SNOMED CT

Importing a SNOMED CT release or extension

You can import a full SNOMED CT RF2 release into Snow Owl. Changes between a newly imported ontology and the existing ontology will be displayed at the end of the import. Previously authored but unreleased components will be retained. This allows importing delta releases as well as snapshot releases. Import is restricted to the administrator. The import can only be done from MAIN through the UI. If the assigned role is Editor, Browser, or Reviewer, it is not possible to import. The import restrictions apply to all import content (all terminologies and classification systems, value domains, mapping sets, local code systems).

Starting the import wizard

Click on File > Import... in the main menu, select Snow Owl > SNOMED CT Release from RF2 from the list, and click Next to bring up the import wizard.

Starting the import wizard

Selecting the import version

Select which version you want to import:

• Delta: All component versions created since the previous release. Only components that were changed or added are included. Delta versions are the fastest way to update your terminology, but you must have previously imported a snapshot or full release.
• Snapshot: Most recent version of every component. Even components that did not change are included. If you don't work with historical information, the snapshot release might be sufficient for your needs. It can be imported in an empty database or if there is already an older SNOMED CT release.
• Full: Every version of every component ever released. The full historical information is included on every component. If you need historical information, you should start out with the full release, and use the delta version to update your terminology. An import is only possible if there is no SNOMED CT content in Snow Owl.
• Create versions for each effective time: This option is only available when importing a full release. It creates a separate version for each release, which allows to switch between versions, for example if you want to work with older versions. If you run the import without creating versions, you will still be able to see historical information in the History view, but won't be able to switch between versions.

SNOMED CT import

Note: If you are working with a standalone version of Snow Owl the SNOMED CT release is already part of the application and you don't need to run an import. Once a new release comes out, it's sufficient to run a delta import to update the existing content. For this reason, only the delta import is enabled, the other import options are disabled.

Selecting the import files

The wizard allows you to specify the release files in three different ways:

• From archive file: Use this if you have a SNOMED CT release in ZIP format.
• From root directory: Use this when you have already unzipped a SNOMED CT release into a directory.
• Manually specify location: Use this if you have the release files in a different directory structure than the official release. This allows you to specify individual files for concepts, descriptions, relationships, language reference set, description type reference set, and stated relationships.

Click the Browse.. button to select your file. If you choose to import from a zip file or a root directory, the wizard will automatically identify the necessary files. The individual files will be displayed in the bottom section of the wizard (see screenshot below). If you manually specify the location, you will have to fill this section by browsing for each file individually.

Selecting a SNOMED CT release in ZIP format

Selecting the language

New releases of SNOMED CT (in RF2 format) no longer include preferred term information with the concept descriptions. Instead, a language reference set is used to identify preferred terms. The importer will scan the release for available language reference sets and prompt you to select a language. Select a language and click Next to proceed.

Selecting the language to import

If only one language is found, as in the Australian language reference set pictured below, it will still be displayed for confirmation before proceeding to the next step.

Display of language for confirmation

Selecting the release version

The next page prompts you to specify whether you would like to import the full version including all history, or only the most recent version (referred to by IHTSDO as a snapshot release), which is the default.

Selecting the release version to import

Selecting reference sets

Check the reference sets you want to import from the list. You can add a new reference set file to the list manually by clicking on the Add... button and selecting the reference set file to import. To exclude a reference set from the import uncheck the box. Click Finish to start the import.

Selecting the reference sets to import

Running the import

During the import, messages and a status bar will keep you updated on the import process. The import process will analyze the description logic basis of the ontology and create several types of indexes, including a semantic cache. Depending on the number and size of the input files you selected, the import can vary between a few minutes (delta) and several hours (full release).

You can cancel the import by clicking on the small red square next to the status bar.

Running the import

Reviewing results

Once the import is completed, the differences between the original ontology and the newly imported release will be presented. You can review details about the changes for each component by clicking on the components in the upper section of the page. The details will be displayed in the tables on the bottom.

Highlighting differences during import

Publishing a SNOMED CT release

Snow Owl allows you to export a SNOMED CT release in RF1 and RF2 format for publication.

Starting the export

To start the export

• Go to File > Export... in the Menu to open export wizard.
• Select Snow Owl > SNOMED CT to RF1 and RF2 from the list, and click Next.

Selecting the export wizard

Specifying the export settings

Specify the export settings on the SNOMED CT Publication page:

• File path: Specify a location on your computer. The exported output includes the core terminology files, the structural and the clinical reference sets organized into the standard file structure.
• Publication format: You can choose between Full, Snapshot and Delta release format.
  • A Full release contains every version of every component ever released. This includes historical information about the components.
  • A Snapshot release contains only the most recent version of every component ever released (both active and inactive components).
  • A Delta release contains only component versions created since the last release. Each component version represents a new component or a change in an existing component. If you chose this option, you have to specify starting and finishing effective date by clicking the calendar icons.
• RF1: Check this box, if you want to include the RF1 (Release Format 1). This is optional.

Specifying SNOMED CT export settings

Defining the scope of the export

On the next page, you can select whether you want to export the core ontology files, the reference sets or both.

Defining the components to export

Selecting the reference sets to export

This page allows you to select which reference sets you want to export. At least one SNOMED CT reference set should be selected to export. If you want to export all reference sets, use the Select all button. Note: If you selected to export only the core components, this page will be skipped.

Selecting the reference sets to export

Selecting modules for export and adding dependent modules

On the last page of the wizard, you can select which module or modules you want to export.

Selecting modules for export

When selecting a particular module to export, the export wizard supports the addition of the dependent modules. By adding the dependencies the export output will be universally valid, and can be used in other systems. More information about Module Dependency reference sets in the Reference sets, Subsets, and Value Sets section.

Show Dependencies lists the selected modules (source module) and their dependencies (target module). If the list is empty, the selected modules have no dependencies that need to be considered for the export.

Module dependencies

Click on Add required dependencies to automatically include the affected modules in the export. Hit Next to start the export.

Export wizard after adding module dependencies

Starting the export

Once you have selected the modules, hit Next to start the export. The export process is fairly quick. A full SCT RF2 publication is about 5-6 minutes. When you are exporting a full RF 1 and RF 2, the process can take up to half an hour.

Exporting a SNOMED CT release

Once the export is finished, you will be presented with a hyperlink to the exported file. Click the link to get to the file, or Finish to close the dialog.

SNOMED CT export review with hyperlink to exported file

Exporting SNOMED CT to OWL 2

You can export the SNOMED CT ontology in OWL2 formats (OWL functional syntax, Manchester OWL Syntax, OWL/XML). To start the export

• Go to File > Export... in the Menu to open the wizard.
• Select Snow Owl > SNOMED CT to OWL 2 from the list, and click Next.

Wizard for exporting SNOMED CT to OWL

Specify the name and location of the destination file, select the syntax, and click Finish to start the export.

Selecting the syntax for OWL export

The export is fairly quick, taking less than a minute.

OWL export progress dialog