Lexical analysis and stoplists
Information retrieval
Some advances in transformation-based part of speech tagging
AAAI '94 Proceedings of the twelfth national conference on Artificial intelligence (vol. 1)
Foundations of statistical natural language processing
Foundations of statistical natural language processing
Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Constructing Biological Knowledge Bases by Extracting Information from Text Sources
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
A Literature Based Method for Identifying Gene-Disease Connections
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
EACL '99 Proceedings of the ninth conference on European chapter of the Association for Computational Linguistics
Extracting the names of genes and gene products with a hidden Markov model
COLING '00 Proceedings of the 18th conference on Computational linguistics - Volume 1
Identification and classification of proper nouns in Chinese texts
COLING '96 Proceedings of the 16th conference on Computational linguistics - Volume 1
Notions of correctness when evaluating protein name taggers
COLING '02 Proceedings of the 19th international conference on Computational linguistics - Volume 1
Gene name extraction using FlyBase resources
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Enhancing performance of protein name recognizers using collocation
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Boosting precision and recall of dictionary-based protein name recognition
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Protein name tagging for biomedical annotation in text
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Introduction: named entity recognition in biomedicine
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Translating–transliterating named entities for multilingual information access
Journal of the American Society for Information Science and Technology
Two learning approaches for protein name extraction
Journal of Biomedical Informatics
Boosting performance of gene mention tagging system by hybrid methods
Journal of Biomedical Informatics
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Named entity (NE) recognition is a fundamental task in biological relationship mining. This paper considers protein/gene collocates extracted from biological corpora as restrictions to enhance the precision rate of protein/gene name recognition. In addition, we integrate the results of multiple NE recognizers to improve the recall rates. Yapex and KeX, and ABGene and Idgene are taken as examples of protein and gene name recognizers, respectively. The precision of Yapex increases from 70.90 to 85.84% at the low expense of the recall rate (i.e., it only decreases 2.44%) when collocates are incorporated. When both filtering and integration strategies are employed together, the Yapex-based integration with KeX shows good performance, i.e., the F-score increases by 7.83% compared to the pure Yapex method. The results of gene recognition show the same tendency. The ABGene-based integration with Idgene shows a 10.18% F-score increase compared to the pure ABGene method. These successful methodologies can be easily extended to other name finders in biological documents.