Bootstrapping and evaluating named entity recognition in the biomedical domain

HLT-NAACL 2006 - BioNLP 2006: Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, Proceedings of the Workshop

Volumn , Issue , 2006, Pages 138-145

  Vlachos, Andreas ^a   Gasperin, Caroline ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTER RECOGNITION; GENES; COMPUTATIONAL LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS;

ANNOTATION SCHEME; BIOMEDICAL DOMAIN; BIOMEDICAL TEXT; NAMED ENTITY RECOGNITION; SUPERVISED TRAININGS; TASK-BASED; TEST SETS; TRAINING DATA; CURATION; PERFORMANCE;

NATURAL LANGUAGE PROCESSING SYSTEMS; GENES;

EID: 84872974254     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.3115/1654415.1654448     Document Type: Conference Paper

References (17)

1. ACE. 2004. Annotation guidelines for entity detection and tracking (EDT).
2. Christian Blaschke, Lynette Hirschman, and Alexander Yeh, editors. 2004. Proceedings of the BioCreative Workshop, Granada, March.
3. Avrim Blum and Tom Mitchell. 1998. Combining labeled and unlabeled data with co-training. In Proceedings of COLT 1998.
4. E. J. Briscoe and J. Carroll. 2002. Robust accurate statistical annotation of general text. In Proceedings of the 3rd International Conference on Language Resources and Evaluation, pages 1499-1504.
5. Jean Carletta. 1996. Assessing agreement on classification tasks: The kappa statistic. Computational Linguistics, 22(2):249-254.
6. M. Collins and Y. Singer. 1999. Unsupervised models for named entity classification. In Proceedings of the Joint SIGDAT Conference on EMNLP and VLC.
7. J. Curran and S. Clark. 2003. Investigating gis and smoothing for maximum entropy taggers. In Proceedings of the 11th Annual Meeting of the European Chapter of the Association for Computational Linguistics.
8. S. Dingare, J. Finkel, M. Nissim, C. Manning, and C. Grover. 2004. A system for identifying named entities in biomedical text: How results from two evaluations reflect on both the system and the evaluations. In The 2004 BioLink meeting at ISMB.
9. R. Gaizauskas, G. Demetriou, P. J. Artymiuk, and P. Willet. 2003. Protein structures and information extraction from biological texts: The "PASTA" system. BioInformatics, 19(1):135-143.
10. L. Hirschman, J. C. Park, J. Tsujii, L. Wong, and C. H. Wu. 2002. Accomplishments and challenges in literature data mining for biology. Bioinformatics, 18(12):1553-1561.
11. J. Kim, T. Ohta, Y. Tsuruoka, Y. Tateisi, and N. Collier, editors. 2004. Proceedings of JNLPBA, Geneva.
12. H. Liu and C. Friedman. 2003. Mining terminological knowledge in large biomedical corpora. In Pacific Symposium on Biocomputing, pages 415-426.
13. A. A. Morgan, L. Hirschman, M. Colosimo, A. S. Yeh, and J. B. Colombe. 2004. Gene name identification and normalization using a model organism database. J. of Biomedical Informatics, 37(6):396-410.
14. D. Shen, J. Zhang, J. Su, G. Zhou, and C. L. Tan. 2004. Multi-criteria-based active learning for named entity recongition. In Proceedings of ACL 2004, Barcelona.
15. Erik F. Tjong, Kim Sang and Fien De Meulder. 2003. Introduction to the conll-2003 shared task: Languageindependent named entity recognition. In Walter Daelemans and Miles Osborne, editors, Proceedings of CoNLL-2003, pages 142-147. Edmonton, Canada.
16. C. J. Van Rijsbergen. 1979. Information Retrieval, 2nd edition. Dept. of Computer Science, University of Glasgow.
17. A. Vlachos, C. Gasperin, I. Lewin, and T. Briscoe. 2006. Bootstrapping the recognition and anaphoric linking of named entities in drosophila articles. In Proceedings of PSB 2006.