The human phenotype ontology: semantic unification of common and rare disease

Groza, Tudor, Kohler, Sebastian, Moldenhauer, Dawid, Vasilevsky, Nicole, Baynam, Gareth, Zemojtel, Tomasz, Schriml, Lynn Marie, Kibbe, Warren Alden, Schofield, Paul N., Beck, Tim, Vasant, Drashtti, Brookes, Anthony J., Zankl, Andreas, Washington, Nicole L., Mungall, Christopher J., Lewis, Suzanna E., Haendel, Melissa A., Parkinson, Helen and Robinson, Peter N. (2015) The human phenotype ontology: semantic unification of common and rare disease. American Journal of Human Genetics, 97 1: 111-124. doi:10.1016/j.ajhg.2015.05.020


Author Groza, Tudor
Kohler, Sebastian
Moldenhauer, Dawid
Vasilevsky, Nicole
Baynam, Gareth
Zemojtel, Tomasz
Schriml, Lynn Marie
Kibbe, Warren Alden
Schofield, Paul N.
Beck, Tim
Vasant, Drashtti
Brookes, Anthony J.
Zankl, Andreas
Washington, Nicole L.
Mungall, Christopher J.
Lewis, Suzanna E.
Haendel, Melissa A.
Parkinson, Helen
Robinson, Peter N.
Title The human phenotype ontology: semantic unification of common and rare disease
Journal name American Journal of Human Genetics   Check publisher's open access policy
ISSN 1537-6605
0002-9297
Publication date 2015-07-02
Sub-type Article (original research)
DOI 10.1016/j.ajhg.2015.05.020
Open Access Status DOI
Volume 97
Issue 1
Start page 111
End page 124
Total pages 14
Place of publication Cambridge, MA United States
Publisher Cell Press [Elsevier]
Collection year 2016
Language eng
Abstract 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.
Keyword Human phenotype ontology
Rare disease community
Phenotype-driven analysis
Concept-recognition procedure
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2016 Collection
School of Information Technology and Electrical Engineering Publications
 
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