loading
Papers

Research.Publish.Connect.

Paper

Authors: Dongsheng Zhao ; Fan Tong and Zheheng Luo

Affiliation: Information Center, Academy of Military Medical Science, Beijing and China

ISBN: 978-989-758-353-7

Keyword(s): Semantic Type, Text Mining, Curation, Gene, Mutation, Disease.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Data Mining and Machine Learning

Abstract: Background: Current semantic type of “gene-mutation-disease” relation lacks fine-grained classification and corresponding relation signal words, which limits its usage in relation extraction from biomedical literature using text mining approach. Methods: We propose a computer-aided curation pipeline in which open relation extraction, signal word clustering, relation type mapping are used to analyze biomedical abstracts for semantic type of “gene-mutation-disease” construction. Coverage metrics are used to evaluate the defined relation type while ClinVar is chosen as a target to test our semantic type’s usability and performance on guiding relation extraction from biomedical literature. Results: We have constructed a 5-layer and 16-category semantic type of “gene-mutation-disease” relation with a vocabulary list containing 58 commonly used relation signal words. The vocabulary list has coverage of 95.08% and the semantic type has coverage of 94.12%. From 25 abstracts linked to 30 ClinV ar records, 15 relations are correctly mapped and 8 novel relations are discovered additionally. Conclusion: The results show that our semantic type can cover the main relations between “gene”, “mutation” and “disease” and can achieve good performance on guiding relation extraction from biomedical text even using relatively out-of-date dictionary-based text mining methods. (More)

PDF ImageFull Text

Download
CC BY-NC-ND 4.0

Sign In Guest: Register as new SciTePress user now for free.

Sign In SciTePress user: please login.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 100.26.176.182

In the current month:
Recent papers: 100 available of 100 total
2+ years older papers: 200 available of 200 total

Paper citation in several formats:
Zhao, D.; Tong, F. and Luo, Z. (2019). Construct Semantic Type of “Gene-mutation-disease” Relation by Computer-aided Curation from Biomedical Literature.In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3 BIOINFORMATICS: BIOINFORMATICS, ISBN 978-989-758-353-7, pages 123-130. DOI: 10.5220/0007688101230130

@conference{bioinformatics19,
author={Dongsheng Zhao. and Fan Tong. and Zheheng Luo.},
title={Construct Semantic Type of “Gene-mutation-disease” Relation by Computer-aided Curation from Biomedical Literature},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3 BIOINFORMATICS: BIOINFORMATICS,},
year={2019},
pages={123-130},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007688101230130},
isbn={978-989-758-353-7},
}

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3 BIOINFORMATICS: BIOINFORMATICS,
TI - Construct Semantic Type of “Gene-mutation-disease” Relation by Computer-aided Curation from Biomedical Literature
SN - 978-989-758-353-7
AU - Zhao, D.
AU - Tong, F.
AU - Luo, Z.
PY - 2019
SP - 123
EP - 130
DO - 10.5220/0007688101230130

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.