Introduction

The Alpha release of the SNOMED CT to Orphanet Map is the product of a joint project carried out under a collaboration agreement between Institut national de la sante et de la recherche medicale (Inserm) and the International Health Terminology Standards Organisation (IHTSDO). Based on agreed priority set,  missing Rare Diseases defined in Orphanet have been added to SNOMED CT and a map from SNOMED CT to Orphanet has been created.

This document is intended to give a brief description, background context and explanatory notes on the SNOMED CT International/INSERM work and and the resulting SNOMED CT to Orphanet map, which is being published as an Alpha release at this time with intention to publish a production release in April 2021. This document covers the background to the collaboration between SNOMED International and INSERM, and goes on to cover the consequent release artefacts. It is not a detailed technical document of SNOMED CT or Orphanet. Nor does it seek to provide an editorial policy for this content .

This ALPHA release package is distributed for evaluation purposes only.  It must not be used in production clinical systems or in clinical settings, or distributed to Affiliate Licensees or any third parties.   

Audience for this document

This document should be read by all those (SNOMED International National Release Centers, vendors of electronic health records, terminology developers, Researchers, Genomics experts etc) with an interest in the usage of this content in SNOMED CT and its linkage with Orphanet for Rare Disease content.

Background

SNOMED International (then IHTSDO) and INSERM first started exploring opportunities for linking SNOMED CT and Orphanet Rare Disease in 2012 because of the drivers to link between clinical data using SNOMED CT and the mandated use of Orphanet for rare disease research purposes in Europe and other countries outside Europe. As a consequence, an Agreement was signed in 2014 and a set of Rare Diseases in Orphanet was agreed as a priority for linking. Since then, the two organisations have worked closely as follows to:

1. Undertake a gap analysis for the defined set
2. Develop definitions for the Rare Diseases based on expert input through the INSERM community
3. Create new content in SNOMED CT
4. Create a map between existing and new content in SNOMED CT and Orphanet
5. Ensure content throughout the period is in line with changes in Orphanet.

Approximately 3500 new Rare Disease concepts have been added to SNOMED CT as part of this collaboration and the map contains 5,721 SNOMED CT and Orphanet concepts/terms.

In parallel to the content development and mapping work, the operational aspects have been worked on to agree activities and processes to enable the Map to move in to Production in April 2021 and from there to be maintained and updated according to changes within the 2 terminologies. As a consequence, an updated Agreement was signed in March 2020 signalling both organisations commitment to maintaining and updating the content and map.

At this time, SNOMED International and INSERM are seeking feedback on the Alpha version of the Map. The Review period ends on 31 November 2020, after which work will be undertaken to update the content of the Map in line with January 2021 SNOMED CT International Release and Orphanet July 2020 coding release. A report of the feedback will be made available. Please note that the Map will NOT be extended beyond current scope for the Production release. The Production release will be April 2021.

Scope and Purpose of the collaborative work going forward. 

The scope of the SNOMED International and INSERM work has been outlined above, and the 2 organisations has formalised the next steps as part of a new Collaboration agreement which ensures that the Map is updated, after feedback from the Alpha release, to form the Production release in April 2021. 

Under the terms of the Collaboration agreement between SNOMED International and INSERM, the Map will be issued annually by both SNOMED International in RF2 format and INSERM in spreadsheet format. Documented quality assurance processes will ensure both formats are the same and supporting materials are produced jointly. In addition, criteria for extending the Map will be agreed and managed through agreed processes to ensure that the products meet the needs of the different stakeholder groups based on Use Cases.

Design

Decisions concerning source concepts, target concepts and validity of equivalencies were made by consensus of both parties

4.1 Versions

The version of Orphanet used is January 2020.  

The version of SNOMED CT used is the January 2020 International Release.

Source

The source data is a subset of 5721 Orphanet concepts.

4.3 Target

All target concepts are drawn from SNOMED CT Clinical Findings and Situation. As part of the work, new concepts were identified as relevant and needed within SNOMED CT. These were modeled as Clinical Findings. PLEASE CONFIRM THIS

4.4 Direction

The direction is from SNOMED CT International Release to the Orphanet classification in line with the stated use case in section 3.

4.5 Cardinality

The cardinality for all equivalencies in the table is one-to-one.

5 Content

The SNOMED CT to Orphanet Map covers just one semantic type – Rare Diseases (clinical findings) – with equivalent SNOMED CT and Oprhanet content for each. The table comprises 5721 concepts for each, representing a subset of Orphanet and a subset of SNOMED CT – equivalencies have not been identified other Orphanet content- (DMO -what does this last statement mean?)

6 Obtaining the Alpha release

Access within IHTSDO member countries is provided by the Member National Release Centre in each country, via the relevant Member page. Affiliates of IHTSDO in non-member countries can access the table through their Member Licensing and Distribution Service (MLDS) account. Please contact info@snomed.org for more information if required. 

The Map in spreadsheet form is available for download from the Orphanet website: 
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Users of the table should comply with licensing arrangements for both Orphanet and SNOMED CT.

7 Feedback

Feedback should be sent jointly to info@snomed.org and INSERT INSERM DETAILS. Feedback should include any issues relating to implementation, suggestions for future content inclusion or general comments regarding the set.

8 Technical Notes

RF2 package format

The RF2 package convention dictates that it contains all relevant files, regardless of whether or not there is content to be included in each particular release.  Therefore, the package contains a mixture of files which contain both header rows and content data, and also files that are intentionally left blank (including only a header record).  The reason that these files are not removed from the package is to draw a clear distinction between:

1. ...files that have been deprecated (and therefore removed from the package completely), due to the content no longer being relevant to RF2 in this or future releases, and 
2. ...files that just happen to contain no data in this particular release (and are therefore included in the package but left blank, with only a header record), but are still relevant to RF2, and could therefore potentially contain data in future releases.

This allows users to easily distinguish between files that have purposefully been removed or not, as otherwise if files in option 2 above were left out of the package it could be interpreted as an error, rather than an intentional lack of content in that release.