March-2017 

Phenotypes associated with rare disorders


The Orphanet inventory of rare disorders is now annotated with the Human Phenotype Ontology (HPO) terms, a standardized and controlled terminology covering phenotypic abnormalities in human diseases.

Files available in XML format.

Language links size
English http://www.orphadata.org/data/xml/en_product4_HPO.xml 20.37 MB
English http://www.orphadata.org/data/xml/en_product4_HPO_status.xml 1.19 MB
French http://www.orphadata.org/data/xml/fr_product4_HPO.xml 17.89 MB
French http://www.orphadata.org/data/xml/fr_product4_HPO_status.xml 1.19 MB
Spanish http://www.orphadata.org/data/xml/es_product4_HPO.xml 17.89 MB
Spanish http://www.orphadata.org/data/xml/es_product4_HPO_status.xml 1.19 MB
Italian http://www.orphadata.org/data/xml/it_product4_HPO.xml 17.96 MB
Italian http://www.orphadata.org/data/xml/it_product4_HPO_status.xml 1.19 MB
Portuguese http://www.orphadata.org/data/xml/pt_product4_HPO.xml 17.92 MB
Portuguese http://www.orphadata.org/data/xml/pt_product4_HPO_status.xml 1.19 MB
German http://www.orphadata.org/data/xml/de_product4_HPO.xml 17.85 MB
German http://www.orphadata.org/data/xml/de_product4_HPO_status.xml 1.19 MB
Dutch http://www.orphadata.org/data/xml/nl_product4_HPO.xml 17.90 MB
Dutch http://www.orphadata.org/data/xml/nl_product4_HPO_status.xml 1.19 MB

This new product contains two different files. The first one contains rare disorders listed in Orphanet annotated with HPO phenotypes. The alignment is characterized by frequency (obligate, very frequent, frequent, occasional, very rare or excluded) and whether the annotated HPO term is a major diagnostic criterion or a pathognomonic sign of the rare disease. The second file contains the source, the date and the status of validation of the association between the rare disease and HPO terms.

  • Definitions
    • Frequencies
      • Obligate: the phenotype is always present and the diagnosis could not be achieved in its absence;
      • Very frequent: the phenotype is present in 80 to 99% of the patient population ;
      • Frequent: the phenotype is present in 30 to 79% of the patient population ;
      • Occasional: the phenotype is present in 5 to 29% of the patient population ;
      • Very rare: the phenotype is present in 1 to 4% of the patient population ;
      • Excluded: the phenotype is always absent AND is an exclusion criteria for diagnosing the disorder.
    • Diagnostic criterion:
      • A diagnostic criterion is a phenotypic abnormality used consensually to assess the diagnosis of a disorder. Multiple sets of diagnostic criteria are necessary to achieve the diagnosis. Orphanet indicates only diagnostic criteria that are consensually accepted by the experts of the medical domain AND published in medical literature. Depending of the medical consensus, they could be further qualified as minor, major, etc... This level of precision is yet not informed in the Orphanet dataset.
    • Pathognomonic sign:
      • A pathognomonic phenotype is a feature sufficient by itself to establish definitively and beyond any doubt the diagnosis of the disease concerned (i.e. heliotrope erytheme for dermatomyosistis).

Files are available in 7 different languages (diseases name, frequency, diagnostic criterion and pathognomonic sign are translated): English, French, Italian, Spanish, German, Portuguese and Dutch. If terms are not yet translated from English, they remain in English by default.

The previous version compiling rare diseases annotated with the clinical signs of the "Orphanet thesaurus of clinical signs" is outdated and no longer maintained. However, if you want to access this file, please contact us using the contact form.

For more information, see the user's guide

For more information, go to the presentation "Orphadata : how are the data produced ?"

For other types of products please contact us using the contact form.