SNOMED2HL7: a tool to normalize and bind SNOMED CT concepts to the HL7 Reference Information Model

[Abstract] BACKGROUND: Current clinical research and practice requires interoperability among systems in a complex and highly dynamic domain. There has been a significant effort in recent years to develop integrative common data models and domain terminologies. Such efforts have not completely solved the challenges associated with clinical data that are distributed among different and heterogeneous institutions with different systems to encode the information. Currently, when providing homogeneous interfaces to exploit clinical data, certain transformations still involve manual and time-consuming processes that could be automated. OBJECTIVES: There is a lack of tools to support data experts adopting clinical standards. This absence is especially significant when links between data model and vocabulary are required. The objective of this work is to present SNOMED2HL7, a novel tool to automatically link biomedical concepts from widely used terminologies, and the corresponding clinical context, to the HL7 Reference Information Model (RIM). METHODS: Based on the recommendations of the International Health Terminology Standards Development Organisation (IHTSDO), the SNOMED Normal Form has been implemented within SNOMED2HL7 to decompose and provide a method to reduce the number of options to store the same information. The binding of clinical terminologies to HL7 RIM components is the core of SNOMED2HL7, where terminology concepts have been annotated with the corresponding options within the interoperability standard. A web-based tool has been developed to automatically provide information from the normalization mechanisms and the terminology binding. RESULTS: SNOMED2HL7 binding coverage includes the majority of the concepts used to annotate legacy systems. It follows HL7 recommendations to solve binding overlaps and provides the binding of the normalized version of the concepts. The first version of the tool, available at http://kandel.dia.fi.upm.es:8078, has been validated in EU funded projects to integrate real world data for clinical research with an 88.47% of accuracy. CONCLUSIONS: This paper presents the first initiative to automatically retrieve concept-centered information required to transform legacy data into widely adopted interoperability standards. Although additional functionality will extend capabilities to automate data transformations, SNOMED2HL7 already provides the functionality required for the clinical interoperability community.Instituto de Salud Carlos III; PI13/0202

How to report COVID-19 laboratory data

Updated Jan. 26, 2021The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding COVID-19\u2019s impact and testing coverage and can contribute to the identification of supply chain issues for reagents and other materials. The information below outlines reporting requirements for laboratories.Who must reportWhat to report -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.2021903

How to report COVID-19 laboratory data

Updated July 29, 2020The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding disease incidence and testing coverage, and can contribute to the identification of supply chain issues for reagents and other material. The information below outlines reporting requirements for laboratories.CDC is working with state health departments to collect SARS-CoV-2 laboratory testing data that they already receive from most clinical laboratories. CDC also receives SARS-CoV-2 testing data directly from state and local public health laboratories, a few large commercial laboratories, and its own laboratories. For assistance with reporting SARS-CoV-2 testing results, please send an email to [email protected] public health laboratories and select large commercial laboratories that currently report directly to CDC should continue sending that data.Who must report -- How to report -- What to report -- What to include -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.2020807

Harmonization and standardization of data for a pan-European cohort on SARS- CoV-2 pandemic

The European project ORCHESTRA intends to create a new pan-European cohort to rapidly advance the knowledge of the effects and treatment of COVID-19. Establishing processes that facilitate the merging of heterogeneous clusters of retrospective data was an essential challenge. In addition, data from new ORCHESTRA prospective studies have to be compatible with earlier collected information to be efficiently combined. In this article, we describe how we utilized and contributed to existing standard terminologies to create consistent semantic representation of over 2500 COVID-19-related variables taken from three ORCHESTRA studies. The goal is to enable the semantic interoperability of data within the existing project studies and to create a common basis of standardized elements available for the design of new COVID-19 studies. We also identified 743 variables that were commonly used in two of the three prospective ORCHESTRA studies and can therefore be directly combined for analysis purposes. Additionally, we actively contributed to global interoperability by submitting new concept requests to the terminology Standards Development Organizations

How to report COVID-19 laboratory data

Updated Nov. 25, 2020The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding disease incidence and testing coverage, and can contribute to the identification of supply chain issues for reagents and other material. The information below outlines reporting requirements for laboratories.CDC is working with state health departments to collect SARS-CoV-2 laboratory testing data that they already receive from most clinical laboratories. CDC also receives SARS-CoV-2 testing data directly from state and local public health laboratories, a few large commercial laboratories, and its own laboratories. For assistance with reporting SARS-CoV-2 testing results, please send an email to [email protected] public health laboratories and select large commercial laboratories that currently report directly to CDC should continue sending that data.Who must report -- What to report -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.2020E:\cpapFiles\WebServer\COVIDlabData2020nov25.pdfhttps://www.cdc.gov/coronavirus/2019-ncov/lab/reporting-lab-data.html872

How to report COVID-19 laboratory data

Updated Aug. 17, 2020The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding disease incidence and testing coverage, and can contribute to the identification of supply chain issues for reagents and other material. The information below outlines reporting requirements for laboratories.CDC is working with state health departments to collect SARS-CoV-2 laboratory testing data that they already receive from most clinical laboratories. CDC also receives SARS-CoV-2 testing data directly from state and local public health laboratories, a few large commercial laboratories, and its own laboratories. For assistance with reporting SARS-CoV-2 testing results, please send an email to [email protected] public health laboratories and select large commercial laboratories that currently report directly to CDC should continue sending that data.Who must report -- How to report -- What to report -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.2020816

How to report COVID-19 laboratory data

Updated Mar. 4, 2022The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding COVID-19\u2019s impact and testing coverage and can contribute to the identification of supply chain issues for reagents and other materials. The information below outlines reporting requirements for laboratories.The Coronavirus Aid, Relief, and Economic Security (CARES) Act and its June 4 implementation guidanceexternal icon require every CLIA certified COVID-19 testing site to report every diagnostic and screening test result (both positive and negative results) performed to detect SARS-CoV-2 or to diagnose a possible case of COVID-19 (e.g., molecular, antigen, antibody) to the appropriate state or local public health department, based on the individual\u2019s residence. Laboratories that currently report directly to CDC should continue sending these data to CDC.Who must report -- What to report -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.20221104

How to report COVID-19 laboratory data

Updated Jan. 26, 2021The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding COVID-19\u2019s impact and testing coverage and can contribute to the identification of supply chain issues for reagents and other materials. The information below outlines reporting requirements for laboratories.Who must reportWhat to report -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.2021903

How to report COVID-19 laboratory data

Updated Apr. 4, 2022Effective April 4, 2022, HHS and CDC announced revisions to COVID-19 laboratory reporting guidance.. Reporting of negative results for non-NAAT tests (rapid or antigen test results) is no longer required. However, testing sites must still report data for all positive diagnostic and screening testing completed for each individual test.The public health response to COVID-19 depends on comprehensive laboratory testing data. These data will contribute to understanding COVID-19\u2019s impact and testing coverage and can contribute to the identification of supply chain issues for reagents and other materials. The information below outlines reporting requirements for laboratories.The Coronavirus Aid, Relief, and Economic Security (CARES) Act and its June 4 implementation guidanceexternal icon require every CLIA certified COVID-19 testing site to report every diagnostic and screening test result (both positive and negative results) performed to detect SARS-CoV-2 or to diagnose a possible case of COVID-19 (e.g., molecular, antigen, antibody) to the appropriate state or local public health department, based on the individual\u2019s residence. Laboratories that currently report directly to CDC should continue sending these data to CDC.Who must report -- What to report -- Using Standard Terminology -- Assistance with Electronic Reporting -- FAQs.20221117