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

Research output: Contribution to journal › Article › peer-review

161 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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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.",

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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.

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

Abstract

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