Cascaded classifiers for confidence-based chemical named entity recognition

BMC Bioinformatics

Volumn 9, Issue SUPPL. 11, 2008, Pages

  Corbett, Peter ^a   Copestake, Ann ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL TEXT; CASCADED CLASSIFIERS; F-SCORE; MAXIMUM ENTROPY MARKOV MODEL; NAMED ENTITIES; NAMED ENTITY RECOGNITION; PRECISION AND RECALL; THRESHOLD SETS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

FLUORINE;

ACCURACY; COMPUTER ANALYSIS; COMPUTER PROGRAM; CONFERENCE PAPER; CONFIDENCE INTERVAL; DATA EXTRACTION; MEDLINE; NOMENCLATURE; STATISTICAL MODEL; SYSTEM ANALYSIS; ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL MODEL; INFORMATION RETRIEVAL; METHODOLOGY; NATURAL LANGUAGE PROCESSING;

ALGORITHMS; COMPUTATIONAL BIOLOGY; INFORMATION STORAGE AND RETRIEVAL; MODELS, CHEMICAL; MODELS, STATISTICAL; NATURAL LANGUAGE PROCESSING; SOFTWARE; TERMINOLOGY AS TOPIC;

EID: 56649102386     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S11-S4     Document Type: Conference Paper

References (26)

1. Reyle U Understanding chemical terminology Terminology 2006, 12:111-126.
2. Corbett P Batchelor C Teufel S Annotation of Chemical Named Entities Proceedings of BioNLP 2007: Biological, translational, and clinical language processing (ACL 2007 workshop) 2007:57-64.
3. Wilbur WJ Hazard G Divita G Mork J Aronson A Browne A Analysis of Biomedical Text for Chemical Names: A Comparison of Three Methods Proceedings of the Annual Fall Symposium of the American Medical Informatics Association (AMIA 99) 1999:176-180.
4. Vasserman A Identifying Chemical Names in Biomedical Text: An Investigation of Substring Co-occurrence Based Approaches Proceedings of the Student Research Workshop at HLT-NAACL 2004:7-12.
5. Townsend J Copestake A Murray-Rust P Teufel S Waudby C Language Technology for Processing Chemistry Publications Proceedings of the UK e-Science All Hands Meeting 2005:247-253.
6. McCallum A Freitag D Pereira F Maximum Entropy Markov Models for Information Extraction and Segmentation Proceedings of the 17th International Conference on Machine Learning (ICML 2000) 2000:591-598.
7. 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) 2001:282-289.
8. Krallinger M Hirschman L (Eds) Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007.
9. Culotta A McCallum A Confidence Estimation for Information Extraction Proceedings of the Human Language Technology Conference of the North American Chapter of the Association for Computational Linguistics (HLT-NAACL 2004) 109-112.
10. Carpenter B LingPipe for 99.99% Recall of Gene Mentions Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007:307-309.
11. Copestake A Corbett P Murray-Rust P Rupp C Siddharthan A Teufel S Waldron B An Architecture for Language Technology for Processing Scientific Texts Proceedings of the UK e-Science All Hands Meeting 2006.
12. Roth D Yih W Probabilistic reasoning for entity & relation recognition Proceedings of the 19th International Conference on Computational Linguistics (COLING 2002) 2002:1-7.
13. Roth D Yih W A Linear Programming Formulation for Global Inference in Natural Language Tasks Proceedings of the 8th Conference on Computational Natural Language Learning (CoNLL 2004) 2004:1-8.
14. Finkel JR Manning C Ng A Solving the Problem of Cascading Errors: Approximate Bayesian Inference for Linguistic Annotation Pipelines Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing (EMNLP 2006) 2006:618-626.
15. Batchelor C Corbett P Semantic enrichment of journal articles using chemical named entity recognition Proceedings of the 45th Annual Meeting of the Association for Computational Linguistics (ACL 2007) Demo and Poster Sessions 2007:45-48.
16. Alex B Grover C Haddow B Kabadjor M Klein E Matthews M Roebuck S Tobin R Wang X Assisted Curation: Does Text Mining Really Help? Proceedings of the 13th Pacific Symposium on Biocomputing (PSB 2008) 2008:556-567.
17. Krishnan V Manning C An Effective Two-Stage Model for Exploiting Non-Local Dependencies in Named Entity Recognition Proceedings of the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics (COLING-ACL 2006) 2006:1121-1128.
18. Yoshida K Tsujii J Reranking for Biomedical Named-Entity Recognition Proceedings of BioNLP 2007: Biological, translational, and clinical language processing (ACL 2007 workshop) 2007:209-216.
19. Ji H Grishman R Applying Coreference to Improve Name Recognition Proceedings of the Workshop on Reference Resolution and its Applications (ACL 2004 workshop) 2004:32-39.
20. Ji H Grishman R Improving Name Tagging by Reference Resolution and Relation Detection Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL 2005) 2005:411-418.
21. Ji H Grishman R Analysis and Repair of Name Tagger Errors Proceedings of the COLING/ACL 2006 Main Conference Poster Sessions 2006:420-427.
22. Degtyarenko K Matos PdD Ennis M Hastings J Zbinden M McNaught A Alcántara R Darsow M Guedj M Ashburner M ChEBI: A database and ontology for chemical entities of biological interest Nucleic Acids Res 2007, 36 2238832 17932057
23. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29. http://dx.doi.org/10.1038/75556 10802651
24. OpenNLP Maxent http://maxent.sourceforge.net/
25. LingPipe http://alias-i.com/lingpipe/
26. Oscar3 https://sourceforge.net/projects/oscar3-chem