Human Phenotype Ontology (HPO) gene set. This set contains genes that have been annotated to the HPO term "Migraine with aura", which is defined as "A type of migraine in which there is an aura characterized by focal neurological phenomena that usually proceed, but may accompany or occur in the absence of, the headache. The symptoms of an aura may include fully reversible visual, sensory, and speech symptoms but not motor weakness. Visual symptoms may include flickering lights, spots and lines and/or loss of vision and/or unilateral sensory symptoms such as paresthesias or numbness. At least one of the symptoms of an aura develops gradually over 5 or more minutes and/or different symptoms occur in succession." This gene set was automatically constructed using annotation and ontology data provided by HPO and includes gene-phenotypes annotations from all HPO sources. The transitive closure of this term is taken into account using is_a relationships. For more information: The Human Phenotype Ontology Consortium (HPOC), http://human-phenotype-ontology.org This gene set was generated using the GeneWeaver HPO loader v. 0.1.5, HPO OBO v. hp/releases/2020-03-27, and HPO Genes to Phenotypes (all sources, all frequencies) v. 2020.05.06.
S Köhler, SC Doelken, CJ Mungall, S Bauer, HV Firth, I Bailleul-Forestier, GC Black, DL Brown, M Brudno, J Campbell, DR FitzPatrick, JT Eppig, AP Jackson, K Freson, M Girdea, I Helbig, JA Hurst, J Jähn, LG Jackson, AM Kelly, DH Ledbetter, S Mansour, CL Martin, C Moss, A Mumford, WH Ouwehand, SM Park, ER Riggs, RH Scott, S Sisodiya, S Van Vooren, RJ Wapner, AO Wilkie, CF Wright, AT Vulto-van Silfhout, N de Leeuw, BB de Vries, NL Washingthon, CL Smith, M Westerfield, P Schofield, BJ Ruef, GV Gkoutos, M Haendel, D Smedley, SE Lewis, PN Robinson
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.
PUBMED: 24217912
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