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. The broad solution space to achieve interoperability with different health data standards is part of the problem, resulting in different standards used at various institutions. For cross-institutional use cases like federated feasibility queries, the issue of heterogeneity is reintroduced. This work showcases how the existing German infrastructure for federated feasibility queries based on Hl7 FHIR can be extended to support openEHR without further data transformation. By utilizing an intermediate query format that can be transferred to FHIR Search, CQL, and AQL.

The Urethral Perfusion Index During Off-Pump Coronary Artery Bypass Surgery: An Observational Study.

OBJECTIVES: The IKORUS system (Vygon, Écouen, France) allows continuous monitoring of the urethral perfusion index (uPI) using a photoplethysmographic sensor mounted near the base of the balloon of a dedicated urinary catheter. We aimed to test the hypothesis that the uPI decreases during off-pump coronary artery bypass (OPCAB) surgery and to investigate the relationship between the uPI and macrocirculatory variables. DESIGN: Prospective observational study. SETTING: University Medical Center Hamburg-Eppendorf, Hamburg, Germany. PARTICIPANTS: Twenty patients having OPCAB surgery. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The primary endpoint was changes in the uPI during OPCAB surgery. We additionally investigated associations between the uPI and cardiac output, mean arterial pressure, heart rate, and point-of-care variables. Twenty patients with 24,137 uPI measurements were included. Overall, there was a high interindividual variability in the uPI. Compared with the preparation phase (during which the median [interquartile range] uPI was 7.7 [5.6-12.0]), the uPI decreased by 14% (95% CI 13%-15%) during the bypass grafting phase, by 35% (95% CI 34%-36%) during the cardiac positioning phase, and by 7% (95% CI 6%-9%) during hemostasis. There was no clinically important association between uPI and either cardiac output, mean arterial pressure, or heart rate. CONCLUSIONS: The uPI decreases during OPCAB surgery, specifically during the cardiac positioning phase. There was no clinically important association between uPI and either cardiac output, mean arterial pressure, or heart rate. It, therefore, remains to be determined whether intraoperative uPI decreases are clinically important, reflect alterations in intra-abdominal tissue perfusion that are not reflected by systemic macrohemodynamics, and can help clinicians guide therapeutic interventions.

Towards a Bavarian Oncology Real World Data Research Platform.

INTRODUCTION: In the last decade numerous real-world data networks have been established in order to leverage the value of data from electronic health records for medical research. In Germany, a nation-wide network based on electronic health record data from all German university hospitals has been established within the Medical Informatics Initiative (MII) and recently opened for researcherst' access through the German Portal for Medical Research Data (FDPG). In Bavaria, the six university hospitals have joined forces within the Bavarian Cancer Research Center (BZKF). The oncology departments aim at establishing a federated observational research network based on the framework of the MII/FDPG and extending it with a clear focus on oncological clinical data, imaging data and molecular high throughput analysis data. METHODS: We describe necessary adaptions and extensions of existing MII components with the goal of establishing a Bavarian oncology real world data research platform with its first use case of performing federated feasibility queries on clinical oncology data. RESULTS: We share insights from developing a feasibility platform prototype and presenting it to end users. Our main discovery was that oncological data is characterized by a higher degree of interdependence and complexity compared to the MII core dataset that is already integrated into the FDPG. DISCUSSION: The significance of our work lies in the requirements we formulated for extending already existing MII components to match oncology specific data and to meet oncology researchers needs while simultaneously transferring back our results and experiences into further developments within the MII.

Towards a National Portal for Medical Research Data (FDPG): Vision, Status, and Lessons Learned.

Harmonizing medical data sharing frameworks is challenging. Data collection and formats follow local solutions in individual hospitals; thus, interoperability is not guaranteed. The German Medical Informatics Initiative (MII) aims to provide a Germany-wide, federated, large-scale data sharing network. In the last five years, numerous efforts have been successfully completed to implement the regulatory framework and software components for securely interacting with decentralized and centralized data sharing processes. 31 German university hospitals have today established local data integration centers that are connected to the central German Portal for Medical Research Data (FDPG). Here, we present milestones and associated major achievements of various MII working groups and subprojects which led to the current status. Further, we describe major obstacles and the lessons learned during its routine application in the last six months.

Empowering Researchers to Query Medical Data and Biospecimens by Ensuring Appropriate Usability of a Feasibility Tool: Evaluation Study.

BACKGROUND: The Aligning Biobanking and Data Integration Centers Efficiently project aims to harmonize technologies and governance structures of German university hospitals and their biobanks to facilitate searching for patient data and biospecimens. The central element will be a feasibility tool for researchers to query the availability of samples and data to determine the feasibility of their study project. OBJECTIVE: The objectives of the study were as follows: an evaluation of the overall user interface usability of the feasibility tool, the identification of critical usability issues, comprehensibility of the underlying ontology operability, and analysis of user feedback on additional functionalities. From these, recommendations for quality-of-use optimization, focusing on more intuitive usability, were derived. METHODS: To achieve the study goal, an exploratory usability test consisting of 2 main parts was conducted. In the first part, the thinking aloud method (test participants express their thoughts aloud throughout their use of the tool) was complemented by a quantitative questionnaire. In the second part, the interview method was combined with supplementary mock-ups to collect users' opinions on possible additional features. RESULTS: The study cohort rated global usability of the feasibility tool based on the System Usability Scale with a good score of 81.25. The tasks assigned posed certain challenges. No participant was able to solve all tasks correctly. A detailed analysis showed that this was mostly because of minor issues. This impression was confirmed by the recorded statements, which described the tool as intuitive and user friendly. The feedback also provided useful insights regarding which critical usability problems occur and need to be addressed promptly. CONCLUSIONS: The findings indicate that the prototype of the Aligning Biobanking and Data Integration Centers Efficiently feasibility tool is headed in the right direction. Nevertheless, we see potential for optimization primarily in the display of the search functions, the unambiguous distinguishability of criteria, and the visibility of their associated classification system. Overall, it can be stated that the combination of different tools used to evaluate the feasibility tool provided a comprehensive picture of its usability.

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. Our tool considers differences across all levels required, i.e. metadata and concept differences, as well as differences in the edge graph, and surfaces them in a visually digestible fashion.

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. 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.

The Architecture of a Feasibility Query Portal for Distributed COVID-19 Fast Healthcare Interoperability Resources (FHIR) Patient Data Repositories: Design and Implementation Study.

BACKGROUND: An essential step in any medical research project after identifying the research question is to determine if there are sufficient patients available for a study and where to find them. Pursuing digital feasibility queries on available patient data registries has proven to be an excellent way of reusing existing real-world data sources. To support multicentric research, these feasibility queries should be designed and implemented to run across multiple sites and securely access local data. Working across hospitals usually involves working with different data formats and vocabularies. Recently, the Fast Healthcare Interoperability Resources (FHIR) standard was developed by Health Level Seven to address this concern and describe patient data in a standardized format. The Medical Informatics Initiative in Germany has committed to this standard and created data integration centers, which convert existing data into the FHIR format at each hospital. This partially solves the interoperability problem; however, a distributed feasibility query platform for the FHIR standard is still missing. OBJECTIVE: This study described the design and implementation of the components involved in creating a cross-hospital feasibility query platform for researchers based on FHIR resources. This effort was part of a large COVID-19 data exchange platform and was designed to be scalable for a broad range of patient data. METHODS: We analyzed and designed the abstract components necessary for a distributed feasibility query. This included a user interface for creating the query, backend with an ontology and terminology service, middleware for query distribution, and FHIR feasibility query execution service. RESULTS: We implemented the components described in the Methods section. The resulting solution was distributed to 33 German university hospitals. The functionality of the comprehensive network infrastructure was demonstrated using a test data set based on the German Corona Consensus Data Set. A performance test using specifically created synthetic data revealed the applicability of our solution to data sets containing millions of FHIR resources. The solution can be easily deployed across hospitals and supports feasibility queries, combining multiple inclusion and exclusion criteria using standard Health Level Seven query languages such as Clinical Quality Language and FHIR Search. Developing a platform based on multiple microservices allowed us to create an extendable platform and support multiple Health Level Seven query languages and middleware components to allow integration with future directions of the Medical Informatics Initiative. CONCLUSIONS: We designed and implemented a feasibility platform for distributed feasibility queries, which works directly on FHIR-formatted data and distributed it across 33 university hospitals in Germany. We showed that developing a feasibility platform directly on the FHIR standard is feasible.

Comparing susceptibility and contagiousness in concurrent outbreaks with a non-VOC and the VOC SARS-CoV-2 variant B.1.1.7 in daycare centers in Hamburg, Germany.

We describe two outbreaks of SARS-CoV-2 in daycare centers in the metropolitan area of Hamburg, Germany. The outbreaks occurred in rapid chronological succession, in neighborhoods with a very similar sociodemographic structure, thus allowing for cross-comparison of these events. We combined classical and molecular epidemiologic investigation methods to study infection entry, spread within the facilities, and subsequent transmission of infections to households. Epidemiologic and molecular evidence suggests a superspreading event with a non-variant of concern (non-VOC) SARS CoV-2 strain at the root of the first outbreak. The second outbreak involved two childcare facilities experiencing infection activity with the variant of concern (VOC) B.1.1.7 (Alpha). We show that the index cases in all outbreaks had been childcare workers, and that children contributed substantially to secondary transmission of SARS-CoV-2 infection from childcare facilities to households. The frequency of secondary transmissions in households originating from B.1.1.7-infected children was increased compared to children with non-VOC infections. Self-reported symptoms, particularly cough and rhinitis, occurred more frequently in B.1.1.7-infected children. Especially in light of the rapidly spreading VOC B.1.617.2 (Delta), our data underline the notion that rigorous SARS-CoV-2 testing in combination with screening of contacts regardless of symptoms is an important measure to prevent SARS-CoV-2 infection of unvaccinated individuals in daycare centers and associated households.