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

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-phenotypeontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [3];  [4];  [2]; ORCiD logo [3];  [2];  [5];  [6]; ORCiD logo [7];  [6]; ORCiD logo [8]; ORCiD logo [9]; ORCiD logo [7]; ORCiD logo [2];  [10];  [11];  [12];  [13];  [14] more »;  [15];  [16];  [17];  [18]; ORCiD logo [19]; ORCiD logo [20]; ORCiD logo [21];  [18];  [22];  [23];  [24];  [25];  [17]; ORCiD logo [26];  [27];  [27]; ORCiD logo [28];  [29];  [30];  [24]; ORCiD logo [31];  [23];  [32];  [33];  [23]; ORCiD logo [34];  [27];  [30];  [18];  [18]; ORCiD logo [2];  [35]; ORCiD logo [36];  [37];  [38];  [28]; ORCiD logo [30];  [39]; ORCiD logo [26];  [18];  [37];  [27];  [18];  [18];  [16];  [4];  [7];  [5]; ORCiD logo [40] « less
+ Show Author Affiliations
  1. Charité Centrum für Therapieforschung, Charité—Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Inst. of Health, Berlin (Germany); Einstein Center Digital Future, Berlin (Germany); Monarch Initiative (monarchinitiative.org)
  2. Monarch Initiative (monarchinitiative.org); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  3. Monarch Initiative (monarchinitiative.org); Oregon Health & Science Univ., Portland, OR (United States)
  4. Monarch Initiative (monarchinitiative.org); Queen Mary University of London (United Kingdom). Genomics England
  5. Monarch Initiative (monarchinitiative.org); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
  6. Monarch Initiative (monarchinitiative.org); Wellcome Trust Genome Campus, Cambridge (United Kingdom). European Bioinformatics Institute (EMBL-EBI)
  7. Monarch Initiative (monarchinitiative.org); Oregon State Univ., Corvallis, OR (United States). Linus Pauling Inst.
  8. Monarch Initiative (monarchinitiative.org); Queen Mary Univ. College of London (United Kingdom). William Harvey Research Inst.; Univ. College of London (United Kingdom). UCL Genetics Inst.; University College of London (United Kingdom). UCL Inst. of Ophthalmology
  9. Monarch Initiative (monarchinitiative.org); Univ. of North Carolina, Chapel Hill, NC (United States). Renaissance Computing Inst.
  10. Government of Western Australia, Perth, WA (Australia). Dept. of Health. Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and The Office of Population Health Genomics; Univ. of Western Australia, Perth, WA (Australia). School of Paediatrics and Telethon Kids Inst.; Murdoch Univ., WA (Australia). Inst. for Immunology and Infectious Diseases; Curtin Univ., Perth, WA (Australia). Dept. of Science and Engineering. Spatial Sciences
  11. Curtin Univ., Perth, WA (Australia). Dept. of Science and Engineering. Spatial Sciences
  12. Government of Western Australia, Perth, WA (Australia). Dept. of Health. Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and The Office of Population Health Genomics
  13. Government of Western Australia, Perth, WA (Australia). Dept. of Health. The Office of Population Health Genomics
  14. SimulConsult, Chestnut Hill, MA, (United States)
  15. Vrije Univ., Brussels (Belgium). Neurogenetics Research Group; UZ Brussels (Belgium). Dept. of Pediatrics. Pediatric Neurology Unit
  16. Monarch Initiative (monarchinitiative.org); Garvan Inst. of Medical Research, Sydney, NSW (Australia)
  17. Univ. of Toronto, ON (Canada). Centre for Computational Medicine. Hospital for Sick Children. Dept. of Computer Science
  18. National Institutes of Health (NIH), Bethesda, MD (United States). National Inst. of Allergy and Infectious Diseases
  19. Marquette Univ., Milwaukee, WI (United States). Medical College of Wisconsin. Dept. of Biomedical Engineering. Rat Genome Database
  20. Bioscientia GmbH, Ingelheim (Germany)
  21. Barcelona Institute of Science and Technology (BIST), Barcelona (Spain). CNAG-CRG, Centre for Genomic Regulation (CRG); Univ. Pompeu Fabra, Barcelona (Spain)
  22. Univ. of Manchester (United Kingdom). Manchester Royal Eye Hospital
  23. The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  24. ICF, Rockville, MD, (United States); National Institutes of Health (NIH), Bethesda, MD (United States). National Center for Advancing Translational Sciences. Office of Rare Diseases Research
  25. Orphanet, Paris (France). Plateforme Maladies Rares. INSERM
  26. The Jackson Lab., Bar Harbor, ME (United States)
  27. Sanford Health, Sioux Falls, SD (United States). Sanford Imagenetics
  28. Stanford Univ., CA (United States). School of Medicine. Center for Undiagnosed Diseases
  29. Univ. of Utrecht (Netherlands). Univ. Medical Center. Dept. of Genetics
  30. Orphanet, Paris (France). Plateforme Maladies Rares. INSERM
  31. Newcastle Univ., Newcastle upon Tyne (United Kingdom). Inst. of Genetic Medicine
  32. Stanford Univ., CA (United States). School of Medicine. Dept. of Pediatrics
  33. Icahn School of Medicine at Mount Sinai, New York, NY (United States)
  34. Univ. College London (United Kingdom). Inst. of Cardiovascular Science
  35. Vall d’Hebron Research Inst. (VHIR), Barcelona (Spain). Hospital Universitari Vall d’Hebron. Child Neurology Unit
  36. Barcelona Institute of Science and Technology (BIST), Barcelona (Spain). CNAG-CRG, Centre for Genomic Regulation (CRG); Univ. of Freiburg (Germany). Medical Center. Faculty of Medicine. Dept. of Neuropediatrics and Muscle Disorders; Univ. of Ottawa (Canada). Children’s Hospital of Eastern Ontario Research Inst.; The Ottawa Hospital, Ottawa (Canada). Dept. of Medicine. Division of Neurology
  37. Strasbourg Univ. Hospital, Strasbourg (France). SENSGENE FSMR Network. Centre for Rare Eye Diseases CARGO
  38. National Institutes of Health (NIH), Bethesda, MD (United States). Clinical Center. Dept. of Lab. Medicine. Immunology Service
  39. Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine. The Children’s Hospital of Philadelphia. Dept. of Pediatrics. Division of Allergy Immunology
  40. Monarch Initiative (monarchinitiative.org); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States); Univ. of Connecticut, Farmington, CT (United States). Inst. for Systems Genomics
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1625571
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 47; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

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 A., Mungall, Chris, and Robinson, Peter N. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. United States: N. p., 2018. Web. doi:10.1093/nar/gky1105.
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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 A., Mungall, Chris, & Robinson, Peter N. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. United States. https://doi.org/10.1093/nar/gky1105
Copy to clipboard
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 A., Mungall, Chris, and Robinson, Peter N. Thu . "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources". United States. https://doi.org/10.1093/nar/gky1105. https://www.osti.gov/servlets/purl/1625571.
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@article{osti_1625571,
title = {Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources},
author = {Köhler, Sebastian and Carmody, Leigh and Vasilevsky, Nicole and Jacobsen, Julius O B and Danis, Daniel and Gourdine, Jean-Philippe and Gargano, Michael and Harris, Nomi L. and Matentzoglu, Nicolas and McMurry, Julie A. and Osumi-Sutherland, David and Cipriani, Valentina and Balhoff, James P. and Conlin, Tom and Blau, Hannah and Baynam, Gareth and Palmer, Richard and Gratian, Dylan and Dawkins, Hugh and Segal, Michael and Jansen, Anna C. and Muaz, Ahmed and Chang, Willie H. and Bergerson, Jenna and Laulederkind, Stanley J F and Yüksel, Zafer and Beltran, Sergi and Freeman, Alexandra F. and Sergouniotis, Panagiotis I. and Durkin, Daniel and Storm, Andrea L. and Hanauer, Marc and Brudno, Michael and Bello, Susan M. and Sincan, Murat and Rageth, Kayli and Wheeler, Matthew T. and Oegema, Renske and Lourghi, Halima and Della Rocca, Maria G. and Thompson, Rachel and Castellanos, Francisco and Priest, James and Cunningham-Rundles, Charlotte and Hegde, Ayushi and Lovering, Ruth C. and Hajek, Catherine and Olry, Annie and Notarangelo, Luigi and Similuk, Morgan and Zhang, Xingmin A. and Gómez-Andrés, David and Lochmüller, Hanns and Dollfus, Hélène and Rosenzweig, Sergio and Marwaha, Shruti and Rath, Ana and Sullivan, Kathleen and Smith, Cynthia and Milner, Joshua D. and Leroux, Dorothée and Boerkoel, Cornelius F. and Klion, Amy and Carter, Melody C. and Groza, Tudor and Smedley, Damian and Haendel, Melissa A. and Mungall, Chris and Robinson, Peter N.},
abstractNote = {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-phenotypeontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.},
doi = {10.1093/nar/gky1105},
journal = {Nucleic Acids Research},
number = D1,
volume = 47,
place = {United States},
year = {Thu Nov 22 00:00:00 EST 2018},
month = {Thu Nov 22 00:00:00 EST 2018}
}
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