrate Common Data Models: Development of a Tool and Quantitative Validation Study. JMIR Med Inform 2019; 7:e15199. [PMID: 31621639 PMCID: PMC6913576 DOI: 10.2196/15199] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 11/13/2022] Open
Abstract
Background In a multisite clinical research collaboration, institutions may or may not use the same common data model (CDM) to store clinical data. To overcome this challenge, we proposed to use Health Level 7’s Fast Healthcare Interoperability Resources (FHIR) as a meta-CDM—a single standard to represent clinical data. Objective In this study, we aimed to create an open-source application termed the Clinical Asset Mapping Program for FHIR (CAMP FHIR) to efficiently transform clinical data to FHIR for supporting source-agnostic CDM-to-FHIR mapping. Methods Mapping with CAMP FHIR involves (1) mapping each source variable to its corresponding FHIR element and (2) mapping each item in the source data’s value sets to the corresponding FHIR value set item for variables with strict value sets. To date, CAMP FHIR has been used to transform 108 variables from the Informatics for Integrating Biology & the Bedside (i2b2) and Patient-Centered Outcomes Research Network data models to fields across 7 FHIR resources. It is designed to allow input from any source data model and will support additional FHIR resources in the future. Results We have used CAMP FHIR to transform data on approximately 23,000 patients with asthma from our institution’s i2b2 database. Data quality and integrity were validated against the origin point of the data, our enterprise clinical data warehouse. Conclusions We believe that CAMP FHIR can serve as an alternative to implementing new CDMs on a project-by-project basis. Moreover, the use of FHIR as a CDM could support rare data sharing opportunities, such as collaborations between academic medical centers and community hospitals. We anticipate adoption and use of CAMP FHIR to foster sharing of clinical data across institutions for downstream applications in translational research.
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Affiliation(s)
- Emily Rose Pfaff
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - James Champion
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Robert Louis Bradford
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marshall Clark
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hao Xu
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Karamarie Fecho
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ashok Krishnamurthy
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Steven Cox
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | | | - Stan Ahalt
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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18
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Abstract
Emerging applications of machine learning and artificial intelligence offer the opportunity to discover new clinical knowledge through secondary exploration of existing patient medical records. This new knowledge may in turn offer a foundation to build new types of clinical decision support (CDS) that provide patient-specific insights and guidance across a wide range of clinical questions and settings. This article will provide an overview of these emerging approaches to CDS, discussing both existing technologies as well as challenges that health systems and informaticists will need to address to allow these emerging approaches to reach their full potential.
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Affiliation(s)
- Jason M Baron
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02214, USA.
| | - Danielle E Kurant
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02214, USA
| | - Anand S Dighe
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02214, USA
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19
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Vaidyam A, Halamka J, Torous J. Actionable digital phenotyping: a framework for the delivery of just-in-time and longitudinal interventions in clinical healthcare. Mhealth 2019; 5:25. [PMID: 31559270 PMCID: PMC6737424 DOI: 10.21037/mhealth.2019.07.04] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
Designed to improve health, today numerous wearables and smartphone apps are used by millions across the world. Yet the wealth of data generated from the many sensors on these wearables and smartwatches has not yet transformed routine clinical care. One central reason for this gap between data and clinical insights is the lack of transparency and standards around data generated from mobile device that hinders interoperability and reproducibility. The clinical informatics community has offered solutions via the Fast Healthcare Interoperability Resources (FHIR) standard which facilities electronic health record interoperability but is less developed towards precision temporal contextually-tagged sensor measurements generated from today's ubiquitous mobile devices. In this paper we explore the opportunities and challenges of various theoretical approaches towards FHIR compatible digital phenotyping, and offer a concrete example implementing one such framework as an Application Programming Interface (API) for the open-source mindLAMP platform. We aim to build a community with contributions from statisticians, clinicians, patients, family members, researchers, designers, engineers, and more.
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Affiliation(s)
- Aditya Vaidyam
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - John Halamka
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - John Torous
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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20
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Saripalle RK. Fast Health Interoperability Resources (FHIR). INTERNATIONAL JOURNAL OF E-HEALTH AND MEDICAL COMMUNICATIONS 2019. [DOI: 10.4018/ijehmc.2019010105] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The inception of EHR has shown a lot of potentials and virtually eliminated the drawbacks of paper-based medical notes. However, the transition has not been seamless due to various technical and political drawbacks. One of the major technical challenges is interoperability. The biomedical community has established various structural and semantic standards to capture and share medical data across heterogeneous systems such as ASTM Community Care Record, Health Level 7 (HL7) Clinical Care Document, etc. The HL7 organization has recently published Fast Health Interoperability Resources (FHIR) – a standard to improve interoperability, overcome shortcomings of the previous standard and integrate lightweight web services. This article provides an overview of HL7 FHIR, its concepts and literature review on its current status, usage, and adoption. Based on the thorough research and literature review, the authors strongly believe that FHIR can bridge interoperability gap between the growing number of disparate and variety of healthcare entities.
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21
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Solbrig HR, Hong N, Murphy SN, Jiang G. Automated Population of an i2b2 Clinical Data Warehouse using FHIR. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2018:979-988. [PMID: 30815141 PMCID: PMC6371332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
HL7 Fast Healthcare Information Resources (FHIR) is rapidly becoming the de-facto standard for the exchange of clinical and healthcare related information. Major EHR vendors and healthcare providers are actively developing transformations between existing EHR databases and their corresponding FHIR representation. Many of these organizations are concurrently creating a second set of transformations from the same sources into integrated data repositories (IDRs). Considerable cost savings could be realized and overall quality could be improved were it possible to transformation primary FHIR EHR data directly into an IDR. We developed a FHIR to i2b2 transformation toolkit and evaluated the viability of such an approach.
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Affiliation(s)
- Harold R Solbrig
- Department of Health Sciences Research, Mayo Clinic, Rochester MN, USA
| | - Na Hong
- Department of Health Sciences Research, Mayo Clinic, Rochester MN, USA
| | - Shawn N Murphy
- Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA, USA
| | - Guoqian Jiang
- Department of Health Sciences Research, Mayo Clinic, Rochester MN, USA
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22
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Wagholikar KB, Dessai P, Sanz J, Mendis ME, Bell DS, Murphy SN. Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers. BMC Med Inform Decis Mak 2018; 18:66. [PMID: 30012140 PMCID: PMC6048900 DOI: 10.1186/s12911-018-0646-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 06/27/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at over 200 healthcare institutions for querying patient data. The i2b2 platform has several components with numerous dependencies and configuration parameters, which renders the task of installing or upgrading i2b2 a challenging one. Even with the availability of extensive documentation and tutorials, new users often require several weeks to correctly install a functional i2b2 platform. The goal of this work is to simplify the installation and upgrade process for i2b2. Specifically, we have containerized the core components of the platform, and evaluated the containers for ease of installation. RESULTS We developed three Docker container images: WildFly, database, and web, to encapsulate the three major deployment components of i2b2. These containers isolate the core functionalities of the i2b2 platform, and work in unison to provide its functionalities. Our evaluations indicate that i2b2 containers function successfully on the Linux platform. Our results demonstrate that the containerized components work out-of-the-box, with minimal configuration. CONCLUSIONS Containerization offers the potential to package the i2b2 platform components into standalone executable packages that are agnostic to the underlying host operating system. By releasing i2b2 as a Docker container, we anticipate that users will be able to create a working i2b2 hive installation without the need to download, compile, and configure individual components that constitute the i2b2 cells, thus making this platform accessible to a greater number of institutions.
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Affiliation(s)
| | - Pralav Dessai
- University of California Los Angeles, Los Angeles, CA USA
| | - Javier Sanz
- University of California Los Angeles, Los Angeles, CA USA
| | | | | | - Shawn N. Murphy
- Massachusetts General Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
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23
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Wagholikar KB, Mendis M, Dessai P, Sanz J, Law S, Gilson M, Sanders S, Vangala M, Bell DS, Murphy SN. Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform. BIOMEDICAL INFORMATICS INSIGHTS 2018; 10:1178222618777749. [PMID: 29887730 PMCID: PMC5989048 DOI: 10.1177/1178222618777749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/25/2018] [Indexed: 11/17/2022]
Abstract
Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at more than 150 institutions for querying patient data. An i2b2 installation (called hive) comprises several i2b2 cells that provide different functionalities. Given the complex architecture of i2b2 installation, creating a working installation of the platform is challenging for new users. This is despite the availability of extensive documentation for i2b2 and access to a large and active mailing list community of i2b2 users. To address this problem, we have created an automated installation package, called i2b2-quickstart, which automatically downloads the latest i2b2 source code and dependencies, and compiles and configures the i2b2 cells to create a functional i2b2 hive installation. This package will serve as a convenient starting point and reference implementation that will facilitate researchers in the installation and exploration of the i2b2 platform.
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Affiliation(s)
- Kavishwar B Wagholikar
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Partners HealthCare, Boston, MA, USA
| | | | - Pralav Dessai
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Javier Sanz
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Sindy Law
- University of California, San Francisco, San Francisco, CA, USA
| | - Micheal Gilson
- University of California, San Francisco, San Francisco, CA, USA
| | - Stephan Sanders
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Douglas S Bell
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Shawn N Murphy
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Partners HealthCare, Boston, MA, USA
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24
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Paris N, Mendis M, Daniel C, Murphy S, Tannier X, Zweigenbaum P. i2b2 implemented over SMART-on-FHIR. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2018; 2017:369-378. [PMID: 29888095 PMCID: PMC5961782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Integrating Biology and the Bedside (i2b2) is the de-facto open-source medical tool for cohort discovery. Fast Healthcare Interoperability Resources (FHIR) is a new standard for exchanging health care information electronically. Substitutable Modular third-party Applications (SMART) defines the SMART-on-FHIR specification on how applications shall interface with Electronic Health Records (EHR) through FHIR. Related work made it possible to produce FHIR from an i2b2 instance or made i2b2 able to store FHIR datasets. In this paper, we extend i2b2 to search remotely into one or multiple SMART-on-FHIR Application Programming Interfaces (APIs). This enables the federation of queries, security, terminology mapping, and also bridges the gap between i2b2 and modern big-data technologies.
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Affiliation(s)
- Nicolas Paris
- WIND-DSI, AP-HP, Paris, France,LIMSI, CNRS, Université Paris-Saclay, Orsay, France,INSERM, UMR S 1142, LIMICS, Paris, France
| | | | - Christel Daniel
- WIND-DSI, AP-HP, Paris, France,INSERM, UMR S 1142, LIMICS, Paris, France
| | | | - Xavier Tannier
- INSERM, UMR S 1142, LIMICS, Paris, France,Sorbonne Universités, UPMC Univ Paris 06, France
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25
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Kramer F, Just S, Zeller T. New perspectives: systems medicine in cardiovascular disease. BMC SYSTEMS BIOLOGY 2018; 12:57. [PMID: 29699591 PMCID: PMC5921396 DOI: 10.1186/s12918-018-0579-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/28/2018] [Indexed: 01/22/2023]
Abstract
Background Cardiovascular diseases (CVD) represent one of the most important causes of morbidity and mortality worldwide. Innovative approaches to increase the understanding of the underpinnings of CVD promise to enhance CVD risk assessment and might pave the way to tailored therapies. Within the last years, systems medicine has emerged as a novel tool to study the genetic, molecular and physiological interactions. Conclusion In this review, we provide an overview of the current molecular-experimental, epidemiological and bioinformatical tools applied in systems medicine in the cardiovascular field. We will discuss the status and challenges in implementing interdisciplinary systems medicine approaches in CVD.
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Affiliation(s)
- Frank Kramer
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee, 32, Göttingen, Germany
| | - Steffen Just
- Molecular Cardiology, Department of Medicine II, University of Ulm, Ulm, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany. .,German Center for Cardiovascular Research (DZHK e.V.), Partner Site Hamburg, Lübeck, Kiel, Hamburg, Germany.
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