BioPPIExtractor: A protein-protein interaction extraction system for biomedical literature

Authors:
Zhihao Yang;Hongfei Lin;Baodong Wu
Affiliations:
Department of Computer Science and Technology, DaLian University of Technology, No. 2 LingGong Road, ShaHeKou district, DaLian 116023, China;Department of Computer Science and Technology, DaLian University of Technology, No. 2 LingGong Road, ShaHeKou district, DaLian 116023, China;Department of Computer Science and Technology, DaLian University of Technology, No. 2 LingGong Road, ShaHeKou district, DaLian 116023, China
Venue:
Expert Systems with Applications: An International Journal
Year:
2009

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Abstract

Automatic extracting protein-protein interaction information from biomedical literature can help to build protein relation network, predict protein function and design new drugs. This paper presents a protein-protein interaction extraction system BioPPIExtractor for biomedical literature. This system applies Conditional Random Fields model to tag protein names in biomedical text, then uses a link grammar parser to identify the syntactic roles in sentences and at last extracts complete interactions by analyzing the matching contents of syntactic roles and their linguistically significant combinations. Experimental evaluations with two other state of the art extraction systems indicate that BioPPIExtractor system achieves better performance.