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

Köhler, S; Doelken, SC; Mungall, CJ; Bauer, S; Firth, HV; Bailleul-Forestier, I; Black, GC; Brown, DL; Brudno, M; Campbell, J; et al. Köhler, S; Doelken, SC; Mungall, CJ; Bauer, S; Firth, HV; Bailleul-Forestier, I; Black, GC; Brown, DL; Brudno, M; Campbell, J; FitzPatrick, DR; Eppig, JT; Jackson, AP; Freson, K; Girdea, M; Helbig, I; Hurst, JA; Jähn, J; Jackson, LG; Kelly, AM; Ledbetter, DH; Mansour, S; Martin, CL; Moss, C; Mumford, A; Ouwehand, WH; Park, SM; Riggs, ER; Scott, RH; Sisodiya, S; Van Vooren, S; Wapner, RJ; Wilkie, AO; Wright, CF; Vulto-van Silfhout, AT; de Leeuw, N; de Vries, BB; Washingthon, NL; Smith, CL; Westerfield, M; Schofield, P; Ruef, BJ; Gkoutos, GV; Haendel, M; Smedley, D; Lewis, SE; Robinson, PN (2014) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research, 42 (Database issue). D966-D974. ISSN 1362-4962 https://doi.org/10.1093/nar/gkt1026
SGUL Authors: Mansour, Sahar

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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.

Item Type: Article
Additional Information: © The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Animals, Biological Ontologies, Databases, Factual, Genetic Diseases, Inborn, Genomics, Humans, Internet, Mice, Phenotype, Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, BIOCHEMISTRY & MOLECULAR BIOLOGY, INTERNATIONAL STANDARDS, GENE DISCOVERY, INFORMATICS, INTEGRATION, EVOLUTION, MEDICINE, SEARCHES, Developmental Biology, 05 Environmental Sciences, 06 Biological Sciences, 08 Information And Computing Sciences
SGUL Research Institute / Research Centre: Academic Structure > Molecular and Clinical Sciences Research Institute (MCS) > Cell Sciences (INCCCS)
Journal or Publication Title: Nucleic Acids Research
ISSN: 1362-4962
Language: eng
Dates:
DateEvent
1 January 2014Published
PubMed ID: 24217912
Web of Science ID: WOS:000331139800142
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URI: https://openaccess.sgul.ac.uk/id/eprint/105377
Publisher's version: https://doi.org/10.1093/nar/gkt1026

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