1. An ontological foundation for ocular phenotypes and rare eye diseases
- Author
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Sergouniotis, Panagiotis I., Maxime, Emmanuel, Leroux, Dorothée, Olry, Annie, Thompson, Rachel, Rath, Ana, Robinson, Peter N., Dollfus, Hélèneashworth, Jl, Audo, I, Balciuniene, Vj, Banin, E, Black, Gc, Böhringer, D, Boon, Cjf, Bremond-Gignac, D, Calvas, P, Castela, G, Dagnelie, G, Dollfus, H, Downes, Sm, Fasolo, A, Fasser, C, Gelzinis, A, Goetz, K, Hamann, S, Héon, E, Iarossi, G, Kawasaki, A, Keegan, D, Kessel, L, Khan, K, Klett, A, Köhler, S, Leroux, D, Leroy, Bp, Lisch, W, Liskova, P, Lorenz, B, Maggi, R, Maxime, E, Meunier, I, Mohand-Said, S, Nowomiejska, K, Perdomo, Y, Petzold, A, Preising, M, Robinson, Pn, Scholl, Hpn, Sergouniotis, Pi, Sodi, A, Stingl, K, Studer, F, Suppiej, A, Thompson, R, Touitou, V, Traboulsi, E, Trumpaitis, J, Tuft, Sj, Vaclavik, V, Valeina, S, Van Cauwenbergh, C, Verloes, A, Vighetto, A, Wheeler, R, Wheeler-Schilling, T, Yu-Wai-Man, P, Zobor, D, Zrenner, E., Sergouniotis, Panagiotis I [0000-0003-0986-4123], Apollo - University of Cambridge Repository, University of Manchester [Manchester], Plateforme d'information et de services pour les maladies rares et les médicaments orphelins (Orphanet), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Broussais-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO) et Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Newcastle University [Newcastle], The Jackson Laboratory for Genomic Medicine, Laboratoire de Génétique Médicale (LGM), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), and European Project: 0305444(2003)
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0301 basic medicine ,Eye Diseases ,Computer science ,Evidence-based precision medicine, Rare eye disease, Human phenotype ontology, Orphanet rare disease ontology ,lcsh:Medicine ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,030105 genetics & heredity ,Ontology (information science) ,Terminology ,NO ,Open Biomedical Ontologies ,MESH: Eye Diseases / classificationHumans Precision Medicine / methods* Rare Diseases / classification ,03 medical and health sciences ,0302 clinical medicine ,Rare Diseases ,Human Phenotype Ontology ,Eye Diseases/classification ,Humans ,Pharmacology (medical) ,Precision Medicine ,Letter to the Editor ,MESH: Humans Precision Medicine / methods ,Genetics (clinical) ,Information exchange ,Evidence-Based Medicine ,Orphanet rare disease ontology ,Rare Diseases/classification ,MESH: Computational Biology / methods ,lcsh:R ,Computational Biology ,Human phenotype ontology ,Biological Ontologies ,Precision Medicine/methods ,General Medicine ,Evidence-based medicine ,Rare eye disease ,Computational Biology/methods ,Data science ,MESH: Rare Diseases / classification ,3. Good health ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Evidence-based precision medicine ,Eye disorder ,MESH: Biological Ontologies ,MESH: Evidence-Based Medicine ,030217 neurology & neurosurgery - Abstract
Background The optical accessibility of the eye and technological advances in ophthalmic diagnostics have put ophthalmology at the forefront of data-driven medicine. The focus of this study is rare eye disorders, a group of conditions whose clinical heterogeneity and geographic dispersion make data-driven, evidence-based practice particularly challenging. Inter-institutional collaboration and information sharing is crucial but the lack of standardised terminology poses an important barrier. Ontologies are computational tools that include sets of vocabulary terms arranged in hierarchical structures. They can be used to provide robust terminology standards and to enhance data interoperability. Here, we discuss the development of the ophthalmology-related component of two well-established biomedical ontologies, the Human Phenotype Ontology (HPO; includes signs, symptoms and investigation findings) and the Orphanet Rare Disease Ontology (ORDO; includes rare disease nomenclature/nosology). Methods A variety of approaches were used including automated matching to existing resources and extensive manual curation. To achieve the latter, a study group including clinicians, patient representatives and ontology developers from 17 countries was formed. A broad range of terms was discussed and validated during a dedicated workshop attended by 60 members of the group. Results A comprehensive, structured and well-defined set of terms has been agreed on including 1106 terms relating to ocular phenotypes (HPO) and 1202 terms relating to rare eye disease nomenclature (ORDO). These terms and their relevant annotations can be accessed in http://www.human-phenotype-ontology.org/ and http://www.orpha.net/; comments, corrections, suggestions and requests for new terms can be made through these websites. This is an ongoing, community-driven endeavour and both HPO and ORDO are regularly updated. Conclusions To our knowledge, this is the first effort of such scale to provide terminology standards for the rare eye disease community. We hope that this work will not only improve coding and standardise information exchange in clinical care and research, but also it will catalyse the transition to an evidence-based precision ophthalmology paradigm. Electronic supplementary material The online version of this article (10.1186/s13023-018-0980-6) contains supplementary material, which is available to authorized users.
- Published
- 2019
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