Moara: A Java library for extracting and normalizing gene and protein mentions

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Neves, Mariana L ^a   Carazo, José María ^a   Pascual Montano, Alberto ^a,b  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EFFECTIVE SOLUTION; INTEGRATED TOOLS; JAVA LIBRARY; MODEL ORGANISMS; OPEN SOURCE SYSTEM; PROTEIN-PROTEIN INTERACTIONS; SEMANTIC INFORMATION; STANDALONE APPLICATIONS;

BIOLOGY; DATA MINING;

PROTEINS;

PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; DATA MINING; GENE; GENETIC DATABASE; INFORMATION RETRIEVAL; METHODOLOGY; PROTEIN DATABASE;

DATA MINING; DATABASES, GENETIC; DATABASES, PROTEIN; GENES; INFORMATION STORAGE AND RETRIEVAL; PROTEINS; SOFTWARE;

EID: 77952310847     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-157     Document Type: Article

References (26)

1. Tamames J, Valencia A. The success (or not) of HUGO nomenclature. Genome Biol 2006, 7(5):402. 10.1186/gb-2006-7-5-402, 1779514, 16707004.
2. Crim J, McDonald R, Pereira F. Automatically annotating documents with normalized gene lists. BMC Bioinformatics 2005, 6(Suppl 1):S13. 10.1186/1471-2105-6-S1-S13, 1771968, 15960825.
3. 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. 10.1186/1471-2105-6-S1-S14, 1869006, 15960826.
4. Fundel K, Guttler D, Zimmer R, Apostolakis J. A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 2005, 6(Suppl 1):S15. 10.1186/1471-2105-6-S1-S15, 1869007, 15960827.
5. Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, Hsu CN, Lin YS, Klinger R, Friedrich CM, Ganchev K, et al. Overview of BioCreative II gene mention recognition. Genome Biology 2008, 9(Suppl 2):S2. 10.1186/gb-2008-9-s2-s2, 2559986, 18834493.
6. Hirschman L, Colosimo M, Morgan A, Yeh A. Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 2005, 6(Suppl 1):S11. 10.1186/1471-2105-6-S1-S11, 1869004, 15960823.
7. Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, et al. Overview of BioCreative II gene normalization. Genome Biology 2008, 9(Suppl 2):S3. 10.1186/gb-2008-9-s2-s3, 2559987, 18834494.
8. Leaman R, Gonzalez G. BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput 2008, 652-663.
9. 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.
10. Tsuruoka Y, Tateishi Y, Kim J-D, Ohta T, McNaught J, Ananiadou S, Tsujii J. Developing a Robust Part-of-Speech Tagger for Biomedical Text. Advances in Informatics - 10th Panhellenic Conference on Informatics: 2005: LNCS 2005, 282-392.
11. McDonald R, Pereira F. Identifying gene and protein mentions in text using conditional random fields. BMC Bioinformatics 2005, 6(Suppl 1):S6. 10.1186/1471-2105-6-S1-S6, 1869020, 15960840.
12. Kano Y, Baumgartner WA, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J. U-Compare: share and compare text mining toolswith UIMA. Bioinformatics 2009, 2712335, 19414535.
13. Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G. Inter-species normalization of gene mentions with GNAT. Bioinformatics 2008, 24(16):i126-132. 10.1093/bioinformatics/btn299, 18689813.
14. Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through Web services: calling Whatizit. Bioinformatics 2008, 24(2):296-298. 10.1093/bioinformatics/btm557, 18006544.
15. Witten IH, Frank E. Data mining: Practical machine learning tools and techniques. 2005, San Francisco: Morgan Kaufmann, 2.
16. Neves M, Chagoyen M, Carazo JM, Pascual-Montano A. CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem. BioNLP 2008 Workshop at ACL 2008: 2008; Columbus, OH, USA 2008,
17. Aamodt A, Plaza E. Case-Based Reasoning: Foundational Issues, Methodological Variations, and System Approaches. AI Communications 1994, 7(1):39-59.
18. Daelemans W, Zavrel J, Berck P, Gillis S. MBT: A Memory-Based Part of Speech Tagger-Generator. Fourth Workshop on Very Large Corpora: 1996; Copenhagen, Denmark 1996, 14-27.
19. 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.
20. Cohen WC, Ravikumar P, Fienberg SE. A Comparison of String Distance Metrics for Name-Matching Tasks. IIWeb Workshop on International Joint Conference on Artificial Intelligence: 2003; Acapulco, Mexico 2003, 73-78.
21. Shatkay H, Feldman R. Mining the biomedical literature in the genomic era: an overview. J Comput Biol 2003, 10(6):821-855. 10.1089/106652703322756104, 14980013.
22. Wermter J, Tomanek K, Hahn U. High-performance gene name normalization with GeNo. Bioinformatics 2009, 25(6):815-821. 10.1093/bioinformatics/btp071, 19188193.
23. Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, et al. Introducing meta-services for biomedical information extraction. Genome Biol 2008, 9(Suppl 2):S6. 10.1186/gb-2008-9-s2-s6, 2559990, 18834497.
24. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007, (35 Database):D26-31. 10.1093/nar/gkl993, 1761442, 17148475.
25. The Universal Protein Resource (UniProt) 2009 Nucleic Acids Res 2009, (37 Database):D169-174. 2686606, 18836194, The Universal Protein Resource (UniProt) 2009.
26. Povey S, Lovering R, Bruford E, Wright M, Lush M, Wain H. The HUGO Gene Nomenclature Committee (HGNC). Hum Genet 2001, 109(6):678-680. 10.1007/s00439-001-0615-0, 11810281.