Genes associated with rare diseases

Table with ORPHAcode of the disease linked to the associated genes, with a characterisation of the relationship between gene and disease (causative, modifier, susceptibility, or playing a role in the phenotype) and the kind of mutation germline or somatic. In addition, the table includes the name of the gene in English, its ORPHAcode, chromosomal location, symbol and synonyms and cross-referenced with UniProtKB, HGNC, OMIM, Genatlas, ensembl, Reactome and IUPHAR-DB.
Here are XSD (XML Schema Definitions) and JPG representations for this product.

If you need a generation using the old format, do not hesitate to contact us by email
data.orphanet@inserm.fr


Changes during the past month are only available for the english version
in a HTML version or in a Git diff version, and some extensions for browsers (if locally installed) let you to display XML by opening the file in a new tab/window.
We would advise Pretty XML or XML Viewer Plus for Firefox or Google Chrome

Please consult the Orphadata Github  for previous versions (since April 2020)
Historical versions (before April 2020) are available on request (please use contact form)


Here is a PDF file describing Orphanet free access products.

Video tutorials

What is the Orphanet nomenclature of rare disorders?

Frequently Asked Questions

Free access products description

Orphanet procedures

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Orphanet nomenclature and classification of rare diseases

Orphanet Advisory Board on Genetics Rules of procedures

Orphanet inventory of genes related to rare diseases

Orphanet Standard Operating Procedures

Phenotypes associated with rare disorders

Table with diseases listed in Orphanet annotated with HPO phenotypes.
The alignment is characterised by frequency (obligatory, 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 source, the date and the validation status of the association between the rare disease and HPO terms are also indicated.
Here are XSD (XML Schema Definitions) and JPEG representations for this product that contains rare disorders listed in Orphanet annotated with HPO phenotypes, and which embeds the status of validation of the association.

If you need a generation using the old format, do not hesitate to contact us by email
data.orphanet@inserm.fr


Changes during the past month are only available for the english version
in a HTML version or in a Git diff version, and some extensions for browsers (if locally installed) let you to display XML by opening the file in a new tab/window.
We would advise Pretty XML or XML Viewer Plus for Firefox or Google Chrome

Please consult the Orphadata Github  for previous versions (since April 2020)
Historical versions (before April 2020) are available on request (please use contact form)


Here is a PDF file describing Orphanet free access products.

Rare diseases and functional consequences

Table with diseases listed in Orphanet annotated with functional consequences or environmental factors leading to limitation of activity or restriction of participation.
Here are xsd (XML Schema Definitions) and JPEG representations for this product.

Changes during the past month are only available for the english version
in a HTML version or in a Git diff version, and some extensions for browsers (if locally installed) let you to display XML by opening the file in a new tab/window.
We would advise Pretty XML or XML Viewer Plus for Firefox or Google Chrome

Please consult the Orphadata Github  for previous versions (since April 2020)
Historical versions (before April 2020) are available on request (please use contact form)


Here is a PDF file describing Orphanet free access products.

Orphanet Rare
Disease Ontology

The Orphanet Rare Disease ontology (ORDO) was jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epidemiological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Genatlas) or classifications (ICD-10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated every six months and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).

A document describing ORDO is available for consultation.
These products have been recognised as an Elixir Core Data Resource  

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HPO - ORDO Ontological Module

Orphanet provides phenotypic annotations of the rare diseases in the Orphanet nomenclature using the Human Phenotype Ontology (HPO). HOOM is a module that qualifies the annotation between a clinical entity and phenotypic abnormalities according to a frequency and by integrating the notion of diagnostic criterion. In ORDO a clinical entity is either a group of rare disorders, a rare disorder or a subtype of disorder. The "Clinical Entity" branch of ORDO has been refactored as a logical import of HPO, and the HPO-ORDO phenotype disease-annotations have been provided in a series of triples in OBAN format in which associations, frequency and provenance are modeled. HOOM is provided as an OWL (Ontologies Web Languages) file, using OBAN, the Orphanet Rare Disease Ontology (ORDO), and HPO ontological models. HOOM provides extra possibilities for researchers, pharmaceutical companies and others wishing to co-analyse rare and common disease phenotype associations, or re-use the integrated ontologies in genomic variants repositories or match-making tools.

A document describing HOOM is available for consultation.
These products have been recognised as an Elixir Core Data Resource  

HPO & ORDO Ontological Module (HOOM) versions

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