SR4GN: A species recognition software tool for gene normalization

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Wei, Chih Hsuan ^a,b   Kao, Hung Yu ^b   Lu, Zhiyong ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA MINING; GENE NORMALIZATION; INFORMATION PROCESSING; INTERMETHOD COMPARISON; PROCESS OPTIMIZATION; SPECIES IDENTIFICATION; ALGORITHM; BIOLOGY; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA MINING; SOFTWARE;

EID: 84861856856     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038460     Document Type: Article

References (22)

1. Lu Z, Kao H-Y, Wei C-H, Huang M, Liu J, et al. (2011) The Gene Normalization Task in BioCreative III. BMC Bioinformatics 12: S9.
2. Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, et al. (2008) Overview of BioCreative II gene normalization. Genome Biology 9: S3.
3. Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A, (2008) Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biology 9: S4.
4. Krallinger M, Vazquez M, Leitner F, Salgado D, Chatraryamontri A, et al. (2011) The Protein-Protein Interaction tasks of BioCreative III: classication/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics 12: S3.
5. William A Baumgartner J, Lu Z, Johnson HL, Caporaso JG, Paquette J, et al. (2008) Concept recognition for extracting protein interaction relations from biomedical text. Genome Biology 9: S9.
6. Gerner M, Nenadic G, Bergman CM, (2010) LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics 11.
7. Bontcheva K, Tablan v, Maynard d, Cunningham HS, (2004) Evolving GATE to Meet New Challenges in Language Engineering. Natural Language Engineering 10: 349-373.
8. Cunningham H, Maynard D, Bontcheva K, Tablan V, (2002) A framework and graphical development environment for robust NLP tools and applications pp. 168-175.
9. Wang X, Tsujii Ji, Ananiadou S, (2010) Disambiguating the Species of Biomedical Named Entities using Natural Language Parsers. Bioinformatics 26: 661-667.
10. Mu T, Wang X, Tsujii Ji, Ananiadou S, (2010) Imbalanced Classification Using Dictionary-based Prototypes and Hierarchical Decision Rules for Entity Sense Disambiguation; 851-859.
11. Hirschman L, Colosimo M, Morgan A, Yeh A, (2005) Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 6: S11.
12. Kano Y Jr, WAB McCrohon L, Ananiadou S, Cohen KB, et al. (2009) U-Compare: share and compare text mining tools with UIMA. Bioinformatics 25: 1997-1998.
13. Wei C-H, Kao H-Y, (2011) Cross-species gene normalization by species inference. BMC Bioinformatics 12: S6.
14. Wei C-H, Kao H-Y, (2010) Represented Indicator Measurement and corpus distillation on focus species detection; 2010 pp. 657-662.
15. Kappeler T, Kaljurand K, Rinaldi F TX, (2009) Task:Automatic Detection of Focus Organisms in Biomedical Publications; 2009; Boulder, Colorado, USA pp. 80-88.
16. Hakenberg J, Gerner M, Haeussler M, Solt I, Plake C, et al. (2011) The GNAT library for local and remote gene mention normalization. Bioinformatics 27: 2769-2771.
17. Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G, (2008) Inter-species normalization of gene mentions with GNAT. Bioinformatics 24: i126-i132.
18. Hsu C-N, Chang Y-M, Kuo C-J, Lin Y-S, Huang H-S, et al. (2008) Integrating High Dimensional Bi-directional Parsing Models for Gene Mention Tagging. Bioinformatics 24: i286-i294.
19. Naderi N, Kappler T, Baker CJO, Witte R, (2011) OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents. Bioinformatics 27: 2721-2729.
20. D B, (1980) Randomization Analysis of Experimental Data: The Fisher Randomization Test. Journal of the American Statistical Association 75: 575-582.
21. Wei C-H, Kao H-Y, Lu Z, (2012) PubTator: A PubMed-like interactive curation system for document triage and literature curation. BioCreative 2012 workshop pp. 145-150.
22. Carroll HD, Kann MG, Sheetlin SL, Spouge JL, (2010) Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. Bioinformatics 26: 1708-1713.