A machine learning approach for phenotype name Recognition

24th International Conference on Computational Linguistics - Proceedings of COLING 2012: Technical Papers

Volumn , Issue , 2012, Pages 1425-1440

  Khordad, Maryam ^a   Mercer, Robert E ^a   Rogan, Peter ^a  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

Human phenotype ontology; Metamap; Named entity recognition; Phenotype

Indexed keywords

AUTOMATIC PROCESSING; BIOMEDICAL LITERATURE; EVALUATION RESULTS; MACHINE LEARNING APPROACHES; METAMAP; NAMED ENTITY RECOGNITION; PHENOTYPE; SEMI-SUPERVISED LEARNING METHODS;

SUPERVISED LEARNING;

COMPUTATIONAL LINGUISTICS;

EID: 84876803741     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (41)

1. Andrade, M. A. and Valencia, A. (1998). Automatic extraction of keywords from scientific text: Application to the knowledge domain of protein families. Bioinformatics, 14(7):600-607.
2. Aronson, A. R. (2001). Effective mapping of biomedical text to the umls metathesaurus: The metamap program. In AMIA Symposium, pages 17-21.
3. Bui, Q.-C., Katrenko, S., and Sloot, P. M. A. (2011). A hybrid approach to extract protein-protein interactions. Bioinformatics, 27(2):259-265.
4. Burgun, A., Mougin, F., and Bodenreider, O. (2009). Two approaches to integrating phenotype and clinical information. AMIA Annual Symposium proceedings, 2009:75-79.
5. Coulet, A., Shah, N. H., Garten, Y., Musen, M. A., and Altman, R. B. (2010). Using text to build semantic networks for pharmacogenomics. Journal of Biomedical Informatics, 43(6):1009- 1019.
6. Dai, M., Shah, N. H., Xuan, W., Musen, M. A., Watson, S. J., Athey, B. D., and Meng, F. (2008). An efficient solution for mapping free text to ontology terms. In AMIA Summit on Translational Bioinformatics, San Francisco, CA.
7. Day-Richter, J., Harris, M. A., Haendel, M., OBO, T. G. O., and Lewis, S. (2007). OBO-Edit an ontology editor for biologists. Bioinformatics, 23(16):2198-2200.
8. Friedman, C., Kra, P., Yu, H., Krauthammer, M., and Rzhetsky, A. (2001). GENIES: A naturallanguage processing system for the extraction of molecular pathways from journal articles. Bioinformatics (Oxford, England), 17 Suppl 1(suppl-1):S74-82.
9. Fukuda, K., Tamura, A., Tsunoda, T., and Takagi, T. (1998). Toward information extraction: identifying protein names from biological papers. Pac Symp Biocomput, pages 707-718.
10. Fundel, K., Küffner, R., and Zimmer, R. (2007). Relex - relation extraction using dependency parse trees. Bioinformatics, 23(3):365-371.
11. Gaizauskas, R., Demetriou, G., Artymiuk, P. J., and Willett, P. (2003). Protein structures and information extraction from biological texts: The PASTA system. Bioinformatics, 19(1):135-143.
12. Gong, L.-J., Yuan, Y., Wei, Y.-B., and Sun, X. (2009). A hybrid approach for biomedical entity name recognition. In Biomedical Engineering and Informatics, 2009. BMEI '09. 2nd International Conference on, pages 1 -5.
13. He, X. and DiMarco, C. (2005). Using lexical chaining to rank protein-protein interactions in biomedical texts. In BioLink 2005: Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, Conference of the Association for Computational Linguistics (poster Presentation).
14. Horn, F., Lau, A. L., and Cohen, F. E. (2004). Automated extraction of mutation data from the literature: Application of MuteXt to G protein-coupled receptors and nuclear hormone receptors. Bioinformatics, 20(4):557-568.
15. Hristovski, D., Friedman, C., Rindflesch, T. C., and Peterlin, B. (2006). Exploiting semantic relations for literature-based discovery. AMIA Annual Symposium proceedings, pages 349-353.
16. Hristovski, D., Peterlin, B., Mitchell, J. A., and Humphrey, S. M. (2005). Using literature-based discovery to identify disease candidate genes. I. J. Medical Informatics, 74(2-4):289-298.
17. Humphreys, B. L., Lindberg, D. A., Schoolman, H. M., and Barnett, G. O. (1998). The Unified Medical Language System: An informatics research collaboration. J Am Med Inform Assoc, 5(1):1-11.
18. Humphreys, K., Demetriou, G., and Gaizauskas, R. (2000). Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pages 505-516.
19. Khordad, M., Mercer, R. E., and Rogan, P. (2011). Improving phenotype name recognition. Canadian Conference on AI, 6657:246-257.
20. kiong Ng, S. and Wong, M. (1999). Toward routine automatic pathway discovery from on-line scientific text abstracts. Genome Informatics, 10:104-112.
21. Klein, T. E., Chang, J. T., Cho, M. K., Easton, K. L., Fergerson, R., Hewett, M., Lin, Z., Liu, Y., Liu, S., Oliver, D. E., Rubin, D. L., Shafa, F., Stuart, J. M., and Altman, R. B. (2001). Integrating genotype and phenotype information: An overview of the PharmGKB project. The pharmacogenomics journal, 1(3):167-170.
22. Krauthammer, M., Rzhetsky, A., Morozov, P., and Friedman, C. (2000). Using BLAST for identifying gene and protein names in journal articles. Gene, 259(1-2):245-252.
23. Leaman, R. and Gonzalez, G. (2008). Banner: An executable survey of advances in biomedical named entity recognition. In Pacific Symposium on Biocomputing, pages 652-663.
24. Leroy, G., Chen, H., and Martinez, J. D. (2003). A shallow parser based on closed-class words to capture relations in biomedical text. Journal of Biomedical Informatics, 36(3):145-158.
25. Leser, U. and Hakenberg, J. (2005). What makes a gene name? named entity recognition in the biomedical literature. Briefings in Bioinformatics, 6(4):357-369.
26. McCallum, A. K. (2002). Mallet: A machine learning for language toolkit. http://mallet.cs.umass.edu.
27. McCray, A., Burgun, A., and Bodenreider, O. (2001). Aggregating UMLS semantic types for reducing conceptual complexity. Proceedings of Medinfo, 10(pt 1):216-20.
28. McKusick, V. (2007). Mendelian Inheritance in Man and Its Online Version, OMIM. The American Journal of Human Genetics, 80(4):588-604.
29. Nobata, C., Collier, N., and ichi Tsujii, J. (1999). Automatic term identification and classification in biology texts. In In Proc. of the 5th NLPRS, pages 369-374.
30. Rindflesch, T. C., Libbus, B., Hristovski, D., Aronson, A. R., and Kilicoglu, H. (2003). Semantic relations asserting the etiology of genetic diseases. AMIA Annual Symposium Proceedings, pages 554-558.
31. Rindflesch, T. C., Tanabe, L., Weinstein, J. N., and Hunter, L. (2000). Edgar: Extraction of drugs, genes and relations from the biomedical literature. In Pacific Symposium on Biocomputing, volume 5, pages 514-525.
32. Robinson, P. N. and Mundlos, S. (2010). The human phenotype ontology. Clinical genetics, 77(6):525-534.
33. Rocktäschel, T., Weidlich, M., and Leser, U. (2012). Chemspot: A hybrid system for chemical named entity recognition. Bioinformatics, 28(12):1633-1640.
34. Schwartz, A. S. and Hearst, M. A. (2003). A simple algorithm for identifying abbreviation definitions in biomedical text. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pages 451-462.
35. Segura-Bedmar, I., Martinez, P., and Segura-Bedmar, M. (2008). Drug name recognition and classification in biomedical texts: A case study outlining approaches underpinning automated systems. Drug Discovery Today, 13(17-18):816 - 823.
36. Seki, K. and Mostafa, J. (2005). A hybrid approach to protein name identification in biomedical texts. Inf. Process. Manage., 41(4):723-743.
37. Swanson, D. (1986). Fish oil, raynaud's syndrome, and undiscovered public knowledge. Perspect. Bio. Med, 30:7-18.
38. Tanabe, L., Scherf, U., Smith, L. H., Lee, J. K., Hunter, L., and Weinstein, J. N. (1999). MedMiner: An Internet text-mining tool for biomedical information, with application to gene expression profiling. BioTechniques, 27(6):1210-1217.
39. Valencia, A. (2005). Automatic annotation of protein function. Current opinion in structural biology, 15(3):267-274.
40. Xu, R., Supekar, K., Morgan, A., Das, A., and Garber, A. (2008). Unsupervised method for automatic construction of a disease dictionary from a large free text collection. AMIA Annual Symposium proceedings, pages 820-824.
41. Yu, H., Zhu, X., Huang, M., and Li, M. (2005). Discovering patterns to extract protein-protein interactions from the literature: Part ii. Bioinformatics, 21(15):3294-3300.