DCC Terminology Service—An Automated CI/CD Pipeline for Converting Clinical and Biomedical Terminologies in Graph Format for the Swiss Personalized Health Network
Abstract
:1. Introduction
2. Materials and Methods
2.1. Design
2.2. Implementation
2.2.1. Data Collection
2.2.2. Conversion Scripts
2.2.3. Test
2.2.4. Bundling
2.2.5. GitLab Runner Pipeline
- Setup: The pipeline run is initialized and some local temporary exchanges are created.
- Prepare: The files are loaded from the sources/current folder on the virtual machine (VM) where the GitLab runner is executed.
- Convert: The provided terminology is converted with the corresponding conversion script. Each terminology has its own job that is only executed in case there is valid input data for the job.
- Test: Technical and semantic tests are run. All tests are run in a single job.
- Publish: A single zip file is created containing all the newest RDF files of SNOMED CT, LOINC, ATC, ICD-10-GM, UCUM and CHOP. This bundle is signed and copied to the MinIO server in the ontologies/current folder. The previous bundle is moved to the ontologies/archive folder. If all steps are successful, the source files are moved from sources/current to sources/archive.
2.2.6. Containerized Execution
- GitLab Runner: This is the main container that registers to the GitLab CI/CD pipeline. Besides the MinIO service, it is the only prerequisite to be installed on a machine in order for it to be able to execute the pipelines.
- Python: Besides the pipeline for SNOMED CT, all pipelines use Python in their conversion. The Python container gives a simple abstraction of a plain Linux with a basic Python installation. Additional packages that are needed are installed using a requirements.txt file through the Python package manager, pip, in the “install” target of the Makefile of the individual pipeline.
- Ubuntu Linux: For the SNOMED CT conversion, Java is used. As additional tools are needed in the conversion, the generic Ubuntu Linux container is used, and the necessary tools are installed using the “install” target of the Makefile. The generic Ubuntu Linux container is also used for interaction with MinIO using the mc client tool.
- Apache Jena Fuseki: As part of the pipeline, the triplestore Apache Jena Fuseki is used to test the terminologies in RDF. To be able to make use of the scripts locally in a hospital or BioMedIT node, the triplestore is also offered as a docker container. The same docker container is used in the testing step to ensure correctness. For service providers that do not have a local triplestore of choice, this container can be used to deploy a triplestore. Apache Jena Fuseki is open-source software under the Apache 2.0 license.
3. Results
- CHOP (including historical versions since 2016)
- ICD-10-GM (including historical versions since 2014)
- SNOMED CT (including historical versions since 31 January 2021)
- LOINC (including historical versions since v2.69)
- ATC (2021 version)
- UCUM
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Code Availability Statement
Acknowledgments
Conflicts of Interest
References
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ID | Description |
---|---|
Q0 | Every element must be at least of type rdfs:Class |
Q1 | Only the listed roots are present in the terminology |
Q2 | The number of concepts is between x and y |
Q3 | Every concept must have at least one rdfs:label |
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Krauss, P.; Touré, V.; Gnodtke, K.; Crameri, K.; Österle, S. DCC Terminology Service—An Automated CI/CD Pipeline for Converting Clinical and Biomedical Terminologies in Graph Format for the Swiss Personalized Health Network. Appl. Sci. 2021, 11, 11311. https://doi.org/10.3390/app112311311
Krauss P, Touré V, Gnodtke K, Crameri K, Österle S. DCC Terminology Service—An Automated CI/CD Pipeline for Converting Clinical and Biomedical Terminologies in Graph Format for the Swiss Personalized Health Network. Applied Sciences. 2021; 11(23):11311. https://doi.org/10.3390/app112311311
Chicago/Turabian StyleKrauss, Philip, Vasundra Touré, Kristin Gnodtke, Katrin Crameri, and Sabine Österle. 2021. "DCC Terminology Service—An Automated CI/CD Pipeline for Converting Clinical and Biomedical Terminologies in Graph Format for the Swiss Personalized Health Network" Applied Sciences 11, no. 23: 11311. https://doi.org/10.3390/app112311311