title: LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems.
abstract: Characterizing a rare disease diagnosis for a given patient is often made through expert's networks. It is a complex task that could evolve over time depending on the natural history of the disease and the evolution of the scientific knowledge. Most rare diseases have genetic causes and recent improvements of sequencing techniques contribute to the discovery of many new diseases every year. Diagnosis coding in the rare disease field requires data from multiple knowledge bases to be aggregated in order to offer the clinician a global information space from possible diagnosis to clinical signs (phenotypes) and known genetic mutations (genotype). Nowadays, the major barrier to the coding activity is the lack of consolidation of such information scattered in different thesaurus such as Orphanet, OMIM or HPO. The Linking Open data for Rare Diseases (LORD) web portal we developed stands as the first attempt to fill this gap by offering an integrated view of 8,400 rare diseases linked to more than 14,500 signs and 3,270 genes. The application provides a browsing feature to navigate through the relationships between diseases, signs and genes, and some Application Programming Interfaces to help its integration in health information systems in routine.
authors.affiliation: Banque Nationale de Données Maladies Rares, Hôpital Necker Enfants Malades, APHP, F-75015, Paris, France; INSERM, U1142, LIMICS, F-75006, Paris, France.
authors.forename: Remy
authors.initials: R
authors.lastname: Choquet
authors.affiliation: Banque Nationale de Données Maladies Rares, Hôpital Necker Enfants Malades, APHP, F-75015, Paris, France; INSERM, U1142, LIMICS, F-75006, Paris, France.
authors.forename: Meriem
authors.initials: M
authors.lastname: Maaroufi
authors.affiliation: Banque Nationale de Données Maladies Rares, Hôpital Necker Enfants Malades, APHP, F-75015, Paris, France.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Fonjallaz
authors.affiliation: Banque Nationale de Données Maladies Rares, Hôpital Necker Enfants Malades, APHP, F-75015, Paris, France.
authors.forename: Albane
authors.initials: A
authors.lastname: de Carrara
authors.affiliation: INSERM, U1142, LIMICS, F-75006, Paris, France.
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Vandenbussche
authors.affiliation: INSERM, U1142, LIMICS, F-75006, Paris, France; Service de Médecine Foetale, Hôpital Armand Trousseau, APHP, UPMC, Paris, France.
authors.forename: Ferdinand
authors.initials: F
authors.lastname: Dhombres
authors.affiliation: Banque Nationale de Données Maladies Rares, Hôpital Necker Enfants Malades, APHP, F-75015, Paris, France; Montpellier1 University, EA2415 & BESPIM, University Hospital, Nîmes, France.
authors.forename: Paul
authors.initials: P
authors.lastname: Landais
mesh_terms: D059019:Clinical Coding / Q000379:methods*; D057225:Data Mining; D016208:Databases, Factual; D005838:Genotype; D063005:Health Information Systems; D006801:Humans; D008498:Medical Record Linkage / Q000379:methods*; D010641:Phenotype; D035583:Rare Diseases / Q000175:diagnosis* / Q000235:genetics; D012660:Semantics