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

Sebastian Koehler, 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 Yueksel, 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 Gomez-Andres, Hanns Lochmueller, Helene Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia Smith, Joshua D. Milner, Dorothee Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

The Human Phenotype Ontology (HPO)a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseasesis 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
Pages (from-to)D1018-D1027
Number of pages10
JournalNucleic Acids Research
Volume47
Issue numberD1
DOIs
Publication statusPublished - 8 Jan 2019

Cite this

Koehler, 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
Koehler, 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. ; Yueksel, 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. ; Gomez-Andres, David ; Lochmueller, Hanns ; Dollfus, Helene ; Rosenzweig, Sergio ; Marwaha, Shruti ; Rath, Ana ; Sullivan, Kathleen ; Smith, Cynthia ; Milner, Joshua D. ; Leroux, Dorothee ; Boerkoel, Cornelius F. ; Klion, Amy ; Carter, Melody C. ; Groza, Tudor ; Smedley, Damian ; Haendel, Melissa A. ; 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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abstract = "The Human Phenotype Ontology (HPO)a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseasesis 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.",
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Koehler, S, Carmody, L, Vasilevsky, N, Jacobsen, JOB, Danis, D, Gourdine, J-P, 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, Yueksel, 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, Gomez-Andres, D, Lochmueller, 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, MA, 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

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. / Koehler, 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.; Yueksel, 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.; Gomez-Andres, David; Lochmueller, Hanns; Dollfus, Helene; Rosenzweig, Sergio; Marwaha, Shruti; Rath, Ana; Sullivan, Kathleen; Smith, Cynthia; Milner, Joshua D.; Leroux, Dorothee; Boerkoel, Cornelius F.; Klion, Amy; Carter, Melody C.; Groza, Tudor; Smedley, Damian; Haendel, Melissa A.; Mungall, Chris; Robinson, Peter N.

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

Research output: Contribution to journalArticle

TY - JOUR

T1 - Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

AU - Koehler, Sebastian

AU - Carmody, Leigh

AU - Vasilevsky, Nicole

AU - Jacobsen, Julius O. B.

AU - Danis, Daniel

AU - Gourdine, Jean-Philippe

AU - Gargano, Michael

AU - Harris, Nomi L.

AU - Matentzoglu, Nicolas

AU - McMurry, Julie A.

AU - Osumi-Sutherland, David

AU - Cipriani, Valentina

AU - Balhoff, James P.

AU - Conlin, Tom

AU - Blau, Hannah

AU - Baynam, Gareth

AU - Palmer, Richard

AU - Gratian, Dylan

AU - Dawkins, Hugh

AU - Segal, Michael

AU - Jansen, Anna C.

AU - Muaz, Ahmed

AU - Chang, Willie H.

AU - Bergerson, Jenna

AU - Laulederkind, Stanley J. F.

AU - Yueksel, Zafer

AU - Beltran, Sergi

AU - Freeman, Alexandra F.

AU - Sergouniotis, Panagiotis I.

AU - Durkin, Daniel

AU - Storm, Andrea L.

AU - Hanauer, Marc

AU - Brudno, Michael

AU - Bello, Susan M.

AU - Sincan, Murat

AU - Rageth, Kayli

AU - Wheeler, Matthew T.

AU - Oegema, Renske

AU - Lourghi, Halima

AU - Della Rocca, Maria G.

AU - Thompson, Rachel

AU - Castellanos, Francisco

AU - Priest, James

AU - Cunningham-Rundles, Charlotte

AU - Hegde, Ayushi

AU - Lovering, Ruth C.

AU - Hajek, Catherine

AU - Olry, Annie

AU - Notarangelo, Luigi

AU - Similuk, Morgan

AU - Zhang, Xingmin A.

AU - Gomez-Andres, David

AU - Lochmueller, Hanns

AU - Dollfus, Helene

AU - Rosenzweig, Sergio

AU - Marwaha, Shruti

AU - Rath, Ana

AU - Sullivan, Kathleen

AU - Smith, Cynthia

AU - Milner, Joshua D.

AU - Leroux, Dorothee

AU - Boerkoel, Cornelius F.

AU - Klion, Amy

AU - Carter, Melody C.

AU - Groza, Tudor

AU - Smedley, Damian

AU - Haendel, Melissa A.

AU - Mungall, Chris

AU - Robinson, Peter N.

PY - 2019/1/8

Y1 - 2019/1/8

N2 - The Human Phenotype Ontology (HPO)a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseasesis 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.

AB - The Human Phenotype Ontology (HPO)a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseasesis 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.

KW - RD-CONNECT

KW - DISEASE

KW - VARIANTS

KW - PLATFORM

KW - MUTATIONS

KW - DISCOVERY

KW - DATABASES

KW - TOOL

U2 - 10.1093/nar/gky1105

DO - 10.1093/nar/gky1105

M3 - Article

VL - 47

SP - D1018-D1027

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -

Koehler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine J-P 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