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) 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;
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).
3)What is the difference between obsoleted and deprecated entities?
The ORPHAcode is deprecated when it is no longer an independent entity in itself, becomes part of another one as a result of the evolution of knowledge. The deprecated entity 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).
The ORPHAcode is obsoleted for upkeep purposes. Reasons are duplicates or categories that are not used anymore to organize the Orphanet classifications. 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: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.
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.
4) 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.
5) 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.
6) Where can I download the “Master file”?
The “Master file” was an excel file promoted by the RD-Action Joint Action. It included a reduced list of ORPHAcodes and their ICD-10 cross referencing in order to allow data sharing and statistical analysis at EU-level. This list was based on the disorder level of the Orphanet classification, excluding groups and subtypes. Orphanet no longer produces the Master file as a separate table, but instead provides a suite of files that covers the various codification needs, along with the right method to produce easily the master file. These files are available for download in xml format on the Orphadata website. It includes:
the Orphanet nomenclature file;
the Orphanet – ICD-10 mapping file;
a directory containing the Orphanet classifications files.
7) What is the difference between ORDO and the Orphanet nomenclature files?
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 (MeSH, UMLS, MedDRA), 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. ORDO is not primary intended for coding.
The Orphanet nomenclature xml files have been specifically set up for coding purposes. The content is limited to 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. This piece of information is missing in ORDO.
8) 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.