Prototypical Clinical Trial Registry Based on Fast Healthcare Interoperability Resources (FHIR): Design and Implementation Study.
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ABSTRACT: Background
Clinical trial registries increase transparency in medical research by making information and results of planned, ongoing, and completed studies publicly available. However, the registration of clinical trials remains a time-consuming manual task complicated by the fact that the same studies often need to be registered in different registries with different data entry requirements and interfaces.Objective
This study investigates how Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) may be used as a standardized format for exchanging and storing clinical trial records.Methods
We designed and prototypically implemented an open-source central trial registry containing records from university hospitals, which are automatically exported and updated by local study management systems.Results
We provided an architecture and implementation of a multisite clinical trials registry based on HL7 FHIR as a data storage and exchange format.Conclusions
The results show that FHIR resources establish a harmonized view of study information from heterogeneous sources by enabling automated data exchange between trial centers and central study registries.
SUBMITTER: Gulden C
PROVIDER: S-EPMC7837997 | biostudies-literature | 2021 Jan
REPOSITORIES: biostudies-literature
Publications
Prototypical Clinical Trial Registry Based on Fast Healthcare Interoperability Resources (FHIR): Design and Implementation Study.
Gulden Christian C Blasini Romina R Nassirian Azadeh A Stein Alexandra A Altun Fatma Betül FB Kirchner Melanie M Prokosch Hans-Ulrich HU Boeker Martin M
JMIR medical informatics 20210112 1
<h4>Background</h4>Clinical trial registries increase transparency in medical research by making information and results of planned, ongoing, and completed studies publicly available. However, the registration of clinical trials remains a time-consuming manual task complicated by the fact that the same studies often need to be registered in different registries with different data entry requirements and interfaces.<h4>Objective</h4>This study investigates how Health Level 7 (HL7) Fast Healthcare ...[more]
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| S-EPMC5557515 | biostudies-other
Project description:BackgroundThe harmonization and standardization of digital medical information for research purposes is a challenging and ongoing collaborative effort. Current research data repositories typically require extensive efforts in harmonizing and transforming original clinical data. The Fast Healthcare Interoperability Resources (FHIR) format was designed primarily to represent clinical processes; therefore, it closely resembles the clinical data model and is more widely available across modern electronic health records. However, no common standardized data format is directly suitable for statistical analyses, and data need to be preprocessed before statistical analysis.ObjectiveThis study aimed to elucidate how FHIR data can be queried directly with a preprocessing service and be used for statistical analyses.MethodsWe propose that the binary JavaScript Object Notation format of the PostgreSQL (PSQL) open source database is suitable for not only storing FHIR data, but also extending it with preprocessing and filtering services, which directly transform data stored in FHIR format into prepared data subsets for statistical analysis. We specified an interface for this preprocessor, implemented and deployed it at University Hospital Erlangen-Nürnberg, generated 3 sample data sets, and analyzed the available data.ResultsWe imported real-world patient data from 2016 to 2018 into a standard PSQL database, generating a dataset of approximately 35.5 million FHIR resources, including "Patient," "Encounter," "Condition" (diagnoses specified using International Classification of Diseases codes), "Procedure," and "Observation" (laboratory test results). We then integrated the developed preprocessing service with the PSQL database and the locally installed web-based KETOS analysis platform. Advanced statistical analyses were feasible using the developed framework using 3 clinically relevant scenarios (data-driven establishment of hemoglobin reference intervals, assessment of anemia prevalence in patients with cancer, and investigation of the adverse effects of drugs).ConclusionsThis study shows how the standard open source database PSQL can be used to store FHIR data and be integrated with a specifically developed preprocessing and analysis framework. This enables dataset generation with advanced medical criteria and the integration of subsequent statistical analysis. The web-based preprocessing service can be deployed locally at the hospital level, protecting patients' privacy while being integrated with existing open source data analysis tools currently being developed across Germany.
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| S-EPMC9135115 | biostudies-literature
Project description:BackgroundThe introduction of next-generation sequencing (NGS) into molecular cancer diagnostics has led to an increase in the data available for the identification and evaluation of driver mutations and for defining personalized cancer treatment regimens. The meaningful combination of omics data, ie, pathogenic gene variants and alterations with other patient data, to understand the full picture of malignancy has been challenging.ObjectiveThis study describes the implementation of a system capable of processing, analyzing, and subsequently combining NGS data with other clinical patient data for analysis within and across institutions.MethodsOn the basis of the already existing NGS analysis workflows for the identification of malignant gene variants at the Institute of Pathology of the University Hospital Erlangen, we defined basic requirements on an NGS processing and analysis pipeline and implemented a pipeline based on the GEMINI (GEnome MINIng) open source genetic variation database. For the purpose of validation, this pipeline was applied to data from the 1000 Genomes Project and subsequently to NGS data derived from 206 patients of a local hospital. We further integrated the pipeline into existing structures of data integration centers at the University Hospital Erlangen and combined NGS data with local nongenomic patient-derived data available in Fast Healthcare Interoperability Resources format.ResultsUsing data from the 1000 Genomes Project and from the patient cohort as input, the implemented system produced the same results as already established methodologies. Further, it satisfied all our identified requirements and was successfully integrated into the existing infrastructure. Finally, we showed in an exemplary analysis how the data could be quickly loaded into and analyzed in KETOS, a web-based analysis platform for statistical analysis and clinical decision support.ConclusionsThis study demonstrates that the GEMINI open source database can be augmented to create an NGS analysis pipeline. The pipeline generates high-quality results consistent with the already established workflows for gene variant annotation and pathological evaluation. We further demonstrate how NGS-derived genomic and other clinical data can be combined for further statistical analysis, thereby providing for data integration using standardized vocabularies and methods. Finally, we demonstrate the feasibility of the pipeline integration into hospital workflows by providing an exemplary integration into the data integration center infrastructure, which is currently being established across Germany.
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Project description:BackgroundReferral linkages are crucial for efficient functioning of primary health care (PHC) systems. Fast Healthcare Interoperability Resource (FHIR) is an open global standard that facilitates structuring of health information for coordinated exchange among stakeholders.ObjectiveThe objective of this study is to design FHIR profiles and present methodology and the profiled FHIR resource for Maternal and Child Health referral use cases in Ebonyi state, Nigeria-a typical low- and middle-income country (LMIC) setting.MethodsPracticing doctors, midwives, and nurses were purposefully sampled and surveyed. Different referral forms were reviewed. The union of data sets from surveys and forms was aggregated and mapped to base patient FHIR resource elements, and extensions were created for data sets not in the core FHIR specification. This study also introduced FHIR and its relation to the World Health Organization's (WHO's) International Classification of Diseases.ResultsWe found many different data elements from the referral forms and survey responses even in urban settings. The resulting FHIR standard profile is published on GitHub for adaptation or adoption as necessary to aid alignment with WHO recommendations. Understanding data sets used in health care and clinical practice for information sharing is crucial in properly standardizing information sharing, particularly during the management of COVID-19 and other infectious diseases. Development organizations and governments can use this methodology and profile to fast-track FHIR standards adoption for paper and electronic information sharing at PHC systems in LMICs.ConclusionsWe presented our methodology for profiling the referral resource crucial for the standardized exchange of new and expectant moms' information. Using data from frontline providers and mapping to the FHIR profile helped contextualize the standardized profile.
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Project description:BackgroundThe 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.ObjectiveThe 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.MethodsA 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.ResultsA 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.ConclusionsThis 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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Project description:This study aimed to develop a model to predict the 5-year risk of developing end-stage renal disease (ESRD) in patients with type 2 diabetes mellitus (T2DM) using machine learning (ML). It also aimed to implement the developed algorithms into electronic medical records (EMR) system using Health Level Seven (HL7) Fast Healthcare Interoperability Resources (FHIR). The final dataset used for modeling included 19,159 patients. The medical data were engineered to generate various types of features that were input into the various ML classifiers. The classifier with the best performance was XGBoost, with an area under the receiver operator characteristics curve (AUROC) of 0.95 and area under the precision recall curve (AUPRC) of 0.79 using three-fold cross-validation, compared to other models such as logistic regression, random forest, and support vector machine (AUROC range, 0.929-0.943; AUPRC 0.765-0.792). Serum creatinine, serum albumin, the urine albumin-to-creatinine ratio, Charlson comorbidity index, estimated GFR, and medication days of insulin were features that were ranked high for the ESRD risk prediction. The algorithm was implemented in the EMR system using HL7 FHIR through an ML-dedicated server that preprocessed unstructured data and trained updated data.
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Project description:PURPOSE:For patients with time-critical acute coronary syndrome, reporting electrocardiogram (ECG) findings is the most important component of the treatment process. We aimed to develop and validate an automated Fast Healthcare Interoperability Resources (FHIR)-based 12-lead ECG mobile alert system for use in an emergency department (ED). MATERIALS AND METHODS:An automated FHIR-based 12-lead ECG alert system was developed in the ED of an academic tertiary care hospital. The system was aimed at generating an alert for patients with suspected acute coronary syndrome based on interpretation by the legacy device. The alert is transmitted to physicians both via a mobile application and the patient's electronic medical record (EMR). The automated FHIR-based 12-lead ECG alert system processing interval was defined as the time from ED arrival and 12-lead ECG capture to the time when the FHIR-based notification was transmitted. RESULTS:During the study period, 3812 emergency visits and 1581 12-lead ECGs were recorded. The FHIR system generated 155 alerts for 116 patients. The alerted patients were significantly older [mean (standard deviation): 68.1 (12.4) years vs. 59.6 (16.8) years, p<0.001], and the cardiac-related symptom rate was higher (34.5% vs. 19%, p<0.001). Among the 155 alerts, 146 (94%) were transmitted successfully within 5 minutes. The median interval from 12-lead ECG capture to FHIR notification was 2.7 min [interquartile range (IQR) 2.2-3.1 min] for the group with cardiac-related symptoms and 3.0 min (IQR 2.5-3.4 min) for the group with non-cardiac-related symptoms. CONCLUSION:An automated FHIR-based 12-lead ECG mobile alert system was successfully implemented in an ED.
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Project description:ObjectiveDevelop and evaluate an interactive information visualization embedded within the electronic health record (EHR) by following human-centered design (HCD) processes and leveraging modern health information exchange standards.Materials and methodsWe applied an HCD process to develop a Fast Healthcare Interoperability Resources (FHIR) application that displays a patient's asthma history to clinicians in a pediatric emergency department. We performed a preimplementation comparative system evaluation to measure time on task, number of screens, information retrieval accuracy, cognitive load, user satisfaction, and perceived utility and usefulness. Application usage and system functionality were assessed using application logs and a postimplementation survey of end users.ResultsUsability testing of the Asthma Timeline Application demonstrated a statistically significant reduction in time on task (P < .001), number of screens (P < .001), and cognitive load (P < .001) for clinicians when compared to base EHR functionality. Postimplementation evaluation demonstrated reliable functionality and high user satisfaction.DiscussionFollowing HCD processes to develop an application in the context of clinical operations/quality improvement is feasible. Our work also highlights the potential benefits and challenges associated with using internationally recognized data exchange standards as currently implemented.ConclusionCompared to standard EHR functionality, our visualization increased clinician efficiency when reviewing the charts of pediatric asthma patients. Application development efforts in an operational context should leverage existing health information exchange standards, such as FHIR, and evidence-based mixed methods approaches.
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