Overview of BioCreative II gene mention recognition

Genome Biology

Volumn 9, Issue SUPPL. 2, 2008, Pages

  Smith, Larry ^a   Tanabe, Lorraine K ^a   Ando, Rie ^b   Kuo, Cheng Ju ^c   Chung, I Fang ^c   Hsu, Chun Nan ^d   Lin, Yu Shi ^d   Klinger, Roman ^e   Friedrich, Christoph M ^e   Ganchev, Kuzman ^f   Torii, Manabu ^g   Liu, Hongfang ^g   Haddow, Barry ^h   Struble, Craig A ⁱ   Povinelli, Richard J ^j   Vlachos, Andreas ^k   Baumgartner Jr , William A ^l   Hunter, Lawrence ^l   Carpenter, Bob ^m   Tsai, Richard Tzong Han ^d,n   Dai, Hong Jie ^d,o   Liu, Feng ^p   Chen, Yifei ^p   Sun, Chengjie ^q   Katrenko, Sophia ^r   Adriaans, Pieter ^r   Blaschke, Christian ^s   Torres, Rafael ^s   Neves, Mariana ^t   Nakov, Preslav ^u,v   Divoli, Anna ^w   Maña López, Manuel ^x   Mata, Jacinto ^x   Wilbur, W John ^a   more..

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b IBM T J WATSON RESEARCH CENTER   (United States)

^c NATIONAL YANG MING UNIVERSITY   (Taiwan)

^d INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^e FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

^f UNIVERSITY OF PENNSYLVANIA   (United States)

^g GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^h UNIVERSITY OF EDINBURGH   (United Kingdom)

ⁱ MARQUETTE UNIVERSITY   (United States)

^j Marquette University   (United States)

^k UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^l UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^m Alias i Inc   (United States)

ⁿ YUAN ZE UNIVERSITY   (Taiwan)

^o NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^p VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^q HARBIN INSTITUTE OF TECHNOLOGY   (China)

^r UNIVERSITY OF AMSTERDAM   (Netherlands)

^s Bioalma   (Spain)

^t UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^u UNIVERSITY OF CALIFORNIA   (United States)

^v BULGARIAN ACADEMY OF SCIENCES   (Bulgaria)

^w UNIVERSITY OF CALIFORNIA   (United States)

^x UNIVERSITY OF HUELVA   (Spain)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; BIOINFORMATICS; COMPUTER PROGRAM; FEASIBILITY STUDY; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC DATABASE; INFORMATION RETRIEVAL; MACHINE LEARNING; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; NATURAL LANGUAGE PROCESSING; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN PROTEIN INTERACTION; RECALL; REVIEW; SCORING SYSTEM; STATISTICAL ANALYSIS; SYSTEM ANALYSIS; ARTICLE; BIOLOGY; GENE; HEALTH CARE ORGANIZATION; METHODOLOGY; ORGANIZATION;

COMPUTATIONAL BIOLOGY; CONGRESSES AS TOPIC; GENES; SOCIETIES, SCIENTIFIC;

EID: 51049088874     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-s2-s2     Document Type: Review

References (49)

1. Chinchor N MUC-7 named entity task definition. Proceedings of the Seventh Message Understanding Conference (MUC-7); April 1998; Fairfax, Virginia 1998 http://www.itl.nist.gov/iaui/894.02/related_projects/muc/ proceedings/ne_task.html
2. Morgan AA Hirschman L Overview of BioCreative II gene normalization. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:17-27
3. Yeh AS Morgan A Colosimo M Hirschman L BioCreAtIvE task 1A: Gene mention finding evaluation. BMC Bioinformatics 2005, 6(suppl 1):S2. 1869012 15960832
4. Voorhees EM Overview of TREC 2005. Proceedings of the 14th Text Retrieval Conference; 2005; Gaithersburg, Maryland http://trec.nist.gov/ pubs/trec14/t14_proceedings.html
5. Wilbur WJ Smith LH Tanabe LK BioCreative 2. Gene mention task. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:7-16.
6. Tanabe L Wilbur WJ Tagging gene and protein names in biomedical text. Bioinformatics 2002, 18:1124-1132. 12176836
7. Tanabe L Xie N Thom LH Matten W Wilbur WJ GENETAG: A tagged corpus for gene/protein named entity recognition. BMC Bioinformatics 2005, 6(suppl 1):S3. 1869017 15960837
8. Smith LH Tanabe L Rindflesch T Wilbur WJ MedTag: A collection of biomedical annotations. Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics; 2005; Detroit 2005:32-37.
9. Jurafsky D Martin J Speech and Language Processing. An Introduction to Natural Language Processing, Computational Linguistics, and Speech Recognition Upper Saddle River, NJ, Prentice Hall 2000.
10. Manning C Schütz H Foundations of Statistical Natural Language Processing Cambridge, MA: MIT Press 1999.
11. Witten IH Frank E Data mining: Practical machine learning tools and techniques San Francisco, CA: Morgan Kaufmann 2005.
12. Ando RK Zhang T A framework for learning predictive structures from multiple tasks and unlabeled data. J Machine Learning Res 2005, 6:1817-1853.
13. Ando RK BioCreative II Gene Mention Tagging System at IBM Watson. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:101-103.
14. Kuo CJ Chang YM Huang HS Lin KT Yang BH Lin YS Hsu CN Chung IF Rich feature set, unification of bidirectional parsing and dictionary filtering for high F-score gene mention tagging. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:105-107.
15. Kudo T Matsumoto Y Chunking with support vector machines. Proceedings of the Second Meeting of North American Chapter of the Association for Computational Linguistics; 2 to 7 June 2001; Pittsburgh, PA 2001:192-199.
16. Huang HS Lin YS Lin KT Kuo CJ Chang YM Yang BH Chung IF Hsu CN High-recall gene mention recognition by unification of multiple backward parsing models. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:109-111.
17. Klinger R Friedrich CM Fluck J Hofmann-Apitius M Named entity recognition with combinations of conditional random fields. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:89-91.
18. Hanisch D Fundel K Mevissen HT Zimmer R Fluck J ProMiner: organism-specific protein name detection using approximate string matching. Proceedings of the BioCreative Challenge Evaluation Workshop 2004.
19. Ganchev K Crammer K Pereira F Mann G Bellare K McCallum A Carroll S Jin Y White P Penn/UMass/CHOP Biocreative II Systems. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:119-124.
20. Crammer K Dekel O Keshet J Shalev-Shwartz S Singer Y Online passive-aggressive algorithms. J Machine Learning Res 2006, 7:551-585.
21. Liu H Torii M Hu ZZ Wu C Gene mention and gene normalization based on machine learning and online resources. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:135-140.
22. Liu H Hu ZZ Zhang J Wu C BioThesaurus: A web-based thesaurus of protein and gene names. Bioinformatics 2006, 22:103-105. 16267085
23. Bodenreider O The Unified Medical Language System (UMLS): Integrating biomedical terminology. Nucleic Acids Res 2004, 32:D267-D270. 308795 14681409
24. Grover C Haddow B Klein E Matthews M Nielsen L Tobin R Wang X Adapting a relation extraction pipeline for the BioCreAtIvE II tasks. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:273-286.
25. Tsuruoka Y Tsujii J Bidirectional Inference with the easiest-first strategy for tagging sequence data. Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing; 2005; Vancouver, Canada 2005:467-474.
26. Schwartz A Hearst M A simple algorithm for identifying abbreviation definitions in biomedical text. Proceedings of the Pacific Symposium on Biocomputing (PSB 2003); Kauai, Hawaii
27. Tjong Kim Sang EF De Meulder F Introduction to the CoNLL-2003 shared task: Language-independent named entity recognition. Proceedings of CoNLL-2003 2003:142-147.
28. Struble CA Povinelli RJ Johnson MT Berchanskiy D Tao J Trawicki M Combined conditional random fields and n-gram language models for gene mention recognition. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:81-83.
29. Vlachos A Tackling the BioCreative2 gene mention task with conditional random fields and syntactic parsing. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:85-87.
30. Baumgartner WA Jr Lu Z Johnson HL Caporaso JG Paquette J Lindemann A White EK Medvedeva O Fox LM Cohen KB Hunter L An integrated approach to concept recognition in biomedical text. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:257-271.
31. Carpenter B LingPipe for 99.99% recall of gene mentions. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:307-309.
32. Carpenter B Character language models for Chinese word segmentation and named entity recogntion. Proceedings of the 5th SIGHAN Workshop on Chinese Language Processing; July 2006; Sydney, Australia 2006:169-172.
33. Tsai RTH Sung CL Dai HJ Sung HCHTY Hsu WL NERBio: Using selected word conjunction, term normalization, and global patterns to improve biomedical named entity recognition. BMC Bioinformatics 2006, 7(suppl 5):S11. 1764467 17254295
34. Dai HJ Hung HC Tsai RTH Hsu WL IASL systems in the gene mention tagging task and protein interaction article sub-task. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:69-76.
35. Chen Y Liu F Manderick B Gene mention recognition using lexicon match based two-layer support vector machines. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:93-95.
36. Smith LH Rindflesch T Wilbur WJ MedPost: A part of speech tagger for biomedical text. Bioinformatics 2004, 20:2320-2321. 15073016
37. Chen Y Liu F Manderick B Improving the performance of gene mention recognition system using reformed lexicon-based support vector machine. Proceedings of the International Conference on Data Mining; 25 to 28 June 2007; Las Vegas, NV 2007.
38. Sun C Lei L Xiaolong W Yi G A study for application of discriminative models in biomedical literature mining. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:319-321.
39. Katrenko S Pieter Adriaans P Using semi-supervised techniques to detect gene mentions. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:97-100.
40. Krogel MA Scheffer T Multi-relational learning, text mining, and semi-supervised learning for functional genomics. Machine Learning 2004, 57:61-81.
41. Torres R Sánchez PD Pascual L Blaschke C Text Detective: Gene/ proteins annotation tool by Alma Bioinformatics. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:125-130.
42. Neves M Identifying gene mentions by case-based reasoning. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:77-79.
43. Nakov P Divoli A BioText report for the Second BioCreAtIvE Challenge. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:297-306.
44. Bhalotia G Nakov P Schwartz AS Hearst MA BioText Team report for the TREC 2003 Genomics Track. Proceedings of the 12th Text Retrieval Conference; 2003; Gaithersburg, Maryland 2003:612-621.
45. Avancini H Rauber A Sebastiani F Organizing digital libraries by automated text categorization. Proceedings of the International Conference on Digital Libraries; 24 to 27 February 2004; New Delhi 2004:919-931.
46. Carrero F Gómez JM Puertas E Maña MJ Mata J Attribute Analysis in Biomedical Text Clasification. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 23 to 25 April 2007; Madrid, Spain 2007:113-118.
47. Carreras X Marquez L Boosting trees for anti-spam email filtering. Proceedings of RANLP-01, 4th International Conference on Recent Advances in Language Processing; 2001; Tzigov Chark, Bulgaria 2001:58-64.
48. Schapire RE Singer Y Improved boosting algorithms using confidence-rated predictions. Machine Learning 1999, 37:297-336.
49. McCallum A Efficiently inducing features of conditional random fields. Proceedings of the Nineteenth Conference on Uncertainty in Artificial Intelligence; 7 to 10 August 2003; Acapulco 2003:403-410.