Using human phenotype ontology for phenotypic analysis of clinical notes

Feichen Shen; Liwei Wang; Hongfang Liu

doi:10.3233/978-1-61499-830-3-1285

Using human phenotype ontology for phenotypic analysis of clinical notes

Feichen Shen, Liwei Wang, Hongfang Liu

Digital Health Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

11 Scopus citations

Abstract

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.

Original language	English (US)
Title of host publication	MEDINFO 2017
Subtitle of host publication	Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics
Editors	Adi V. Gundlapalli, Jaulent Marie-Christine, Zhao Dongsheng
Publisher	IOS Press BV
Pages	1285
Number of pages	1
ISBN (Electronic)	9781614998297
DOIs	https://doi.org/10.3233/978-1-61499-830-3-1285
State	Published - 2017
Event	16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017 - Hangzhou, China Duration: Aug 21 2017 → Aug 25 2017

Publication series

Name	Studies in Health Technology and Informatics
Volume	245
ISSN (Print)	0926-9630
ISSN (Electronic)	1879-8365

Other

Other	16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017
Country/Territory	China
City	Hangzhou
Period	8/21/17 → 8/25/17

Keywords

Human phenotype ontology
Phenotypic analysis
Semantics

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

Access to Document

10.3233/978-1-61499-830-3-1285

Cite this

Shen, F., Wang, L., & Liu, H. (2017). Using human phenotype ontology for phenotypic analysis of clinical notes. In A. V. Gundlapalli, J. Marie-Christine, & Z. Dongsheng (Eds.), MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics (pp. 1285). (Studies in Health Technology and Informatics; Vol. 245). IOS Press BV. https://doi.org/10.3233/978-1-61499-830-3-1285

Using human phenotype ontology for phenotypic analysis of clinical notes. / Shen, Feichen; Wang, Liwei; Liu, Hongfang.

MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. ed. / Adi V. Gundlapalli; Jaulent Marie-Christine; Zhao Dongsheng. IOS Press BV, 2017. p. 1285 (Studies in Health Technology and Informatics; Vol. 245).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Shen, F, Wang, L & Liu, H 2017, Using human phenotype ontology for phenotypic analysis of clinical notes. in AV Gundlapalli, J Marie-Christine & Z Dongsheng (eds), MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. Studies in Health Technology and Informatics, vol. 245, IOS Press BV, pp. 1285, 16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017, Hangzhou, China, 8/21/17. https://doi.org/10.3233/978-1-61499-830-3-1285

Shen F, Wang L, Liu H. Using human phenotype ontology for phenotypic analysis of clinical notes. In Gundlapalli AV, Marie-Christine J, Dongsheng Z, editors, MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. IOS Press BV. 2017. p. 1285. (Studies in Health Technology and Informatics). https://doi.org/10.3233/978-1-61499-830-3-1285

Shen, Feichen ; Wang, Liwei ; Liu, Hongfang. / Using human phenotype ontology for phenotypic analysis of clinical notes. MEDINFO 2017: Precision Healthcare through Informatics - Proceedings of the 16th World Congress on Medical and Health Informatics. editor / Adi V. Gundlapalli ; Jaulent Marie-Christine ; Zhao Dongsheng. IOS Press BV, 2017. pp. 1285 (Studies in Health Technology and Informatics).

@inproceedings{1d309aa4e75e4988bd20a9ee82d95c39,

title = "Using human phenotype ontology for phenotypic analysis of clinical notes",

abstract = "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.",

keywords = "Human phenotype ontology, Phenotypic analysis, Semantics",

author = "Feichen Shen and Liwei Wang and Hongfang Liu",

note = "Funding Information: This work was made possible by internal funding from Center for Individualized Medicine of Mayo Clinic and NCATS Biomedical Translator Award, OT3TR00201901. Publisher Copyright: {\textcopyright} 2017 International Medical Informatics Association (IMIA) and IOS Press.; 16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017 ; Conference date: 21-08-2017 Through 25-08-2017",

year = "2017",

doi = "10.3233/978-1-61499-830-3-1285",

language = "English (US)",

series = "Studies in Health Technology and Informatics",

publisher = "IOS Press BV",

pages = "1285",

editor = "Gundlapalli, {Adi V.} and Jaulent Marie-Christine and Zhao Dongsheng",

booktitle = "MEDINFO 2017",

address = "Netherlands",

}

TY - GEN

T1 - Using human phenotype ontology for phenotypic analysis of clinical notes

AU - Shen, Feichen

AU - Wang, Liwei

AU - Liu, Hongfang

N1 - Funding Information: 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 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.

AB - 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.

KW - Human phenotype ontology

KW - Phenotypic analysis

KW - Semantics

UR - http://www.scopus.com/inward/record.url?scp=85040529028&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040529028&partnerID=8YFLogxK

U2 - 10.3233/978-1-61499-830-3-1285

DO - 10.3233/978-1-61499-830-3-1285

M3 - Conference contribution

C2 - 29295370

AN - SCOPUS:85040529028

T3 - Studies in Health Technology and Informatics

SP - 1285

BT - MEDINFO 2017

A2 - Gundlapalli, Adi V.

A2 - Marie-Christine, Jaulent

A2 - Dongsheng, Zhao

PB - IOS Press BV

T2 - 16th World Congress of Medical and Health Informatics: Precision Healthcare through Informatics, MedInfo 2017

Y2 - 21 August 2017 through 25 August 2017

ER -

Using human phenotype ontology for phenotypic analysis of clinical notes

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this