The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

Tudor Groza; Sebastian Köhler; Dawid Moldenhauer; Nicole Vasilevsky; Gareth Baynam; Tomasz Zemojtel; Lynn Marie Schriml; Warren Alden Kibbe; Paul N. Schofield; Tim Beck; Drashtti Vasant; Anthony J. Brookes; Andreas Zankl; Nicole L. Washington; Christopher J. Mungall; Suzanna E. Lewis; Melissa A. Haendel; Helen Parkinson; Peter N. Robinson

doi:10.1016/j.ajhg.2015.05.020

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

Tudor Groza, Sebastian Köhler, Dawid Moldenhauer, Nicole Vasilevsky, Gareth Baynam, Tomasz Zemojtel, Lynn Marie Schriml, Warren Alden Kibbe, Paul N. Schofield, Tim Beck, Drashtti Vasant, Anthony J. Brookes, Andreas Zankl, Nicole L. Washington, Christopher J. Mungall, Suzanna E. Lewis, Melissa A. Haendel, Helen Parkinson, Peter N. Robinson

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157 Scopus citations

Abstract

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.

Original language	English (US)
Pages (from-to)	111-124
Number of pages	14
Journal	American Journal of Human Genetics
Volume	97
Issue number	1
DOIs	https://doi.org/10.1016/j.ajhg.2015.05.020
State	Published - 2015

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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Groza, T., Köhler, S., Moldenhauer, D., Vasilevsky, N., Baynam, G., Zemojtel, T., Schriml, L. M., Kibbe, W. A., Schofield, P. N., Beck, T., Vasant, D., Brookes, A. J., Zankl, A., Washington, N. L., Mungall, C. J., Lewis, S. E., Haendel, M. A., Parkinson, H., & Robinson, P. N. (2015). The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. American Journal of Human Genetics, 97(1), 111-124. https://doi.org/10.1016/j.ajhg.2015.05.020

Groza, T, Köhler, S, Moldenhauer, D, Vasilevsky, N, Baynam, G, Zemojtel, T, Schriml, LM, Kibbe, WA, Schofield, PN, Beck, T, Vasant, D, Brookes, AJ, Zankl, A, Washington, NL, Mungall, CJ, Lewis, SE, Haendel, MA, Parkinson, H & Robinson, PN 2015, 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease', American Journal of Human Genetics, vol. 97, no. 1, pp. 111-124. https://doi.org/10.1016/j.ajhg.2015.05.020

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title = "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease",

abstract = "The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.",

author = "Tudor Groza and Sebastian K{\"o}hler and Dawid Moldenhauer and Nicole Vasilevsky and Gareth Baynam and Tomasz Zemojtel and Schriml, {Lynn Marie} and Kibbe, {Warren Alden} and Schofield, {Paul N.} and Tim Beck and Drashtti Vasant and Brookes, {Anthony J.} and Andreas Zankl and Washington, {Nicole L.} and Mungall, {Christopher J.} and Lewis, {Suzanna E.} and Haendel, {Melissa A.} and Helen Parkinson and Robinson, {Peter N.}",

note = "Funding Information: This work was supported by the Bundesministerium f{\"u}r Bildung und Forschung (project 0313911 ), the European Commission Seventh Framework Programme (FP7; grant 602300 ; SYBIL project), the Raine Clinician Research Fellowship ( 20140101 ), and the National Health and Medical Research Council of Australia (grant APP1055319 , which is partnered with FP7 grant 305444 ). Oregon Health and Science University acknowledges the support of grant 1R24OD011883-01 from the NIH Office of the Director . T.G. was supported by an Australian Research Council Discovery Early Career Researcher Award ( DE120100508 ). D.V. was supported in part by the BioMedBridges project funded by Research Infrastructures of the FP7 (grant 284209 ). H.P. was supported by European Molecular Biology Laboratory Core Funds . This work was supported by the director, Basic Energy Sciences, Office of Science, US Department of Energy under contract DE-AC02-05CH11231 and NIH contract 1R24OD011883-01 . This document was prepared as an account of work sponsored by the US Government . While this document is believed to contain correct information, neither the US Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed or represents that its use would not infringe privately owned rights. The views and opinions of authors expressed herein do not necessarily state or reflect those of the US Government or any agency thereof or the Regents of the University of California. Publisher Copyright: {\textcopyright} 2015 The Authors.",

year = "2015",

doi = "10.1016/j.ajhg.2015.05.020",

language = "English (US)",

volume = "97",

pages = "111--124",

journal = "American Journal of Human Genetics",

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T2 - Semantic Unification of Common and Rare Disease

AU - Groza, Tudor

AU - Köhler, Sebastian

AU - Moldenhauer, Dawid

AU - Vasilevsky, Nicole

AU - Baynam, Gareth

AU - Zemojtel, Tomasz

AU - Schriml, Lynn Marie

AU - Kibbe, Warren Alden

AU - Schofield, Paul N.

AU - Beck, Tim

AU - Vasant, Drashtti

AU - Brookes, Anthony J.

AU - Zankl, Andreas

AU - Washington, Nicole L.

AU - Mungall, Christopher J.

AU - Lewis, Suzanna E.

AU - Haendel, Melissa A.

AU - Parkinson, Helen

AU - Robinson, Peter N.

N1 - Funding Information: This work was supported by the Bundesministerium für Bildung und Forschung (project 0313911 ), the European Commission Seventh Framework Programme (FP7; grant 602300 ; SYBIL project), the Raine Clinician Research Fellowship ( 20140101 ), and the National Health and Medical Research Council of Australia (grant APP1055319 , which is partnered with FP7 grant 305444 ). Oregon Health and Science University acknowledges the support of grant 1R24OD011883-01 from the NIH Office of the Director . T.G. was supported by an Australian Research Council Discovery Early Career Researcher Award ( DE120100508 ). D.V. was supported in part by the BioMedBridges project funded by Research Infrastructures of the FP7 (grant 284209 ). H.P. was supported by European Molecular Biology Laboratory Core Funds . This work was supported by the director, Basic Energy Sciences, Office of Science, US Department of Energy under contract DE-AC02-05CH11231 and NIH contract 1R24OD011883-01 . This document was prepared as an account of work sponsored by the US Government . While this document is believed to contain correct information, neither the US Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed or represents that its use would not infringe privately owned rights. The views and opinions of authors expressed herein do not necessarily state or reflect those of the US Government or any agency thereof or the Regents of the University of California. Publisher Copyright: © 2015 The Authors.

PY - 2015

Y1 - 2015

N2 - The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.

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The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

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