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Title: The Human Phenotype Ontology in 2017

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 PhenotypeOntology (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.
Authors:
 [1] ; ORCiD logo [2] ;  [2] ;  [2] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [8] ;  [9] ;  [10] ;  [11] ;  [12] ;  [11] ;  [13] ;  [14] ;  [15] more »;  [16] ;  [9] ;  [17] ;  [18] ;  [8] ;  [19] ;  [9] ;  [20] ; ORCiD logo [21] ;  [22] ;  [23] ;  [24] ;  [25] ;  [26] ;  [10] ;  [25] ;  [27] ;  [13] ;  [28] ;  [29] ;  [11] ;  [5] ;  [22] ;  [22] ;  [22] ;  [9] ;  [26] ;  [13] ;  [30] ;  [31] ;  [32] ;  [33] ;  [1] ;  [13] ;  [34] ;  [13] ;  [35] ;  [2] ;  [36] « less
  1. Charite-Universitatsmedizin, Berlin (Germany)
  2. Oregon Health and Science Univ., Portland, OR (United States)
  3. Institut du Cerveau et de la Moelle epiniere, Paris (France)
  4. Univ. of Western Australia, Perth, WA (Australia); King Edward Memorial Hospital Department of Health, Perth, WA (Austrailia)
  5. The Jackson Laboratory, Bar Harbor, ME (United States)
  6. Sanford Health, Sioux Falls, SD (United States)
  7. Univ. of Ottawa, ON (Canada)
  8. Univ. of Toronto, ON (Canada); Hospital for Sick Children, Toronto, ON (Canada)
  9. Univ. of Cambridge (United Kingdom); Cambridge Biomedical Campus, Cambridge (United Kingdom)
  10. Univ. College London, London (United Kingdom)
  11. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (United States)
  12. Health Department of Western Australia, Perth, WA (Australia)
  13. Queen Mary Univ. of London (United Kingdom)
  14. Radboud Univ., Nijmegen (Netherlands)
  15. Wellcome Genome Campus, Hinxton, Cambridge (United Kingdom)
  16. Univ. of Leuven (Belgium)
  17. Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)
  18. The Children's Hospital of Philadelphia, PA (United States); Univ. Medical Center Schleswig-Holstein (UKSH), Kiel (Germany)
  19. Univ. Medical Center Schleswig-Holstein (UKSH), Kiel (Germany
  20. Univ. of Luxembourg (Luxembourg)
  21. Medical College of Wisconsin, Milwaukee, WI (United States)
  22. Univ. of Newcastle, Newcastle upon Tyne (United Kingdom)
  23. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (United States)
  24. Tohoku Univ., Sendai (Japan)
  25. Orphanet, Paris (France)
  26. Cambridge Biomedical Campus, Cambridge (United Kingdom)
  27. Center for Pediatrics and Adolescent Medicine, Heidelberg (Germany)
  28. SimulConsult Inc., Chestnut Hill, MA (United States)
  29. Univ. of Manchester (United Kingdom)
  30. Univ. of Oxford (United Kingdom)
  31. Univ. of Cambridge (United Kingdom)
  32. Univ. of Sydney, NSW (Australia); Sydney Childrens Hospitals Network, Sydney, NSW (Australia)
  33. Univ. of Miami, FL (United States)
  34. Garvan Inst. of Medical Research, Sydney, NSW (Australia); St. Vincent's Clinical School, Sydney, NSW (Australia)
  35. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  36. Univ. of Connecticut, Farmington, CT (United States); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 45; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1408411

Köhler, Sebastian, Vasilevsky, Nicole A., Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M., Boerkoel, Cornelius F., Boycott, Kym M., Brudno, Michael, Buske, Orion J., Chinnery, Patrick F., Cipriani, Valentina, Connell, Laureen E., Dawkins, Hugh J. S., DeMare, Laura E., Devereau, Andrew D., de Vries, Bert B. A., Firth, Helen V., Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A., James, Roger, Krause, Roland, F. Laulederkind, Stanley J., Lochmüller, Hanns, Lyon, Gholson J., Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H., Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H., Segal, Michael, Sergouniotis, Panagiotis I., Sever, Richard, Smith, Cynthia L., Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke W. M., Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius O. B., Groza, Tudor, Smedley, Damian, Mungall, Christopher J., Haendel, Melissa, and Robinson, Peter N.. The Human Phenotype Ontology in 2017. United States: N. p., Web. doi:10.1093/nar/gkw1039.
Köhler, Sebastian, Vasilevsky, Nicole A., Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M., Boerkoel, Cornelius F., Boycott, Kym M., Brudno, Michael, Buske, Orion J., Chinnery, Patrick F., Cipriani, Valentina, Connell, Laureen E., Dawkins, Hugh J. S., DeMare, Laura E., Devereau, Andrew D., de Vries, Bert B. A., Firth, Helen V., Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A., James, Roger, Krause, Roland, F. Laulederkind, Stanley J., Lochmüller, Hanns, Lyon, Gholson J., Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H., Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H., Segal, Michael, Sergouniotis, Panagiotis I., Sever, Richard, Smith, Cynthia L., Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke W. M., Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius O. B., Groza, Tudor, Smedley, Damian, Mungall, Christopher J., Haendel, Melissa, & Robinson, Peter N.. The Human Phenotype Ontology in 2017. United States. doi:10.1093/nar/gkw1039.
Köhler, Sebastian, Vasilevsky, Nicole A., Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M., Boerkoel, Cornelius F., Boycott, Kym M., Brudno, Michael, Buske, Orion J., Chinnery, Patrick F., Cipriani, Valentina, Connell, Laureen E., Dawkins, Hugh J. S., DeMare, Laura E., Devereau, Andrew D., de Vries, Bert B. A., Firth, Helen V., Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A., James, Roger, Krause, Roland, F. Laulederkind, Stanley J., Lochmüller, Hanns, Lyon, Gholson J., Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H., Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H., Segal, Michael, Sergouniotis, Panagiotis I., Sever, Richard, Smith, Cynthia L., Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke W. M., Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius O. B., Groza, Tudor, Smedley, Damian, Mungall, Christopher J., Haendel, Melissa, and Robinson, Peter N.. 2016. "The Human Phenotype Ontology in 2017". United States. doi:10.1093/nar/gkw1039. https://www.osti.gov/servlets/purl/1408411.
@article{osti_1408411,
title = {The Human Phenotype Ontology in 2017},
author = {Köhler, Sebastian and Vasilevsky, Nicole A. and Engelstad, Mark and Foster, Erin and McMurry, Julie and Aymé, Ségolène and Baynam, Gareth and Bello, Susan M. and Boerkoel, Cornelius F. and Boycott, Kym M. and Brudno, Michael and Buske, Orion J. and Chinnery, Patrick F. and Cipriani, Valentina and Connell, Laureen E. and Dawkins, Hugh J. S. and DeMare, Laura E. and Devereau, Andrew D. and de Vries, Bert B. A. and Firth, Helen V. and Freson, Kathleen and Greene, Daniel and Hamosh, Ada and Helbig, Ingo and Hum, Courtney and Jähn, Johanna A. and James, Roger and Krause, Roland and F. Laulederkind, Stanley J. and Lochmüller, Hanns and Lyon, Gholson J. and Ogishima, Soichi and Olry, Annie and Ouwehand, Willem H. and Pontikos, Nikolas and Rath, Ana and Schaefer, Franz and Scott, Richard H. and Segal, Michael and Sergouniotis, Panagiotis I. and Sever, Richard and Smith, Cynthia L. and Straub, Volker and Thompson, Rachel and Turner, Catherine and Turro, Ernest and Veltman, Marijcke W. M. and Vulliamy, Tom and Yu, Jing and von Ziegenweidt, Julie and Zankl, Andreas and Züchner, Stephan and Zemojtel, Tomasz and Jacobsen, Julius O. B. and Groza, Tudor and Smedley, Damian and Mungall, Christopher J. and Haendel, Melissa and Robinson, Peter N.},
abstractNote = {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 PhenotypeOntology (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.},
doi = {10.1093/nar/gkw1039},
journal = {Nucleic Acids Research},
number = D1,
volume = 45,
place = {United States},
year = {2016},
month = {11}
}