Köhler, S., Doelken, S.C., Mungall, C.J., Bauer, S., Firth, H.V., Bailleul-Forestier, I., Black, G.C., 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.M., Riggs, E.R., Scott, R.H., Sisodiya, S., Vooren, S.V., Wapner, R.J., Wilkie, A.O., Wright, C.F., Vulto-van Silfhout, A.T., Leeuw, N.D., de Vries, B.B., Washingthon, N.L., Smith, C.L., Westerfield, M., Schofield, P., Ruef, B.J., Gkoutos, G.V., Haendel, M., Smedley, D., Lewis, S.E., and Robinson, P.N. (2013) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic acids research. 42(1):D966-74.
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.