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 journalArticlepeer-review

157 Scopus citations


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 languageEnglish (US)
Pages (from-to)111-124
Number of pages14
JournalAmerican Journal of Human Genetics
Issue number1
StatePublished - 2015

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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