DCC Terminology Service—An Automated CI/CD Pipeline for Converting Clinical and Biomedical Terminologies in Graph Format for the Swiss Personalized Health Network

Kristin Gnodtke,Katrin Crameri,Vasundra Touré,Sabine Österle,Philip Krauss

doi:10.3390/app112311311

Kristin Gnodtke, Katrin Crameri + Show 3 more

Open Access

https://doi.org/10.3390/app112311311

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Abstract

One goal of the Swiss Personalized Health Network (SPHN) is to provide an infrastructure for FAIR (Findable, Accessible, Interoperable and Reusable) health-related data for research purposes. Semantic web technology and biomedical terminologies are key to achieving semantic interoperability. To enable the integrative use of different terminologies, a terminology service is a important component of the SPHN Infrastructure for FAIR data. It provides both the current and historical versions of the terminologies in an SPHN-compliant graph format. To minimize the usually high maintenance effort of a terminology service, we developed an automated CI/CD pipeline for converting clinical and biomedical terminologies in an SPHN-compatible way. Hospitals, research infrastructure providers, as well as any other data providers, can download a terminology bundle (currently composed of SNOMED CT, LOINC, UCUM, ATC, ICD-10-GM, and CHOP) and deploy it in their local terminology service. The distributed service architecture allows each party to fulfill their local IT and security requirements, while still having an up-to-date interoperable stack of SPHN-compliant terminologies. In the future, more terminologies and mappings will be added to the terminology service according to the needs of the SPHN community.

Highlights

Many national and international terminologies are available to describe biomedical concepts and to encode health-related data in Switzerland
Swiss Personalized Health Network [1] (SPHN) national research infrastructure initiative, the SPHN Data Coordination Center (DCC) is developing a data ecosystem [2] using semantic web technologies to manage and link data according to the SPHN Semantic
DCC Terminology Service consists of the following two main parts, as depicted in Figure 2: the terminology server, where the source files and ready-to-use terminologies are stored in the object storage, and second, the continuous integration/continuous deployment (CI/CD) pipeline

Summary

Introduction

Therapeutic Chemical Classification System [10] (ATC) and the Unified Code for Units of Measure [11] (UCUM). Using these semantic standards across different hospitals enables better interoperability between all kinds of data, ranging from routine care data to clinical research data, and leverages the additional information that these semantic standards provide. Classifications, such as ATC, ICD-10-GM, or CHOP, provide hierarchical information, whereas multi-axial terminologies such as LOINC allow for the use of contextual machine-readable information. For LOINC, additional attributes have been generated for the six axes (component, property, time, system, scale, and method) to provide individual

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