Identifying gene and protein names from biological texts

Abstract

Extracting and identifying gene and protein names from literature is a critical step for mining functional information of genes and proteins. While extensive efforts have been devoted to this important task, most of them were aiming at extracting gene/protein name per se without paying much attention to associate the extracted name with existing gene and protein database entries. We developed a simple and efficient method to identify gene and protein names in literature using a combination of heuristic and statistical strategies. Our approach will map the extracted names to individual LocusLink entries thus enable the seamless integration of literature information with existing gene/protein databases. Evaluation on a test corpus shows that our method can achieve both high recall and precision. Our method exhibits good performance and can be used as a building block for large biomedical literature mining systems.