The Human Phenotype Ontology in 2017

被引：590

作者：

Koehler, Sebastian ^{[1
]}

Vasilevsky, Nicole A. ^{[2
]}

Engelstad, Mark ^{[2
]}

Foster, Erin ^{[2
]}

McMurry, Julie ^{[2
]}

Ayme, Segolene ^{[3
]}

Baynam, Gareth ^{[4
,5
]}

Bello, Susan M. ^{[6
]}

Boerkoel, Cornelius F. ^{[7
]}

Boycott, Kym M. ^{[8
]}

Brudno, Michael ^{[9
,10
]}

Buske, Orion J. ^{[9
,10
]}

Chinnery, Patrick F. ^{[11
,12
]}

Cipriani, Valentina ^{[13
,14
]}

Connell, Laureen E. ^{[15
]}

Dawkins, Hugh J. S. ^{[16
]}

DeMare, Laura E. ^{[15
]}

Devereau, Andrew D. ^{[17
]}

de Vries, Bert B. A. ^{[18
]}

Firth, Helen V. ^{[19
]}

Freson, Kathleen ^{[20
]}

Greene, Daniel ^{[21
,22
]}

Hamosh, Ada ^{[23
]}

Helbig, Ingo ^{[24
,25
]}

Hum, Courtney ^{[26
]}

Jahn, Johaenna A. ^{[25
]}

James, Roger ^{[12
,22
]}

Krause, Roland ^{[27
]}

Laulederkind, Stanley J. F. ^{[28
]}

Lochmuller, Hanns ^{[29
]}

Lyon, Gholson J. ^{[30
]}

Ogishima, Soichi ^{[31
]}

Olry, Annie ^{[32
]}

Ouwehand, Willem H. ^{[21
]}

Pontikos, Nikolas ^{[13
,14
]}

Rath, Ana ^{[32
]}

Schaefer, Franz ^{[33
,34
]}

Scott, Richard H. ^{[17
]}

Segal, Michael ^{[35
]}

Sergouniotis, Panagiotis I. ^{[36
,37
]}

Sever, Richard ^{[15
]}

Smith, Cynthia L. ^{[6
]}

Straub, Volker ^{[29
]}

Thompson, Rachel ^{[29
]}

Turner, Catherine ^{[29
]}

Turro, Ernest ^{[21
,22
]}

Veltman, Marijcke W. M. ^{[12
]}

Vulliamy, Tom ^{[38
]}

Yu, Jing ^{[39
]}

von Ziegenweidt, Julie ^{[21
]}

机构：

[1] Charite, Inst Med Genet & Human Genet, Augustenburger Pl 1, D-13353 Berlin, Germany

[2] Oregon Hlth & Sci Univ, Library & Dept Med Informat & Clin Epidemiol, Portland, OR 97239 USA

[3] CNRS, Inst Cerveau & Moelle Epiniere ICM, UMR 7225,Inserm U1127,UPMC P6 UMR S 1127, Hop La Pitie Salpetriere, 47 Bd Hop, F-75013 Paris, France

[4] Govt Western Australia, King Edward Mem Hosp Dept Hlth, Western Australian Register Dev Anomalies & Genet, Perth, WA 6008, Australia

[5] Univ Western Australia, Sch Paediat & Child Hlth, Perth, WA 6008, Australia

[6] Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA

[7] Sanford Hlth, Imagenet Res, POB 5039,Route 5001, Sioux Falls, SD 57117 USA

[8] Univ Ottawa, Childrens Hosp Eastern Ontario Res Inst, Ottawa, ON, Canada

[9] Univ Toronto, Dept Comp Sci, Toronto, ON M5S 2E4, Canada

[10] Hosp Sick Children, Ctr Computat Med, Toronto, ON M5G 1L7, Canada

[11] Univ Cambridge, Sch Clin Med, Dept Clin Neurosci, Cambridge CB2 0QQ, England

[12] NIHR Rare Dis Translat Res Collaborat, Cambridge Biomed Campus, Cambridge CB2 0QQ, England

[13] UCL Inst Ophthalmol, Dept Ocular Biol & Therapeut, 11-43 Bath St, London EC1V 9EL, England

[14] UCL, UCL Genet Inst, London WC1E 6BT, England

[15] Cold Spring Harbor Lab Press, Cold Spring Harbor, NY USA

[16] Hlth Dept Western Australia, Off Populat Hlth Genom, Publ Hlth Div, 189 Royal St, Perth, WA 6004, Australia

[17] Queen Mary Univ London, Genom England, Dawson Hall,Charterhouse Sq, London EC1M 6BQ, England

[18] Radboud Univ Nijmegen, Univ Med Ctr, Dept Human Genet, Nijmegen, Netherlands

[19] Wellcome Trust Sanger Inst, Wellcome Genome Campus, Cambridge CB10 1SA, England

[20] Univ Leuven, Ctr Mol & Vasc Biol, Dept Cardiovasc Sci, Leuven, Belgium

[21] Univ Cambridge, Dept Haematol, NHS Blood & Transplant Ctr, Long Rd, Cambridge CB2 0PT, England

[22] Cambridge Inst Publ Hlth, Med Res Council Biostat Unit, Cambridge Biomed Campus, Cambridge, England

[23] Johns Hopkins Univ, Sch Med, Dept Pediat, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

[24] Childrens Hosp Philadelphia, Div Neurol, 3501 Civ Ctr Blvd, Philadelphia, PA 19104 USA

[25] Univ Med Ctr Schleswig Holstein, Dept Neuropediat, Kiel, Germany

[26] Hosp Sick Children, Ctr Computat Med, Toronto, ON M5G 1H3, Canada

[27] Univ Luxembourg, LuxembourgCtr Syst Biomed, Ave Hauts Fourneaux, L-4362 Luxembourg, Luxembourg

[28] Med Coll Wisconsin, Human & Mol Genet Ctr, Milwaukee, WI 53226 USA

[29] Newcastle Univ, Inst Med Genet, MRC Ctr Neuromuscular Dis, John Walton Muscular Dystrophy Res Ctr, Newcastle Upon Tyne, Tyne & Wear, England

[30] Cold Spring Harbor Lab, Stanley Inst Cognit Genom, New York, NY 11797 USA

[31] Tohoku Univ, Tohoku Med Megabank Org, Dept Bioclin Informat, Aoba Ku, Tohoku Med Megabank Org Bldg 7F Room 741,736,Seir, Sendai, Miyagi 9808573, Japan

[32] Orphanet INSERM, US14, Plateforme Malad Rares, 96 Rue Didot, F-75014 Paris, France

[33] Ctr Pediat & Adolescent Med, Div Pediat Nephrol, D-69120 Heidelberg, Germany

[34] Ctr Pediat & Adolescent Med, KFH Childrens Kidney Ctr, D-69120 Heidelberg, Germany

[35] SimulConsult Inc, 27 Crafts Rd, Chestnut Hill, MA 02467 USA

[36] Manchester Royal Eye Hosp, Manchester M13 9WL, Lancs, England

[37] Univ Manchester, Manchester M13 9WL, Lancs, England

[38] Queen Mary Univ London, Barts & London Sch Med & Dent, Blizard Inst, London E1 2AT, England

[39] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Clin Neurosci, Level 6,West Wing, Oxford OX3 9DU, England

[40] Univ Sydney, Sydney Med Sch, Discipline Genet Med, Sydney, NSW, Australia

[41] Sydney Childrens Hosp Network, Acad Dept Med Genet, Westmead, NSW, Australia

[42] Univ Miami, JD McDonald Dept Human Genet, Miami, FL 33136 USA

[43] Univ Miami, Hussman Inst Human Gen, Miami, FL 33136 USA

[44] Garvan Inst Med Res, Sydney, NSW 2010, Australia

[45] UNSW Australia, Fac Med, St Vincents Clin Sch, Sydney, NSW, Australia

[46] Lawrence Berkeley Natl Lab, Environm Genom & Syst Biol Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA

[47] Jackson Lab Genom Med, 10 Discovery Dr, Farmington, CT 06032 USA

[48] Univ Connecticut, Inst Syst Genom, Farmington, CT 06032 USA

来源：

NUCLEIC ACIDS RESEARCH | 2017年 / 45卷 / D1期

基金：

美国国家卫生研究院;

关键词：

DISEASE-GENE-DISCOVERY; GENOME-WIDE ASSOCIATION; RARE-DISEASE; DEVELOPMENTAL DISORDERS; PLATELET DISORDERS; MODEL ORGANISM; EPILEPTIC ENCEPHALOPATHY; VARIANT PRIORITIZATION; MATCHMAKER EXCHANGE; CANDIDATE GENES;

D O I：

10.1093/nar/gkw1039

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

引用

页码：D865 / D876

页数：12

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