Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations

• Published in: PloS one Vol. 8; no. 4; p. e60954
• Main Authors: Liu, Haibin, Hunter, Lawrence, Kešelj, Vlado, Verspoor, Karin
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.04.2013; Public Library of Science (PLoS)
• Subjects: Algorithms; Amino Acids - metabolism; Associations; Bioinformatics; Biology; Biomedical Technology; Coding; Computer Science; Data mining; Data Mining - methods; Databases, Protein; Engineering; Gene expression; Graph matching; Isomorphism; Language; Linguistics; Natural language; Proteins; Proteins - metabolism; Reproducibility of Results; Semantics; Social and Behavioral Sciences; Texts
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0060954

The biomedical text mining community has focused on developing techniques to automatically extract important relations between biological components and semantic events involving genes or proteins from literature. In this paper, we propose a novel approach for mining relations and events in the biomedical literature using approximate subgraph matching. Extraction of such knowledge is performed by searching for an approximate subgraph isomorphism between key contextual dependencies and input sentence graphs. Our approach significantly increases the chance of retrieving relations or events encoded within complex dependency contexts by introducing error tolerance into the graph matching process, while maintaining the extraction precision at a high level. When evaluated on practical tasks, it achieves a 51.12% F-score in extracting nine types of biological events on the GE task of the BioNLP-ST 2011 and an 84.22% F-score in detecting protein-residue associations. The performance is comparable to the reported systems across these tasks, and thus demonstrates the generalizability of our proposed approach.