Exploring species-based strategies for gene normalization

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 7, Issue 3, 2010, Pages 462-471

  Verspoor, Karin ^a   Roeder, Christophe ^a   Johnson, Helen L ^a   Cohen, Kevin Bretonnel ^a   Baumgartner Jr , William A ^a   Hunter, Lawrence E ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Biomedical natural language processing; gene normalization; information extraction; text mining

Indexed keywords

BIOMEDICAL NATURAL LANGUAGE PROCESSING; DICTIONARY LOOKUP; EXTERNAL KNOWLEDGE; INFORMATION EXTRACTION; NATURAL LANGUAGE PROCESSING; NORMALIZATION STRATEGIES; PROTEIN INTERACTION; SYSTEM VARIATIONS; TEXT MINING;

COMPUTATIONAL LINGUISTICS; INFORMATION ANALYSIS; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS;

CHARACTER RECOGNITION;

ARTICLE; AUTOMATED PATTERN RECOGNITION; BIOLOGY; DATA MINING; GENE; HEALTH CARE ORGANIZATION; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PROTEIN ANALYSIS; SPECIES DIFFERENCE;

COMPUTATIONAL BIOLOGY; DATA MINING; GENES; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PROTEIN INTERACTION MAPPING; SOCIETIES, SCIENTIFIC; SPECIES SPECIFICITY;

EID: 77955439720     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2010.48     Document Type: Article

References (16)

1. M. Krallinger, A. Morgan, L. Smith, F. Leitner, L. Tanabe, J. Wilbur, L. Hirschman, and A. Valencia, "Evaluation of Text- Mining Systems for Biology: Overview of the Second BioCreative Community Challenge," Genome Biology, vol.9, suppl. 2, article no. S1, 2008.
2. L. Hunter, Z. Lu, J. Firby, W.A. Baumgartner, Jr., H.L. Johnson, P.V. Ogren, and K.B. Cohen, "OpenDMAP: An Open-Source, Ontology-Driven Concept Analysis Engine, with Applications to Capturing Knowledge Regarding Protein Transport, Protein Interactions and Cell-Specific Gene Expression," BMC Bioinformatics, vol.9, no.78, 2008.
3. W.A. Baumgartner, Jr., K.B. Cohen, and L. Hunter, "An Open- Source Framework for Large-Scale, Flexible Evaluation of Biomedical Text Mining Systems," J. Biomedical Discovery and Collaboration, vol.3, no.1, 2008.
4. D. Ferrucci and A. Lally, "Building an Example Application with the Unstructured Information Management Architecture," IBM Systems J., vol.43, no.3, pp. 455-475, July 2004.
5. A.A. Morgan et al., "Overview of BioCreative II Gene Normalization," Genome Biology, vol.9, suppl. 2, article no. S3, 2008.
6. W.A. Baumgartner, Jr., Z. Lu, H.L. Johnson, J.G. Caporaso, J. Paquette, A. Lindemann, E.K. White, O. Medvedeva, K.B. Cohen, and L. Hunter, "Concept Recognition for Extracting Protein Interaction Relations from Biomedical Text," Genome Biology, vol.9, suppl. 2, article no. S9, 2008.
7. T. Kappeler, K. Kaljurand, and F. Rinaldi, "TX Task: Automatic Detection of Focus Organisms in Biomedical Publications," Proc. BioNLP '09 Workshop, pp. 80-88, http://www.aclweb.org/ anthology/W09-1310, June 2009.
8. X. Wang, J. Tsujii, and S. Ananiadou, "Disambiguating the Species of Biomedical Named Entities Using Natural Language Parsers," Bioinformatics, vol.26, no.5, pp. 661-667, http://bioinformatics. oxfordjournals.org/cgi/ content/abstract/26/5/661, 2010.
9. H. Xu, J.-W. Fan, and C. Friedman, "Combining Multiple Evidence for Gene Symbol Disambiguation," Proc. Biological, Translational, and Clinical Language Processing, pp. 41-48, http://www.aclweb. org/anthology/ W/W07/W07-1006, June 2007.
10. H. Xu, J.-W. Fan, G. Hripcsa, E.A. Mendon, M. Markatou, and C. Friedman, "Gene Symbol Disambiguation Using Knowledge- Based Profiles," Bioinformatics, vol.23, no.8, pp. 1015-1022, 2007.
11. X. Wang and M. Matthews, "Species Disambiguation for Biomedical Term Identification," Proc. Current Trends in Biomedical Natural Language Processing (BioNLP '08), pp. 71-79, 2008.
12. A. Schwartz and M. Hearst, "A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text," Proc. Pacific Symp. Biocomputing, vol.8, pp. 451-462, 2003.
13. K.B. Cohen, K. Verspoor, H.L. Johnson, C. Roeder, P.V. Ogren, W.A. Baumgartner, Jr., E. White, H. Tipney, and L. Hunter, "High- Precision Biological Event Extraction with a Concept Recognizer," Proc. BioNLP '09 Companion Volume: Shared Task on Entity Extraction, pp. 50-58, 2009.
14. A. Ceol, A. Chatr-Aryamontri, L. Licata, and G. Cesareni, "Linking Entries in Protein Interaction Database to Structured Text: The FEBS Letters Experiment," FEBS Letters, vol.582, no.8, pp. 1171-1177, 2008.
15. F. Leitner et al., "Introducing Meta-Services for Biomedical Information Extraction," Genome Biology, vol.9, suppl. 2, article no. S6, 2008.
16. D. Hanisch, K. Fundel, H.-T. Mevissen, R. Zimmer, and J. Fluck, "ProMiner: Rule-Based Protein and Gene Entity Recognition," BMC Bioinformatics, vol.6, suppl. 1, article no. S14, 2005.