A machine learning-based system to normalise gene mentions to unique database identifiers

作者：Chen Yifei^*; Liu Feng; Manderick Bernard

来源：International Journal of Data Mining and Bioinformatics, 2011, 5(6): 640-660.

DOI：10.1504/ijdmb.2011.045415

• gene normalisation
• gene mention recognition
• disambiguation
• text mining
• bioinformatics
• machine learning
• SVMs
• support vector machines

In this paper, we propose an integrated Gene normaliser (GNer) to assign a unique database identifier for each recognised gene mention in biological literature. The GNer combines Support Vector Machines (SVMs) and some rule-base components. First, we construct a dictionary from EntrezGene and BioThesaurus. Then we reduce variations and ambiguities of synonyms based on a designed pre-processor. Finally, a SVM-based disambiguation filter is developed to eliminate the ambiguity of exact matching. From the experimental results, the proposed GNer can achieve a fairly good performance, which can achieve the precision 80.5%, the recall 86.4% and the F(beta=1) measure 83.4.

• 出版日期2011
• 单位南京审计大学