Terminology Service
External terminologies
If an ontology references existing external standard terminologies, such as
disease or device classifications of interest in the context of SPHN,
it needs to be represented in the RDF format.
The DCC Terminology Service provides SPHN compatible, machine-readable versions
of national (CHOP, ICD-10-GM) and international (SNOMED CT, LOINC, ATC, UCUM, HGNC, GENO, SO)
terminologies and classifications in RDF formats (.ttl or .owl).
This page describes the way DCC distributes the external terminologies.
For further information on the external terminologies, see
here.
The SPHN Terminology Service
The DCC developed the Terminology Service as a way to distribute external terminologies in RDF format without external dependencies and in compliance with the copyright statements of the single terminologies.
The terminologies are available directly in the individual project spaces on the BioMedIT nodes. Furthermore, the DCC provides two modes of distribution, enabling projects and institutions to fetch the external terminologies in RDF format:
via the Terminology Service at the BioMedIT portal
via a standalone Terminology Server that uses the MinIO object storage service.
Terminology Service at the BioMedIT portal |
Terminology Server |
|
|---|---|---|
URL |
||
Access |
SWITCH edu-ID |
A dedicated account to be requested at dcc@sib.swiss |
Terminology format |
Provides a single file per external terminology |
Provides bundles of external terminologies |
Download modality |
Web interface |
Web interface or command-line interface |
Intended users |
Researchers |
BioMedIT nodes, hospitals or other service providers |
The two modes of distribution are always synchronized and regularly provide updated versions of the external terminologies.
The bundle of external terminologies provided in the Terminology Server on the MinIO instance is a compressed folder that contains all versions of the terminologies stated in the Namespace of terminologies used in SPHN.
Versioning of Terminologies
Since 2023, the DCC has adopted the concept of versioning to enhance interoperability of codes from different versions of a terminology. See Versioning of Terminologies for more information.
For a select list terminologies, the Terminology Service now provides a historized RDF turtle file. This historized version contains:
codes from the current version of the terminology
codes from all previous versions of the terminology
with the default unversioned code IRI corresponding to the current (latest) version of the terminology.
Following are the list of terminologies for which a historized RDF turtle is provided:
ATC
CHOP
ICD-10-GM
Downloading terminology files
Both modes of distribution allow for manually downloading the terminologies
via the web browser. An additional tool, the terminology-server-downloader,
enables automatically downloading terminologies from the Terminology Server
via a command-line interface.
For instructions on downloading external terminology files from the Terminology
Service, please see our user guide Download external terminologies from the Terminology Service.
After the terminology files have been downloaded, they can be imported into RDF tools such as Protégé or GraphDB.
Reference
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