The Human Phenotype Ontology in 2017

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenoty...

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Published inNucleic acids research Vol. 45; no. D1; pp. D865 - D876
Main Authors Köhler, Sebastian, Vasilevsky, Nicole A, Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M, Boerkoel, Cornelius F, Boycott, Kym M, Brudno, Michael, Buske, Orion J, Chinnery, Patrick F, Cipriani, Valentina, Connell, Laureen E, Dawkins, Hugh J S, DeMare, Laura E, Devereau, Andrew D, de Vries, Bert B A, Firth, Helen V, Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A, James, Roger, Krause, Roland, F Laulederkind, Stanley J, Lochmüller, Hanns, Lyon, Gholson J, Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H, Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H, Segal, Michael, Sergouniotis, Panagiotis I, Sever, Richard, Smith, Cynthia L, Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke W M, Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius O B, Groza, Tudor, Smedley, Damian, Mungall, Christopher J, Haendel, Melissa, Robinson, Peter N
Format Journal Article
LanguageEnglish
Published England Oxford University Press 04.01.2017
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Abstract Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
AbstractList Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org ) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
Author Baynam, Gareth
Helbig, Ingo
McMurry, Julie
Züchner, Stephan
F Laulederkind, Stanley J
Foster, Erin
von Ziegenweidt, Julie
Zankl, Andreas
Krause, Roland
Pontikos, Nikolas
Boerkoel, Cornelius F
Veltman, Marijcke W M
Rath, Ana
Turro, Ernest
Groza, Tudor
Brudno, Michael
Lyon, Gholson J
Aymé, Ségolène
Sergouniotis, Panagiotis I
Köhler, Sebastian
Thompson, Rachel
Hamosh, Ada
Ogishima, Soichi
Vulliamy, Tom
Haendel, Melissa
Lochmüller, Hanns
Vasilevsky, Nicole A
Chinnery, Patrick F
Engelstad, Mark
Jacobsen, Julius O B
Segal, Michael
Schaefer, Franz
Smedley, Damian
Ouwehand, Willem H
Buske, Orion J
Cipriani, Valentina
Firth, Helen V
Olry, Annie
Smith, Cynthia L
Boycott, Kym M
Dawkins, Hugh J S
Scott, Richard H
Hum, Courtney
DeMare, Laura E
Turner, Catherine
Greene, Daniel
Devereau, Andrew D
Zemojtel, Tomasz
de Vries, Bert B A
Robinson, Peter N
Jähn, Johanna A
James, Roger
Straub, Volker
Bello, Susan M
Sever, Richard
Yu, Jing
Connell, Laureen E
Freson, Kathleen
Mungall, Christopher J
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Snippet Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are...
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StartPage D865
SubjectTerms Algorithms
Biological Ontologies
Computational Biology
Computational Biology - methods
Database Issue
Genetic Association Studies
Genetic Association Studies - methods
Genomics
Genomics - methods
Human health and pathology
Humans
Life Sciences
Phenotype
Precision Medicine
Precision Medicine - methods
Rare Diseases
Rare Diseases - diagnosis
Rare Diseases - etiology
Software
Translational Research, Biomedical
Translational Research, Biomedical - methods
Title The Human Phenotype Ontology in 2017
URI https://www.ncbi.nlm.nih.gov/pubmed/27899602
https://hal.sorbonne-universite.fr/hal-04412294
https://pubmed.ncbi.nlm.nih.gov/PMC5210535
Volume 45
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