FAQ

Here is the list of the most frequently asked questions sent to the Orphanet team. This list will be updated regularly, please take the time to consult it before sending us requests via the helpdesk.

1) What is the correct way to display ORPHAcodes?

ORPHAcodes should be written: ORPHA:XXX

Example: ORPHA:355 Gaucher disease.

2) What does the format of the ORPHAcode mean?

The format of the ORPHAcode has no clinical meaning. The ORPHAcode is a random and never re-used number automatically assigned by the Database to every newly created entity. Shorter digits ORPHAcodes were created earlier in the lifespan of the Database and longer digits ORPHAcodes correspond to more recent creations.

3) I retrieve several ORPHAcodes for the same disease, why that?

ORPHAcodes are unique, and every clinical entity is attributed a single and unique ORPHAcode. However, some names looks like very similar, as they are variants or subtypes, and may make it seem like multiple codes exist for the same disorder (example: Charco-Marie Tooth subtypes). In order to identify the ORPHAcode that better suits your coding situation, you can refer to the classification level (i.e. Group of disorders, disorder or subtypes of disorder) and/or read the ORPHAcode’s definition and/or browse the Orphanet classification. The Orphanet website and the Orphanet datavisualisation tool could help you in this process.

4) Why can’t I find an ORPHAcode anymore?

The Orphanet nomenclature of Rare Diseases evolves continuously according to knowledge development. Three situations can explain the removal of an ORPHAcode from the Orphanet nomenclature:

  • The disease is no longer rare in Europe; (In the EU, a rare disease, is one that affects no more than 1 person in 2,000).

  • Two diseases initially separately described are now recognized as a unique entity. One of the ORPHAcode is deprecated, the second is kept in the nomenclature. Orphanet stores this relationship for a better traceability;

  • The entity has been obsoleted for upkeep purposes (duplicates or categories that are not used anymore to organize the Orphanet classifications). Whenever possible, Orphanet suggests an ORPHAcode in use in replacement.

In any case, the inactive ORPHAcodes are still available in the Orphanet nomenclature files along with the ORPHAcode suggested in replacement (when available).

5) What is the difference between obsoleted and deprecated entities?

  • The ORPHAcode is deprecated when the phenotype was initially considered as an independant diagnosis, but it now considered as part of another diagnosis as a result of the evolution knowledge. The deprecated ORPHAcode is removed from the Orphanet nomenclature of Rare Diseases. However, it is kept in the Orphanet nomenclature files along with the ORPHAcode to be used in replacement (« moved to » relationship).

  • Example: ORPHA:98836 Bilineal acute leukemia, initially recognized as a unique and separate entity, is now part of ORPHA:530995 Mixed phenotype acute leukemia according to the 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia.

  • The ORPHAcode is obsoleted for upkeep purposes encompassing exact duplicate of another existing clinical entity, unclear entity that connot be precisely characterised, only one published case in the litterature, or organisational category that is no longer in use. In case of duplication, a relationship is provided between the obsoleted ORPHAcode and the ORPHAcode retained in the Orphanet nomenclature (“referred to” relationship). Otherwise, a relationship between the obsoleted ORPHAcode and an active ORPHAcode is suggested only if relevant.

  • Example: ORPHA:480773 Fibular aplasia-tibial campomelia-oligosyndactyly syndrome is obsoleted because it duplicates ORPHA:2492 FATCO syndrome, that is the ORPHAcode of replacement.

In any case, it belongs to the user to make sure that the ORPHAcode of replacement is adapted to setting.

6) Where can I access the Orphanet nomenclature?

The Orphanet nomenclature files can be downloaded from the Orphadata website. Links to access directly are also provided on the RD-CODE GitHub. Additional customised queries can be designed using the API.

7) 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 download the Orphanet nomenclature files for coding, use the API, or browse the Orphanet datavisualisation tool.

8) How often is the Orphanet nomenclature of Rare Diseases updated?

The Orphanet nomenclature of Rare Diseases is updated on a daily basis. However, to ensure continuity in the coding process of RD, the Orphanet nomenclature files for coding are delivered on an annual basis, in July. The previous versions stay available on the RD-CODE GitHub project as well as the change logs.

9)Why the Nomenclature Pack is updated annually and in July?

The Nomenclature pack is updated once a year, to ensure stability and continuity of coding, as well as to facilitate updating in the health systems through versioning. July was chosen to allow users to manage this versioning before the actual implementation which often takes place at the end of the year.

This decision was taken during the RD-ACTION project, by a working group that has produced Guidelines for coding with ORPHAcodes (lead by the 3 stakeholders from the countries where ORPHAcodes are implemented: DIMDI now Bfarm in Germany, APHP In Paris and Veneto Region in Italy). It was a consensus decision that accommodates most of national situations involved in the discussions. These guidelines are being updated by the same working group in the new RD-CODE project, DO NOT HESITATE TO SHARE YOUR FEEDBACK with them.

10) How can I get the changes made in the nomenclature at once (i.e. the list of inactive – deprecated, obsolete- codes)?

You can access the list of annual changes in a computable format at the RD-CODE GitHub. The file is called “ChangeLogs”.

For IT: By using git command line (or apps) users could retrieve any changes between versions. The Orphanet team is working at releasing lighter files on new created entities and inactivated ones.

11) What is the difference between the Orphanet nomenclature files and ORDO?

The Orphanet nomenclature xml files have been specifically set up for coding purposes. The content is focused on the Orphanet nomenclature of Rare diseases, the Orphanet classifications and the cross-referencing to ICD-10. Information to allow data sharing and statistical analysis at EU-level is specifically provided.

The Orphanet Rare Disease ontology (ORDO) is a semantic representation of the scientific information produced by Orphanet encompassing the Orphanet Nomenclature of Rare diseases and its relationships with genes, epidemiological data, and connections with other medical terminologies (ICD10, MeSH, UMLS, MedDRA) or databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, GARD) or classifications (ICD-10). It is a useful resource for the computational analysis in the research and development area. Information to allow data sharing and statistical analysis at EU-level is absent from ORDO a it is not primary intended for coding.

12) Where can I find tutorials on using the nomenclature?

We are developing tutorials for helping using our tools. You can find them at Orphanet Tutorials YouTube channel in English and in French. The collection is progressively growing.

13) How can I browse the Orphanet classifications?

The new Orphanet datavisualisation tool is a very good tool to visualise and browse Orphanet classification.

14) What is the Aggregation level?

A subset of ORPHAcodes is recommended to be used for data sharing and statistical analysis at EU-level. This subset, based on the disorder level excluding groups and subtypes, establishes the “Aggregation level”. For every disorder or subtype of the Orphanet nomenclature, the aggregation level is provided in the Orphanet nomenclature file. For more details, see here.

If you have other questions, you can post an issue on our Github Tracker issue.