Phenotypes are defined as observable characteristics of organisms. To facilitate the translation between genotype and phenotype, Human Phenotype Ontology (HPO) was developed as a semantically computable standardized vocabulary to capture phenotypic abnormalities found in human. In this study, we investigated the use of HPO to annotate phenotypic information in clinical domain by leveraging a corpus of 12.8 million clinical notes created from 2010 to 2015 for 729 thousand patients at Mayo Clinic Rochester campus.