The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Köhler, S., Doelken, S. C., Mungall, C. J., Bauer, S., Firth, H. V., Bailleul-Forestier, I., Black, G. C. M., Brown, D. L., Brudno, M., Campbell, J., FitzPatrick, D. R., Eppig, J. T., Jackson, A. P., Freson, K., Girdea, M., Helbig, I., Hurst, J. A., Jähn, J., Jackson, L. G., Kelly, A. M., Ledbetter, D. H., Mansour, S., Martin, C. L., Moss, C., Mumford, A., Ouwehand, W. H., Park, S., Riggs, E. R., Scott, R. H., Sisodiya, S., Van Vooren, S., Wapner, R. J., Wilkie, A. O. M., Wright, C. F., Vulto-van Silfhout, A. T., de Leeuw, N., de Vries, B. B. A., Washingthon, N. L., Smith, C. L., Westerfield, M., Schofield, P., Ruef, B. J., Gkoutos, G. V., Haendel, M., Smedley, D., Lewis, S. E., & Robinson, P. N. Nucleic Acids Research, 42(Database issue):D966–974, January, 2014.
doi  abstract   bibtex   
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.
@article{kohler_human_2014,
	title = {The {Human} {Phenotype} {Ontology} project: linking molecular biology and disease through phenotype data},
	volume = {42},
	issn = {1362-4962},
	shorttitle = {The {Human} {Phenotype} {Ontology} project},
	doi = {10.1093/nar/gkt1026},
	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.},
	language = {eng},
	number = {Database issue},
	journal = {Nucleic Acids Research},
	author = {Köhler, Sebastian and Doelken, Sandra C. and Mungall, Christopher J. and Bauer, Sebastian and Firth, Helen V. and Bailleul-Forestier, Isabelle and Black, Graeme C. M. and Brown, Danielle L. and Brudno, Michael and Campbell, Jennifer and FitzPatrick, David R. and Eppig, Janan T. and Jackson, Andrew P. and Freson, Kathleen and Girdea, Marta and Helbig, Ingo and Hurst, Jane A. and Jähn, Johanna and Jackson, Laird G. and Kelly, Anne M. and Ledbetter, David H. and Mansour, Sahar and Martin, Christa L. and Moss, Celia and Mumford, Andrew and Ouwehand, Willem H. and Park, Soo-Mi and Riggs, Erin Rooney and Scott, Richard H. and Sisodiya, Sanjay and Van Vooren, Steven and Wapner, Ronald J. and Wilkie, Andrew O. M. and Wright, Caroline F. and Vulto-van Silfhout, Anneke T. and de Leeuw, Nicole and de Vries, Bert B. A. and Washingthon, Nicole L. and Smith, Cynthia L. and Westerfield, Monte and Schofield, Paul and Ruef, Barbara J. and Gkoutos, Georgios V. and Haendel, Melissa and Smedley, Damian and Lewis, Suzanna E. and Robinson, Peter N.},
	month = jan,
	year = {2014},
	pmid = {24217912},
	pmcid = {PMC3965098},
	keywords = {Animals, Biological Ontologies, Databases, Factual, Genetic Diseases, Inborn, Genomics, Humans, Internet, Mice, Phenotype},
	pages = {D966--974},
}
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