Incorporating rich background knowledge for gene named entity classification and recognition

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Li, Yanpeng ^a   Lin, Hongfei ^a   Yang, Zhihao ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACK-GROUND KNOWLEDGE; BIOMEDICAL LITERATURE; CO-OCCURRENCE INFORMATIONS; CONDITIONAL RANDOM FIELD; LEARNING-BASED METHODS; NAMED ENTITY CLASSIFICATION; RECOGNITION SYSTEMS; STATE-OF-THE-ART SYSTEM;

DATA MINING; GENES; INDUSTRIAL PLANTS; TEXT PROCESSING;

NATURAL LANGUAGE PROCESSING SYSTEMS;

ARTICLE; AUTOMATED PATTERN RECOGNITION; CLASSIFICATION; CLASSIFIER; CONTROLLED STUDY; GENOMICS; INFORMATION PROCESSING; MACHINE LEARNING; NATURAL LANGUAGE PROCESSING; SUPPORT VECTOR MACHINE; ARTIFICIAL INTELLIGENCE; BIOLOGY; GENE; INFORMATION RETRIEVAL; LINGUISTICS; METHODOLOGY;

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; GENES; INFORMATION STORAGE AND RETRIEVAL; VOCABULARY, CONTROLLED;

EID: 68949148714     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-223     Document Type: Article

References (27)

1. Cohen AM Hersh WR A survey of current work in biomedical text mining Briefings in Bioinformatics 2005, 6:57-71 10.1093/bib/6.1.57 15826357
2. Yeh AS Morgan A Colosimo M Hirschman L BioCreaitve task 1A: Gene mention finding evaluation BMC Bioinformatics. 2005, 6(supp1 1):S3
3. Wilbur J Smith L Tanabe L BioCreative 2. gene mention task Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007:7-16
4. Kim JD Ohta T Tsuruoka Y Tateisi Y Collier N Introduction to the bio-entity recognition task at JNLPBA Proceedings of the International Work-shop on Natural Language Processing in Biomedicine and its Applications (JNLPBA) 2004:70-75
5. Ando RK BioCreative II gene mention tagging system at IBM Watson Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007:101-103
6. Zhou GD Su J Exploring deep knowledge resources in biomedical name recognition Proceedings of Joint Workshop on Natural Language Processing in Biomedicine and Its Applications (JNLPBA) 2004:96-99
7. Settles B Biomedical named entity recognition using conditional random fields and novel feature sets Proceedings of the Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA) 2004:104-107
8. Finkel J Dingare S Manning CD Nissim M Alex B Grover C Exploring the boundaries: Gene and protein identification in biomedical text BMC Bioinformatics 2005, 6(Suppl 1):S5 1869019 15960839 10.1186/ 1471-2105-6-S1-S5
9. Ryan M Pereira P Identifying gene and protein mentions in text using conditional random field BMC Bioinformatics 2005, 6(Suppl 1):S6 1869020 15960840 10.1186/1471-2105-6-S1-S6
10. Hsu CN Chang YM Kuo CJ Lin YS Huang HS Chung IF Integrating high dimensional bi-directional parsing models for gene mention tagging Bioinformatics 2008, 24:i286-i294 10.1093/bioinformatics/btn183 18586726
11. Lanczos C Linear differential operators Van Nostrand, New York 1961
12. Ando RK Zhang T A framework for learning predictive structures from multiple tasks and unlabeled data Journal of Machine Learning Research 2005, 6:1817-1853
13. Etzioni O Cafarella M Downey D Kok S Popescu A Shaked T Soderland S Weld D Yates A Unsupervised named-entity extraction from the web: An experimental study Artificial Intelligence 2005, 165(1):91-134 10.1016/ j.artint.2005.03.001
14. Zhu X Semi-supervised learning literature survey Technical Report (1530) University of Wisconsin-Madison 2008
15. Lafferty J McCallum A Pereira F Conditional random fields: Probabilistic models for segmenting and labeling sequence data Proceedings of the 18th International Conference on Machine Learning (ICML) 2001:282-289
16. Liu H Hu ZZ Zhang J Wu C BioThesaurus: A web-based thesaurus of protein and gene names Bioinformatics 2006, 22:103-105 10.1093/bioinformatics/ bti749 16267085
17. Tanabe L Wilbur WJ Generation of a large gene/protein lexicon by morphological pattern analysis J Bioinform Comput Biol. 2004, 1(4):611-626 10.1142/S0219720004000399 15290756
18. Joachims T "Making large-Scale SVM Learning Practical," Advances in Kernel Methods - Support Vector Learning MIT-Press Schölkopf B, Burges C, Smola A 1999
19. Church KW Hanks P Word association norms, mutual information, and lexicography Computational Linguistics 1989, 16(1):22-29
20. Herbrich R Graepel T A PAC-Bayesian margin bound for linear classifiers: why SVMs work Proceedings of Advances in Neural Information System Processing 13 (NIPS) 2001:224-230
21. Vapnik VN Statistical Learning theory John Wiley and Sons 1998
22. Hersh W Cohen A Roberts P Rekapalli HK TREC 2006 genomics track overview Proceedings of 15th Text REtrieval Conference ((TREC) 2006
23. Yang Z Lin H Li Y Xu L Pan Y Liu B DUTIR at TREC 2006: Genomics and Enterprise Tracks Proceedings of the 15th Text Retrieval Conference 2006
24. Settles B ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text Bioinformatics 2005, 21(14):3191-3192 10.1093/bioinformatics/bti475 15860559
25. Manning CD Raghavan P Schulze H Introduction to Information Retrieval Cambridge, Cambridge University Press 2007
26. Leaman R Gonzalez G BANNER: An executable survey of advances in biomedical named entity recognition Pac Symp Biocomput. 2008, 13:652-663
27. Hakenberg J Plake C Leaman R Schroeder M Gonzalez G Inter-species normalization of gene mentions with GNAT Bioinformatics 2008, 24:i126-132 10.1093/bioinformatics/btn299 18689813