Journal article
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
Nucleic acids research, v 42(D1), pp D966-D974
01 Jan 2014
PMID: 24217912
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, 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.
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Details
- Title
- The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
- Creators
- Sebastian Koehler - Charite, Inst Med Genet & Human Genet, D-13353 Berlin, GermanySandra C. Doelken - Charité - Universitätsmedizin BerlinChristopher J. Mungall - Lawrence Berkeley National LaboratorySebastian Bauer - Charité - Universitätsmedizin BerlinHelen V. Firth - Cambridge University Hospitals NHS Foundation TrustIsabelle Bailleul-Forestier - Université Toulouse III - Paul SabatierGraeme C. M. Black - University of ManchesterDanielle L. Brown - Newcastle UniversityMichael Brudno - University of TorontoJennifer Campbell - Leeds Teaching Hospitals NHS TrustDavid R. FitzPatrick - University of EdinburghJanan T. Eppig - Jackson LaboratoryAndrew P. Jackson - University of EdinburghKathleen Freson - KU LeuvenMarta Girdea - University of TorontoIngo Helbig - Christian-Albrechts-Universität zu KielJane A. Hurst - University College LondonJohanna Jaehn - College Station Medical CenterLaird G. Jackson - Drexel UniversityAnne M. Kelly - University of CambridgeDavid H. Ledbetter - Geisinger Medical CenterSahar Mansour - St George’s University Hospitals NHS Foundation TrustChrista L. Martin - Geisinger Medical CenterCelia Moss - Birmingham Women’s and Children’s NHS Foundation TrustAndrew Mumford - University of BristolWillem H. Ouwehand - Wellcome Sanger InstituteSoo-Mi Park - Cambridge University Hospitals NHS Foundation TrustErin Rooney Riggs - Geisinger Medical CenterRichard H. Scott - University College LondonSanjay Sisodiya - University College LondonSteven Van Vooren - University of CartagenaRonald J. Wapner - Columbia UniversityAndrew O. M. Wilkie - University of OxfordCaroline F. Wright - Wellcome Sanger InstituteAnneke T. Vulto-van Silfhout - Radboud University NijmegenNicole de Leeuw - Radboud University NijmegenBert B. A. de Vries - Radboud University NijmegenNicole L. Washingthon - Lawrence Berkeley National LaboratoryCynthia L. Smith - Jackson LaboratoryMonte Westerfield - University of OregonPaul Schofield - University of CambridgeBarbara J. Ruef - University of OregonGeorgios V. Gkoutos - Aberystwyth UniversityMelissa Haendel - College Station Medical CenterDamian Smedley - Wellcome Sanger InstituteSuzanna E. Lewis - Lawrence Berkeley National LaboratoryPeter N. Robinson - Charité - Universitätsmedizin Berlin
- Publication Details
- Nucleic acids research, v 42(D1), pp D966-D974
- Publisher
- Oxford Univ Press
- Number of pages
- 9
- Grant note
- 0313911 / Bundesministerium fur Bildung und Forschung [BMBF]; Federal Ministry of Education & Research (BMBF) R01MH074090 / NATIONAL INSTITUTE OF MENTAL HEALTH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Mental Health (NIMH) MC_PC_U127580972 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC); European Commission RO 2005/4-2 / Deutsche Forschungsgemeinschaft [DFG]; German Research Foundation (DFG) P41HG000330 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) HG000330; U41-HG002659; R01-HG004838; R24-OD011883 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA NF-SI-0513-10151 / National Institute for Health Research; National Institute for Health Research (NIHR) DE-AC02-05CH11231 / Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy; United States Department of Energy (DOE) National Institute for Health Research University College London Hospitals Biomedical Research Centre; General Electric RG/09/012/28096 / British Heart Foundation R24OD011883 / OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 602300 / European Community; European Commission 1801/02 / Fight for Sight MC_PC_U127561093 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC)
- Resource Type
- Journal article
- Language
- English
- Web of Science ID
- WOS:000331139800142
- Scopus ID
- 2-s2.0-84891749517
- Other Identifier
- 991019350585704721
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- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology