Download external terminologies from the Terminology Service

Note

For background information about the Terminology Service, see the Terminology Service section.

Target Audience

The DCC distributes External terminologies via (i) the Terminology Service in the BioMedIT portal and (ii) a standalone Terminology Server based on MinIO. The first option is intended to be used by researchers; the second one by BioMedIT nodes and data providers. The following document shows how to download these external terminologies in each distribution.

Downloading external terminologies from the BioMedIT portal

Prerequisites

You have a SWITCH edu-ID account. (If you don’t have one, you can quickly generate one following instructions here.)

Download

After logging in to the BioMedIT portal https://terminology.dcc.sib.swiss/ with your SWITCH edu-ID account, you will see a table with the available external terminologies (see Figure 1). Click on the terminology you want to download to expand the entry. You will be presented with a list of available versions including buttons for the available file formats (RDF/OWL and/or RDF/TTL). Clicking on the button will download the terminology file.

Figure 1. Terminology Service in the BioMedIT Portal. The content of the ICD-10-GM classification has been expanded, showing some of the available versions that can be downloaded.

Downloading external terminologies from the Terminology Server

Prerequisites

You have requested a user account for the Terminology Server at biomedit@sib.swiss.
You have accepted the “Acceptable use policy for the Terminology Service”.

Download via the web interface

After logging in at https://terminology-server.dcc.sib.swiss/ with your credentials, you will be presented with the MinIO Browser. It will show two folders (see Figure 2): current/, which has the most recent release of the external terminologies, and archive/, which has all previous releases.

Figure 2. Current and archive folders in the Terminology Server.

After navigating into one of the folders, you will be presented with a list of available packages. A package bundles all available external terminologies and consists of a .zip and a .gpg file (for instance, ontologies-2024-07-08_12-06-22.zip `` and ``ontologies-2024-07-08_12-06-22.gpg). The .zip holds all the terminology files while the .gpg file is a detached gpg signature that allows to verify that the .zip file has been created by the DCC.

Select all relevant files and download them by clicking the Download button appearing on the right side of the screen.

After the download is complete, you can unzip the downloaded file and optionally verify the signatures of the packages.

Note

Verify the signature

Verifying a package’s gpg signature is automatically done if using the terminology-server-downloader (see below). To manually verify the signature, download the “DCC” public gpg key from the Open PGP keyserver by running

$ gpg --keyserver hkps://keys.openpgp.org --recv-keys CB5931C8B32B4BB7DE6D781C95B54DA2D018F7E7

To verify a signature, run gpg --verify, for instance:

$ gpg --verify ontologies-2024-07-08_12-06-22.gpg ontologies-2024-07-08_12-06-22.zip
  gpg: Signature made Mo  8 Jul 12:08:33 2024 CEST
  gpg:                using EDDSA key CB5931C8B32B4BB7DE6D781C95B54DA2D018F7E7
  gpg: Good signature from "DCC <dcc@sib.swiss>" [unknown]
  gpg: WARNING: This key is not certified with a trusted signature!
  gpg:          There is no indication that the signature belongs to the owner.
  Primary key fingerprint: CB59 31C8 B32B 4BB7 DE6D  781C 95B5 4DA2 D018 F7E7

The output below indicates that the file has been signed by the DCC.

An output that includes

gpg: BAD signature from "DCC <dcc@sib.swiss>" [unknown]

indicates that the integrity of the data cannot be verified and that the data should not be used.

Finally, unzip the ontologies-*.zip file to access the terminology files.

Download via the command-line interface

The terminology-server-downloader, accessible in Git can be used to download terminologies from the Terminology Server via a command-line interface.

After installing this Python tool via pip and providing the credentials to the Terminology Server via environmental variables, all or a selected set of ontologies can be downloaded with a single command without further user interaction.

$ terminology-server-downloader ~/data

This process can further be automatized by invoking the command regularly from a cron job.

For further information, see the terminology-server-downloader repository.