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Advances in Bioinformatics
Volume 2012, Article ID 582765, 12 pages
http://dx.doi.org/10.1155/2012/582765
Research Article

Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations

1Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
2Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
3Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland
4Turku BioNLP Group, Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520 Turku, Finland

Received 22 November 2011; Revised 16 March 2012; Accepted 28 March 2012

Academic Editor: Jin-Dong Kim

Copyright © 2012 Sofie Van Landeghem et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J.-D. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, “Overview of BioNLP'09 shared task on event extraction,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 1–9, Association for Computational Linguistics, 2009.
  2. J.-D. Kim, S. Pyysalo, T. Ohta, R. Bossy, N. Nguyen, N. Nguyen, and J. Tsujii, “Overview of BioNLP shared task 2011,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 1–6, Association for Computational Linguistics, 2011.
  3. R. Homann and A. Valencia, “A gene network for navigating the literature,” Nature Genetics, vol. 36, no. 7, aricle 664, 2004. View at Google Scholar
  4. T. Ohta, Y. Miyao, T. Ninomiya et al., “An intelligent search engine and GUI-based efficient MEDLINE search tool based on deep syntactic parsing,” in Proceedings of the COLING/ACL 2006 Interactive Presentation Sessions, pp. 17–20, Association for Computational Linguistics, 2006.
  5. D. Rebholz-Schuhmann, H. Kirsch, M. Arregui, S. Gaudan, M. Riethoven, and P. Stoehr, “EBIMed—text crunching to gather facts for proteins from Medline,” Bioinformatics, vol. 23, no. 2, pp. e237–e244, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. M. A. Hearst, A. Divoli, H. H. Guturu et al., “BioText search engine: beyond abstract search,” Bioinformatics, vol. 23, no. 16, pp. 2196–2197, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. S. Xu, J. McCusker, and M. Krauthammer, “Yale Image Finder (YIF): a new search engine for retrieving biomedical images,” Bioinformatics, vol. 24, no. 17, pp. 1968–1970, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. S. Agarwal, H. Yu, and I. Kohane, “BioNOT: a searchable database of biomedical negated sentences,” BMC Bioinformatics, vol. 12, Article ID 420, 2011. View at Publisher · View at Google Scholar
  9. J. Björne, F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski, “Scaling up biomedical event extraction to the entire PubMed,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 28–36, Association for Computational Linguistics, 2010.
  10. S. Van Landeghem, F. Ginter, Y. Van de Peer, and T. Salakoski, “EVEX: a PubMed-scale resource for homology-based generalization of text mining predictions,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 28–37, Association for Computational Linguistics, 2011.
  11. R. Leaman and G. Gonzalez, “BANNER: an executable survey of advances in biomedical named entity recognition,” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 652–663, 2011. View at Google Scholar · View at Scopus
  12. J. Björne, F. Ginter, and T. Salakoski, “Generalizing biomedical event extraction,” BMC Bioinformatics, vol. 13, supplement 8, article S4, 2012. View at Google Scholar
  13. The UniProt Consortium, “Ongoing and future developments at the universal protein resource,” Nucleic Acids Research, vol. 39, supplement 1, pp. D214–D219, 2011. View at Google Scholar
  14. E. W. Sayers, T. Barrett, D. A. Benson et al., “Database resources of the National Center for Biotechnology Information,” Nucleic Acids Research, vol. 38, supplement 1, pp. D5–D16, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. P. Flicek, M. R. Amode, D. Barrell et al., “Ensembl 2011,” Nucleic Acids Research, vol. 39, no. 1, pp. D800–D806, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. P. J. Kersey, D. Lawson, E. Birney et al., “Ensembl genomes: extending ensembl across the taxonomic space,” Nucleic Acids Research, vol. 38, supplement 1, pp. D563–D569, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Crammer and Y. Singer, “Ultraconservative online algorithms for multiclass problems,” Journal of Machine Learning Research, vol. 3, no. 4-5, pp. 951–991, 2003. View at Google Scholar · View at Scopus
  18. E. Segal, M. Shapira, A. Regev et al., “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data,” Nature Genetics, vol. 34, no. 2, pp. 166–176, 2003. View at Publisher · View at Google Scholar · View at Scopus
  19. J. Björne, F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski, “Complex event extraction at PubMed scale,” Bioinformatics, vol. 26, no. 12, Article ID btq180, pp. i382–i390, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Kaewphan, S. Kreula, S. Van Landeghem, Y. Van de Peer, P. Jones, and F. Ginter, “Integrating large-scale text mining and co-expression networks: targeting NADP(H) metabolism in E. coli with event extraction,” in Proceedings of the 3rd Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM '12), 2012.
  21. T. Ohta, S. Pyysalo, and J. Tsujii, “From pathways to biomolecular events: opportunities and challenges,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 105–113, Association for Computational Linguistics, 2011.
  22. J. A. Carballo and R. S. Cha, “Meiotic roles of Mec1, a budding yeast homolog of mammalian ATR/ATM,” Chromosome Research, vol. 15, no. 5, pp. 539–550, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. Y. Loewenstein, D. Raimondo, O. C. Redfern et al., “Protein function annotation by homology-based inference,” Genome Biology, vol. 10, no. 2, article 207, 2009. View at Google Scholar · View at Scopus
  24. S. Proost, M. Van Bel, L. Sterck et al., “PLAZA: a comparative genomics resource to study gene and genome evolution in plants,” Plant Cell, vol. 21, no. 12, pp. 3718–3731, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. R. Kato and H. Ogawa, “An essential gene, ESR1, is required for mitotic cell growth, DNA repair and meiotic recombination in Saccharomyces cerevisiae,” Nucleic Acids Research, vol. 22, no. 15, pp. 3104–3112, 1994. View at Google Scholar · View at Scopus
  26. P. Stenetorp, G. Topić, S. Pyysalo, T. Ohta, J.-D. Kim, and J. Tsujii, “BioNLP Shared Task 2011: supporting resources,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 112–120, Portland, Oregon, USA, 2011.
  27. J. Björne and T. Salakoski, “Generalizing biomedical event extraction,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 183–191, Association for Computational Linguistics, 2011.
  28. S. Pyysalo, T. Ohta, and J. Tsujii, “Overview of the entity relations (REL) supporting task of BioNLP Shared Task 2011,” in Proceedings of the BioNLP Workshop Companion Volume for Shared Task, pp. 83–88, Association for Computational Linguistics, 2011.
  29. S. Van Landeghem, J. Björne, T. Abeel, B. De Baets, T. Salakoski, and Y. Van de Peer, “Semantically linking molecular entities in literature through entity relationships,” BMC Bioinformatics, vol. 13, supplement 8, article S6, 2012. View at Google Scholar
  30. Z. Lu, H. Y. Kao, C. H. Wei et al., “The gene normalization task in BioCreative III,” BMC Bioinformatics, vol. 12, supplement 8, article S2, 2011. View at Google Scholar