TY - GEN
T1 - Phenotypic analysis of clinical narratives using human phenotype ontology
AU - Shen, Feichen
AU - Wang, Liwei
AU - Liu, Hongfang
N1 - Funding Information:
We would like to thank the support from our colleague Ra-vikumar Komandur Elayavilli for his valuable suggestions on this research. This work was made possible by internal funding from Center for Individualized Medicine of Mayo Clinic and NCATS Biomedical Translator Award, OT3TR00201901.
Publisher Copyright:
© 2017 International Medical Informatics Association (IMIA) and IOS Press.
PY - 2017
Y1 - 2017
N2 - Phenotypes are defined as observable characteristics and clinical traits of diseases and organisms. As connectors between medical experimental findings and clinical practices, phenotypes play vital roles in translational medicine. To facilitate the translation between genotype and phenotype, Human Phenotype Ontology (HPO) was developed as a semantically computable vocabulary to capture phenotypic abnormalities found in human diseases discovered through biomedical research. The use of HPO in annotating phenotypic information in clinical practice remains unexplored. 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 and assessed the distribution information of HPO terms in the corpus. We also analyzed the distributional difference of HPO terms among demographic groups. We further demonstrated the potential application of the annotated corpus to support knowledge discovery in precision medicine through Wilson's Disease.
AB - Phenotypes are defined as observable characteristics and clinical traits of diseases and organisms. As connectors between medical experimental findings and clinical practices, phenotypes play vital roles in translational medicine. To facilitate the translation between genotype and phenotype, Human Phenotype Ontology (HPO) was developed as a semantically computable vocabulary to capture phenotypic abnormalities found in human diseases discovered through biomedical research. The use of HPO in annotating phenotypic information in clinical practice remains unexplored. 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 and assessed the distribution information of HPO terms in the corpus. We also analyzed the distributional difference of HPO terms among demographic groups. We further demonstrated the potential application of the annotated corpus to support knowledge discovery in precision medicine through Wilson's Disease.
KW - Human phenotype ontology
KW - Phenotypic analysis
KW - Semantic annotation
UR - http://www.scopus.com/inward/record.url?scp=85040510435&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85040510435&partnerID=8YFLogxK
U2 - 10.3233/978-1-61499-830-3-581
DO - 10.3233/978-1-61499-830-3-581
M3 - Conference contribution
C2 - 29295162
AN - SCOPUS:85040510435
T3 - Studies in Health Technology and Informatics
SP - 581
EP - 585
BT - MEDINFO 2017
A2 - Dongsheng, Zhao
A2 - Gundlapalli, Adi V.
A2 - Marie-Christine, Jaulent
PB - IOS Press
T2 - 16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017
Y2 - 21 August 2017 through 25 August 2017
ER -