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The Human Phenotype Ontology in 2017

Lookup NU author(s): Professor Patrick Chinnery, Professor Hanns Lochmuller, Professor Volker StraubORCiD, Rachel ThompsonORCiD, Catherine TurnerORCiD



This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).


© The Author(s) 2016. Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Publication metadata

Author(s): Kohler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Ayme S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, De Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jahn JA, James R, Krause R, Laulederkind SJF, Lochmuller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, Von Ziegenweidt J, Zankl A, Zuchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN

Publication type: Article

Publication status: Published

Journal: Nucleic Acids Research

Year: 2017

Volume: 45

Issue: D1

Pages: D865-D876

Print publication date: 01/01/2017

Online publication date: 24/09/2016

Acceptance date: 28/10/2016

Date deposited: 25/04/2017

ISSN (print): 0305-1048

ISSN (electronic): 1362-4962

Publisher: Oxford University Press


DOI: 10.1093/nar/gkw1039


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Funder referenceFunder name
DFG, HE5415 / 5-1
FP7 / 2007-2013
HE5415 / 3-1
HE5415 / 6-1
NIH OD #5R24OD011883
NIH [R24- OD011883]
ZON-MW grants 912-12-109