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) Is there a meaning for the amounts of digits in an ORPHAcode?
Clinically speaking NOT AT ALL. 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) It seems to be several ORPHAcodes for the same disease, why that?
No, ORPHAcodes are unique, and a disorder (or a subtype) are attributed a single and unique ORPHAcode. However, some disorders have several variants or subtypes which names are very similar, giving the impression that multiple codes exist for the same disorder (example: Charco-Marie Tooth subtypes). What can help you deciding which ORPHAcode to use is to navigate the classifications or to visualize the ontology, in which you will have the definition, the links to genes, and other complementary information of help (see: How can I visualize the Orphanet nomenclature and classifications? above). You will then decide whch level in the classification (group, disorder, subtype) better suits your coding situation.
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 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.
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 diseases, you can find the corresponding ICD-10 mapping at the dedicated page in Orphanet: you search for the disease you are interested in, you open its page and you will find the corresponding codes in other terminologies, including ICD-10. However, you won’t know how exact this mapping it is. To retrieve the integrality of ORPHAcodes-ICD-10 mappings, and the relationship between each other term, you can download the “Cross-referencing of rare disease” file in Orphadata. This file is updated the 1st day of the month.
You can also have the annual release of the nomenclature for coding in Health Information Systems including those mappings and the information of the relationship between terms at Orphanet nomenclature files for coding.
Finally, you can use the API.
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?
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 changes in a computable format at the Orphanet GitHub for the monthly releases: Diff files can be found at the History tab for each file (beware, files can be heavy).
You can also use the RD-CODE GitHub (for the annual releases for codification in Health Information Systems). 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 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.
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) Can I visualise the classifications in the the xml files?
Yes, you have to use dedicated tool such as UltraEdit to open XML files, or notepad++. Dedicated XML tools are also useful (Altova, XML explorer, XML tree editor…). Some XML tools could be used as well to perform XPath queries directly on the file.
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.