RESUMEN
Cytomegalovirus (CMV) is the most common congenital infection and cause of birth defects worldwide. Primary CMV infection during pregnancy leads to a higher frequency of congenital CMV (cCMV) than maternal re-infection, suggesting that maternal immunity confers partial protection. However, poorly understood immune correlates of protection against placental transmission contributes to the current lack of an approved vaccine to prevent cCMV. In this study, we characterized the kinetics of maternal plasma rhesus CMV (RhCMV) viral load (VL) and RhCMV-specific antibody binding and functional responses in a group of 12 immunocompetent dams with acute, primary RhCMV infection. We defined cCMV transmission as RhCMV detection in amniotic fluid (AF) by qPCR. We then leveraged a large group of past and current primary RhCMV infection studies in late-first/early-second trimester RhCMV-seronegative rhesus macaque dams, including immunocompetent (n = 15), CD4+ T cell-depleted with (n = 6) and without (n = 6) RhCMV-specific polyclonal IgG infusion before infection to evaluate differences between RhCMV AF-positive and AF-negative dams. During the first 3 weeks after infection, the magnitude of RhCMV VL in maternal plasma was higher in AF-positive dams in the combined cohort, while RhCMV glycoprotein B (gB)- and pentamer-specific binding IgG responses were lower magnitude compared to AF-negative dams. However, these observed differences were driven by the CD4+ T cell-depleted dams, as there were no differences in plasma VL or antibody responses between immunocompetent AF-positive vs AF-negative dams. Overall, these results suggest that levels of neither maternal plasma viremia nor humoral responses are associated with cCMV following primary maternal infection in healthy individuals. We speculate that other factors related to innate immunity are more important in this context as antibody responses to acute infection likely develop too late to influence vertical transmission. Yet, pre-existing CMV glycoprotein-specific and neutralizing IgG may provide protection against cCMV following primary maternal CMV infection even in high-risk, immunocompromised settings.
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Infecciones por Citomegalovirus , Citomegalovirus , Animales , Femenino , Humanos , Embarazo , Citomegalovirus/fisiología , Macaca mulatta , Formación de Anticuerpos , Carga Viral , Placenta , Anticuerpos Antivirales , Glicoproteínas/metabolismo , Transmisión Vertical de Enfermedad Infecciosa , Inmunoglobulina G/metabolismoRESUMEN
The interoperability Working Group of the Medical Informatics Initiative (MII) is the platform for the coordination of overarching procedures, data structures, and interfaces between the data integration centers (DIC) of the university hospitals and national and international interoperability committees. The goal is the joint content-related and technical design of a distributed infrastructure for the secondary use of healthcare data that can be used via the Research Data Portal for Health. Important general conditions are data privacy and IT security for the use of health data in biomedical research. To this end, suitable methods are used in dedicated task forces to enable procedural, syntactic, and semantic interoperability for data use projects. The MII core dataset was developed as several modules with corresponding information models and implemented using the HL7® FHIR® standard to enable content-related and technical specifications for the interoperable provision of healthcare data through the DIC. International terminologies and consented metadata are used to describe these data in more detail. The overall architecture, including overarching interfaces, implements the methodological and legal requirements for a distributed data use infrastructure, for example, by providing pseudonymized data or by federated analyses. With these results of the Interoperability Working Group, the MII is presenting a future-oriented solution for the exchange and use of healthcare data, the applicability of which goes beyond the purpose of research and can play an essential role in the digital transformation of the healthcare system.
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Interoperabilidad de la Información en Salud , Humanos , Conjuntos de Datos como Asunto , Registros Electrónicos de Salud , Alemania , Interoperabilidad de la Información en Salud/normas , Informática Médica , Registro Médico Coordinado/métodos , Integración de SistemasRESUMEN
The German government initiated the Network University Medicine (NUM) in early 2020 to improve national research activities on the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. To this end, 36 German Academic Medical Centers started to collaborate on 13 projects, with the largest being the National Pandemic Cohort Network (NAPKON). The NAPKON's goal is creating the most comprehensive Coronavirus Disease 2019 (COVID-19) cohort in Germany. Within NAPKON, adult and pediatric patients are observed in three complementary cohort platforms (Cross-Sectoral, High-Resolution and Population-Based) from the initial infection until up to three years of follow-up. Study procedures comprise comprehensive clinical and imaging diagnostics, quality-of-life assessment, patient-reported outcomes and biosampling. The three cohort platforms build on four infrastructure core units (Interaction, Biosampling, Epidemiology, and Integration) and collaborations with NUM projects. Key components of the data capture, regulatory, and data privacy are based on the German Centre for Cardiovascular Research. By April 01, 2022, 34 university and 40 non-university hospitals have enrolled 5298 patients with local data quality reviews performed on 4727 (89%). 47% were female, the median age was 52 (IQR 36-62-) and 50 pediatric cases were included. 44% of patients were hospitalized, 15% admitted to an intensive care unit, and 12% of patients deceased while enrolled. 8845 visits with biosampling in 4349 patients were conducted by April 03, 2022. In this overview article, we summarize NAPKON's design, relevant milestones including first study population characteristics, and outline the potential of NAPKON for German and international research activities.Trial registration https://clinicaltrials.gov/ct2/show/NCT04768998 . https://clinicaltrials.gov/ct2/show/NCT04747366 . https://clinicaltrials.gov/ct2/show/NCT04679584.
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COVID-19 , Pandemias , Adulto , COVID-19/epidemiología , Niño , Ensayos Clínicos como Asunto , Femenino , Humanos , Unidades de Cuidados Intensivos , Masculino , Persona de Mediana Edad , Proyectos de Investigación , SARS-CoV-2RESUMEN
Mother-to-child transmission of human immunodeficiency virus type 1 (HIV-1) continues to cause new pediatric cases of infection through breastfeeding, a setting where it is not always possible to initiate early antiretroviral therapy (ART). Without novel interventions that do not rely on daily ART, HIV-1-infected children face lifelong medications to control infection. A detailed analysis of virus persistence following breast milk transmission of HIV-1 and ART has not been performed. Here, we used infant rhesus macaques orally infected with simian/human immunodeficiency virus (SHIV) (SHIV.C.CH505) to identify cellular and anatomical sites of virus persistence under ART. Viral DNA was detected at similar levels in blood and tissue CD4+ T cells after a year on ART, with virus in blood and lymphoid organs confirmed to be replication competent. Viral RNA/DNA ratios were elevated in rectal CD4+ T cells compared to those of other sites (P ≤ 0.0001), suggesting that the gastrointestinal tract is an active site of virus transcription during ART-mediated suppression of viremia. SHIV.C.CH505 DNA was detected in multiple CD4+ T cell subsets, including cells with a naive phenotype (CD45RA+ CCR7+ CD95-). While the frequency of naive cells harboring intact provirus was lower than in memory cells, the high abundance of naive cells in the infant CD4+ T cell pool made them a substantial source of persistent viral DNA (approximately 50% of the total CD4+ T cell reservoir), with an estimated 1:2 ratio of intact provirus to total viral DNA. This viral reservoir profile broadens our understanding of virus persistence in a relevant infant macaque model and provides insight into targets for cure-directed approaches in the pediatric population.IMPORTANCE Uncovering the sanctuaries of the long-lived HIV-1 reservoir is crucial to develop cure strategies. Pediatric immunity is distinct from that of adults, which may alter where the reservoir is established in infancy. Thus, it is important to utilize pediatric models to inform cure-directed approaches for HIV-1-infected children. We used an infant rhesus macaque model of HIV-1 infection via breastfeeding to identify key sites of viral persistence under antiretroviral therapy (ART). The gastrointestinal tract was found to be a site for low-level viral transcription during ART. We also show that naive CD4+ T cells harbored intact provirus and were a major contributor to blood and lymphoid reservoir size. This is particularly striking, as memory CD4+ T cells are generally regarded as the main source of latent HIV/simian immunodeficiency virus (SIV) infection of adult humans and rhesus macaques. Our findings highlight unique features of reservoir composition in pediatric infection that should be considered for eradication efforts.
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Antirretrovirales/uso terapéutico , Linfocitos T CD4-Positivos/inmunología , Infecciones por VIH/veterinaria , Macaca mulatta , Enfermedades de los Monos/virología , Síndrome de Inmunodeficiencia Adquirida del Simio/inmunología , Virus de la Inmunodeficiencia de los Simios/inmunología , Administración Oral , Animales , Animales Recién Nacidos , ADN Viral/análisis , Reservorios de Enfermedades , Femenino , Infecciones por VIH/inmunología , Infecciones por VIH/transmisión , VIH-1 , Masculino , Enfermedades de los Monos/inmunología , Enfermedades de los Monos/transmisión , ARN Viral/análisis , Virus Reordenados/inmunología , Síndrome de Inmunodeficiencia Adquirida del Simio/virología , Carga ViralRESUMEN
BACKGROUND: The current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing fragmentation of information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the "German Corona Consensus Dataset" (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data, in particular for university medicine. METHODS: Based on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats. RESULTS: A core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, medical history, symptoms, therapy, medications or laboratory values of COVID-19 patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined. CONCLUSION: GECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.
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Investigación Biomédica , COVID-19 , Conjuntos de Datos como Asunto , Medicina , Consenso , Humanos , PandemiasRESUMEN
This paper presents an approach to enable interoperability of the research data management system XNAT by the implementation of the HL7 standards framework Fast Healthcare Interoperability Resources (FHIR). The FHIR implementation is realized as an XNAT plugin (Source code: https://github.com/somnonetz/xnat-fhir-plugin ), that allows easy adoption in arbitrary XNAT instances. The approach is demonstrated on patient data exchange between a FHIR reference implementation and XNAT.
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Estándar HL7/organización & administración , Sistemas de Registros Médicos Computarizados/organización & administración , Neuroimagen/métodos , Manejo de Datos , Registros Electrónicos de Salud , Estándar HL7/normas , Humanos , Sistemas de Registros Médicos Computarizados/normas , Integración de SistemasRESUMEN
Cardiac electrical alternans is a period-2 dynamical behavior with alternating long and short action potential durations (APD) that often precedes dangerous arrhythmias associated with cardiac arrest. Despite the importance of alternans, many current ordinary differential equations models of cardiac electrophysiology do not produce alternans, thereby limiting the use of these models for studying the mechanisms that underlie this condition. Because delay differential equations (DDEs) commonly induce complex dynamics in other biological systems, we investigate whether incorporating DDEs can lead to alternans development in cardiac models by studying the Fox et al. canine ventricular action potential model. After suppressing the alternans in the original model, we show that alternans can be obtained by introducing DDEs in the model gating variables, and we quantitatively compare the DDE-induced alternans with the alternans present in the original model. We analyze the behavior of the voltage, currents, and gating variables of the model to study the effects of the delays and to determine how alternans develops in that setting, and we discuss the mathematical and physiological implications of our findings. In future work, we aim to apply our approach to induce alternans in models that do not naturally exhibit such dynamics.
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Potenciales de Acción/fisiología , Electrofisiología , Corazón/fisiología , Modelos Neurológicos , Animales , Canales de Calcio Tipo L/metabolismo , Perros , Activación del Canal Iónico/fisiología , Modelos Biológicos , Factores de TiempoRESUMEN
BACKGROUND: Dengue virus, primarily transmitted by the Aedes aegypti mosquito, is a major public health concern affecting ≈3.83 billion people worldwide. Recent releases of Wolbachia-transinfected Ae. aegypti in several cities worldwide have shown that it can reduce dengue transmission. However, these releases are costly, and, to date, no framework has been proposed for determining economically optimal release strategies that account for both costs associated with disease risk and releases. RESULTS: We present a flexible stochastic dynamic programming framework for determining optimal release schedules for Wolbachia-transinfected mosquitoes that balances the cost of dengue infection with the costs of rearing and releasing transinfected mosquitoes. Using an ordinary differential equation model of Wolbachia and dengue in a hypothetical city loosely describing areas at risk of new dengue epidemics, we determined that an all-or-nothing release strategy that quickly brings Wolbachia to fixation is often the optimal solution. Based on this, we examined the optimal facility size, finding that it was inelastic with respect to the mosquito population size, with a 100% increase in population size resulting in a 50-67% increase in optimal facility size. Furthermore, we found that these results are robust to mosquito life-history parameters and are mostly determined by the mosquito population size and the fitness costs associated with Wolbachia. CONCLUSIONS: These results reinforce that Wolbachia-transinfected mosquitoes can reduce the cost of dengue epidemics. Furthermore, they emphasize the importance of determining the size of the target population and fitness costs associated with Wolbachia before releases occur. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Aedes , Dengue , Control de Mosquitos , Mosquitos Vectores , Wolbachia , Aedes/microbiología , Aedes/virología , Wolbachia/fisiología , Animales , Dengue/prevención & control , Dengue/transmisión , Control de Mosquitos/métodos , Control de Mosquitos/economía , Mosquitos Vectores/microbiologíaRESUMEN
This work presents the Fast Healthcare Interoperability Resources (FHIR®) specification of the NFDI4Health Metadata schema based on FHIR Version 4: We created 16 profiles to facilitate the integration of clinical, epidemiological, and public health study data. Despite challenges arising from the extensive MDS as well as missing concepts in semantic standards, it marks a significant advance in applying information technology standards to health research.
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Interoperabilidad de la Información en Salud , Estándar HL7 , Metadatos , Humanos , Registros Electrónicos de Salud , Estudios Epidemiológicos , Salud Pública , Investigación BiomédicaRESUMEN
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.
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Estándar HL7 , Unified Medical Language System , Interoperabilidad de la Información en Salud , Integración de Sistemas , HumanosRESUMEN
Adhering to FAIR principles (findability, accessibility, interoperability, reusability) ensures sustainability and reliable exchange of data and metadata. Research communities need common infrastructures and information models to collect, store, manage and work with data and metadata. The German initiative NFDI4Health created a metadata schema and an infrastructure integrating existing platforms based on different information models and standards. To ensure system compatibility and enhance data integration possibilities, we mapped the Investigation-Study-Assay (ISA) model to Fast Healthcare Interoperability Resources (FHIR). We present the mapping in FHIR logical models, a resulting FHIR resources' network and challenges that we encountered. Challenges mainly related to ISA's genericness, and to different structures and datatypes used in ISA and FHIR. Mapping ISA to FHIR is feasible but requires further analyses of example data and adaptations to better specify target FHIR elements, and enable possible automatized conversions from ISA to FHIR.
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Medicamentos Genéricos , Instituciones de Salud , Humanos , Metadatos , Atención a la SaludRESUMEN
To illustrate to health professionals how interoperability may improve patient care we (1) built a prototype to automate the sequential organ failure assessment (SOFA) risk score and (2) designed its display on a medical dashboard. In Accordance with prioritized system requirements from stakeholder interviews, the prototype microservice uses FHIR as the first focus of this work. As the second focus, PretoFaces were used to facilitate user interface design feedback. Our interoperable prototype met all requirements of the highest priority. As a microservice in a SOA, it collects and extracts needed data from a FHIR server and computes the SOFA score and its subscores. Additionally, most requirements of second and third highest priority were met. In parallel, PretoFaces of interfaces were inspired by the requirements. We showed that an automatically computed SOFA score can be speedily developed using FHIR.
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The dynamics of HIV viral load following the initiation of antiretroviral therapy is not well-described by simple, single-phase exponential decay. Several mathematical models have been proposed to describe its more complex behavior, the most popular of which is two-phase exponential decay. The underlying assumption in two-phase exponential decay is that there are two classes of infected cells with different lifespans. However, with the exception of CD4+ T cells, there is not a consensus on all of the cell types that can become productively infected, and the fit of the two-phase exponential decay to observed data from SHIV.C.CH505 infected infant rhesus macaques was relatively poor. Therefore, we propose a new model for viral decay, inspired by the Gompertz model where the decay rate itself is a dynamic variable. We modify the Gompertz model to include a linear term that modulates the decay rate. We show that this simple model performs as well as the two-phase exponential decay model on HIV and SIV data sets, and outperforms it for the infant rhesus macaque SHIV.C.CH505 infection data set. We also show that by using a stochastic differential equation formulation, the modified Gompertz model can be interpreted as being driven by a population of infected cells with a continuous distribution of cell lifespans, and estimate this distribution for the SHIV.C.CH505-infected infant rhesus macaques. Thus, we find that the dynamics of viral decay in this model of infant HIV infection and treatment may be explained by a distribution of cell lifespans, rather than two distinct cell types.
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Infecciones por VIH , VIH-1 , Virus de la Inmunodeficiencia de los Simios , Animales , Macaca mulatta , Longevidad , Carga ViralRESUMEN
OBJECTIVE: The objective was to develop a dataset definition, information model, and FHIR® specification for key data elements contained in a German molecular genomics (MolGen) report to facilitate genomic and phenotype integration in electronic health records. MATERIALS AND METHODS: A dedicated expert group participating in the German Medical Informatics Initiative reviewed information contained in MolGen reports, determined the key elements, and formulated a dataset definition. HL7's Genomics Reporting Implementation Guide (IG) was adopted as a basis for the FHIR® specification which was subjected to a public ballot. In addition, elements in the MolGen dataset were mapped to the fields defined in ISO/TS 20428:2017 standard to evaluate compliance. RESULTS: A core dataset of 76 data elements, clustered into 6 categories was created to represent all key information of German MolGen reports. Based on this, a FHIR specification with 16 profiles, 14 derived from HL7®'s Genomics Reporting IG and 2 additional profiles (of the FamilyMemberHistory and RiskAssessment resources), was developed. Five example resource bundles show how our adaptation of an international standard can be used to model MolGen report data that was requested following oncological or rare disease indications. Furthermore, the map of the MolGen report data elements to the fields defined by the ISO/TC 20428:2017 standard, confirmed the presence of the majority of required fields. CONCLUSIONS: Our report serves as a template for other research initiatives attempting to create a standard format for unstructured genomic report data. Use of standard formats facilitates integration of genomic data into electronic health records for clinical decision support.
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Sistemas de Apoyo a Decisiones Clínicas , Estándar HL7 , Registros Electrónicos de Salud , Genómica , AlemaniaRESUMEN
Background: The COVID-19 pandemic has spurred large-scale, interinstitutional research efforts. To enable these efforts, researchers must agree on data set definitions that not only cover all elements relevant to the respective medical specialty but also are syntactically and semantically interoperable. Therefore, the German Corona Consensus (GECCO) data set was developed as a harmonized, interoperable collection of the most relevant data elements for COVID-19-related patient research. As the GECCO data set is a compact core data set comprising data across all medical fields, the focused research within particular medical domains demands the definition of extension modules that include data elements that are the most relevant to the research performed in those individual medical specialties. Objective: We aimed to (1) specify a workflow for the development of interoperable data set definitions that involves close collaboration between medical experts and information scientists and (2) apply the workflow to develop data set definitions that include data elements that are the most relevant to COVID-19-related patient research regarding immunization, pediatrics, and cardiology. Methods: We developed a workflow to create data set definitions that were (1) content-wise as relevant as possible to a specific field of study and (2) universally usable across computer systems, institutions, and countries (ie, interoperable). We then gathered medical experts from 3 specialties-infectious diseases (with a focus on immunization), pediatrics, and cardiology-to select data elements that were the most relevant to COVID-19-related patient research in the respective specialty. We mapped the data elements to international standardized vocabularies and created data exchange specifications, using Health Level Seven International (HL7) Fast Healthcare Interoperability Resources (FHIR). All steps were performed in close interdisciplinary collaboration with medical domain experts and medical information specialists. Profiles and vocabulary mappings were syntactically and semantically validated in a 2-stage process. Results: We created GECCO extension modules for the immunization, pediatrics, and cardiology domains according to pandemic-related requests. The data elements included in each module were selected, according to the developed consensus-based workflow, by medical experts from these specialties to ensure that the contents aligned with their research needs. We defined data set specifications for 48 immunization, 150 pediatrics, and 52 cardiology data elements that complement the GECCO core data set. We created and published implementation guides, example implementations, and data set annotations for each extension module. Conclusions: The GECCO extension modules, which contain data elements that are the most relevant to COVID-19-related patient research on infectious diseases (with a focus on immunization), pediatrics, and cardiology, were defined in an interdisciplinary, iterative, consensus-based workflow that may serve as a blueprint for developing further data set definitions. The GECCO extension modules provide standardized and harmonized definitions of specialty-related data sets that can help enable interinstitutional and cross-country COVID-19 research in these specialties.
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Cytomegalovirus (CMV) is the most common congenital infection and cause of birth defects worldwide. Primary CMV infection during pregnancy leads to a higher frequency of congenital CMV (cCMV) than maternal re-infection, suggesting that maternal immunity confers partial protection. However, poorly understood immune correlates of protection against placental transmission contributes to the current lack of an approved vaccine to prevent cCMV. In this study, we characterized the kinetics of maternal plasma rhesus CMV (RhCMV) viral load (VL) and RhCMV-specific antibody binding and functional responses in a group of 12 immunocompetent dams with acute, primary RhCMV infection. We defined cCMV transmission as RhCMV detection in amniotic fluid (AF) by qPCR. We then leveraged a large group of past and current primary RhCMV infection studies in late-first/early-second trimester RhCMV-seronegative rhesus macaque dams, including immunocompetent (n=15), CD4+ T cell-depleted with (n=6) and without (n=6) RhCMV-specific polyclonal IgG infusion before infection to evaluate differences between RhCMV AF-positive and AF-negative dams. During the first 3 weeks after infection, the magnitude of RhCMV VL in maternal plasma was higher in AF-positive dams in the combined cohort, while RhCMV glycoprotein B (gB)- and pentamer-specific binding IgG responses were lower magnitude compared to AF-negative dams. However, these observed differences were driven by the CD4+ T cell-depleted dams, as there were no differences in plasma VL or antibody responses between immunocompetent AF-positive vs AF-negative dams. Overall, these results suggest that levels of neither maternal plasma viremia nor humoral responses are associated with cCMV following primary maternal infection in healthy individuals. We speculate that other factors related to innate immunity are more important in this context as antibody responses to acute infection likely develop too late to influence vertical transmission. Yet, pre-existing CMV glycoprotein-specific and neutralizing IgG may provide protection against cCMV following primary maternal CMV infection even in high-risk, immunocompromised settings.
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SNOMED CT fosters interoperability in healthcare and research. This use case implemented SNOMED CT for browsing COVID-19 questionnaires in the open-software solutions OPAL/MICA. We implemented a test server requiring files in a given YAML format for implementation of taxonomies with only two levels of hierarchy. Within this format, neither the implementation of SNOMED CT hierarchies and post-coordination nor the use of release files were possible. To solve this, Python scripts were written to integrate the required SNOMED CT concepts (Fully Specified Name, FSN and SNOMED CT Identifier, SCTID) into the YAML format (YAML Mode). Mappings of SNOMED CT to data items of the questionnaires had to be provided as Excel files for implementation into Opal/MICA and further Python scripts were established within the Excel Mode. Finally, a total of eight questionnaires containing 1.178 data items were successfully mapped to SNOMED CT and implemented in OPAL/MICA. This use case showed that implementing SNOMED CT for browsing COVID-19 questionnaires is feasible despite software solutions not supporting SNOMED CT. However, limitations of not being able to implement SNOMED CT release files and its provided hierarchy and post-coordination still have to be overcome.
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COVID-19 , Systematized Nomenclature of Medicine , Atención a la Salud , Humanos , Programas Informáticos , Encuestas y CuestionariosRESUMEN
COVID-19 has challenged the healthcare systems worldwide. To quickly identify successful diagnostic and therapeutic approaches large data sharing approaches are inevitable. Though organizational clinical data are abundant, many of them are available only in isolated silos and largely inaccessible to external researchers. To overcome and tackle this challenge the university medicine network (comprising all 36 German university hospitals) has been founded in April 2020 to coordinate COVID-19 action plans, diagnostic and therapeutic strategies and collaborative research activities. 13 projects were initiated from which the CODEX project, aiming at the development of a Germany-wide Covid-19 Data Exchange Platform, is presented in this publication. We illustrate the conceptual design, the stepwise development and deployment, first results and the current status.
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COVID-19 , Atención a la Salud , Alemania , Hospitales Universitarios , Humanos , Difusión de la InformaciónRESUMEN
Electronic documentation of medication data is one of the biggest challenges associated with digital clinical documentation. Despite its importance, it has not been consistently implemented in German university hospitals. In this paper we describe the approach of the German Medical Informatics Initiative (MII) towards the modelling of a medication core dataset using FHIR® profiles and standard-compliant terminologies. The FHIR profiles for Medication and MedicationStatement were adapted to the core dataset of the MIl. The terminologies to be used were selected based on the criteria of the ISO-standard for the Identification of Medicinal Products (IDMP). For a first use case with a minimal medication dataset, the entries in the medication chapter of the German Procedure Classification (OPS codes) were analyzed and mapped to IDMP-compliant medication terminology. OPS data are available at all German hospitals as they are mandatory for reimbursement purposes. Reimbursement-relevant encounter data containing OPS medication procedures were used to create a FHIR representation based on the FHIR profiles MedicationStatement and Medication. This minimal solution includes - besides the details on patient and start-/end-dates - the active ingredients identified by the IDMP-compliant codes and - if specified in the OPS code - the route of administration and the range of the amount of substance administered to the patient, using the appropriate unit of measurement code. With FHIR, the medication data can be represented in the data integration centers of the MII to provide a standardized format for data analysis across the MII sites.
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Informática Médica , Registros Electrónicos de Salud , Humanos , Cooperación del PacienteRESUMEN
Studies investigating the suitability of SNOMED CT in COVID-19 datasets are still scarce. The purpose of this study was to evaluate the suitability of SNOMED CT for structured searches of COVID-19 studies, using the German Corona Consensus Dataset (GECCO) as example. Suitability of the international standard SNOMED CT was measured with the scoring system ISO/TS 21564, and intercoder reliability of two independent mapping specialists was evaluated. The resulting analysis showed that the majority of data items had either a complete or partial equivalent in SNOMED CT (complete equivalent: 141 items; partial equivalent: 63 items; no equivalent: 1 item). Intercoder reliability was moderate, possibly due to non-establishment of mapping rules and high percentage (74%) of different but similar concepts among the 86 non-equal chosen concepts. The study shows that SNOMED CT can be utilized for COVID-19 cohort browsing. However, further studies investigating mapping rules and further international terminologies are necessary.