Statistical principle-based approach for gene and protein related object recognition

• Main Authors: Po-Ting Lai, Ming-Siang Huang, Ting-Hao Yang, Wen-Lian Hsu, Richard Tzong-Han Tsai
• Format: Article
• Language: English
• Published: BMC 2018-12-01
• Series: Journal of Cheminformatics
• Subjects: Named entity recognition; Information extraction; Natural language processing; Biomedical text mining; Machine learning; Medical chemical patent
• Online Access: http://link.springer.com/article/10.1186/s13321-018-0314-7

Abstract The large number of chemical and pharmaceutical patents has attracted researchers doing biomedical text mining to extract valuable information such as chemicals, genes and gene products. To facilitate gene and gene product annotations in patents, BioCreative V.5 organized a gene- and protein-related object (GPRO) recognition task, in which participants were assigned to identify GPRO mentions and determine whether they could be linked to their unique biological database records. In this paper, we describe the system constructed for this task. Our system is based on two different NER approaches: the statistical-principle-based approach (SPBA) and conditional random fields (CRF). Therefore, we call our system SPBA-CRF. SPBA is an interpretable machine-learning framework for gene mention recognition. The predictions of SPBA are used as features for our CRF-based GPRO recognizer. The recognizer was developed for identifying chemical mentions in patents, and we adapted it for GPRO recognition. In the BioCreative V.5 GPRO recognition task, SPBA-CRF obtained an F-score of 73.73% on the evaluation metric of GPRO type 1 and an F-score of 78.66% on the evaluation metric of combining GPRO types 1 and 2. Our results show that SPBA trained on an external NER dataset can perform reasonably well on the partial match evaluation metric. Furthermore, SPBA can significantly improve performance of the CRF-based recognizer trained on the GPRO dataset.