ABSTRACT
Phenotype-based analysis of WES/WGS data is one of the most powerful approaches towards gene prioritization. This chapter presents the Human Phenotype Ontology (HPO) and explains how HPO-based computational phenotype analysis works. The HPO is being used by numerous databases in the field of human genetics to annotate patient data and to enable phenotype- based searching and analysis. Annotations within the ontologies such as the Gene Ontology and the HPO follow the so-called Annotation Propagation Rule. One of the most important tasks of a clinician is to determine the phenotype of patients and to use the phenotypic information to make a correct diagnosis. One obvious advantage of capturing phenotypic information in the form of an ontology is that search routines can be designed to exploit the semantic relationships between terms. Semantic similarity metrics can be adapted to measure phenotypic similarity between queries and hereditary diseases annotated using the HPO.
