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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • 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

Published Date

  • July 2, 2015

Published In

Volume / Issue

  • 97 / 1

Start / End Page

  • 111 - 124

PubMed ID

  • 26119816

Pubmed Central ID

  • PMC4572507

Electronic International Standard Serial Number (EISSN)

  • 1537-6605

Digital Object Identifier (DOI)

  • 10.1016/j.ajhg.2015.05.020


  • eng

Conference Location

  • United States