Towards interoperability in infection control: a standard data model for microbiology

Abstract

The COVID-19 pandemic has made it clear: sharing and exchanging data among research institutions is crucial in order to efficiently respond to global health threats. This can be facilitated by defining health data models based on interoperability standards. In Germany, a national effort is in progress to create common data models using international healthcare IT standards. In this context, collaborative work on a data set module for microbiology is of particular importance as the WHO has declared antimicrobial resistance one of the top global public health threats that humanity is facing. In this article, we describe how we developed a common model for microbiology data in an interdisciplinary collaborative effort and how we make use of the standard HL7 FHIR and terminologies such as SNOMED CT or LOINC to ensure syntactic and semantic interoperability. The use of international healthcare standards qualifies our data model to be adopted beyond the environment where it was first developed and used at an international level.

Decomposition of post-coordinated SNOMED CT expressions for storage as HL7 FHIR resources (PCEtoFHIR) (Preprint)

“…Nevertheless, the PCE should be stored in the metadata so that the missing information is not lost. The FHIR StructureMaps have not yet been reviewed with domain experts for quality assurance purposes, although the authors have some experience with FHIR modeling [40] and a lot of experience with SNOMED CT from previous projects [4,8,18]. However, it became apparent that the mapping could be successfully solved for the considered categories and can be extended to other sub-hierarchies of SNOMED CT without any problems.…”

Arbeitsgruppe Interoperabilität: Kerndatensatz und Informationssysteme für Integration und Austausch von Daten in der Medizininformatik-Initiative

“…B. im IG des Moduls Medikation [ 22 , 23 ] beschrieben, wie die Angabe einer Medikamentenpackung mit Pharmazentralnummer erfolgt, sodass in Deutschland gebräuchliche Medikationen für die Sekundärnutzung in der Forschung erschließbar werden. Zusätzlich kommen internationale Terminologien wie LOINC (Logical Observation Identifiers Names and Codes) für Laboruntersuchungen oder SNOMED CT [ 7 ] zum Einsatz, etwa für die Klassifikation von Erregern im Erweiterungsmodul Mikrobiologie [ 24 ] oder für die Angabe von Verwandtschaftsverhältnissen im molekulargenetischen Befundbericht [ 27 ].…”