Snow Owl® is a highly scalable, open source terminology server and collaborative authoring platform. It allows you to store, search and author high volumes of terminology artifacts quickly and efficiently.

Here are a few use-cases that Snow Owl could be used for:

• You work in the healthcare industry and are interested in using a terminology server for browsing, accessing and distributing components of various terminologies and classifications to third-party consumers. In this case, you can use Snow Owl to load the necessary terminologies and access them via FHIR and proprietary APIs.

• You are responsible for maintaining and publishing new versions of a particular terminology. In this case, you can use Snow Owl to collaboratively access and author the terminology content and at the end of your release schedule publish it with confidence and zero errors.

• You have an Electronic Health Record system and would like to capture, maintain and query clinical information in a structured and standardized manner. Your Snow Owl terminology server can integrate with your EHR server via standard APIs to provide the necessary access for both terminology binding and data processing and analytics.

In this tutorial, you will be guided through the process of getting Snow Owl up and running, taking a peek inside it, and performing basic operations like importing SNOMED CT RF2 content, searching, and modifying your data. At the end of this tutorial, you should have a good idea of what Snow Owl is, how it works, and hopefully be inspired to see how you can use it for your needs.

Coming soon!

Snow Owl is both a simple and complex product. We’ve so far learned the basics of what it is, how to look inside of it, and how to work with it using some of the available APIs. Hopefully this tutorial has given you a better understanding of what Snow Owl is and more importantly, inspired you to further experiment with the rest of its great features!

You should rarely need to change Java Virtual Machine (JVM) options. If you do, the most likely change is setting the heap size.

The preferred method of setting JVM options (including system properties and JVM flags) is via the the SO_JAVA_OPTS environment variable. For instance:

export SO_JAVA_OPTS="$SO_JAVA_OPTS -Djava.io.tmpdir=/path/to/temp/dir"
./bin/startup

When using the RPM or Debian packages, SO_JAVA_OPTS can be specified in the system configuration file.

Let’s start with a basic health check, which we can use to see how our instance is doing. We’ll be using curl to do this but you can use any tool that allows you to make HTTP/REST calls. Let’s assume that we are still on the same node where we started Snow Owl on and open another command shell window.

To check the instance status/health, we will be using the . You can run the command by clicking the "Copy" link on the right side and pasting it into a terminal.

And the response:

In the response, we can see the version of our instance along with the available repositories and their health status (eg. SNOMED CT with status GREEN).

Snow Owl ships with good defaults and requires very little configuration.

Config files location

Snow Owl has three configuration files:

Snow Owl is provided in the following package formats:

By default, Snow Owl is starting and connecting to an embedded Elasticsearch cluster available on http://localhost:9200. This cluster has only a single node and its discovery method is set to single-node, which means it is not able to connect to other Elasticsearch clusters and will be used exclusively by Snow Owl.

This single node Elasticsearch cluster can easily serve Snow Owl in testing, evaluation and small authoring environments, but it is recommended to customize how Snow Owl connects to an Elasticsearch cluster in larger environments (especially when planning to scale with user demand).

You have two options to configure Elasticsearch used by Snow Owl.

There are a few concepts that are core to Snow Owl. Understanding these concepts from the outset will tremendously help ease the learning process.

Terminology / Code System

A terminology (also known as code system, classification and/or ontology) defines and encapsulates a set of terminology components (eg. set of codes with their meanings) and versions. A terminology is identified by a unique name and stored in a repository. Multiple code systems can exist in a single repository besides each other as long as their name is unique.

An orderly shutdown of Snow Owl ensures that Snow Owl has a chance to cleanup and close outstanding resources. For example, an instance that is shutdown in an orderly fashion will initiate an orderly shutdown of the embedded Elasticsearch instance, gracefully close and disconnect connections and perform other related cleanup activities. You can help ensure an orderly shutdown by properly stopping Snow Owl.

If you’re running Snow Owl as a service, you can stop Snow Owl via the service management functionality provided by your installation.

If you’re running Snow Owl directly, you can stop Snow Owl by sending Ctrl-C if you’re running Snow Owl in the console, or by invoking the provided shutdown script as follows:

Now that we have our instance up and running, the next step is to understand how to communicate with it. Fortunately, Snow Owl provides very comprehensive and powerful APIs to interact with your instance.

REST API

Among the few things that can be done with the API are as follows:

This section describes the use case scenarios present in the world of SNOMED CT and how Snow Owl can be used in those scenarios to maximize its full potential. Each scenario comes with a summary and a pros/cons section to help your decision making process when selecting the appropriate scenario for your use case.

Detailed API documentation is coming soon! Until then we recommend to check out the official Swagger documentation available on your Snow Owl instance at .

This section includes information on how to setup Snow Owl and get it running, including:

• Downloading

• Installing

Snow Owl uses a number of thread pools for different types of operations. It is important that it is able to create new threads whenever needed. Make sure that the number of threads that the Snow Owl user can create is at least 4096.

This can be done by setting ulimit -u 4096 as root before starting Snow Owl, or by setting nproc to 4096 in /etc/security/limits.conf.

The package distributions when run as services under systemd will configure the number of threads for the Snow Owl process automatically. No additional configuration is required.

Snow Owl uses SLF4J and Logback for logging.

The logging configuration file (serviceability.xml) can be used to configure Snow Owl logging. The logging configuration file location depends on your installation method, by default it is located in the ${SO_HOME}/configuration folder.

Extensive information on how to customize logging and all the supported appenders can be found on the Logback documentation.

Scheduler

# noop I/O scheduler, should be set in eg. /etc/rc.local for solid state disks:
echo noop > /sys/block/sdX/queue/scheduler

Snow Owl uses a mmapfs directory by default to store its data. The default operating system limits on mmap counts is likely to be too low, which may result in out of memory exceptions.

On Linux, you can increase the limits by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf. To verify after rebooting, run sysctl vm.max_map_count.

The RPM and Debian packages will configure this setting automatically. No further configuration is required.

Now let's import an official SNOMED CT RF2 SNAPSHOT distribution archive so that we can further explore the available SNOMED CT APIs.

To import an RF2 archive you must first create an import configuration using the SNOMED CT Import API as follows:

curl -X POST http://localhost:8080/snowowl/snomed-ct/v3/imports -d
{
  "type": "SNAPSHOT",
  "branchPath": "MAIN"
}

And the response:

The import configuration specifies the type of the RF2 release (in this case SNAPSHOT) and the target branchPath where the content should imported. The response returns an empty body along with a Location header with a URL pointing to the created import configuration. You can extract the last part of the URL to get the import configuration ID which can be used to retrieve the configuration and to upload the actual archive and start the import.

The import will start automatically when you upload the archive to the /imports/:id/archive endpoint:

The import process is asynchronous and its status can be checked by sending a GET request to the /imports/:id endpoint with the extracted import identifier as follows:

And the response:

The status field describes the current state of the import, while the startDate and completionDate fields specify start and completion timestamps.

The method for starting Snow Owl varies depending on how you installed it.

Archive packages (.tar.gz, .zip)

If you installed Snow Owl with a .tar.gz or zip package, you can start Snow Owl from the command line.

Running Snow Owl from the command line

Snow Owl can be started from the command line as follows:

By default, Snow Owl runs in the foreground, prints some of its logs to the standard output (stdout), and can be stopped by pressing Ctrl-C.

Running as a daemon

To run Snow Owl as a daemon, use the following command:

Log messages can be found in the $SO_HOME/serviceability/logs/ directory.

RPM packages

Snow Owl is not started automatically after installation. How to start and stop Snow Owl depends on whether your system uses SysV init or systemd (used by newer distributions). You can tell which is being used by running this command:

Running Snow Owl with SysV init

Use the chkconfig command to configure Snow Owl to start automatically when the system boots up:

Snow Owl can be started and stopped using the service command:

If Snow Owl fails to start for any reason, it will print the reason for failure to STDOUT. Log files can be found in /var/log/snowowl/.

Running Snow Owl with systemd

To configure Snow Owl to start automatically when the system boots up, run the following commands:

Snow Owl can be started and stopped as follows:

These commands provide no feedback as to whether Snow Owl was started successfully or not. Instead, this information will be written in the log files located in /var/log/snowowl/.

Debian packages (Coming Soon)

Docker images (Coming Soon)

While Snow Owl requires very little configuration, there are a number of settings which need to be considered before going into production.

The following settings must be considered before going to production:

Elasticsearch settings

By default, Snow Owl includes the OSS version of Elasticsearch and runs it in embedded mode to store terminology data and make it available for search. This is convenient for single node environments (eg. for evaluation, testing and development), but it might not be sufficient when you go into production.

Now let's take a peek at our code systems:

And the response:

Which means, we have a single Code System in Snow Owl, called SNOMED CT. It has been created by the SNOMED CT module by default on the first startup of your instance. A Code System lives in a repository and its working branchPath is currently associated with the default MAIN branch in the snomedStore repository.

Now that we have a SNOMED CT Code System, let's take a look at its content. We can query its content using either the or the .

For sake of simplicity, let's search for the available concepts using the . For that we will need the branch we would like to query, but fortunately we already know the value from our previous call to the Code Systems API, it was MAIN. To list all available concepts in a SNOMED CT Code System, use the following command:

And the response is:

Which simply means we have no SNOMED CT concepts yet in our instance.

Multi Extension Authoring and Distribution

On top of single Edition/Extension distribution and authoring, Snow Owl provides full support for multi-SNOMED CT distribution and authoring even if the Extensions depend on different versions of the SNOMED CT International Edition.

To achieve a deployment like this you need to perform the same initialization steps for each desired SNOMED CT Extension as if it were a single extension scenario (see ). Development and maintenance of each managed extension can happen in parallel without affecting one or the other. Each of them can have their own release cycles, maintenance and upgrade schedules, and so on.

Most operating systems try to use as much memory as possible for file system caches and eagerly swap out unused application memory. This can result in parts of the JVM heap or even its executable pages being swapped out to disk.

Swapping is very bad for performance, and should be avoided at all costs. It can cause garbage collections to last for minutes instead of milliseconds and can cause services to respond slowly or even time out.

There are two approaches to disabling swapping. The preferred option is to completely disable swap, but if this is not an option, you can minimize swappiness.

When an Extension reaches the end of its current development cycle, it needs to be prepared for release and distribution.

Workflows and Authoring Branches

All planned content changes that are still on their dedicated branch either need to be integrated with the main development version or removed from the scope of the next release.

You can manage and authenticate users with the built-in file realm. All the data about the users for the file realm is stored in the users file. The file is located in SO_PATH_CONF and is read on startup.

You need to explicitly select the file realm in the snowowl.yml configuration file in order to use it for authentication.

In the above configuration the file realm is using the users file to read your users from. Each row in the file represents a username and password delimited by : character. The passwords are BCrypt encrypted hashes. The default users

Snow Owl requires Java 11 or newer version. Specifically as of this writing, it is recommended that you use JDK (Oracle of OpenJDK is preferred) version 11.0.2. Java installation varies from platform to platform so we won’t go into those details here. Oracle’s recommended installation documentation can be found on Oracle’s website. Suffice to say, before you install Snow Owl, please check your Java version first by running (and then install/upgrade accordingly if needed):

Once we have Java set up, we can then download and run Snow Owl. The binaries are available at the pages. For each release, you have a choice among a zip or tar archive, a DEB or RPM package.

Installation example with zip

Snow Owl (with embedded Elasticsearch) uses a lot of file descriptors or file handles. Running out of file descriptors can be disastrous and will most probably lead to data loss. Make sure to increase the limit on the number of open files descriptors for the user running Snow Owl to 65,536 or higher.

For the .zip and .tar.gz packages, set ulimit -n 65536

Snow Owl 7 uses a single data source, an Elasticsearch cluster (either embedded or external). To backup and restore the data, we highly recommend the official Snapshot and Restore feature from Elasticsearch. On top of that API, we highly recommend using tools, like Curator to ease the lifecycle management of your Elasticsearch cluster and your indices. See Curator here.

Below you can find a very simple guide on how to configure the backup and restore process for your Snow Owl Terminology Server using Curator.

Coming soon!

This describes the resources that make up the official Snow Owl® CIS API.

Coming soon!

Snow Owl is a multi-purpose terminology server with a main focus on SNOMED CT International Edition and its Extensions. Whether you are a producer of a SNOMED CT Extension or a consumer of one, Snow Owl has you covered. As always, feel free to ask your questions regarding any of the content you read here (raise a ticket on GitHub Issues).

Snow Owl Concepts

Snow Owl uses the following basic concepts to provide authoring and maintenance support for SNOMED CT Extensions.

Code Systems

From the page, we've learned what is a Repository and how Code Systems are defined as part of a Repository.

SNOMED CT Extensions in Snow Owl are basically Code Systems with their own set of properties and characteristics. With Snow Owl's Code System API, a Code System can be created for each SNOMED CT Extension to easily identify the Code System and its components with a single unique identifer, called the Code System short name. The recommended naming approach when selecting the unique short name identifier is the following:

• SNOMED CT International Edition: SNOMEDCT - often included in other editions for distribution purposes

• National Release Center (single maintained extension) - SNOMEDCT-US - represents the SNOMED CT United States of America Extension

The primary namespace identifer and set of modules and languages can be set during the creation of the Code System, and can be updated later on if required. These properties can be used when users are accessing the terminology server for authoring purposes to provide a seamless authoring experience for the user without them needing to worry about selecting the proper namespace, modules, language tags, etc. (NOTE: this feature is not available yet in the OSS version of Snow Owl)

Extension Of

A Snow Owl Code System can be marked as an extensionOf another Code System, which ties them together, forming a dependency between the two Code Systems. A Code System can have multiple Extension Code Systems, but a Code System can only be extensionOf a single Code System.

Branching

In Snow Owl, a Repository maintains a set of branches and Code Systems are always attached to a dedicated branch. For example, the default root Code Systems are always tied to the default branch, called MAIN. When creating a new Code System, the "working" branchPath can be specified and doing so assigns the branch to the Code System. A Code System cannot be attached to multiple branches at the same time, and a branch can only be assigned to a single Code System in a Repository. Snow Owl's branching infrastructure allows the use of isolated environments for both distribution and authoring workflows, therefore they play crucial role in SNOMED CT Extension managament as well. They also provide the support for seamless upgrade mechanism, which can be done whenever there is a new version available in one of your SNOMED CT Extension's dependent Code Systems.

Versions

As in real life, a Code System can have zero or more versions (or with another name, releases). A version is a special branch that is created during the versioning process and makes the currently available latest content accessible later in its current form. Since SNOMED CT Extensions can have releases as well, creating a Code System Version in Snow Owl is a must in order to produce the release packages.

Examples

The following image shows the repository content rendered from the available commits, after a successful International Edition import.

Dots represent commits made with the commit message on the right. Green boxes represent where the associated branch's HEAD is currently located. Blue tag labels represent versions created during the commit.

If your use case would be to import the SNOMED CT US Extension 2019-09-01 version into this repository, then ideally it would look like this:

The next section describes the use case scenarios in the world of SNOMED CT and the recommended approaches for deploying these scenarios in Snow Owl.

A typical extension scenario is the development of the extension itself. Whether you are starting your extension from scratch or already have a well-developed version that you need to maintain, the first choice you need to make is to identify the dependencies of your SNOMED CT Extension.

Extending the International Edition

If your Extension extends the SNOMED CT International Edition directly, then you need to pick one of the available International Edition versions:

• If you are starting from scratch, it is always recommended to select the latest International Release as the starting point of your Extension.

• If you have an existing Extension then you probably already know the International Release version your Extension depends on.

When you have identified the version you need to depend on then you need to import that version (or a later release packages that also includes that version in its FULL RF2 package) first into Snow Owl. Make sure that the createVersion feature of the RF2 import process is enabled, so it will automatically create the versions for each imported RF2 effectiveTime value.

After you have successfully imported all dependencies into Snow Owl, the next step is to create a Code System that represents your SNOMED CT Extension (see ). When creating the Code System, besides specifying the namespace and optional modules and languages, you need to enter a Code System shortName, which will serve as the unique identifier of your Extension and select the extensionOf value, which represents the dependency of the Code System.

After you have successfully created the Code System representing your Extension, you can import any existing content from a most recent release or start from scratch by creating the module concept of your extension.

Extending another Extension

If your Extension needs to extend another Extension and not the International Edition itself, then you need to identify the version you'd like to depend on in that Extension (that indirectly will select the International Edition dependency as well). When you have identified all required versions, then starting from the International Edition recursively traverse back and repeat the RF2 Import and Code System creation steps described in the previous section until you have finally imported your extension. In the end your extension might look like this, depending on how many Extensions you are depending on.

Summary

Setting up a Snow Owl deployment like this is not an easy task. It requires a thorough understanding of each SNOMED CT Extension you'd like to import and their dependencies as well. However, after the initial setup, the maintenance of your Extension becomes straightforward, thanks to the clear distinction from the International Edition and from its other dependencies. The release process is easier and you can choose to publish your Extension as an extension only release, or as an Edition or both (see ). Additionally, when a new version is available in one of the dependencies, you will be able to upgrade your Extension with the help of automated validation rules and upgrade processes (see ). From the distribution perspective, this scenario shines when you need to maintain multiple Extensions/Editions in a single deployment.

Pros:

• Excellent for authoring and maintenance

• Good for distribution

Cons:

• Harder to set up the initial deployment

Authoring is the process by which content is created in an extension in accordance with a set of authoring principles. These principles ensure the quality of content and referential integrity between content in the extension and content in the International Edition (the principles are set by SNOMED International, can be found here).

During the extension development process authors are:

• creating, modifying or inactivating content according to editorial principles and policies

• running validation processes to verify the quality and integrity of their Extension

• classifying their authored content with an OWL Reasoner to produce its distribution normal form

The authors directly (via the available REST and FHIR APIs) or indirectly (via user interfaces, scripts, etc.) work with the Snow Owl Terminology Server to make the necessary changes for the next planned Extension release.

Workflow and Editing

Authors often require a dedicated editing environment where they can make the necessary changes and let others review the changes they have made, so errors and issues can be corrected before integrating the change with the rest of the Extension. Similarly to how SNOMED CT Extensions are separated from the SNOMED CT International Edition and other dependencies, this can be achieved by using branches.

• - to create and merge branches

• - to compare branches

Authoring APIs

To let authors make the necessary changes they need, Snow Owl offers the following SNOMED CT component endpoints to work with:

• - to create, edit SNOMED CT Concepts

• - to create, edit SNOMED CT Descriptions

• - to create, edit SNOMED CT Relationships

Validation

To verify quality and integrity of the changes they have made, authors often generate reports and make further fixes according to the received responses. In Snow Owl, reports and rules can be represented with validation queries and scripts.

• - to run validation rules and fetch their reported issues on a per branch basis

Classification

Last but not least, authors run an OWL Reasoner to classify their changes and generate the necessary normal form of their Extension. The provides support for running these reasoner instances and generating the necessary normal form.

The most common use case to consume a SNOMED CT Release Package is to import it directly into a Terminology Server (like Snow Owl) and make it available as read-only content for both human and machine access (via REST and FHIR APIs).

SNOMED CT International Edition

Since Snow Owl by default comes with a pre-initialized SNOMED CT Code System called SNOMEDCT, it is just a single call to import the official RF2 package using the SNOMED CT RF2 Import API The import by default creates a Code System Version for each SNOMED CT Effective Date available in the supplied RF2 package. After a successful import the content is immediately available via REST and FHIR APIs.

SNOMED CT Extension Edition

National Release Centers and other Care Providers provide their own SNOMED CT Edition distribution for third-party consumers in RF2 format. Importing their Edition distribution instead of the International Edition directly into the SNOMEDCT pre-initialized SNOMED CT Code System with the same makes both the International Edition (always included in Edition packages) and the National Extension available for read-only access.

Summary

The single edition scenario without much effort provides access to any SNOMED CT Edition directly on the pre-initialized SNOMEDCT Code System. It is easy to set up and maintain. Because of its flat structure, it is good for distribution and extension consumers. Although it can be used for authoring in certain scenarios, due to the missing distinction between the International Edition and the Extension, it is not the best choice for extension authoring and maintenance.

Pros:

• Good for maintaining the SNOMED CT International Edition

• Good for distribution

• Simple to set up and maintain

Cons:

• Not recommended for extension authoring and maintenance

• Not recommended for multi-extension distribution scenarios

GET the ROOT concept:

curl 'http://localhost:8080/snowowl/snomed-ct/v3/MAIN/concepts/138875005'

And the response:

{
  "id": "138875005",
  "released": true,
  "active": true,
  "effectiveTime": "20020131",
  "moduleId": "900000000000207008",
  "iconId": "138875005",
  "definitionStatus": "PRIMITIVE",
  "subclassDefinitionStatus": "NON_DISJOINT_SUBCLASSES"
}

Search by ECL:

And the response:

Snow Owl security features enable you to easily secure your terminology server. You can password-protect your data as well as implement more advanced security measures such as role-based access control and auditing.

Realms

By default Snow Owl comes without any security features enabled and all read and write operations are unprotected. To configure a security realm, you can choose from the following built-in identity providers:

Ideally, Snow Owl should run alone on a server and use all of the resources available to it. In order to do so, you need to configure your operating system to allow the user running Snow Owl to access more resources than allowed by default.

The following settings must be considered before going to production:

This describes the resources that make up the official Snow Owl® SNOMED CT Terminology API.

ConceptMap API

The endpoints /ConceptMap and /ConceptMap/{conceptMapId} and corresponding operations expose the following types of terminology resources:

Snow Owl^® is a highly scalable, open source terminology server with revision-control capabilities and collaborative authoring platform features. It allows you to store, search and author high volumes of terminology artifacts quickly and efficiently.

Introduction

Features include:

• Revision-controlled authoring

  • Maintains multiple versions (including unpublished and published) for each terminology artifact and provides APIs to access them all

  • Independent work branches offer work-in-process isolation, external business workflow integration and team collaboration

Download

• -

• -

• -

View the detailed release notes .

Not the version you're looking for? View .

Install and Run

NOTE: You need to have a recent version of Java installed (Java 11+, https://adoptium.net/).

Once you have downloaded the appropriate package:

• Run bin/snowowl.sh on unix, or bin/snowowl.bat on windows

• Run curl http://localhost:8080/snowowl/admin/info

Learn Snow Owl

Building from source

Snow Owl uses Maven for its build system. In order to create a distribution, you will only need the installed.

Simply run the following command in the cloned directory. The Maven Wrapper will automatically download the required Maven version (and store it under ~/.m2/wrapper/dists).

The distribution packages can be found in the releng/com.b2international.snowowl.server.update/target folder, when the build is complete.

To run the test cases, use the following command:

Development

These instructions will get Snow Owl up and running on your local machine for development and testing purposes.

Prerequisites

Snow Owl is an Equinox-OSGi based server. To develop plug-ins for Snow Owl you need to use Eclipse as IDE:

• Download Eclipse IDE for Eclipse Committers 2020-09 package from here: https://www.eclipse.org/downloads/packages/release/2020-09/r/eclipse-ide-eclipse-committers

Required Eclipse plug-ins (install the listed features via Help -> Install New Software...):

Note: you may have to untick the Show only the latest versions of the available software checkbox to get older versions of a feature. Please use the exact version specified below, not the latest point release.

• Xtext/Xtend (https://download.eclipse.org/modeling/tmf/xtext/updates/releases/2.23.0/)

  • Xtend IDE 2.23.0 (Xtext)

  • Xtext Complete SDK 2.23.0 (Xtext)

Eclipse Preferences

Make sure you have the following preferences enabled/disabled.

• Plug-in development API baseline errors is set to Ignored (Preferences > Plug-in Development > API Baselines)

• The Plugin execution not covered by lifecycle configuration: org.apache.maven.plugins:maven-clean-plugin:2.5:clean type of errors can be ignored or changed to Warnings in Preferences->Maven->Errors/Warnings.

• Set the workspace encoding to UTF-8 (Preferences->General->Workspace)

Git configuration

• Make sure the Git line endings are set to input (Preferences->Team->Git->Configuration - add key if missing core.autocrlf = input)

Maven Settings

• Make sure the settings.xml in your ~/.m2/settings.xml location is updated with the content from the settings.xml from this repository's root folder.

First steps

1. Import all projects into your Eclipse workspace and wait for the build to complete

2. Select all projects and hit Alt + F5 and trigger an update to all Maven projects manually (to download dependencies from Maven)

3. Open the

Contributing

Please see for details.

Versioning

Our use . You can find a chronologically ordered list of notable changes in .

License

This project is licensed under the Apache 2.0 License. See for details and refer to for additional licensing notes and uses of third-party components.

Acknowledgements

In March 2015, generously licensed the Snow Owl Terminology Server components supporting SNOMED CT. They subsequently made the licensed code available to their and the global community under an open-source license.

In March 2017, licensed the Snow Owl Terminology Server to support the mandatory adoption of SNOMED CT throughout all care settings in the United Kingdom by April 2020. In addition to driving the UK’s clinical terminology efforts by providing a platform to author national clinical codes, Snow Owl will support the maintenance and improvement of the dm+d drug extension which alone is used in over 156 million electronic prescriptions per month. Improvements to the terminology server made under this agreement will be made available to the global community.

Many other organizations have directly and indirectly contributed to Snow Owl, including: Singapore Ministry of Health; American Dental Association; University of Nebraska Medical Center (USA); Federal Public Service of Public Health (Belgium); Danish Health Data Authority; Health and Welfare Information Systems Centre (Estonia); Department of Health (Ireland); New Zealand Ministry of Health; Norwegian Directorate of eHealth; Integrated Health Information Systems (Singapore); National Board of Health and Welfare (Sweden); eHealth Suisse (Switzerland); and the National Library of Medicine (USA).

Introduction

The Snow Owl Terminology Server is capable of managing multiple SNOMED CT extensions for both distribution and authoring purposes in a single deployment. This guide describes the typical scenarios, like creating, managing, releasing and upgrading SNOMED CT Extensions in great detail with images. If you are unfamiliar with SNOMED CT Extensions, the next section walks you through their logical model and basic characteristics, while the following pages describe distribution and authoring scenarios as well as how to use the Snow Owl Terminology Server for SNOMED CT Extensions.

Extensions and Snow Owl

What is a SNOMED CT Extension?

Common Structure

SNOMED CT is a multilingual clinical terminology that covers a broad scope. However, some users may need additional concepts, relationships, descriptions or reference sets to support national, local or organizational needs.

The extension mechanism allows SNOMED CT to be customized to address the terminology needs of a country or organization that are not met by the International Edition.

A SNOMED CT Extension may contain components and/or derivatives (e.g. reference sets used to represent subsets, maps or language preferences). Since the international edition and all extensions share a common structure, the same application software can be used to enter, store and process information from different extensions. Similarly, reference sets can be constructed to refer to content from both the international release and extensions. The common structure also makes it easier for content developed by an extension producer to be submitted for possible inclusion in a National Edition or the International Edition.

Therefore, a SNOMED CT Extension uses the same Release Format version 2 as the International Edition, they share a common structure and schema (see ).

Namespace

Extensions are managed by SNOMED International, and Members or Affiliate Licensees who have been issued a namespace identifier by SNOMED International. A namespace identifier is used to create globally unique SNOMED CT identifiers for each component (i.e. concept, description and relationship) within a Member or Affiliate extension. This ensures that references to extension concepts contained in health record data are unambiguous and can be clearly attributed to a specific issuing organization.

A national or local extension uses a namespace identifier issued by SNOMED International to ensure that all extension components can be uniquely identified (across all extensions).

Therefore, a SNOMED CT Extension uses a single namespace identifier to identify all core components in the SNOMED CT Extension (see ).

Modules

Every SNOMED CT Extension includes one or more modules, and each module contains either SNOMED CT components or reference sets (or both). Modules may be dependent on other modules. A SNOMED CT Edition includes the contents of a focus module together with the contents of all the modules on which it depends. This includes the modules in the International Edition and possibly other modules from a national and/or local extension.

An edition is defined based on a single focus module. This focus module must be the most dependent module, in that the focus module is dependent on all the other modules in the edition.

Therefore, a SNOMED CT Extension uses one or more modules to categorize the components into meaningful groups (see ).

Language

SNOMED CT extensions can support a variety of use cases, including:

Translating SNOMED CT, for example

• Adding terms used in a local language or dialect

• Adding terms used by a specific user group, such as patient-friendly terms

Therefore, an Extension can have its own language to support patient-friendly terms, local user groups, etc. (see ).

Dependency

A SNOMED CT extension is a set of components and reference set members that add to the SNOMED CT International Edition. An extension is created, structured, maintained and distributed in accordance with SNOMED CT specifications and guidelines. Unlike, the International Edition an extension is not a standalone terminology. The content in an extension depends on the SNOMED CT International Edition, and must be used together with the International Edition and any other extension module on which it depends.

Therefore, a SNOMED CT Extension depends on the SNOMED CT International Edition directly or indirectly through another SNOMED CT Extension (see ).

Versions

A specific version of an extension can be referred to using the date on which the extension was published.

There are many use cases that require a date specific version of an edition, including specifying the substrate of a SNOMED CT query, and specifying the version of SNOMED CT used to code a specific data element in a health record. A versioned edition includes the contents of the specified version of the focus module, plus the contents of all versioned modules on which the versioned focus module depends (as specified in the |Module dependency reference set|). The version of an edition is based on the date on which the edition was released. Many extension providers release their extensions as a versioned edition, using regular and predictable release cycles.

Therefore, a SNOMED CT Extension can be versioned and have a different release cycle than the SNOMED CT International Edition (see ).

Characteristics

To summarize, a SNOMED CT Extension has the following characteristics:

• Uses the same RF2 structure as the SNOMED CT International Edition

• Uses a single namespace identifer to globally identify its content

• Uses one or more modules to categorize the content into groups

Now that we have a clear understanding of what SNOMED CT Extensions are, let's take a look at how can we use them in Snow Owl.

Maintenance of a SNOMED CT Extension is essential to ensure that

• it incorporates changes requested by terminology consumers

• it remains aligned with the SNOMED CT International Edition

While both of these maintenance related tasks are potentially assigned to one of the upcoming Extension development cycles, there is a clear distinction between the two maintenance tasks.

Change requests

Changes requested by your terminology consumers are typically content authoring tasks that you would assign to an Extension authoring team. They usually come with a well-described problem you need to address in the terminology as you would do in the usual development cycle.

See the section on how you can address change requests and incorporate them as regular tasks into the main version of your Extension.

International Edition Changes

Aligning content to the SNOMED CT International Edition is one of the main responsibilities of an Extension maintainer. However, keeping up with the changes introduced in SNOMED CT International Edition biannually (on January 31st and July 31st) can be an overwhelming task, especially if:

• you are under pressure from your terminology consumers to make the requested changes ASAP, especially in mission critical scenarios.

• the changes introduced in the International Edition are conflicting with your local changes and/or causing maintenance related issues after the upgrade.

To address SNOMED CT International Edition upgrade tasks in a reliable and reproducible way, Snow Owl offers an upgrade flow for SNOMED CT Extensions.

Upgrades

A Code System upgrade in Snow Owl is a complex workflow with states and steps. The workflow involves a special Upgrade Code System, a series of automated migration processes and validation rules to ensure the quality and reliability of the operation. The upgrade can be done quickly if there were no conflicts between the Extension and the International Edition. However, updates can also be a long-running process spanning over many months when significant structural changes (e.g. in substances, anatomy, or modeling approach) are made in the International Edition.

Starting the Upgrade

In Snow Owl, SNOMED CT Extension are linked to their SNOMED CT dependency with the extensionOf property. This property describes the International Edition and its version that the Extension depends on. For example, the SNOMEDCT/2019-07-31 value specifies that our Extension depends on the 2019-07-31 version of the International Edition.

Extension upgrades can be started when there is a new version available in the Extension/Edition we have selected as our dependency in the extensionOf property. When fetching a SNOMED CT Code System via the Code System API, Snow Owl will check if there are any upgrades availables and return them in the availableUpdates array property. If there are no upgrades available the array will be empty.

To start an Extension upgrade to a newer International Edition (or to a newer Extension dependency version), you can use the . The only thing that needs to be specified there is the desired new version of the Extension's extensionOf dependency.

When the upgrade is started, Snow Owl creates a special <codeSystemShortName>-UP-<newExtensionOf> (eg. SNOMEDCT-MYEXT-UP-SNOMEDCT-2020-01-31) Code System to allow authors and the automated processes to migrate the latest development version of the Extension to the new dependency.

Regular Maintenance

Regular daily Extension development tasks still need to be resolved and pushed somewhere in order to continue the development of the Extension, even if an upgrade process is in progress. Each Extension still has an active development version, even if an upgrade is in progress, which can be used to push daily maintenance changes and business as usual tasks.

Changes pushed to the development area will regularly need to be synced with the upgrade until the upgrade completes, so the upgrade team will be able to resolve all remaining conflicts and issues.

Upgrade Checks

Upgrade Checks ensure the quality of the upgrade process and execute certain tasks/checks automatically. An Upgrade Check can be any logic or function to be run during the upgrade. Upgrade Checks can access the underlying upgrade Code System's content and report any issues (validation rules) or fix content automatically (migration rules). For example, a validation rule (like Active relationships must have active source, type, destination references) can be executed after each change pushed to the upgrade branch to verify whether there is any potentially invalid relationship left to fix or you are ready to go.

Completing the Upgrade

Once the upgrade authoring team is done with the necessary changes to align the Extension with the new International Edition and all the checks are completed successfully the upgrade can be completed. Completing the upgrade performs the following steps:

• Creates a <codeSystemShortName>-DO-<previousExtensionOf> Code System to refer to the previous state of the Extension

• Changes the current working branch of the Extension Code System to the branch that was used during the upgrade process

• Deletes the <codeSystemShortName>-UP-<newExtensionOf>

Two categories make up Snow Owl's Reference Set API:

1. Reference Sets category to get, search, create and modify reference sets

2. Reference Set Members category to get, search, create and modify reference set members

Basic operations like create, update, delete are supported for both category.

Actions API

On top of the basic operations, reference sets and members support actions. Actions have an action property to specify which action to execute, the rest of the JSON properties will be used as body for the Action.

Supported reference set actions are:

1. sync - synchronize all members of a query type reference set by executing their query and comparing the results with the current members of their referenced target reference set

Supported reference set member actions are:

1. create - create a reference set member (uses the same body as POST /members)

2. update - update a reference set member (uses the same body as PUT /members)

3. delete - delete a reference set member

For example the following will sync a query type reference set member's referenced component with the result of the reevaluated member's ESCG query

Bulk API

Members list of a single reference set can be modified by using the following bulk-like update endpoint:

Input

The request body should contain the commitComment property and a request array. The request array must contain actions (see Actions API) that are enabled for the given set of reference set members. Member create actions can omit the referenceSetId parameter, those will use the one defined as path parameter in the URL. For example by using this endpoint you can create, update and delete members of a reference set at once in one single commit.

Compare API

Comparison for current terminology changes committed to a source or target branch can be conducted by creating a compare resource.

A review identifier can be added to merge requests as an optional property. If the source or target branch state is different from the values captured when creating the review, the merge/rebase attempt will be rejected. This can happen, for example, when additional commits are added to the source or the target branch while a review is in progress; the review resource state becomes STALE in such cases.

Reviews and concept change sets have a limited lifetime. CURRENT reviews are kept for 15 minutes, while review objects in any other states are valid for 5 minutes by default. The values can be changed in the server's configuration file.

Compare two branches

Response

Read component state from comparison

Terminology components (and in fact any content) can be read from any point in time by using the special path expression: {branch}@{timestamp}. To get the state of a SNOMED CT Concept from the previous comparison on the compareBranch at the returned compareHeadTimestamp, you can use the following request:

Request

Response

To get the state of the same SNOMED CT Concept but on the base branch, you can use the following request:

Request

Response

Additionally, if required to compute what's changed on the component since the creation of the task, it is possible to get back the base version of the changed component by using another special path expression: {branch}^.

Request

Response

Code systems maintained within Snow Owl are exposed (read-only) via the endpoints /CodeSystem and /CodeSystem/{codeSystemId}. Supported concept properties are handled and returned if requested. The currently exposed code systems are:

Snow Owl OSS:

• SNOMED CT

• Internal (FHIR) Code Systems (terminology subset)

Snow Owl Pro:

• ATC

• ICD-10

• LOINC

SNOMED CT

All standard and default SNOMED CT properties are supported, including the relationship type properties. In addition to the FHIR SNOMED CT properties, Snow Owl can return the effective time property, with the URI http://snomed.info/field/Concept.effectiveTime.

Operations

$lookup

Both GET as well as POST HTTP methods are supported. Concepts are queried based on code, version, system or Coding. Designations are included as part of the response as well as supported concept properties when requested. No date parameter is supported.

Example for looking up a code from the Issue-type FHIR code system:

Example for looking up properties (inactive and method) of the latest version of a SNOMED CT procedure by method code:

For SNOMED CT, all common and SNOMED CT properties are supported, including all active relationship types.

$validate-code

Both GET as well as POST HTTP methods are supported for all exposed terminologies. Example for validating a SNOMED CT code:

$subsumes

Both GET as well as POST HTTP methods are supported. Subsumption testing is supported for ICD-10 and SNOMED CT terminologies.

Example for SNOMED CT (version 2018-01-31):

The Debian package for Snow Owl can be downloaded from the Downloads section. It can be used to install Snow Owl on any Debian-based system such as Debian and Ubuntu.

Download and install

The RPM for Snow Owl can be downloaded from the Downloads section. It can be used to install Snow Owl on any RPM-based system such as OpenSuSE, SLES, Centos, Red Hat, and Oracle Enterprise.

Snow Owl is also available as Docker images. The images use as the base image.

A list of all published Docker images and tags is available at .

These images are free to use under the Apache 2.0 license. They contain open source features only.

Pulling the image

This describes the resources that make up the official Snow Owl® RESTful API.

Media Types

Custom media types are used in the API to let consumers choose the format of the data they wish to receive. This is done by adding one of the following types to the Accept header when you make a request. Media types are specific to resources, allowing them to change independently and support formats that other resources don’t.

The most basic media types the API supports are:

Snow Owl is provided as a .zip and as a .tar.gz package. These packages can be used to install Snow Owl on any system and are the easiest package format to use when trying out Snow Owl.

The latest stable version of Snow Owl can be found on the Snow Owl Releases page.

Download and install the zip package

The .zip archive for Snow Owl can be downloaded and installed as follows:

Download and install the .tar.gz package

The .tar.gz archive for Snow Owl can be downloaded and installed as follows:

Running Snow Owl from the command line

Snow Owl can be started from the command line as follows:

By default, Snow Owl runs in the foreground, prints its logs to the standard output (stdout), and can be stopped by pressing Ctrl-C.

Checking that Snow Owl is running

You can test that your instance is running by sending an HTTP request to Snow Owl's status endpoint:

which should give you a response like this:

Running in the background

You can send the Snow Owl process to the background using the combination of nohup and the & character:

Log messages can be found in the $SO_HOME/serviceability/logs/ directory.

To shut down Snow Owl, you can kill the process ID directly:

or using the provided shutdown script:

Directory layout of .zip and .tar.gz archives:

The .zip and .tar.gz packages are entirely self-contained. All files and directories are, by default, contained within $SO_HOME — the directory created when unpacking the archive.

This is very convenient because you don’t have to create any directories to start using Snow Owl, and uninstalling Snow Owl is as easy as removing the $SO_HOME directory. However, it is advisable to change the default locations of the config directory, the data directory, and the logs directory so that you do not delete important data later on.

Next steps

You now have a test Snow Owl environment set up. Before you start serious development or go into production with Snow Owl, you must do some additional setup:

• Learn how to .

• Configure .

• Configure .

You can configure security to communicate with a Lightweight Directory Access Protocol (LDAP) server to authenticate and authorize users.

To integrate with LDAP, you configure an ldap realm in the snowowl.yml configuration file.

Configuration

The following configuration settings are supported:

The default configuration values are selected to support both OpenLDAP and Active Directory without needing to customize the default schema that comes with their default installation.

Configure Authentication

When users send their username and password with their request in the Authorization header, the LDAP security realm performs the following steps to authenticate the user: 1. Searches for a user entry in the configured baseDn to get the DN 2. Authenticates with the LDAP instance using the received DN and the provided password

If any of the above-mentioned steps fails for any reason, the user is not allowed to access the terminology server's content and the server will respond with HTTP 401 Unauthorized.

To configure authentication, you need to configure the uri, baseDn, bindDn, bindDnPassword, userObjectClass and userIdProperty configuration settings.

Adding a user

To add a user in the LDAP realm, create an entry under the specified baseDn using the configured userObjectClass as class and the userIdProperty as the property where the user's username/e-mail address is configured.

Example user entry:

Configure Authorization

On top of the authentication part, the LDAP realm provides configuration values to support full role-based access control and authorization.

When a user's request is successfully authenticated with the LDAP realm, Snow Owl authorizes the request using the user's currently set roles and permissions in the configured LDAP instance.

Adding a role

To add a role in the LDAP realm, create an entry under the specified baseDn using the configured roleObjectClass as class and the configured permissionProperty and memberProperty properties for permission and user mappings, respectively.

Example read-only role:

The following major differences, features and topics are worth mentioning when comparing features present in Snow Owl 6 and 7 and migrating an existing 6.x deployment to Snow Owl 7.x.

NOTE: It is highly recommended to keep the previous Snow Owl 6 deployment up and running until you have the data and all connected services migrated to the new version successfully. The new Snow Owl 7 system should get its own dedicated machine and deployment environment. Rolling back to the previous state should be available and must be executed when the upgrade cannot be performed successfully.

Java 11

From Snow Owl 7.1, Snow Owl compiles and runs on Java 11+ versions. It is recommended to use the latest OpenJDK or OracleJDK 11 LTS version. Install from , or . The Oracle JDK comes with commercial usage restrictions, see before installing.

RDBMS vs Elasticsearch

While Snow Owl 6 was relying on two data sources for reading and writing data, a primary RDBMS (MySQL) for writing and a secondary Elasticsearch index for full-text search, queries and quick access, Snow Owl 7 in the other hand requires only a single data source, an Elasticsearch cluster.

If you were using an external Elasticsearch cluster then we recommended installing the new Elasticsearch 7.x version first, then installing Snow Owl 7.x and finally connecting the two (or using the appropriate Docker images). If you were using the embedded version, then installing the new Snow Owl 7 version is enough.

After the migration, the MySQL software dependency can be uninstalled from the machine if there are no other services depending on it.

Database content

Due to schema changes the old content present in the RDBMS and index cannot be used by a Snow Owl 7 installation. To migrate an existing dataset to the new version, perform an export in the old system and use the exported files to import the content back into the new Snow Owl 7 version.

LDAP Authorization

The new Snow Owl 7 version comes with complete authorization support using JWT authorization tokens. The old User - Role - Permission system can be used by performing the following migration steps:

1. Add the administrator permission to all administrator roles: *:*

2. Remove the unused permission values from all roles used by Snow Owl

3. Add the classify:*

Configuration changes

Snow Owl 7 configuration file has been renamed to snowowl.yml (from snowowl_config.yml) and moved to the <HOME>/configuration folder.

The following configuration settings have been changed:

• repository.database configuration setting has been removed completely

• repository.numberOfWorkers has been renamed to repository.maxThreads and its default value became 200.

Apply these changes to the configuration before starting your Snow Owl Terminology Server.

Startup and shutdown

The old startup.bat, startup.sh, shutdown.bat, shutdown.sh have been replaced with the new snowowl.sh, snowowl.bat and shutdown.sh scripts.

Packaging

Snow Owl 7 comes in four distribution formats:

• zip/tar.gz for manual deployments

• rpm for CentOS/RHEL based Linux system deployments

Snow Owl provides branching support for terminology repositories. In each repository there is an always existing and UP_TO_DATE branch called MAIN. The MAIN branch represents the latest working version of your terminology (similar to a master branch on GitHub).

You can create your own branches and create/edit/delete components and other resources on them. Branches are identified with their full path, which should always start with MAIN. For example the branch MAIN/a/b/c/d represents a branch under the parent MAIN/a/b/c with name d

ValueSet API

The endpoints /ValueSet and /ValueSet/{valueSetId} and corresponding operations expose the following types of terminology resources: