Load SNOMED CT into Aidbox
Start working with SNOMED CT terminology in Aidbox
SNOMED CT is a large medical terminology which can be used in FHIR ValueSet resources. It is distributed under a free license which you have to set up with them.
We provide out-of-the-box integration with SNOMED CT through Aidbox Configuration project. You may start using it after we make sure you have the required SNOMED license.
There is a step-by-step guide below which takes you from our default Aidbox Configuration project to a fully enabled SNOMED terminology.
You need to have an Aidbox Configuration project to load prepackaged SNOMED CT terminology. One of the easiest way is to start with our Docker Getting started guide.
SNOMED CT is distributed under a license which means that we can not redistribute it without making sure that other people have this license. You can confirm your eligibility for accessing SNOMED CT by contacting Aidbox team. See our contacts here.
We distribute SNOMED CT through a private Github repository. This means that you have to provide us with your public SSH key which we’ll add to the repository’s access list.
You also need to set Aidbox environment variables to use this public key and its corresponding private key. They are required so that Aidbox is able to work with private SNOMED CT repository.
The required environment variables are listed below:
BOX_PROJECT_GIT_PRIVATE__KEY="-----BEGIN …
…
-----END … -----
"
BOX_PROJECT_GIT_PUBLIC__KEY="ssh-…"
Be aware that there’s a newline at the end of
BOX_PROJECT_GIT_PRIVATE__KEY. Make sure that it is present otherwise the key becomes invalid.Edit
zen-package.edn to include SNOMED CT repository in the dependencies:You also need to import
snomed namespace in your Aidbox entrypoint file. Assuming you are working with docker-compose-template from Prerequisites, it is zrc/system.edn file.{:ns system
:import {some-other-dep
snomed}
…}
Set the following environment variable:
BOX_FEATURES_FTR_PULL_ENABLE=true
By default, Aidbox does not load terminologies into the database as that can take a lot of disk space. This means that full terminology functionality won’t be available until you enable it manually. BOX_FEATURES_FTR_PULL_ENABLE environment variable is just for that. When you set it to
true, Aidbox will load terminologies into the database on the next startup and start functioning as a fully-featured terminology server.Currently, we support various SNOMED CT terminology translations, and we can incorporate additional translation variants as needed. Translations are stored in the concept .
designation property, and when a package includes multiple languages, the original language is also retained within the .designation property. To select the desired translation, simply modify the link to the corresponding package in zen-package.edn.Zen Package Link | Languages (IETF BCP 47 tags) |
|---|---|
[email protected]:zen-fhir/snomed.git | en |
[email protected]:zen-fhir/snomedca.git | en, fr |
If you want to customize Aidbox startup behavior when using FTR, read more about FTR environment variables.
One of the options you may want to consider is enabling
BOX_FEATURES_FTR_BUILD__INDEX__ON__STARTUP_SYNC. Setting this environment variable to true will make Aidbox startup blocked until SNOMED CT terminology is fully available for fast and efficient validation.Last modified 14d ago