Metadata Driven Integration of Clinical Data for Secondary Use in FHIR - A Pilot Study at the UKSH.

Introduction: The reuse of clinical data from clinical routine is a topic of research within the field of medical informatics under the term secondary use. In order to ensure the correct use and interpretation of data, there is a need for context information of data collection and a general understanding of the data. The use of metadata as an effective method of defining and maintaining context is well-established, particularly in the field of clinical trials.

Development, Involvement and Use of an Overarching In-House Registry for Clinical Trials.

Introduction: Conducting clinical studies is an integral part of the clinical research repertoire of university hospitals. A wealth of organizational competences must always be available in a central location and in an up-to-date form for appropriate administration. Information such as the number of ongoing studies, and the number of enrolled participants is required for tasks related to e.

Reformatted Crosswalk-Tables Between Annual ICD-10-Versions for Cross Version Data Analysis.

The International Statistical Classification of Diseases and Related Health Problems, 10th Revision (ICD-10) is internationally used for coding diagnoses, with the ICD-10 German Modification (GM) being prescribed for morbidity coding in Germany. ICD-10-GM is subject to annual revisions. This can lead to backward compatibility issues leading to undesirable consequences for cross-version data analysis.

Uncovering Harmonization Potential in Health Care Data Through Iterative Refinement of Fast Healthcare Interoperability Resources Profiles Based on Retrospective Discrepancy Analysis: Case Study.

Background: Cross-institutional interoperability between health care providers remains a recurring challenge worldwide. The German Medical Informatics Initiative, a collaboration of 37 university hospitals in Germany, aims to enable interoperability between partner sites by defining Fast Healthcare Interoperability Resources (FHIR) profiles for the cross-institutional exchange of health care data, the Core Data Set (CDS). The current CDS and its extension modules define elements representing patients' health care records.

Structured Queries to AQL: Querying OpenEHR Data Leveraging a FHIR-Based Infrastructure for Federated Feasibility Queries.

In digital healthcare, data heterogeneity is a reoccurring issue caused by proprietary source systems. It is often overcome by utilizing ETL processes resulting in data warehouses, which ensure common data models for interoperability. Unfortunately, the achieved interoperability is usually limited to an institutional level.

Mettertron - Bridging Metadata Repositories and Terminology Servers.

To provide clinical data in distributed research architectures, a fundamental challenge involves defining and distributing suitable metadata within Metadata Repositories. Especially for structured data, data elements need to be bound against suitable terminologies; otherwise, other systems will only be able to interpret the data with complex and error-prone manual involvement. As current Metadata Repository implementations lack support for querying externally defined terminologies in FHIR terminology servers, we propose an intermediate solution that uses appropriate annotations on metadata elements to allow run-time Terminology Services mediated queries of that metadata.

Performance Benchmarking of FHIR Terminology Operations in ETL Jobs.

Interoperability in healthcare cannot be achieved without mapping local data to standardized terminology. In this paper, we investigate the performance of different approaches for implementing HL7 FHIR Terminology Module operations using a benchmarking methodology, to gather evidence on the benefits and pitfalls of these methods in terms of performance from the point-of-view of a terminology client. The approaches perform very differently, while having a local client-side cache for all operations is of supreme importance.

TermiCron - Bridging the Gap Between FHIR Terminology Servers and Metadata Repositories.

The large variability of data models, specifications, and interpretations of data elements is particular to the healthcare domain. Achieving semantic interoperability is the first step to enable reuse of healthcare data. To ensure interoperability, metadata repositories (MDR) are increasingly used to manage data elements on a structural level, while terminology servers (TS) manage the ontologies, terminologies, coding systems and value sets on a semantic level.

Improving Findability of Digital Assets in Research Data Repositories Using the W3C DCAT Vocabulary.

Research data management requires stable, trustworthy repositories to safeguard scientific research results. In this context, rich markup with metadata is crucial for the discoverability and interpretability of the relevant resources. SEEK is a web-based software to manage all important artifacts of a research project, including project structures, involved actors, documents and datasets.

TerminoDiff - Detecting Semantic Differences in HL7 FHIR CodeSystems.

While HL7 FHIR and its terminology package have seen a rapid uptake by the research community, in no small part due to the wide availability of tooling and resources, there are some areas where tool availability is still lacking. In particular, the comparison of terminological resources, which supports the work of terminologists and implementers alike, has not yet been sufficiently addressed. Hence, we present TerminoDiff, an application to semantically compare FHIR R4 CodeSystem resources.

Proposal of Semantic Annotation for German Metadata Using Bidirectional Recurrent Neural Networks.

The distributed nature of our digital healthcare and the rapid emergence of new data sources prevents a compelling overview and the joint use of new data. Data integration, e.g.

Mapping of ICD-O Tuples to OncoTree Codes Using SNOMED CT Post-Coordination.

Around 500,000 oncological diseases are diagnosed in Germany every year which are documented using the International Classification of Diseases for Oncology (ICD-O). Apart from this, another classification for oncology, OncoTree, is often used for the integration of new research findings in oncology. For this purpose, a semi-automatic mapping of ICD-O tuples to OncoTree codes was developed.

Generation of a Fast Healthcare Interoperability Resources (FHIR)-based Ontology for Federated Feasibility Queries in the Context of COVID-19: Feasibility Study.

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.

Understanding the Nature of Metadata: Systematic Review.

Background: Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example, data identification and classification. However, a clear definition of metadata is crucial for further use. Unfortunately, extensive experience with the processing and management of metadata has shown that the term "metadata" and its use is not always unambiguous.

Providing ART-DECOR ValueSets via FHIR Terminology Servers - A Technical Report.

To ensure semantic interoperability within healthcare systems, using common, curated terminological systems to identify relevant concepts is of fundamental importance. The HL7 FHIR standard specifies means of modelling terminological systems and appropriate ways of accessing and querying these artefacts within a terminology server. Hence, initiatives towards healthcare interoperability like IHE specify not only software interfaces, but also common codes in the form of value sets and code systems.

Hands on the Medical Informatics Initiative Core Data Set - Lessons Learned from Converting the MIMIC-IV.

With the steady increase in the connectivity of the healthcare system, new requirements and challenges are emerging. In addition to the seamless exchange of data between service providers on a national level, the local legacy data must also meet the new requirements. For this purpose, the applications used must be tested securely and sufficiently.

openEHR Mapper - A Tool to Fuse Clinical and Genomic Data Using the openEHR Standard.

Precision medicine is an emerging and important field for health care. Molecular tumor boards use a combination of clinical and molecular data, such as somatic tumor mutations to decide on personalized therapies for patients who have run out of standard treatment options. Personalized treatment decisions require clinical data from the hospital information system and mutation data to be accessible in a structured way.

Fit for Purpose: Analyzing the German Archiving and Exchange Interface for Medical Practice Management Systems.

The archiving and exchange interface for practice management systems of the Kassenärztliche Bundesvereinigung, defined by FHIR (Fast Healthcare Interoperability Resources) profiles with extensions, describes a new opportunity for medical practitioner to change the system provider. The expectation is to transfer an entire database of a legacy system to another system without data loss. In this paper the potential loss of data is analyzed by comparing parameters.

FhirSpark - Implementing a Mediation Layer to Bring FHIR to the cBioPortal for Cancer Genomics.

cBioPortal is a commonly used data warehousing solution for genomic cancer studies. The software is being extended for patient care application in a molecular tumor board by the MIRACUM consortium within the Medical Informatics Initiative Germany. A key feature for this use case is the ability to enter therapy recommendations for individual patients, which requires interoperability with the hospital information system.