The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Research output: Contribution to journalArticlepeer-review


  • S. Kohler
  • S. C. Doelken
  • C. J. Mungall
  • S. Bauer
  • H. V. Firth
  • I. Bailleul-Forestier
  • G. C. Black
  • D. L. Brown
  • M. Brudno
  • J. Campbell
  • D. R. FitzPatrick
  • J. T. Eppig
  • A. P. Jackson
  • K. Freson
  • M. Girdea
  • I. Helbig
  • J. A. Hurst
  • J. Jahn
  • L. G. Jackson
  • A. M. Kelly
  • D. H. Ledbetter
  • S. Mansour
  • C. L. Martin
  • C. Moss
  • A. Mumford
  • W. H. Ouwehand
  • S. M. Park
  • E. R. Riggs
  • R. H. Scott
  • S. Sisodiya
  • S. Van Vooren
  • R. J. Wapner
  • A. O. Wilkie
  • C. F. Wright
  • A. T. Vulto-van Silfhout
  • N. de Leeuw
  • B. B. de Vries
  • N. L. Washingthon
  • C. L. Smith
  • M. Westerfield
  • P. Schofield
  • B. J. Ruef
  • M. Haendel
  • D. Smedley
  • S. E. Lewis
  • P. N. Robinson

Colleges, School and Institutes


The Human Phenotype Ontology (HPO) project, available at, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.


Original languageEnglish
Pages (from-to)D966-974
JournalNucleic Acids Research
Issue numberDatabase issue
Early online date11 Nov 2013
Publication statusPublished - 1 Jan 2014

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