TY - JOUR
T1 - The Human Phenotype Ontology project
T2 - Linking molecular biology and disease through phenotype data
AU - Köhler, Sebastian
AU - Doelken, Sandra C.
AU - Mungall, Christopher J.
AU - Bauer, Sebastian
AU - Firth, Helen V.
AU - Bailleul-Forestier, Isabelle
AU - Black, Graeme C.M.
AU - Brown, Danielle L.
AU - Brudno, Michael
AU - Campbell, Jennifer
AU - Fitzpatrick, David R.
AU - Eppig, Janan T.
AU - Jackson, Andrew P.
AU - Freson, Kathleen
AU - Girdea, Marta
AU - Helbig, Ingo
AU - Hurst, Jane A.
AU - Jähn, Johanna
AU - Jackson, Laird G.
AU - Kelly, Anne M.
AU - Ledbetter, David H.
AU - Mansour, Sahar
AU - Martin, Christa L.
AU - Moss, Celia
AU - Mumford, Andrew
AU - Ouwehand, Willem H.
AU - Park, Soo Mi
AU - Riggs, Erin Rooney
AU - Scott, Richard H.
AU - Sisodiya, Sanjay
AU - Vooren, Steven Van
AU - Wapner, Ronald J.
AU - Wilkie, Andrew O.M.
AU - Wright, Caroline F.
AU - Vulto-Van Silfhout, Anneke T.
AU - Leeuw, Nicole De
AU - De Vries, Bert B.A.
AU - Washingthon, Nicole L.
AU - Smith, Cynthia L.
AU - Westerfield, Monte
AU - Schofield, Paul
AU - Ruef, Barbara J.
AU - Gkoutos, Georgios V.
AU - Haendel, Melissa
AU - Smedley, Damian
AU - Lewis, Suzanna E.
AU - Robinson, Peter N.
N1 - Funding Information:
The Deutsche Forschungsgemeinschaft [DFG RO 2005/ 4-2]; Bundesministerium für Bildung und Forschung [BMBF project number 0313911]; the European Community’s Seventh Framework Programme [Grant Agreement 602300; SYBIL]. Additional support was received from the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under [Contract No. DE-AC02-05CH11231]; the MGD grant from the National Institutes of Health [HG000330]; the ZFIN grant from the National Institutes of Health [U41-HG002659]; National Institutes of Health [R01-HG004838 and R24-OD011883]; National Institute for Health Research University College London Hospitals Biomedical Research Centre. Funding for open access charge: Institutional support.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkt1026
DO - 10.1093/nar/gkt1026
M3 - Article
C2 - 24217912
AN - SCOPUS:84891749517
SN - 0305-1048
VL - 42
SP - D966-D974
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -