The human phenotype ontology: Semantic unification of common and rare disease

T. Groza; S. Kohler; D. Moldenhauer; N. Vasilevsky; G. Baynam; T. Zemojtel; L.M. Schriml; W.A. Kibbe; P.N. Schofield; T. Beck; D. Vasant; A.J. Brookes; A. Zankl; N.L. Washington; C.J. Mungall; S.E. Lewis; M.A. Haendel; H. Parkinson; P.N. Robinson

doi:10.1016/j.ajhg.2015.05.020

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The human phenotype ontology: Semantic unification of common and rare disease

Journal article

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The human phenotype ontology: Semantic unification of common and rare disease

T. Groza, S. Kohler, D. Moldenhauer, N. Vasilevsky, G. Baynam, T. Zemojtel, L.M. Schriml, W.A. Kibbe, P.N. Schofield, T. Beck, …

The American Journal of Human Genetics, Vol.97(1), pp.111-124

2015

DOI: 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.

Details

Title: The human phenotype ontology: Semantic unification of common and rare disease
Authors/Creators: T. Groza (Author/Creator)
S. Kohler (Author/Creator)
D. Moldenhauer (Author/Creator)
N. Vasilevsky (Author/Creator)
G. Baynam (Author/Creator)
T. Zemojtel (Author/Creator)
L.M. Schriml (Author/Creator)
W.A. Kibbe (Author/Creator)
P.N. Schofield (Author/Creator)
T. Beck (Author/Creator)
D. Vasant (Author/Creator)
A.J. Brookes (Author/Creator)
A. Zankl (Author/Creator)
N.L. Washington (Author/Creator)
C.J. Mungall (Author/Creator)
S.E. Lewis (Author/Creator)
M.A. Haendel (Author/Creator)
H. Parkinson (Author/Creator)
P.N. Robinson (Author/Creator)
Publication Details: The American Journal of Human Genetics, Vol.97(1), pp.111-124
Publisher: Cell Press
Identifiers: 991005544404307891
Copyright: 2015 The Authors
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.79 Genomic Bioinformatics
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics