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References
- The MIT Press
- Chapter
- Additional Information
1. Ahmed, A., E. Xing, W. Cohen, and R. F. Murphy. Structured correspondence topic models for mining captioned figures in biological literature. In Proceedings of the Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. New York: ACM, 2009, 39–48. 2.Altman, R. B. 2007 . PharmGKB:A logical home for knowledge relating genotype to drug response phenotype. Nature Genetics 39 (4): 426. 3. Altschul, S., T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman. 1997 . Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25 (17): 3389–3402. 4. Ananiadou, S., B. Kell, and J. Tsujii. 2006. Text mining and its potential applications in systems biology. Trends in Biotechnology 24 (12): 571–579. 5. Ananiadou, S., and J. McNaught. 2006. Text Mining for Biology and Biomedicine. Norwood, MA: Artech House. 6. Ananiadou, S., D. Sullivan, W. Black, G.-A. Levow, J. Gillespie, C. Mao, S. Pyysalo, B. Kolluru, J. Tsujii, and B. Sobrai. 2010. Systematic association of genes to phenotypes by genome and literature mining. PLoS ONE 6 (3): e14780. 7. Angluin, D. 1981. A note on the number of queries needed to identify regular languages. Information and Control 51: 76–87 . 8. Angluin, D. 1988. Queries and concept learning. Machine Learning 2: 319–342. 9. Aranda, B., P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann , et al. 2010. The IntAct molecular interaction database in 2010. Nucleic Acids Research 38 (Database Issue): D525–D531. 10.Arighi, C. N., P. M. Roberts, S.Agarwal, S. Bhattacharya, G. Cesareni,A. Chatraryamontri , S. Clematide, P. Gaudet, M. G. Giglio, I. Harrow, E. Huala, M. Krallinger, U. Leser, D. Li, F. Liu, Z. Lu, L. J. Maltais, N. Okazaki, L. Perfetto, F. Rinaldi, R. Sætre, D. Salgado, P. Srinivasan, P. E. Thomas, L. Toldo, L. Hirschman, and C. H. Wu. 2011. BioCreative III interactive task: An overview. BMC Bioinformatics 12 (Suppl. 8): S4. 11. Bader, G., D. Betel, and C. Hogue. 2003. BIND: The biomolecular interaction network database. Nucleic Acids Research 31 (1): 248–250. 12. Barthelmes, J., C. Ebeling,A. Chang, I. Schomburg, and D. Schomburg. 2007 . BRENDA, AMENDA and FRENDA:The enzyme information system in 2007. Nucleic Acids Research 35 (Database Issue): D511–D514. 13. Beissbarth, T., and T. P. Speed. 2004. GOstat: Find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20 (9): 1464–1465. 14. Berger,A., and J. Lafferty. Information retrieval as statistical translation. In Proceedings of the Twenty-Second ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 1999, 222–229. References 116 References 15. Bhattacharya, S.,A. K. Sehgal, and P. Srinivasan. Online gene indexing and retrieval for BioCreative III at the University of Iowa. In Proceedings of the BioCreative III Workshop, 2010, 52–54. 16. BIND. Biomolecular Interaction Network Database. http://www.bind.ca, 2011. 17. BioCreative Critical Assessment of Information Extraction in Biology. http://www .biocreative.org/, 2011. 18. BioGRID. http://thebiogrid.org/, 2011. 19. Björne, J., F. Ginter, S. Pyysalo, J. Tsujii, and T. Salakoski. Scaling up biomedical event extraction to the entire PubMed. In Proceedings of the 2010 Workshop on Biomedical Natural Language Processing. Stroudsburg, PA:Association for Computational Linguistics, 2010. 20.Blaschke,C.,M.Andrade,C.Ouzounis,andA.Valencia.Automatic extraction of biological information from scientific text: Protein-protein interactions. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAAI Press, 1999, 60–67. 21. Blaschke, C., and A. Valencia. 2001. Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comparative and Functional Genomics 2: 196–206. 22. Blei, D. M., A. Y. Ng, M. I. Jordan, and J. Lafferty. 2003. Latent Dirichlet allocation. Journal of Machine Learning Research 3: 993–1022. 23. Brady, S., and H. Shatkay. EpiLoc:A (working) text-based system for predicting protein subcellular location. In Proceedings of the Pacific Symposium on Biocomputing. Hackensack , NJ: World Scientific, 2008, 604–615. 24. Breiman, L., J. Friedman, R. Olshen, and C. Stone. 1984. Classification and Regression Trees. Monterey, CA: Wadsworth and Brooks. 25.Breitkreutz,B.,C.Stark,T.Reguly,L.Boucher,A.Breitkreutz,M.Livstone,R.Oughtred, et al. 2008.The BioGRID interaction database: 2008 update. Nucleic Acids Research (Database Issue) 36: 637–640. 26. BRENDA. http://www.brenda-enzymes.org/, 2011. 27 . BRENDA Tissue Ontology. http://www.brenda-enzymes.org/ontology/tissue/tree/update/ update_files/BrendaTissueOBO, 2011. 28...