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):

java -version
echo $JAVA_HOME

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

Installation example with zip

For simplicity, let's use a zip file.

Let's download the most recent Snow Owl release as follows:

curl -L -O https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.zip

Then extract it as follows:

unzip snow-owl-oss-<version>.zip

It will then create a bunch of files and folders in your current directory. We then go into the bin directory as follows:

cd snow-owl-oss-<version>/bin

And now we are ready to start the instance:

./startup

Successfully running instance

If everything goes well with the installation, you should see a bunch of log messages that look like below:

TODO example output

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!

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.

Terminology Component

A terminology component is a basic element in a code system with actual clinical meaning or use. For example in SNOMED CT, the Concept, Description, Relationship and Reference Set Member are terminology components.

Version

A version that refers to an important snapshot in time, consistent across many terminology components, also known as tag or label. It is often created when the state of the terminology is deemed to be ready to be published and distributed to downstream customers or for internal use. A version is identified by its version ID (or version tag) within a given code system.

Repository

A repository manages changes to a set of data over time in the form of revisions. Conceptually very similar to a source code repository (like a Git repository), but information stored in the repository must conform to a predefined schema (eg. SNOMED CT Concepts RF2 schema) as opposed to storing it in pure binary or textual format. This way a repository can support various full-text search functionalities, semantical queries and evaluations on the stored, revision-controlled terminology data.

A repository is identified by a name and this name is used to refer to the repository when performing create, read, update, delete and other operations against the revisions in it. Repositories organize revisions into branches and commits.

Revision

A revision is the basic unit of information stored in a repository about a terminology component or artifact. It contains two types of information:

• one is the actual data that you care about, for example a single code from a code system with its meaining and properties.

• the other is revision control information (aka revision metadata). Each revision is identified by a random Universally Unique IDentifier (UUID) that is assigned when performing a commit in the repository. Also, during a commit each revision is associated with a branch and timestamp. Revisions can be compared, restored, and merged.

Branch

A set of components under version control may be branched or forked at a point in time so that, from that time forward, two copies of those components may develop at different speeds or in different ways independently of each other. At later point in time the changes made on one of these branches can be merged into the other.

Branches are organized into hierarchies like directories in file systems. A child branch has access to all of the information that is stored on its parent branch up until its baseTimestamp, which is the time the branch was created. Each repository has a predefined root branch, called MAIN.

Commit

A commit represents a set of changes made against a branch in a repository. After a successful commit, the changes made by the commit are immediately available and searchable on the given branch.

Merge / Rebase

A merge/rebase is an operation in which two sets of changes are applied to set of components. A merge/rebase always happens between two branches, denoting one as the source and the other as the target of the operation.

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

• SNOMED CT and others

  • Full SNOMED CT terminology support (full RF2 support, ECL v1.3, SCG 2.3.1, ETL 1.0, Reference Sets, OWL Axioms, OWL 2 EL/DL support, SNOMED Query Language draft specification)

  • With its modular design, the server can maintain multiple terminologies (including local codes, mapping sets, value sets)

• Various set of APIs

  • SNOMED CT API (RESTful and native Java API)

  • FHIR API

  • CIS API

• Highly extensible and configurable

  • Simple to use plug-in system makes it easy to develop and add new terminology tooling/API or any other functionality

• • Connect to your existing cluster or use the embedded instance

  • All the power of Elasticsearch is available (full-text search support, monitoring, analytics and many more)

Download

Install and Run

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

• Navigate to http://localhost:8080/snowowl

Learn Snow Owl

Building from source

Snow Owl uses Maven for its build system. In order to create a distribution, simply run the following command in the cloned directory.

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:

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.

• • MWE 2 language SDK 2.11.2 (MWE)

  • Xtend IDE 2.21.0 (Xtext)

  • Xtext Complete SDK 2.21.0 (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)

• Set the line endings to Unix style (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)

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 target-platform/target-platform-local.target file

4. Wait until Eclipse resolves the target platform (click on the Resolve button if it refuses to do so) and then click on Set as Active Target platform

5. Wait until the build is complete and you have no compile errors

6. Launch snow-owl-oss launch configuration in the Run Configurations menu

7. Navigate to http://localhost:8080/snowowl

Contributing

Versioning

License

Acknowledgements

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).

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

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.