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An ontological foundation for ocular phenotypes and rare eye diseases

Research output: Contribution to journalLetterpeer-review

Harvard

Sergouniotis, PI, Maxime, E, Leroux, D, Olry, A, Thompson, R, Rath, A, Robinson, PN, Dollfus, H, ERN-EYE Ontology Study Group, Hamann, SE, Kessel, L & Larsen, M 2019, 'An ontological foundation for ocular phenotypes and rare eye diseases', Orphanet Journal of Rare Diseases, vol. 14, no. 1, pp. 8. https://doi.org/10.1186/s13023-018-0980-6

APA

Sergouniotis, P. I., Maxime, E., Leroux, D., Olry, A., Thompson, R., Rath, A., Robinson, P. N., Dollfus, H., ERN-EYE Ontology Study Group, Hamann, S. E., Kessel, L., & Larsen, M. (2019). An ontological foundation for ocular phenotypes and rare eye diseases. Orphanet Journal of Rare Diseases, 14(1), 8. https://doi.org/10.1186/s13023-018-0980-6

CBE

Sergouniotis PI, Maxime E, Leroux D, Olry A, Thompson R, Rath A, Robinson PN, Dollfus H, ERN-EYE Ontology Study Group, Hamann SE, Kessel L, Larsen M. 2019. An ontological foundation for ocular phenotypes and rare eye diseases. Orphanet Journal of Rare Diseases. 14(1):8. https://doi.org/10.1186/s13023-018-0980-6

MLA

Vancouver

Author

Sergouniotis, Panagiotis I ; Maxime, Emmanuel ; Leroux, Dorothée ; Olry, Annie ; Thompson, Rachel ; Rath, Ana ; Robinson, Peter N ; Dollfus, Hélène ; ERN-EYE Ontology Study Group ; Hamann, Steffen Ellitsgaard ; Kessel, Line ; Larsen, Michael. / An ontological foundation for ocular phenotypes and rare eye diseases. In: Orphanet Journal of Rare Diseases. 2019 ; Vol. 14, No. 1. pp. 8.

Bibtex

@article{526d1578a9ee40aebd12ebf845965bd6,
title = "An ontological foundation for ocular phenotypes and rare eye diseases",
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.",
keywords = "Evidence-based precision medicine, Human phenotype ontology, Orphanet rare disease ontology, Rare eye disease",
author = "Sergouniotis, {Panagiotis I} and Emmanuel Maxime and Doroth{\'e}e Leroux and Annie Olry and Rachel Thompson and Ana Rath and Robinson, {Peter N} and H{\'e}l{\`e}ne Dollfus and {ERN-EYE Ontology Study Group} and Hamann, {Steffen Ellitsgaard} and Line Kessel and Michael Larsen",
year = "2019",
month = jan,
day = "9",
doi = "10.1186/s13023-018-0980-6",
language = "English",
volume = "14",
pages = "8",
journal = "Orphanet Journal of Rare Diseases",
issn = "1750-1172",
publisher = "BioMed Central Ltd",
number = "1",

}

RIS

TY - JOUR

T1 - An ontological foundation for ocular phenotypes and rare eye diseases

AU - Sergouniotis, Panagiotis I

AU - Maxime, Emmanuel

AU - Leroux, Dorothée

AU - Olry, Annie

AU - Thompson, Rachel

AU - Rath, Ana

AU - Robinson, Peter N

AU - Dollfus, Hélène

AU - ERN-EYE Ontology Study Group

A2 - Hamann, Steffen Ellitsgaard

A2 - Kessel, Line

A2 - Larsen, Michael

PY - 2019/1/9

Y1 - 2019/1/9

N2 - 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.

AB - 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.

KW - Evidence-based precision medicine

KW - Human phenotype ontology

KW - Orphanet rare disease ontology

KW - Rare eye disease

U2 - 10.1186/s13023-018-0980-6

DO - 10.1186/s13023-018-0980-6

M3 - Letter

C2 - 30626441

VL - 14

SP - 8

JO - Orphanet Journal of Rare Diseases

JF - Orphanet Journal of Rare Diseases

SN - 1750-1172

IS - 1

ER -

ID: 56563967