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1.
Stud Health Technol Inform ; 294: 649-653, 2022 May 25.
Article in English | MEDLINE | ID: covidwho-1865428

ABSTRACT

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.


Subject(s)
COVID-19 , Systematized Nomenclature of Medicine , Delivery of Health Care , Humans , Software , Surveys and Questionnaires
2.
Stud Health Technol Inform ; 287: 73-77, 2021 11 18.
Article in English | MEDLINE | ID: covidwho-1594908

ABSTRACT

Adopting international standards within health research communities can elevate data FAIRness and widen analysis possibilities. The purpose of this study was to evaluate the mapping feasibility against HL7® Fast Healthcare Interoperability Resources® (FHIR)® of a generic metadata schema (MDS) created for a central search hub gathering COVID-19 health research (studies, questionnaires, documents = MDS resource types). Mapping results were rated by calculating the percentage of FHIR coverage. Among 86 items to map, total mapping coverage was 94%: 50 (58%) of the items were available as standard resources in FHIR and 31 (36%) could be mapped using extensions. Five items (6%) could not be mapped to FHIR. Analyzing each MDS resource type, there was a total mapping coverage of 93% for studies and 95% for questionnaires and documents, with 61% of the MDS items available as standard resources in FHIR for studies, 57% for questionnaires and 52% for documents. Extensions in studies, questionnaires and documents were used in 32%, 38% and 43% of items, respectively. This work shows that FHIR can be used as a standardized format in registries for clinical, epidemiological and public health research. However, further adjustments to the initial MDS are recommended - and two additional items even needed when implementing FHIR. Developing a MDS based on the FHIR standard could be a future approach to reduce data ambiguity and foster interoperability.


Subject(s)
COVID-19 , Metadata , Delivery of Health Care , Electronic Health Records , Health Level Seven , Humans , Registries , SARS-CoV-2
3.
Stud Health Technol Inform ; 287: 78-82, 2021 Nov 18.
Article in English | MEDLINE | ID: covidwho-1526756

ABSTRACT

The German Central Health Study Hub COVID-19 is an online service that offers bundled access to COVID-19 related studies conducted in Germany. It combines metadata and other information of epidemiologic, public health and clinical studies into a single data repository for FAIR data access. In addition to study characteristics the system also allows easy access to study documents, as well as instruments for data collection. Study metadata and survey instruments are decomposed into individual data items and semantically enriched to ease the findability. Data from existing clinical trial registries (DRKS, clinicaltrails.gov and WHO ICTRP) are merged with epidemiological and public health studies manually collected and entered. More than 850 studies are listed as of September 2021.


Subject(s)
COVID-19 , Germany , Humans , Metadata , SARS-CoV-2 , Surveys and Questionnaires
4.
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz ; 64(9): 1084-1092, 2021 Sep.
Article in German | MEDLINE | ID: covidwho-1321726

ABSTRACT

Public health research and epidemiological and clinical studies are necessary to understand the COVID-19 pandemic and to take appropriate action. Therefore, since early 2020, numerous research projects have also been initiated in Germany. However, due to the large amount of information, it is currently difficult to get an overview of the diverse research activities and their results. Based on the "Federated research data infrastructure for personal health data" (NFDI4Health) initiative, the "COVID-19 task force" is able to create easier access to SARS-CoV-2- and COVID-19-related clinical, epidemiological, and public health research data. Therefore, the so-called FAIR data principles (findable, accessible, interoperable, reusable) are taken into account and should allow an expedited communication of results. The most essential work of the task force includes the generation of a study portal with metadata, selected instruments, other study documents, and study results as well as a search engine for preprint publications. Additional contents include a concept for the linkage between research and routine data, a service for an enhanced practice of image data, and the application of a standardized analysis routine for harmonized quality assessment. This infrastructure, currently being established, will facilitate the findability and handling of German COVID-19 research. The developments initiated in the context of the NFDI4Health COVID-19 task force are reusable for further research topics, as the challenges addressed are generic for the findability of and the handling with research data.


Subject(s)
Biomedical Research/trends , COVID-19 , Information Dissemination , Germany , Humans , Metadata , Pandemics , SARS-CoV-2
5.
Stud Health Technol Inform ; 281: 794-798, 2021 May 27.
Article in English | MEDLINE | ID: covidwho-1247808

ABSTRACT

COVID-19 poses a major challenge to individuals and societies around the world. Yet, it is difficult to obtain a good overview of studies across different medical fields of research such as clinical trials, epidemiology, and public health. Here, we describe a consensus metadata model to facilitate structured searches of COVID-19 studies and resources along with its implementation in three linked complementary web-based platforms. A relational database serves as central study metadata hub that secures compatibilities with common trials registries (e.g. ICTRP and standards like HL7 FHIR, CDISC ODM, and DataCite). The Central Search Hub was developed as a single-page application, the other two components with additional frontends are based on the SEEK platform and MICA, respectively. These platforms have different features concerning cohort browsing, item browsing, and access to documents and other study resources to meet divergent user needs. By this we want to promote transparent and harmonized COVID-19 research.


Subject(s)
COVID-19 , Epidemiologic Studies , Humans , Metadata , Registries , SARS-CoV-2
6.
Stud Health Technol Inform ; 281: 88-92, 2021 May 27.
Article in English | MEDLINE | ID: covidwho-1247789

ABSTRACT

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.


Subject(s)
COVID-19 , Systematized Nomenclature of Medicine , Consensus , Humans , Reproducibility of Results , SARS-CoV-2
8.
Chirurg ; 92(1): 30-33, 2021 Jan.
Article in German | MEDLINE | ID: covidwho-976992

ABSTRACT

In order to improve the care of patients with chronic inflammatory bowel diseases during the coronavirus disease 2019 (COVID-19) pandemic, the currently valid guidelines of the German Society for Gastroenterology, Digestive and Metabolic Diseases (DGVS) on Crohn's disease and ulcerative colitis were extended within a virtual conference to include current and practically relevant recommendations. The addendum addresses in particular the risk of COVID-19 infections in patients with chronic inflammatory bowel diseases, the diagnostics under the conditions of the pandemic, the consequences for the pharmacotherapy and operative treatment of the underlying disease. It also addresses general measures for protection against infections and for adjunctive treatment of patients with chronic inflammatory bowel diseases.


Subject(s)
COVID-19 , Colitis, Ulcerative , Crohn Disease , Inflammatory Bowel Diseases , Humans , Pandemics , SARS-CoV-2
9.
Z Gastroenterol ; 58(10): 982-1002, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-886826

ABSTRACT

The COVID-19 pandemic is a global outbreak of new onset infections with the SARS-CoV-2 virus. To date, more than 3.4 million people have been infected throughout the world. In Germany, approximately 450,000 patients suffer from inflammatory bowel disease; these patients generally require continuous expert care and support. Against the background of a rapidly accumulating knowledge base on SARS-CoV-2, 68 expert authors of the current DGVS guidelines for Crohn's disease and ulcerative colitis took part in a virtual meeting to compile up-to-date, practice-orientated recommendations aimed at improving the care of patients with IBD. These recommendations address the risk of infection, including the risk for specific patient groups, the possible course of the disease, and consequences for pharmacological and surgical therapies of the underlying disease, as well as general measures for infection prevention and adjuvant prophylactic and therapeutic options.


Subject(s)
Colitis, Ulcerative , Coronavirus Infections , Crohn Disease , Inflammatory Bowel Diseases , Pneumonia, Viral , Practice Guidelines as Topic , Betacoronavirus , COVID-19 , Colitis, Ulcerative/diagnosis , Colitis, Ulcerative/therapy , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Crohn Disease/diagnosis , Crohn Disease/therapy , Germany , Humans , Inflammatory Bowel Diseases/diagnosis , Inflammatory Bowel Diseases/therapy , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , SARS-CoV-2
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