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

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.
Authors:
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Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
American Journal of Human Genetics
Additional Journal Information:
Journal Volume: 97; Journal Issue: 1; Journal ID: ISSN 0002-9297
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1242998
Alternate Identifier(s):
OSTI ID: 1208651