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Extracting Biomedical Entity Relations using Biological Interaction Knowledge.

Authors :
Guo, Shuyu
Huang, Lan
Yao, Gang
Wang, Ye
Guan, Haotian
Bai, Tian
Source :
Interdisciplinary Sciences: Computational Life Sciences; Jun2021, Vol. 13 Issue 2, p312-320, 9p
Publication Year :
2021

Abstract

Discovering relations of cross-type biomedical entities is crucial for biology research. A large amount of potential or indirect connected biological relations is hidden in millions of biomedical literatures and biological databases. The previous rules-based and deep learning approaches rely on plenty of manual annotations, which is laborious, time-consuming and unsatisfactory. It is necessary to be able to combine available annotated gene databases, chemical, genomic, clinical and other types of data repositories as domain knowledge to assist the extraction of biological entity relations from numerous literatures. Under this scenario, this paper proposes BioGraphSAGE model, a Siamese graph neural network with structured databases as domain knowledge to extract biological entity relations from literatures. Our model combines both biological semantic features and positional features to improve the recognition of relations between distant entities in the same literature. The experiment results show that BioGraphSAGE achieves the best F1 score among other relation extraction models on smaller annotated samples. Moreover, the proposed model can still maintain a F1 score of 0.526 without using annotated training samples. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
19132751
Volume :
13
Issue :
2
Database :
Complementary Index
Journal :
Interdisciplinary Sciences: Computational Life Sciences
Publication Type :
Academic Journal
Accession number :
150556134
Full Text :
https://doi.org/10.1007/s12539-021-00425-8