Analyzing factors involved in the HPO-based semantic similarity calculation

Jiajie Peng; Qianqian Li; Bolin Chen; Jialu Hu; Xuequn Shang

doi:10.1109/BIBM.2016.7822766

Analyzing factors involved in the HPO-based semantic similarity calculation

Jiajie Peng
, Qianqian Li
, Bolin Chen
, Jialu Hu
, Xuequn Shang

School of Computer Science

Northwestern Polytechnical University Xian

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

Abstract

Although disease diagnosis have greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis based on purely sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically. In this study, we propose a new framework called HPOFactor to evaluate these factors.

Original language	English
Title of host publication	Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Editors	Kevin Burrage, Qian Zhu, Yunlong Liu, Tianhai Tian, Yadong Wang, Xiaohua Tony Hu, Qinghua Jiang, Jiangning Song, Shinichi Morishita, Kevin Burrage, Guohua Wang
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1653-1656
Number of pages	4
ISBN (Electronic)	9781509016105
DOIs	https://doi.org/10.1109/BIBM.2016.7822766
State	Published - 17 Jan 2017
Event	2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China Duration: 15 Dec 2016 → 18 Dec 2016

Publication series

Name	Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Conference

Conference	2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Country/Territory	China
City	Shenzhen
Period	15/12/16 → 18/12/16

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Access to Document

10.1109/BIBM.2016.7822766

Cite this

Peng, J., Li, Q., Chen, B., Hu, J., & Shang, X. (2017). Analyzing factors involved in the HPO-based semantic similarity calculation. In K. Burrage, Q. Zhu, Y. Liu, T. Tian, Y. Wang, X. T. Hu, Q. Jiang, J. Song, S. Morishita, K. Burrage, & G. Wang (Eds.), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 (pp. 1653-1656). Article 7822766 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2016.7822766

Peng, Jiajie ; Li, Qianqian ; Chen, Bolin et al. / Analyzing factors involved in the HPO-based semantic similarity calculation. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. editor / Kevin Burrage ; Qian Zhu ; Yunlong Liu ; Tianhai Tian ; Yadong Wang ; Xiaohua Tony Hu ; Qinghua Jiang ; Jiangning Song ; Shinichi Morishita ; Kevin Burrage ; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1653-1656 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

@inproceedings{e0a534d4fe4c4c94a13fe17f4488d48c,

title = "Analyzing factors involved in the HPO-based semantic similarity calculation",

abstract = "Although disease diagnosis have greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis based on purely sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically. In this study, we propose a new framework called HPOFactor to evaluate these factors.",

author = "Jiajie Peng and Qianqian Li and Bolin Chen and Jialu Hu and Xuequn Shang",

note = "Publisher Copyright: {\textcopyright} 2016 IEEE.; 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 ; Conference date: 15-12-2016 Through 18-12-2016",

year = "2017",

month = jan,

day = "17",

doi = "10.1109/BIBM.2016.7822766",

language = "英语",

series = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "1653--1656",

editor = "Kevin Burrage and Qian Zhu and Yunlong Liu and Tianhai Tian and Yadong Wang and Hu, \{Xiaohua Tony\} and Qinghua Jiang and Jiangning Song and Shinichi Morishita and Kevin Burrage and Guohua Wang",

booktitle = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",

}

Peng, J, Li, Q, Chen, B, Hu, J & Shang, X 2017, Analyzing factors involved in the HPO-based semantic similarity calculation. in K Burrage, Q Zhu, Y Liu, T Tian, Y Wang, XT Hu, Q Jiang, J Song, S Morishita, K Burrage & G Wang (eds), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016., 7822766, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Institute of Electrical and Electronics Engineers Inc., pp. 1653-1656, 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, 15/12/16. https://doi.org/10.1109/BIBM.2016.7822766

Analyzing factors involved in the HPO-based semantic similarity calculation. / Peng, Jiajie; Li, Qianqian; Chen, Bolin et al.
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. ed. / Kevin Burrage; Qian Zhu; Yunlong Liu; Tianhai Tian; Yadong Wang; Xiaohua Tony Hu; Qinghua Jiang; Jiangning Song; Shinichi Morishita; Kevin Burrage; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1653-1656 7822766 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

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

TY - GEN

T1 - Analyzing factors involved in the HPO-based semantic similarity calculation

AU - Peng, Jiajie

AU - Li, Qianqian

AU - Chen, Bolin

AU - Hu, Jialu

AU - Shang, Xuequn

PY - 2017/1/17

Y1 - 2017/1/17

N2 - Although disease diagnosis have greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis based on purely sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically. In this study, we propose a new framework called HPOFactor to evaluate these factors.

AB - Although disease diagnosis have greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis based on purely sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically. In this study, we propose a new framework called HPOFactor to evaluate these factors.

UR - https://www.scopus.com/pages/publications/85013301471

U2 - 10.1109/BIBM.2016.7822766

DO - 10.1109/BIBM.2016.7822766

M3 - 会议稿件

AN - SCOPUS:85013301471

T3 - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

SP - 1653

EP - 1656

BT - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

A2 - Burrage, Kevin

A2 - Zhu, Qian

A2 - Liu, Yunlong

A2 - Tian, Tianhai

A2 - Wang, Yadong

A2 - Hu, Xiaohua Tony

A2 - Jiang, Qinghua

A2 - Song, Jiangning

A2 - Morishita, Shinichi

A2 - Burrage, Kevin

A2 - Wang, Guohua

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Y2 - 15 December 2016 through 18 December 2016

ER -

Peng J, Li Q, Chen B, Hu J, Shang X. Analyzing factors involved in the HPO-based semantic similarity calculation. In Burrage K, Zhu Q, Liu Y, Tian T, Wang Y, Hu XT, Jiang Q, Song J, Morishita S, Burrage K, Wang G, editors, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1653-1656. 7822766. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). doi: 10.1109/BIBM.2016.7822766

Analyzing factors involved in the HPO-based semantic similarity calculation

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