Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O.B. Jacobsen, Daniel Danis, Jean Philippe Gourdine, Michael 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 Segal & 49 others Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna 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 Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin A. Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa Haendel, Chris Mungall, Peter N. Robinson

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)D1018-D1027
JournalNucleic Acids Research
Volume47
Issue numberD1
DOIs
StatePublished - Jan 8 2019

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Knowledge Bases
Phenotype
Exome
Vocabulary
Electronic Health Records
Rare Diseases
Language
Research Personnel
Genome
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Köhler, S., Carmody, L., Vasilevsky, N., Jacobsen, J. O. B., Danis, D., Gourdine, J. P., ... Robinson, P. N. (2019). Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Research, 47(D1), D1018-D1027. https://doi.org/10.1093/nar/gky1105

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. / Köhler, Sebastian; Carmody, Leigh; Vasilevsky, Nicole; Jacobsen, Julius O.B.; Danis, Daniel; Gourdine, Jean Philippe; Gargano, Michael; Harris, Nomi L.; Matentzoglu, Nicolas; McMurry, Julie A.; Osumi-Sutherland, David; Cipriani, Valentina; Balhoff, James P.; Conlin, Tom; Blau, Hannah; Baynam, Gareth; Palmer, Richard; Gratian, Dylan; Dawkins, Hugh; Segal, Michael; Jansen, Anna C.; Muaz, Ahmed; Chang, Willie H.; Bergerson, Jenna; Laulederkind, Stanley J.F.; Yüksel, Zafer; Beltran, Sergi; Freeman, Alexandra F.; Sergouniotis, Panagiotis I.; Durkin, Daniel; Storm, Andrea L.; Hanauer, Marc; Brudno, Michael; Bello, Susan M.; Sincan, Murat; Rageth, Kayli; Wheeler, Matthew T.; Oegema, Renske; Lourghi, Halima; Della Rocca, Maria G.; Thompson, Rachel; Castellanos, Francisco; Priest, James; Cunningham-Rundles, Charlotte; Hegde, Ayushi; Lovering, Ruth C.; Hajek, Catherine; Olry, Annie; Notarangelo, Luigi; Similuk, Morgan; Zhang, Xingmin A.; Gómez-Andrés, David; Lochmüller, Hanns; Dollfus, Hélène; Rosenzweig, Sergio; Marwaha, Shruti; Rath, Ana; Sullivan, Kathleen; Smith, Cynthia; Milner, Joshua D.; Leroux, Dorothée; Boerkoel, Cornelius F.; Klion, Amy; Carter, Melody C.; Groza, Tudor; Smedley, Damian; Haendel, Melissa; Mungall, Chris; Robinson, Peter N.

In: Nucleic Acids Research, Vol. 47, No. D1, 08.01.2019, p. D1018-D1027.

Research output: Contribution to journalArticle

Köhler, S, Carmody, L, Vasilevsky, N, Jacobsen, JOB, Danis, D, Gourdine, JP, Gargano, M, Harris, NL, Matentzoglu, N, McMurry, JA, Osumi-Sutherland, D, Cipriani, V, Balhoff, JP, Conlin, T, Blau, H, Baynam, G, Palmer, R, Gratian, D, Dawkins, H, Segal, M, Jansen, AC, Muaz, A, Chang, WH, Bergerson, J, Laulederkind, SJF, Yüksel, Z, Beltran, S, Freeman, AF, Sergouniotis, PI, Durkin, D, Storm, AL, Hanauer, M, Brudno, M, Bello, SM, Sincan, M, Rageth, K, Wheeler, MT, Oegema, R, Lourghi, H, Della Rocca, MG, Thompson, R, Castellanos, F, Priest, J, Cunningham-Rundles, C, Hegde, A, Lovering, RC, Hajek, C, Olry, A, Notarangelo, L, Similuk, M, Zhang, XA, Gómez-Andrés, D, Lochmüller, H, Dollfus, H, Rosenzweig, S, Marwaha, S, Rath, A, Sullivan, K, Smith, C, Milner, JD, Leroux, D, Boerkoel, CF, Klion, A, Carter, MC, Groza, T, Smedley, D, Haendel, M, Mungall, C & Robinson, PN 2019, 'Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources' Nucleic Acids Research, vol. 47, no. D1, pp. D1018-D1027. https://doi.org/10.1093/nar/gky1105
Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP et al. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Research. 2019 Jan 8;47(D1):D1018-D1027. https://doi.org/10.1093/nar/gky1105
Köhler, Sebastian ; Carmody, Leigh ; Vasilevsky, Nicole ; Jacobsen, Julius O.B. ; Danis, Daniel ; Gourdine, Jean Philippe ; Gargano, Michael ; Harris, Nomi L. ; Matentzoglu, Nicolas ; McMurry, Julie A. ; Osumi-Sutherland, David ; Cipriani, Valentina ; Balhoff, James P. ; Conlin, Tom ; Blau, Hannah ; Baynam, Gareth ; Palmer, Richard ; Gratian, Dylan ; Dawkins, Hugh ; Segal, Michael ; Jansen, Anna C. ; Muaz, Ahmed ; Chang, Willie H. ; Bergerson, Jenna ; Laulederkind, Stanley J.F. ; Yüksel, Zafer ; Beltran, Sergi ; Freeman, Alexandra F. ; Sergouniotis, Panagiotis I. ; Durkin, Daniel ; Storm, Andrea L. ; Hanauer, Marc ; Brudno, Michael ; Bello, Susan M. ; Sincan, Murat ; Rageth, Kayli ; Wheeler, Matthew T. ; Oegema, Renske ; Lourghi, Halima ; Della Rocca, Maria G. ; Thompson, Rachel ; Castellanos, Francisco ; Priest, James ; Cunningham-Rundles, Charlotte ; Hegde, Ayushi ; Lovering, Ruth C. ; Hajek, Catherine ; Olry, Annie ; Notarangelo, Luigi ; Similuk, Morgan ; Zhang, Xingmin A. ; Gómez-Andrés, David ; Lochmüller, Hanns ; Dollfus, Hélène ; Rosenzweig, Sergio ; Marwaha, Shruti ; Rath, Ana ; Sullivan, Kathleen ; Smith, Cynthia ; Milner, Joshua D. ; Leroux, Dorothée ; Boerkoel, Cornelius F. ; Klion, Amy ; Carter, Melody C. ; Groza, Tudor ; Smedley, Damian ; Haendel, Melissa ; Mungall, Chris ; Robinson, Peter N. / Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. In: Nucleic Acids Research. 2019 ; Vol. 47, No. D1. pp. D1018-D1027.
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