Orphanet Rare Disease Ontology (ORDO)

The Orphanet Rare Disease Ontology (ORDO) is an open-access ontology developed from the Orphanet information system, enabling complex queries of a rare disorder and its epidemiological data (age of onset, prevalence, mode of inheritance) and gene-disorder functional relationships.

Within RD-Connect, the ORDO is recommended as the primary “disease nomenclature” ontology – i.e. to enable the precise “naming” of a specific rare disease. It consists of 11,699 classes and 76,554 annotation assertion axioms. Each concept from the Orphanet database forms a distinct OWL (Web Ontology Language) class and is associated with other classes using a set of defined object properties. ORDO also represents the relationship between the disorders and their genetic cause (if known), the mode of inheritance and associated epidemiological data (age of onset, age of death, prevalence).

An Evidence Code Ontology (ECO) is used to encode the provenance of assertions made in the ORDO. The ORDO also provides disease cross references to the International Classification of Diseases (10th version), SNOMEDCT (SNOMED Clinical Terms), MeSH (Medical Subject Headings), MedDRA (Medical Dictionary for Regulatory Activities), OMIM (Online Mendelian Inheritance in Man) and UMLS (Unified Medical Language System) and genes are cross-referenced to HGNC (HUGO Gene Nomenclature Committee) UniProt (Universal Protein Resource) OMIM (Online Mendelian Inheritance in Man), Ensembl, Reactome and Genatlas.

Efforts are also underway to integrate ORDO with the Human Phenotype Ontology (HPO) annotating Orphanet’s phenome types with appropriate HPO terms. This will provide interoperability between projects such as RD-Connect and Decipher which use the HPO and will drive the revision of the phenome hierarchy once HPO terms have been integrated.