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

Po Ting Lai, Ming Siang Huang, Ting Hao Yang, Wen Lian Hsu, Richard Tzong Han Tsai

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


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.

Original languageEnglish
Article number64
JournalJournal of Cheminformatics
Issue number1
StatePublished - 17 Dec 2018


  • Biomedical text mining
  • Information extraction
  • Machine learning
  • Medical chemical patent
  • Named entity recognition
  • Natural language processing


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