Mining Protein Interaction from Biomedical Literature with Relation Kernel Method

Many interaction data still exist only in the biomedical literature and they require much effort to construct well-structured data. Discovering useful knowledge from large collections of papers is becoming more important for efficient biological and biomedical researches as genomic research advances. In this paper, we present a relation kernel-based interaction extraction method to extract knowledge efficiently. We extract protein interactions of from text documents with relation kernel and Yeast was used as an example target organism. Kernel for relation extraction is constructed with predefined interaction corpus and set of interaction patterns. The proposed method only exploits shallow parsed documents. Experimental results show that the proposed kernel method achieves a recall rate of 79.0% and precision rate of 80.8% for protein interaction extraction from biomedical document without full parsing efforts.