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4. Alignements with other terminologies

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Seed-Orphanet edited this page Aug 7, 2026 · 1 revision

The Orphanet nomenclature is aligned with other international terminologies and reference databases (including ICD-10, ICD-11, SNOMED-CT, OMIM, UMLS, MeSH, MedDRA, GARD and MONDO) in order to enable interoperability between different Health Information Systems (HIS).

Coverage percentages alignements table ORPHAcodes and others terminologies

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Orphanet produces the Orphanet nomenclature (ORPHAcodes), a domain-specific medical terminology dedicated to rare diseases. As ORPHAcodes are progressively introduced into European rare disease registries and information systems, aligning them with other terminologies becomes essential to ensure interoperability. This alignment supports consistent coding of rare diseases across systems, helps identify rare disease patients, and improves epidemiological surveillance through better data retrieval and analysis. Orphanet uses a defined annotation system to characterise the nature of the correspondence between an ORPHAcode and the terminologies with which it is aligned:

Proximity relationships:

  • Exact: The Orphanet entity designated by an ORPHAcode and the target terminology code have the same range of application and describe the same pathological entity (the concepts are equivalent).
  • BTNT (broader term to narrower term): the ORPHAcode covers a wider concept than the target code, meaning the target code represents only part of what the ORPHAcode describes.
  • NTBT (narrower term to broader term): the ORPHAcode covers a more specific concept than the target code, meaning the target code represents a broader category than the ORPHAcode.

Specificity relationships (applicable only to mappings with WHO terminologies):

  • Specific code: the ORPHAcode corresponds specifically to an ICD-10/ICD-11 main term and has its own code in these classifications.
  • Inclusion term (ICD-10 only): The Orphanet entity corresponds to an ICD-10 term that has no standalone code and is displayed as an included term beneath the code and main term of an ICD-10 category.
  • Index term: The Orphanet entity is matched by an ICD-10/ICD-11 term without its own code, appearing either in the ICD-10 alphabetical index or in the ICD-11 foundation with a specific URI.
  • Attributed code: the ORPHAcode has no matching term in ICD-10/ICD-11, and the assigned ICD code corresponds to the closest entity according to Orphanet rules.

International Classification of Diseases (ICD), WHO

Healthcare Information Systems worldwide predominantly use the ICD terminology, produced by the World Health Organization (WHO), for coding purposes.

Specifically, ICD-10 and ICD-11 mappings are managed by a dedicated information scientist in the Orphanet Coordinating team at INSERM, US-14 (Paris, France), under the supervision of the Orphanet Scientific Director.

  1. When a double validation is performed, a mention “Validated” is attributed to the specific mapping (not visible on the website page but available on OrphaData).
  2. On the other hand, the mention “Not yet validated” means that the coding is provisional and has been checked by only one medical expert within Orphanet.

In both cases, if a misalignment is detected, you can contact us here. The project manager will analyse your request and if needed, perform the modification.

ICD-10

Rare diseases of the Orphanet nomenclature have been aligned to, or attributed, a code from the World Heath Organization’s International Classification of Diseases, 10th edition (ICD-10).

ICD-10 examples

  1. Paroxysmal nocturnal hemoglobinuria, ORPHA:447 aligned to D59.5, Relation: Exact specific code Orpha entity is displayed in ICD-10 terminology. Exactly the same concept.
  2. Farber disease, ORPHA:333 aligned to E75.2, Relation: NTBT inclusion term Orpha entity is displayed in the tabulated list under a code corresponding to a broader concept.
  3. Cystic fibrosis, ORPHA:586 aligned to E84.0-E84.1-E84.8, Relation: BTNT specific code Orpha entity is broader than the ICD-10 entity but they represent the same concept.
  4. Canavan disease, ORPHA:141 aligned to E75.2, Relation: NTBT index term Orpha entity is display in the alphabetical index (i.e. ICD-10 search toolbar).
  5. Sialidosis type 1, ORPHA:812 aligned to E77.1, Relation: NTBT attributed Orpha entity does not exist in ICD-10, Orphanet attribute a code corresponding to the closest entity.

How to establish the aligment between ORPHAcodes and ICD-10-CM instead of ICD-10?

ICD-10-Clinical Modification (ICD-10-CM) codes are more granular than ICD-10 and can provide more information about patient care (outpatient care, expanded injury codes, combination codes for diagnosis/symptoms, etc). This classification has been authorised but is country-dependent and not produced by WHO. Orphanet, as an international classification for rare diseases, aligns ORPHAcodes only with other international medical classification codes. We understand that countries needed to update ICD-10 over time while waiting for ICD-11 release, but it is technically impossible to align ORPHAcodes with all the country-specific ICD-10 systems that have been created. Our general advice is to use the ICD-10 source alignment provided by Orphanet to help you to find the right group and refine it step by step.

Where can I find ORPHAcodes-ICD-10 mappings?

If you are looking for a particular disease, you can search for it on the Orphanet website where related codes in other terminologies, including ICD-10, are displayed on every disease page. If you want to know more about the semantic relationships between ORPHAcodes and ICD-10 codes, you should either:

Why the ICD-10 code used by the clinician is not the same that Orphanet has mapped to?

Orphanet tries to align ORPHAcodes to their best corresponding ICD-10 code, taking into consideration the main manifestations of a rare disease. However, every patient can show a different set of manifestations within a disease and an ICD-10 code is assigned to a patient also depending on the reason why the patient is visiting the hospital in the first place (therefore not necessarily corresponding to the patient’s main rare disease diagnosis). This is why, the ICD-10 code assigned to a patient in a specific context might not exactly correspond to the one reported in Orphanet.

ICD-11

ICD-11 coding rules apply to all Orphanet clinical entities and specifically aim to cover the totality of entities at the "Disorder" classification level, which is the first level recommended to be used as the confirmed clinical diagnosis and the aggregation level for statistical reporting. Orphanet has defined specific guidelines for ICD-11 mapping:

  • Subtypes of disorders are aligned with an ICD-11 code when an exact match exists, otherwise they inherit the ICD-11 code attributed to the disorder.
  • Groups of disorders are only aligned with an ICD-11 code when an exact match exists.

The Orphanet entities are preferably aligned with four-character ICD-11 codes which correspond to the WHO-recommended level that should be used as the definitive clinical diagnosis and for statistical reporting. Orphanet is not able to provide coding recommendations for ICD terminologies but only for the use of ORPHAcodes. Please consult the following links for further information: https://icd.who.int/en/docs/ICD-11%20Implementation%20or%20Transition%20Guide_v105.pdf and https://icdcdn.who.int/icd11referenceguide/en/html/index.html

Up to date [September 2023], Orphanet aligned about 5400 ORPHAcodes with ICD-11 corresponding to 62% of Orphanet clinical entities at the disorder and 66% at subtype levels. About the representation of rare diseases and specifically the Orphanet disorder level in ICD-11: less than 1000 ORPHAcodes have been identified in the MMS and fewer than 4000 ORPHAcodes in the Foundation.

The RD domain is in constant evolution and new RD are discovered and characterised every month. This evolution of knowledge is carefully and continuously monitored by Orphanet. Moreover, Orphanet also collects all RD coding needs coming from RD experts and patients/caregivers. Orphanet then updates the Nomenclature of RD not only following this evolution of knowledge in the research and clinical literature, but also by consulting experts of the domain. Rare disease inclusion and modification in the Orphanet Nomenclature is evaluated by Orphanet according to standardised procedures, working with international rare disease expert networks. In this sense, ICD-11 is not indended to replace ORPHAcodes, as it does not provide the expert curation to include newly described rare disease.

ICD-11 examples

  1. Alexander disease (ORPHAcode:58) aligned to 8A44.2 in the MMS and 2023359698 in the foundation, Relation: Exact specific code -> Orphanet entity is displayed in the ICD-11 MMS terminology. Exactly the same concept.

  2. Rheumatic fever (ORPHAcode:3099) aligned to 1B40-1B41 in the MMS and 2058300982-535094176 respectively in the foundation, Relation: BTNT specific code -> Orphanet entity is broader (=BTNT) than the ICD-11 MMS entity but they include the same concept (=specific code).

  3. Systemic monochloroacetate poisoning (ORPHAcode:90069) aligned to NE61 in the MMS, Relation: NTBT attributed
    -> Orphanet entity is included in a broader entity (=NTBT) in the MMS and does not exist in the ICD-11 foundation. Orphanet has attributed an ICD-11 code to the closest concept.

  4. Kennedy disease (ORPHAcode:481) aligned to 8B61.4 in the MMS and 1604214898 in the foundation, Relation: NTBT index term -> Orphanet entity is included in a broader entity (=NTBT) in the MMS but displayed in the alphabetical index (i.e. ICD-11 MMS search toolbar) meaning that the entity exists in the foundation with a specific URI (=index term).

ICD-O-3

ICD-O is a multi-axial classification system for the site, morphology, behaviour, and grading of neoplasms. It is principally used in tumor and cancer registries to code the site (topography) and histology (morphology) of neoplasms, usually based on pathology reports.

  • The topography axis is based on the ICD-10 classification of malignant neoplasms.
  • The morphology axis provides five-digit codes ranging from M-8000/0 to M-9989/3. The first four digits identify the specific histological term. The fifth digit, following the slash (/), is the behaviour code and indicates whether a tumor is malignant, benign, in situ, or of uncertain behaviour.

Recently, the mapping of Orphanet rare cancers to ICD-O-3 has been initiated. The current first phase is limited to exact matches and only involves the first four digits defining the histological term. The fifth digit (behaviour code) is not included at this stage. The mapping rules and procedure for ICD-O-3 will be updated once the process has been validated.

SNOMED CT

SNOMED CT, as for “Systematized Nomenclature of Medecine Clinical Terms”, is a comprehensive, multilingual clinical healthcare terminology that enables the representation of clinical content in electronic health records and is currently used in more than eighty countries.

Orphanet, in collaboration with SNOMED CT, publishes every year in October a mapping files on Orphadata, following an in depth validation process of all alignments between ORPHAcodes and SNOMED IDs. All these alignments concern only exact match. In other words, one ORPHAcode is aligned to one SNOMED ID only if both concepts represent exactly the same entity with the same perimeter. If not, each nomenclature team will review this entity according to their own procedures and decide if this mapping is kept or excluded.

  • SNOMED CT is not a terminology dedicated to code rare diseases and it does not include any mention to specify if a given disease is rare or not.
  • Rare diseases included in SNOMED CT do not have a dedicated classification of rare diseases for data aggregation but are mixed together with non-rare diseases. Therefore, using only SNOMED CT to code rare patients will not allow to retrieve any specific rare disease data nor to make any specific statistical analysis on rare diseases.
  • Interoperability with other systems that does not use SNOMED CT and registers of rare diseases (using ORPHAcodes) is not granted just by using SNOMED CT codification.

About the collaboration process:

  1. ORPHANET is the only existing medical terminology dedicated to Rare Diseases. Orphanet produces the Nomenclature of rare diseases following the evolution of knowledge in the research and clinical literature and by consulting experts of the domain. Rare disease inclusion and modification in the Orphanet Nomenclature is evaluated by Orphanet according to standardized procedures, working with international rare disease expert networks.

  2. The information produced by Orphanet is transmitted to SNOMED CT as part of an ongoing collaboration. This proposed updated information is then evaluated directly by SNOMED CT according to their internal rules for inclusion. Because of the different inclusion criteria, a 100% equivalence between the two nomenclatures is not possible to achieve. Therefore, despite the high level of alignment between both terminologies that consents an optimal level of interoperability, the entirety of rare disease is not represented in SNOMED CT. Therefore, by definition, there is always a delay between the creation of a new ORPHAcode and the mapping with a SNOMED ID due to a reviewing process and the production of a definition (that is necessary to create/align a SNOMED ID).

  3. This collaborative process focuses on aligning entities at the disorder level. Currently, there are no plans to align entities at the subtype or group level, as SNOMED CT does not create entities corresponding to these levels in Orphanet. Subtypes and groups in the Orphanet nomenclature that are aligned with SNOMED CT reflect entities that already existed in SNOMED CT prior to alignment.

Where to find the SNOMED CT mapping?

The SNOMED CT mappings are available on the ORPHAcodes website (scroll down) where you can find the most recent map release regrouping the XLSX ORPHA-SNOMEDCT_Mapping_File_production and the release notes co-produced by Orphanet and SNOMED CT. _Mapping files are usually released in October every year, and they are based on the July Nomenclature release of the same year. For the moment, we don't propose an API due to a licensing agreement signed with SNOMED International. Indeed, SNOMED offer a paid service and we are only authorized to release a human-readable Excel file.

UMLS

  • The UMLS, or Unified Medical Language System is a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems.

  • ORPHAcodes are aligned with UMLS terminology with an exact relationship. Orphanet started a close collaboration with UMLS to update and increase the number of alignments by the end of 2023.

Is it possible to convert OMIM and HPO directly to ORPHAcode?

  • Orphanet database of RD is annotated with the Human Phenotype Ontology (HPO) terms, a standardized and controlled terminology covering phenotypic abnormalities in human diseases. The description of RD by HPO terms can be found on Orphanet and Orphadata.

  • The mapping between Online Mendelian Inheritance in Man (OMIM) and Orphanet is not fully possible. Indeed, alignment is qualified following 3 different relationships: exact, NTBT (narrower term to broader term) or BTNT (broader term to narrower term). The direct conversion is only possible for the exact mapping. On the Orphanet website, you can use the search tool using an OMIM number. The output will give you all the ORPHAcodes linked to this OMIM number.

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