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

T. Groza, S. Köhler, D. Moldenhauer, N. Vasilevsky, Gareth 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

    Research output: Contribution to journalArticlepeer-review

    138 Citations (Scopus)


    © 2015 The Authors. 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
    Pages (from-to)111-124
    Number of pages14
    JournalAmerican Journal of Human Genetics
    Issue number1
    Early online date25 Jun 2015
    Publication statusPublished - 2 Jul 2015


    Dive into the research topics of 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease'. Together they form a unique fingerprint.

    Cite this