Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
Sebastian Köhler,Leigh C. Carmody,Nicole Vasilevsky,Julius O.B. Jacobsen,Daniel Danis,Jean-Philippe F. Gourdine,Michael A. Gargano,Nomi L. Harris,Nicolas Matentzoglu,Julie A. McMurry,David Osumi-Sutherland,Valentina Cipriani,James P. Balhoff,Tom Conlin,Hannah Blau,Gareth Baynam,Richard Palmer,Dylan Gratian,Hugh Dawkins,Michael M. Segal,Anna Jansen,Ahmed Muaz,Willie H. Chang,Jenna R.E. Bergerson,Stanley J. F. Laulederkind,Zafer Yüksel,Sergi Beltran,Alexandra F. Freeman,Panagiotis I. Sergouniotis,Daniel Durkin,Andrea L. Storm,Marc Hanauer,Michael Brudno,Susan M. Bello,Murat Sincan,Kayli Rageth,Matthew T. Wheeler,Renske Oegema,Halima Lourghi,Maria G. Della Rocca,Rachel Thompson,Francisco Castellanos,James R. Priest,Charlotte Cunningham-Rundles,Ayushi Hegde,Ruth C. Lovering,Catherine Hajek,Annie Olry,Luigi D. Notarangelo,Morgan Similuk,Xingmin Aaron Zhang,David Gómez-Andrés,Hanns Lochmüller,Hélène Dollfus,Sergio Rosenzweig,Shruti Marwaha,Ana Rath,Kathleen E. Sullivan,Cynthia L. Smith,Joshua D. Milner,Dorothée Leroux,Cornelius F. Boerkoel,Amy D. Klion,Melody C. Carter,Tudor Groza,Damian Smedley,Melissa A. Haendel,Melissa A. Haendel,Christopher J. Mungall,Peter N. Robinson +69 more
TLDR
The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data and plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data.Abstract:
The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.read more
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g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).
TL;DR: G:Profiler is now capable of analysing data from any organism, including vertebrates, plants, fungi, insects and parasites, and the 2019 update introduces an extensive technical rewrite making the services faster and more flexible.
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The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero,Juan Manuel Ramírez-Anguita,Josep Saüch-Pitarch,Francesco Ronzano,Emilio Centeno,Ferran Sanz,Laura I. Furlong +6 more
TL;DR: The DisGeNET platform, a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.
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Gene Set Knowledge Discovery with Enrichr.
Zhuorui Xie,Allison Bailey,Maxim V. Kuleshov,Daniel J.B. Clarke,John Erol Evangelista,Sherry L. Jenkins,Alexander Lachmann,Megan L. Wojciechowicz,Eryk Kropiwnicki,Kathleen M. Jagodnik,Minji Jeon,Avi Ma'ayan +11 more
TL;DR: Enrichr as discussed by the authors is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets Enrichr uniquely integrates knowledge from many high-profile projects to provide synthesized information about mammalian genes and gene sets.
Journal ArticleDOI
The Human Phenotype Ontology in 2021
Sebastian Köhler,Michael A. Gargano,Nicolas Matentzoglu,Leigh C. Carmody,David Lewis-Smith,David Lewis-Smith,Nicole Vasilevsky,Daniel Danis,Daniel Danis,Ganna Balagura,Gareth Baynam,Gareth Baynam,Amy Brower,Tiffany J. Callahan,Christopher G. Chute,Johanna L. Est,Peter D. Galer,Shiva Ganesan,Matthias Griese,Matthias Haimel,Julia Pazmandi,Julia Pazmandi,Marc Hanauer,Nomi L. Harris,Michael Hartnett,Maximilian Hastreiter,Fabian Hauck,Yongqun He,Tim Jeske,Hugh Kearney,Gerhard Kindle,Christoph Klein,Katrin Knoflach,Roland Krause,David Lagorce,Julie A. McMurry,Jillian A. Miller,Monica Munoz-Torres,Rebecca L. Peters,Christina K Rapp,Ana Rath,Shahmir A. Rind,Avi Z. Rosenberg,Michael M. Segal,Markus G. Seidel,Damian Smedley,Tomer Talmy,Yarlalu Thomas,Samuel A. Wiafe,Julie Xian,Zafer Yüksel,Ingo Helbig,Ingo Helbig,Christopher J. Mungall,Melissa A. Haendel,Melissa A. Haendel,Peter N. Robinson +56 more
TL;DR: Recent major extensions of the Human Phenotype Ontology for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas are presented and new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease are presented.
Journal ArticleDOI
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Christopher J. Mungall,Julie A. McMurry,Sebastian Köhler,James P. Balhoff,Charles D. Borromeo,Matthew H. Brush,Seth Carbon,Tom Conlin,Nathan Dunn,Mark Engelstad,Erin D. Foster,Jean-Philippe F. Gourdine,Julius O.B. Jacobsen,Daniel Keith,Bryan Laraway,Suzanna E. Lewis,Jeremy Nguyen-Xuan,Kent Shefchek,Nicole Vasilevsky,Zhou Yuan,Nicole L. Washington,Harry Hochheiser,Tudor Groza,Damian Smedley,Peter N. Robinson,Melissa A. Haendel +25 more
TL;DR: The Monarch Initiative as discussed by the authors integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search, and develops many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases.
References
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Journal ArticleDOI
The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease
Peter N. Robinson,Sebastian Köhler,Sebastian Bauer,Dominik Seelow,Denise Horn,Stefan Mundlos +5 more
TL;DR: A Human Phenotype Ontology with over 8000 terms representing individual phenotypic anomalies and all clinical entries in Online Mendelian Inheritance in Man with the terms of the HPO are annotated.
Journal ArticleDOI
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
Sebastian Köhler,Sandra C. Doelken,Christopher J. Mungall,Sebastian Bauer,Helen V. Firth,Helen V. Firth,Isabelle Bailleul-Forestier,Graeme C.M. Black,Danielle L. Brown,Michael Brudno,Jennifer Campbell,Jennifer Campbell,David R. FitzPatrick,Janan T. Eppig,Andrew P. Jackson,Kathleen Freson,Marta Girdea,Ingo Helbig,Jane A. Hurst,Johanna A. Jähn,Laird G. Jackson,Anne M. Kelly,David H. Ledbetter,Sahar Mansour,Christa Lese Martin,Celia Moss,Andrew D Mumford,Willem H. Ouwehand,Willem H. Ouwehand,Soo Mi Park,Erin Rooney Riggs,Richard H. Scott,Sanjay M. Sisodiya,Steven Van Vooren,Ronald J. Wapner,Andrew O.M. Wilkie,Caroline F. Wright,Anneke T. Vulto-van Silfhout,Nicole de Leeuw,Bert B.A. de Vries,Nicole L. Washingthon,Cynthia L. Smith,Monte Westerfield,Paul N. Schofield,Barbara J. Ruef,Georgios V. Gkoutos,Melissa A. Haendel,Damian Smedley,Suzanna E. Lewis,Peter N. Robinson,Peter N. Robinson +50 more
TL;DR: The updated HPO database is described, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO, allowing integration of existing datasets and interoperability with multiple biomedical resources.
Journal ArticleDOI
Clinical application of whole-exome sequencing across clinical indications.
Kyle Retterer,Jane Juusola,Megan T. Cho,Patrik Vitazka,Francisca Millan,Federica Gibellini,Annette Vertino-Bell,Nizar Smaoui,Nizar Smaoui,Julie Neidich,Kristin G. Monaghan,Dianalee McKnight,Renkui Bai,Sharon F. Suchy,Bethany Friedman,Jackie Tahiliani,Daniel E. Pineda-Alvarez,Gabriele Richard,Tracy Brandt,Eden Haverfield,Wendy K. Chung,Sherri J. Bale +21 more
TL;DR: The experience with the first 3,040 WES cases suggests that analysis of trios significantly improves the diagnostic yield compared with proband-only testing for genetically heterogeneous disorders and facilitates identification of novel candidate genes.
Journal ArticleDOI
The Human Phenotype Ontology in 2017
Sebastian Köhler,Nicole Vasilevsky,Mark Engelstad,Erin D. Foster,Julie A. McMurry,Ségolène Aymé,Gareth Baynam,Gareth Baynam,Susan M. Bello,Cornelius F. Boerkoel,Kym M. Boycott,Michael Brudno,Orion J. Buske,Patrick F. Chinnery,Valentina Cipriani,Laureen E. Connell,Hugh Dawkins,Laura E. DeMare,Andrew D. Devereau,Bert B.A. de Vries,Helen V. Firth,Kathleen Freson,Daniel Greene,Ada Hamosh,Ingo Helbig,Ingo Helbig,Courtney Hum,Johanna A. Jähn,Roger James,Roland Krause,Stanley J. F. Laulederkind,Hanns Lochmüller,Gholson J. Lyon,Soichi Ogishima,Annie Olry,Willem H. Ouwehand,Nikolas Pontikos,Ana Rath,Franz Schaefer,Richard H. Scott,Michael M. Segal,Panagiotis I. Sergouniotis,Richard Sever,Cynthia L. Smith,Volker Straub,Rachel Thompson,C. Turner,Ernest Turro,Marijcke W. M. Veltman,Tom Vulliamy,Jing Yu,Julie von Ziegenweidt,Andreas Zankl,Stephan Züchner,Tomasz Zemojtel,Julius O.B. Jacobsen,Tudor Groza,Damian Smedley,Christopher J. Mungall,Melissa A. Haendel,Peter N. Robinson +60 more
TL;DR: The progress of the HPO project is reviewed, 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.
Journal ArticleDOI
Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation
Jennifer E. Posey,Tamar Harel,Pengfei Liu,Jill A. Rosenfeld,Regis A. James,Zeynep Coban Akdemir,Magdalena Walkiewicz,Weimin Bi,Rui Xiao,Yan Ding,Fan Xia,Arthur L. Beaudet,Donna M. Muzny,Richard A. Gibbs,Eric Boerwinkle,Christine M. Eng,V. Reid Sutton,Chad A. Shaw,Sharon E. Plon,Sharon E. Plon,Yaping Yang,James R. Lupski,James R. Lupski +22 more
TL;DR: The results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping.
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