SNOMED CT RF2 to OWL

About the tool

Use this tool to quickly convert SNOMED CT RF2 to OWL online.

Demo

Step 0 Extract the RF2 .zip archive to a folder on your computer.
Step 1 Select the folder with the extracted RF2 files. This folder must contain the Snapshot subdirectory.
Clicking the button above will allow access to the RF2 directory.
Axioms read: N/A.
Step 2 Save the generated OWL ontology file.

What is SNOMED CT?

SNOMED CT serves as a global standard terminology / controlled vocabulary for healthcare. It provides a comprehensive set of codes for concepts encompassing diseases, procedures, medications, findings, and more.

The standardized vocabulary facilitates the unambiguous exchange of clinical data across systems, promoting better communication and collaboration among the stakeholders in the healthcare domain.

What is RF2?

The content of SNOMED CT is distributed in the RF2 format, which is a set of text files (database-like exports) containing concept definitions, relationships, refsets, and OWL axioms. You usually don't work with these files directly, but rather load them into a database or process them using specialized tools.

What is OWL?

OWL is used to create and store ontologies-sets of axioms that formally capture the domain model. The logical foundations (formal semantics) of OWL ontologies allow for automated reasoning over the stated axioms to derive new, inferred axioms (new knowledge).

Recently, SNOMED CT transitioned to using OWL axioms as the source of truth in place of simple stated relationships. This allowed for more expressive definitions of SNOMED CT concepts and their relationships.

How does it work?

The tool reads the SNOMED CT RF2 files and extracts the OWL axioms from the refset file. It then produces a complete OWL ontology serialized using the OWL2 Functional Syntax. The resulting OWL ontology can be imported into ontology editors (e.g. Protege), reasoners, and other tools that support OWL.

To read the files from the RF2 directory, the tool uses the File System Access API. The processing is done entirely in the browser, so no files are transmitted over the network.

I'm also looking to add support for reading the RF2 .zip files directly, so you don't have to extract the files manually.

Motivation

The reference implementation of the RF2-to-OWL converter is the SNOMED OWL Toolkit—the official, open-source, and feature-rich tool that supports all versions of SNOMED CT and allows you to execute reasoning over the ontology.

I started diving into the specifics of the RF2 files as I was looking to better understand the OWL-based foundations of SNOMED CT. As a result, I created this unofficial/alternative, online RF2-to-OWL tool that everyone can use to quickly reconstruct the OWL ontology from the RF2 files. Note that you need to use the recent (OWL-first) version of SNOMED CT.

This tool is also a great way to demonstrate the capabilities of the File System Access API.

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Made by Anton Vasetenkov.

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