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


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.

Type Journal
ISBN 1537-6605 (Electronic) 0002-9297 (Linking)
Authors Groza, T. ; Kohler, 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.;
Responsible Garvan Author (missing name)
Publisher Name American Journal Of Human Genetics
Published Date 2015-01-01
Published Volume 97
Published Issue 1
Published Pages 111-24
Status Published in-print
URL link to publisher's version
OpenAccess link to author's accepted manuscript version