Academic literature on the topic 'FHIR Mapping Language'

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.

The conversion of unstructured clinical data into structured formats, such as Fast Healthcare Interoperability Resources (FHIR), is a critical challenge in healthcare informatics. This study explores the potential of large language models (LLMs) to automate this conversion process, aiming to enhance data interoperability and improve healthcare outcomes. The effectiveness of various LLMs in converting clinical reports into FHIR bundles was evaluated using different prompting techniques, including iterative correction and example-based prompting. The findings demonstrate the critical role of prompt engineering, with the two-step approach shown to significantly improve accuracy and completeness. While few-shot learning enhanced performance, it also introduced a risk of overreliance on examples. The performance of the LLMs is assessed based on the precision, hallucination rate, and resource mapping accuracy across mammography and dermatological reports from two clinics, providing insights into effective strategies for reliable FHIR data conversion and highlighting the importance of tailored prompting strategies.

Abstract Objective To design, develop, and evaluate a scalable clinical data normalization pipeline for standardizing unstructured electronic health record (EHR) data leveraging the HL7 Fast Healthcare Interoperability Resources (FHIR) specification. Methods We established an FHIR-based clinical data normalization pipeline known as NLP2FHIR that mainly comprises: (1) a module for a core natural language processing (NLP) engine with an FHIR-based type system; (2) a module for integrating structured data; and (3) a module for content normalization. We evaluated the FHIR modeling capability focusing on core clinical resources such as Condition, Procedure, MedicationStatement (including Medication), and FamilyMemberHistory using Mayo Clinic’s unstructured EHR data. We constructed a gold standard reusing annotation corpora from previous NLP projects. Results A total of 30 mapping rules, 62 normalization rules, and 11 NLP-specific FHIR extensions were created and implemented in the NLP2FHIR pipeline. The elements that need to integrate structured data from each clinical resource were identified. The performance of unstructured data modeling achieved F scores ranging from 0.69 to 0.99 for various FHIR element representations (0.69–0.99 for Condition; 0.75–0.84 for Procedure; 0.71–0.99 for MedicationStatement; and 0.75–0.95 for FamilyMemberHistory). Conclusion We demonstrated that the NLP2FHIR pipeline is feasible for modeling unstructured EHR data and integrating structured elements into the model. The outcomes of this work provide standards-based tools of clinical data normalization that is indispensable for enabling portable EHR-driven phenotyping and large-scale data analytics, as well as useful insights for future developments of the FHIR specifications with regard to handling unstructured clinical data.

IntroductionEcosystem-centered healthcare innovations, such as digital health platforms, patient-centric records, and mobile health applications, depend on the semantic interoperability of health data. This ensures efficient, patient-focused healthcare delivery in a mobile world where citizens frequently travel for work and leisure. Beyond healthcare delivery, semantic interoperability is crucial for secondary health data use. This paper introduces a tool and techniques for achieving health data semantic interoperability, using reusable visual transformation components to create and validate transformation rules and maps, making them usable for domain experts with minimal technical skills.MethodsThe tool and techniques for health data semantic interoperability have been developed and validated using Design Science, a common methodology for developing software artifacts, including tools and techniques.ResultsOur tool and techniques are designed to facilitate the interoperability of Electronic Health Records (EHRs) by enabling the seamless unification of various health data formats in real time, without the need for extensive physical data migrations. These tools simplify complex health data transformations, allowing domain experts to specify and validate intricate data transformation rules and maps. The need for such a solution arises from the ongoing transition of the Estonian National Health Information System (ENHIS) from Clinical Document Architecture (CDA) to Fast Healthcare Interoperability Resources (FHIR), but it is general enough to be used for other data transformation needs, including the European Health Data Space (EHDS) ecosystem.ConclusionThe proposed tool and techniques simplify health data transformation by allowing domain experts to specify and validate the necessary data transformation rules and maps. Evaluation by ENHIS domain experts demonstrated the usability, effectiveness, and business value of the tool and techniques.

The paper presents a visual editor for the FHIR Mapping Language (FML), designed to simplify data transformations for business analysts in healthcare informatics. It aims to make complex data transformation tasks more accessible and manageable without requiring extensive programming knowledge. The paper discusses the development and evaluation of a visual FML editor integrated into the TermX suite. It highlights the challenges of data transformation in healthcare, particularly the need for interoperability between various data standards like HL7 CDA and FHIR. The visual editor is designed to hide the complexity of FML, making it easier for business analysts to create, validate, and maintain data transformations. The usability of the editor was tested with positive results, showing that analysts could effectively use the tool after minimal training. <strong>Problem Addressed</strong>Data transformations in healthcare often require converting between different data standards and versions, which are typically hard-coded and inaccessible to business analysts. This creates challenges in the design, validation, and maintenance of data transformations, making the process resource-intensive and difficult to manage. <strong>Novelty</strong>The visual FML editor is novel in its approach to making FML accessible to business analysts by providing a user-friendly interface that hides the complexity of the underlying language. This tool allows analysts to perform data transformations without needing to write code, which is a significant departure from traditional methods that rely heavily on programming. <strong>Key Contributions</strong> <em>Development of a Visual FML Editor</em>: Created a tool that enables non-technical analysts to design and visualize data transformations using FML without needing programming skills. <em>Integration with TermX</em>: The editor is part of the TermX interoperability suite, enhancing its functionality and usability. <em>Introducing FML</em>: The paper explains the history and design principles of the FML language, addressing gaps in the existing academic literature. <em>Usability Testing</em>: Conducted assessments showing that analysts could effectively use the editor after short training sessions, demonstrating its practicality and effectiveness. <em>Support for Complex Transformations</em>: The editor supports transforming simple and complex data models into FHIR resources, including handling multiple input and output models. This paper contributes to the understanding and application of FML in healthcare data transformations.

Abstract Objective We propose a system, quEHRy, to retrieve precise, interpretable answers to natural language questions from structured data in electronic health records (EHRs). Materials and Methods We develop/synthesize the main components of quEHRy: concept normalization (MetaMap), time frame classification (new), semantic parsing (existing), visualization with question understanding (new), and query module for FHIR mapping/processing (new). We evaluate quEHRy on 2 clinical question answering (QA) datasets. We evaluate each component separately as well as holistically to gain deeper insights. We also conduct a thorough error analysis for a crucial subcomponent, medical concept normalization. Results Using gold concepts, the precision of quEHRy is 98.33% and 90.91% for the 2 datasets, while the overall accuracy was 97.41% and 87.75%. Precision was 94.03% and 87.79% even after employing an automated medical concept extraction system (MetaMap). Most incorrectly predicted medical concepts were broader in nature than gold-annotated concepts (representative of the ones present in EHRs), eg, Diabetes versus Diabetes Mellitus, Non-Insulin-Dependent. Discussion The primary performance barrier to deployment of the system is due to errors in medical concept extraction (a component not studied in this article), which affects the downstream generation of correct logical structures. This indicates the need to build QA-specific clinical concept normalizers that understand EHR context to extract the “relevant” medical concepts from questions. Conclusion We present an end-to-end QA system that allows information access from EHRs using natural language and returns an exact, verifiable answer. Our proposed system is high-precision and interpretable, checking off the requirements for clinical use.

Our novel Intelligent Tutoring System (ITS) architecture integrates HL7 Fast Healthcare Interoperability Resources (FHIR) for data exchange and Unified Medical Language System (UMLS) codes for content mapping.

A significant portion of data in Electronic Health Records is only available as unstructured text, such as surgical or finding reports, clinical notes and discharge summaries. To use this data for secondary purposes, natural language processing (NLP) tools are required to extract structured information. Furthermore, for interoperable use, harmonization of the data is necessary. HL7 Fast Healthcare Interoperability Resources (FHIR), an emerging standard for exchanging healthcare data, defines such a structured format. For German-language medical NLP, the tool Averbis Health Discovery (AHD) represents a comprehensive solution. AHD offers a proprietary REST interface for text analysis pipelines. To build a bridge between FHIR and this interface, we created a service that translates the communication around AHD from and to FHIR. The application is available under an open source license.

Patient summaries grant healthcare providers a concise overview of a patient’s status. This paper showcases to which degree International Patient Summaries (IPS) represented in HL7 FHIR format can be generated using data from the nationwide Austrian Electronic Health Record system ELGA. A solution is presented which enables the automated software-assembled generation of an IPS using the FHIR Mapping Language. The generated document successfully validates against the IPS profiles. Our results show that all required IPS sections can be supplied from ELGA data.

Introduction: 16 million German-language free-text laboratory test results are the basis of the daily diagnostic routine of 17 laboratories within the University Hospital Erlangen. As part of the Medical Informatics Initiative, the local data integration centre is responsible for the accessibility of routine care data for medical research. Following the core data set, international interoperability standards such as FHIR and the English-language medical terminology SNOMED CT are used to create harmonised data. To represent each non-numeric laboratory test result within the base module profile ObservationLab, the need for a map and supporting tooling arose. State of the Art: Due to the requirement of a n:n map and a data safety-compliant local instance, publicly available tools (e.g., SNAP2SNOMED) were insufficient. Concept and Implementation: Therefore, we developed (1) an incremental mapping-validation process with different iteration cycles and (2) a customised mapping tool via Microsoft Access. Time, labour, and cost efficiency played a decisive role. First iterations were used to define requirements (e.g., multiple user access). Lessons Learned: The successful process and tool implementation and the described lessons learned (e.g., cheat sheet) will assist other German hospitals in creating local maps for inter-consortia data exchange and research. In the future, qualitative and quantitative analysis results will be published.