Normalizing biomedical terms by minimizing ambiguity and variability

BMC Bioinformatics

Volumn 9, Issue SUPPL. 3, 2008, Pages

  Tsuruoka, Yoshimasa ^a   McNaught, John ^a   Ananiadou, Sophia ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL INFORMATION EXTRACTIONS; COMPUTATIONAL COSTS; COMPUTATIONAL OVERHEADS; FAST IMPLEMENTATION; HEURISTIC RULES; REALTIME PROCESSING; RULE APPLICATION; STRING MATCHING;

TERMINOLOGY;

MAPPING;

ACCURACY; CONCEPT MAPPING; CONFERENCE PAPER; GENETIC ALGORITHM; GENETIC IDENTIFICATION; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MEDICAL INFORMATION SYSTEM; NOMENCLATURE; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN ANALYSIS; RECALL; ALGORITHM; ARTICLE; ARTIFACT; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BOOK; LINGUISTICS; METHODOLOGY; NATURAL LANGUAGE PROCESSING;

ALGORITHMS; ARTIFACTS; ARTIFICIAL INTELLIGENCE; DICTIONARIES AS TOPIC; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; TERMINOLOGY AS TOPIC; VOCABULARY, CONTROLLED;

EID: 44649194587     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S3-S2     Document Type: Conference Paper

References (27)

1. Kim JD Ohta T Tateisi Y Tsujii J GENIA corpus-semantically annotated corpus for bio-textmining Bioinformatics 2003, 19(Suppl 1):i180-i182. 10.1093/bioinformatics/btg1023 12855455
2. Kulick S Bies A Libeman M Mandel M McDonald R Palmer M Schein A Ungar L Integrated Annotation for Biomedical Information Extraction Proceedings of HLT-NAACL 2004 Workshop: Biolink 2004, 2004:61-68.
3. 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 10.1186/1471-2105-6-S1-S3
4. Tanabe L Wilbur WJ Tagging gene and protein names in biomedical text Bioinformatics 2002, 18(8):1124-1132. 10.1093/bioinformatics/18.8.1124 12176836
5. Zhou G Zhang J Su J Shen D Tan C Recognizing names in biomedical texts: a machine learning approach Bioinformatics 2004, 20(7):1178-1190. 10.1093/bioinformatics/bth060 14871877
6. Hanisch D Fundel K Mevissen HT Zimmer R Fluck J ProMiner: Rule-based protein and gene entity recognition BMC Bioinformatics 2005, 6(Suppl 1):S14. 1869006 15960826 10.1186/1471-2105-6-S1-S14
7. Settles B ABNER: An open source tool for automatically tagging genes, proteins, and other named entities in text Bioinformatics 2005, 21:3191-3192. 10.1093/bioinformatics/bti475 15860559
8. Wren JD A scalable machine-learning approach to recognize chemical names within large text databases BMC Bioinformatics 2006, 7(Suppl 2):S3. 1683569 17118146 10.1186/1471-2105-7-S2-S3
9. Blaschke C Hirschman L Valencia A Information extraction in molecular biology Briefings in Bioinformatics 2002, 3(2):154-165. 10.1093/bib/ 3.2.154 12139435
10. Krauthammer M Rzhetsky A Morozov P Friedman C Using BLAST for identifying gene and protein names in journal articles Gene 2000, 259:245-252. 10.1016/S0378-1119(00)00431-5 11163982
11. Yeganova L Smith L Wilbur WJ Identification of related gene/protein names based on an HMM of name variations Comput Biol Chem 2004, 28:97-107. 10.1016/j.compbiolchem.2003.12.003 15130538
12. Hirschman L Colosimo M Morgan A Yeh A Overview of BioCreAtIvE task 1B: normalized gene lists BMC Bioinformatics 2005, 6(Suppl 1):S11. 1869004 15960823 10.1186/1471-2105-6-S1-S11
13. Cohen WW Minkov E A graph-search framework for associating gene identifies with documents BMC Bioinformatics 2006, 7:440. 1617121 17032441 10.1186/1471-2105-7-440
14. Tsuruoka Y McNaught J Tsujii J Ananiadou S Learning string similarity measures for gene/protein name dictionary look-up using logistic regression Bioinformatics 2007, 23(20):2768-2774. 10.1093/bioinformatics/ btm393 17698493
15. Tsuruoka Y Tsujii J Improving the Performance of Dictionary-based Approaches in Protein Name Recognition Journal of Biomedical Informatics 2004, 37:461-470. 10.1016/j.jbi.2004.08.003 15542019
16. Navarro G A guided tour to approximate string matching ACM Computing Surveys 2001, 33:31-88. 10.1145/375360.375365
17. Cohen KB Dolbey AE Acquaah-Mensah GK Hunter L Contrast And Variability In Gene Names Proceedings of the Workshop on Natural Language Processing in the Biomedical Domain 2002, 14-20.
18. Fang H Murphy K Jin Y Kim JS White PS Human Gene Name Normalization using Text Matching with Automatically Extracted Synonym Dictionaries Proceedings of BioNLP'06 2006.
19. Schuemie MJ Mons B Weeber M Kors JA Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification Journal of Biomedical Informatics 2007, 40:316-324. 10.1016/j.jbi.2006.09.002 17079192
20. Liu H Hu ZZ Torii M Wu C Friedman C Quantitative Assessment of Dictionary-based Protein Named Entity Tagging Journal of the Americal Medical Informatics Association 2006, 13(5):497-507. 10.1197/jamia.M2085
21. 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
22. The Universal Protein Resource (UniProt) The UniProt Consortium Nucleic Acids Research 2007, 35(Database issue):D193-D197. 1669721 17142230
23. Humphreys BL Lindberg DAB Building the unified medical language system Proceedings of the 13th SCAMC 1989, 475-480.
24. Morgan AA Hirschman L Overview of BioCreative II Gene Normalization Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007, 17-22.
25. Brill E Transformation-Based Error-Driven Learning and Natural Language Processing A Case Study in Part-of-Speech Tagging Computational Linguistics 1995, 21(4):543-565.
26. Samuel K Lazy Transformation-Based Learning Proceedings of the Eleventh International Florida Artificial Intelligence Research Society Conference 1998, 235-239.
27. Ngai G Florian R Transformation-Based Learning in the Fast Lane Proceedings of the Second Meeting of the North American Chapter of the Association for Computational Linguistics (NAACL) 2001, 40-47.