Introduction Tools Helpdesk FAQ

The Orphanet nomenclature of rare diseases is a unique and multilingual standardised system aimed at providing a specific terminology for rare diseases. Each clinical entity is assigned a unique and time-stable ORPHAcode, that provides a common language across healthcare and research systems for effective monitoring and reporting on rare diseases.

The tools available below, provide the computable information necessary to achieve implementation of ORPHAcodes in Health Information Systems, and ensure easier and accurate coding.

The Nomenclature Pack ——————————– The Orphanet API ————- The Orphanet Data Visualisation Tool

The files (Orphanet Nomenclature Pack) are designed for codification needs and they are delivered annually (July), a descriptive documentation is also available.

Orphanet also makes available an API (Application Program Interface), in order to facilitate the interrogation of the nomenclature, and a Datavisualisation Tool, in order to provide a human-readable version of the nomenclature files.

The Orphanet nomenclacture pack
In order to allow the implementation of the Orphanet nomenclature in Health Information Systems, Orphanet provides a set of files that includes:
Orphanet nomenclature file (XML file)
Orphanet to ICD-10 mapping file (XML file)
a directory containing the Orphanet classification files  by medical specialties (XML files)
Linearisation file (XML file) attributes one preferential medical specialty to each clinical entity
Master file (Excel file) provides the minimal set of ORPHAcodes, aligned with ICD-10 codes, that should be used for data sharing and statistical purposes at EU-level.
ORPHAnomenclature differential file (Excel file) provides the key changes made to the nomenclature compared to the previous version
Description of the Orphanet nomenclature file for coding (PDF file) describes in details the xml files enclosed in the Orphanet nomenclature pack for coding
Xml files are updated once a year, in 9 different languages: Czech, Dutch, English, French, German, Italian, Polish, Portuguese and Spanish.
Excel and PDF files are available in English only and are common to all Orphanet nomenclature packs.
Download ORPHAnomenclature pack
N.B. The previous versions as well as the related change logs remain accessible and downloadable in this GitHub.
An API (Application Program Interface) facilitates the implementation of the Orphanet nomenclature in Health Information Systems, and enables customised queries for specific use cases.
Access the API
Orphanet Datavisualisation tool
This tool provides a human-readable view of the Orphanet nomenclature pack data and is based on API implementation.
It allows to search for rare diseases, to display the related dataset and to browse through the Orphanet classification branches.
Access the Orphanet Datavisualisation tool
Find out more info about the tool here.

If you have any questions about tools, you can post an issue on our Github Tracker issue.

Recommandations for implementation:

The RD-CODE project has revised the documents below:

  • The document « Specification and implementation manual of the Master file for statistical reporting with ORPHAcodes » has been updated in December 2021 together with the July 2021 release of the Master-file.
  • Also the document the document Standard Procedure and guide for coding with ORPHAcodes has been updated in December 2021.
  • Moreover,to tackle the issue of coding undiagnosed patients’ a collection of existing experiences of coding of undiagnosed or suspected RD patients has been produced, a guidelines proposal has been issued as well as a consensus document on codification of suspected/undiagnosed rare diseases in December 2020, an updated version of this document has been released on the 20/12/ 2021 and it is available here. Those 3 years working together on the best way to give visibility to undiagnosed rare disease patients in health information systems were as interesting as fruitful, and led to the creation of a new ORPHAcode (ORPHA:616874 Rare disorder without a determined diagnosis after full investigation). This code is already visible on the Orphanet website and will be distributed in the Nomenclature Pack of July 2022.

    Background for information only:

    The RD-ACTION Joint Action (2015-2018) codification workpackage published a series of documents to improve the collection of information on rare diseases, and to share standardised and consistent information at European level. These will be expanded by the RD-CODE Workpackage 5 according to real-life codification experiences reported by RD-CODE Workpackage 4 implementing countries.

    According to these recommendations, a reduced list of ORPHAcodes, identified as the ones that allow a definitive diagnosis (disorder level of the Orphanet nomenclature), constitutes the minimal information to allow data sharing and statistical reporting at EU-level.

    This reduced list of ORPHAcodes is provided together with their mappings with ICD-10 codes in the master file, that is included in the Orphanet nomenclature pack. It is also used as the aggregation level for data sharing in Health Information System using the whole list of ORPHAcodes

    Find out more info about the Aggregation level

    Find out more info about the Master file