Automatic approaches for gene-drug interaction extraction from biomedical Text: Corpus and comparative evaluation

BioNLP@HLT-NAACL 2012 - Workshop on Biomedical Natural Language Processing, Proceedings

Volumn , Issue , 2012, Pages 214-222

  Sutton, Nate ^a   Wojtulewicz, Laura ^a   Mehta, Neel ^a   Gonzalez, Graciela ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL LINGUISTICS; DATA MINING; EXTRACTION; GENES; NATURAL LANGUAGE PROCESSING SYSTEMS;

AUTOMATIC APPROACHES; BIOMEDICAL TEXT; CO-OCCURRENCE; COMPARATIVE EVALUATIONS; GENE DRUGS; INTERACTION EXTRACTION; INTERACTION TERM; LINGUISTIC PATTERNS; PHARMACOGENOMICS; TEXT CORPORA;

DRUG INTERACTIONS;

EID: 84883830273     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (20)

1. Ahlers, C., Fiszman, M., Demner-Fushman, D., Lang, F.-M., & Rindflesch, T. (2007). Extracting semantic predications from Medline citations for pharmacogenomics. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 209-220.
2. Bui, Q.-C., Nualláin, B. O., Boucher, C. A., & Sloot, P. M. A. (2010). Extracting causal relations on HIV drug resistance from literature. BMC Bioinformatics, 11, 101. doi:10.1186/1471-2105-11- 101.
3. Cheng, D., Knox, C., Young, N., Stothard, P., Damaraju, S., & Wishart, D. S. (2008). PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Research, 36(Web Server issue), W399-405. doi:10.1093/nar/gkn296.
4. Chowdhary, R., Zhang, J., & Liu, J. S. (2009). Bayesian inference of protein-protein interactions from biological literature. Bioinformatics (Oxford, England), 25(12), 1536-1542. doi:10.1093/bioinformatics/btp245.
5. Coulet, A., Shah, N. H., Garten, Y., Musen, M., & Altman, R. B. (2010). Using text to build semantic networks for pharmacogenomics. Journal of Biomedical Informatics, 43(6), 1009-1019. doi:10.1016/j.jbi.2010.08.005.
6. Garten, Y., & Altman, R. B. (2009). Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics, 10 Suppl 2, S6. doi:10.1186/1471-2105-10-S2-S6
7. Hakenberg, J., Leaman, R., Vo, N. H., Jonnalagadda, S., Sullivan, R., Miller, C., Tari, L., et al. (2010). Efficient extraction of protein-protein interactions from full-text articles. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, 7(3), 481-494. doi:10.1109/TCBB.2010.51.
8. Hewett, M., Oliver, D. E., Rubin, D. L., Easton, K. L., Stuart, J. M., Altman, R. B., & Klein, T. E. (2002). PharmGKB: The Pharmacogenetics Knowledge Base. Nucleic Acids Research, 30(1), 163- 165. doi:10.1093/nar/30.1.163.
9. Krallinger, M., Leitner, F., Rodriguez-Penagos, C., & Valencia, A. (2008). Overview of the proteinprotein interaction annotation extraction task of BioCreative II. Genome Biology, 9 Suppl 2, S4. doi:10.1186/gb-2008-9-s2-s4.
10. Leaman, R., & Gonzalez, G. (2008). BANNER: an executable survey of advances in biomedical named entity recognition. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 652-663.
11. Luis Tari, Jörg Hakenberg, Graciela Gonzalez, & Baral, C. (2009). Querying parse tree database of medline text to synthesize user-specific biomolecular networks. CiteSeerX. Retrieved from http://citeseerx.ist.psu.edu/viewdoc/summary?doi= 10.1.1.140.8574.
12. Pyysalo, S., Ginter, F., Heimonen, J., Björne, J., Boberg, J., Järvinen, J., & Salakoski, T. (2007). BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinformatics, 8, 50. doi:10.1186/1471-2105-8-50.
13. Rebholz-Schuhmann, D., Kirsch, H., Arregui, M., Gaudan, S., Riethoven, M., & Stoehr, P. (2007). EBIMed-text Crunching to Gather Facts for Proteins from Medline. Bioinformatics, 23(2), e237- e244. doi:10.1093/bioinformatics/btl302.
14. Sconce, E. A., Daly, A. K., Khan, T. I., Wynne, H. A., & Kamali, F. (2006). APOE genotype makes a small contribution to warfarin dose requirements. Pharmacogenetics and Genomics, 16(8), 609-611. doi:10.1097/01.fpc.0000220567.98089.b5.
15. Shepherd, A. J., & Clegg, A. B. (2008). Syntactic pattern matching with GraphSpider and MPL. Proceedings of the Third International Symposium on Semantic Mining in Biomedicine SMBM 2008 Turku Finland, 129-132.
16. stav. (n.d.).GitHub. Retrieved March 26, 2012, from https://github.com/TsujiiLaboratory/stav
17. Strijbos, J.-W., Martens, R. L., Prins, F. J., & Jochems, W. M. G. (2006). Content analysis: What are they talking about? Computers & Education, 46(1), 29-48. doi:10.1016/j.compedu.2005.04.002.
18. T1.pdf. (n.d.). Retrieved from http://www.lrecconf.org/proceedings/lrec2008/workshops/T1.pdf.
19. The OpenNLP Homepage. (n.d.). Retrieved March 26, 2012, from http://opennlp.sourceforge.net/projects.html
20. Wishart, D. S. (2006). DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Research, 34(90001), D668- D672. doi:10.1093/nar/gkj067.