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 SNOMED International. Based on an agreed priority set, new concepts for rare diseases as defined in Orphanet have been added to SNOMED CT.  A map from SNOMED CT to Orphanet has been created.

This document is intended to provide a brief description, background context and explanatory notes on the SNOMED International/INSERM collaborative work and and the resulting SNOMED CT to Orphanet map. The map is being published as an Alpha release at this time with the intention to publish a production release in April 2021.  This document is not intended to provide technical specifications about SNOMED CT or Orphanet.  Editorial guidance for SNOMED CT content can be found in the SNOMED CT Editorial Guide.  Editorial guidance for Orphanet Nomenclature of Rare Diseases can be found in Orphanet

(https://www.orpha.net/consor/cgi-bin/Education_Procedure.php?lng=en)

and Orphadata

(http://www.orphadata.org/cgi-bin/ORPHAnomenclature.html)

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

The audience for this document includes National Release Centers, vendors of electronic health records, terminology developers, researchers, genomics experts and individuals who wish to have an understanding of the content of the SNOMED CT to Orphanet map.

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 priority set of rare diseases was agreed. Since then, the two organisations have worked closely as follows to:

1. Undertake a gap analysis for the defined set.
2. Develop textual 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 throughout the development period that new SNOMED CT content aligns with changes in Orphanet.

Approximately 3500 new rare disease concepts have been added to SNOMED CT as part of this collaboration and the resulting map product 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 will end on 31 November 2020, after which time work will be undertaken to update the content of the Map in line with the 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 its current scope for the Production release. The Production release will be April 2021.

Scope and Purpose of Collaborative Work

The scope of the SNOMED International and INSERM work has been outlined above, and the 2 organisations have 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 product meets the needs of the different stakeholder groups based on use cases.

Design

Map

Decisions about maps between pre-existing content in SNOMED CT and Orphanet, the creation of new content for SNOMED CT and also Orphanet, and the validation of the map between SNOMED CT and Orphanet were made by consensus between both organisations.

Version

The version of Orphanet used is January 2020.  

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

Source for Map

The source data is a subset of 5721 SNOMED CT concepts.

Direction of Map

The direction of the map is from SNOMED CT January 2020 International Release to Orphanet.

Cardinality of Map

The cardinality in the table is one-to-one, one SNOMED CT concept maps to one Orphanet entry.

Obtaining the Alpha release

Access within SNOMED International member countries is provided by the Member National Release Centre in each country, via the relevant Member page. Affiliates of SNOMED International in non-member countries can access the map file 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: www.orphadata.org

If you’re having any problems getting hold of the Orphanet Map Package, please contact info@snomed.org.

Users of the map must comply with licensing arrangements for both SNOMED CT and Orphanet.

Feedback

Feedback should be sent jointly to info@snomed.org and contact.orphanet@inserm.fr.

Feedback should include any issues relating to implementation, suggestions for future content inclusion or general comments regarding the map.

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.