Phenotypic analysis of clinical narratives using human phenotype ontology

Feichen Shen, Liwei Wang, Hongfang D Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Title of host publicationMEDINFO 2017
Subtitle of host publicationPrecision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics
PublisherIOS Press
Pages581-585
Number of pages5
Volume245
ISBN (Electronic)9781614998297
DOIs
StatePublished - Jan 1 2017
Event16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017 - Hangzhou, China
Duration: Aug 21 2017Aug 25 2017

Publication series

NameStudies in Health Technology and Informatics
Volume245
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Other

Other16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017
CountryChina
CityHangzhou
Period8/21/178/25/17

Fingerprint

Ontology
Phenotype
Medicine
Data mining
Precision Medicine
Hepatolenticular Degeneration
Translational Medical Research
Information Dissemination
Vocabulary
Biomedical Research
Genotype
Demography

Keywords

  • Human phenotype ontology
  • Phenotypic analysis
  • Semantic annotation

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Shen, F., Wang, L., & Liu, H. D. (2017). Phenotypic analysis of clinical narratives using human phenotype ontology. In MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics (Vol. 245, pp. 581-585). (Studies in Health Technology and Informatics; Vol. 245). IOS Press. https://doi.org/10.3233/978-1-61499-830-3-581

Phenotypic analysis of clinical narratives using human phenotype ontology. / Shen, Feichen; Wang, Liwei; Liu, Hongfang D.

MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. Vol. 245 IOS Press, 2017. p. 581-585 (Studies in Health Technology and Informatics; Vol. 245).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Shen, F, Wang, L & Liu, HD 2017, Phenotypic analysis of clinical narratives using human phenotype ontology. in MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. vol. 245, Studies in Health Technology and Informatics, vol. 245, IOS Press, pp. 581-585, 16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017, Hangzhou, China, 8/21/17. https://doi.org/10.3233/978-1-61499-830-3-581
Shen F, Wang L, Liu HD. Phenotypic analysis of clinical narratives using human phenotype ontology. In MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. Vol. 245. IOS Press. 2017. p. 581-585. (Studies in Health Technology and Informatics). https://doi.org/10.3233/978-1-61499-830-3-581
Shen, Feichen ; Wang, Liwei ; Liu, Hongfang D. / Phenotypic analysis of clinical narratives using human phenotype ontology. MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. Vol. 245 IOS Press, 2017. pp. 581-585 (Studies in Health Technology and Informatics).
@inproceedings{77d67c7e1c334d3fa80a06d0c150f086,
title = "Phenotypic analysis of clinical narratives using human phenotype ontology",
abstract = "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.",
keywords = "Human phenotype ontology, Phenotypic analysis, Semantic annotation",
author = "Feichen Shen and Liwei Wang and Liu, {Hongfang D}",
year = "2017",
month = "1",
day = "1",
doi = "10.3233/978-1-61499-830-3-581",
language = "English (US)",
volume = "245",
series = "Studies in Health Technology and Informatics",
publisher = "IOS Press",
pages = "581--585",
booktitle = "MEDINFO 2017",

}

TY - GEN

T1 - Phenotypic analysis of clinical narratives using human phenotype ontology

AU - Shen, Feichen

AU - Wang, Liwei

AU - Liu, Hongfang D

PY - 2017/1/1

Y1 - 2017/1/1

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

VL - 245

T3 - Studies in Health Technology and Informatics

SP - 581

EP - 585

BT - MEDINFO 2017

PB - IOS Press

ER -