Collaborative semi-automatic annotation of the biomedical literature

International Conference on Intelligent Systems Design and Applications, ISDA

Volumn , Issue , 2011, Pages 1213-1217

  Cano, C ^a   Labarga, A ^a   Blanco, A ^a   Peshkin, L ^b  

^a UNIVERSITY OF GRANADA   (Spain)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

biomedical literature; Collaborative annotation; semi automatic curation; text mining

Indexed keywords

BIOMEDICAL COMMUNITY; BIOMEDICAL LITERATURE; COLLABORATIVE ANNOTATION; CURATION; HIGH-THROUGHPUT; HUMAN GENOMES; HYBRID APPROACH; INFORMATION EXTRACTION SYSTEMS; OPEN SOURCES; SCIENTIFIC LITERATURE; SEMI-AUTOMATIC ANNOTATION; SEMI-AUTOMATICS; SOURCE CODES; TEXT-MINING;

GENES; INTELLIGENT SYSTEMS; SYSTEMS ANALYSIS;

AUTOMATION;

EID: 84857518603     PISSN: 21647143     EISSN: 21647151     Source Type: Conference Proceeding    
DOI: 10.1109/ISDA.2011.6121824     Document Type: Conference Paper

References (17)

1. M. Krallinger, A. Valencia, and L. Hirschman, "Linking genes to literature: text mining, information extraction, and retrieval applications for biology," Genome biology, vol. 9, no. Suppl 2, p. S8, 2008.
2. R. Winnenburg, T. Wachter, C. Plake, A. Doms, and M. Schroeder, "Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?" Briefings in Bioinformatics, vol. 9, no. 6, p. 466, 2008.
3. 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, no. Suppl 2, p. S1, 2008.
4. J. Kim, T. Ohta, S. Pyysalo, Y. Kano, and J. Tsujii, "Overview of BioNLP'09 shared task on event extraction," in Proceedings of the Workshop on BioNLP: Shared Task. Association for Computational Linguistics, 2009, pp. 1-9.
5. F. Leitner, M. Krallinger, C. Rodriguez-Penagos, J. Hakenberg, C. Plake, C. Kuo, C. Hsu, R. Tsai, H. Hung, W. Lau et al., "Introducing meta-services for biomedical information extraction," Genome Biology, vol. 9, no. Suppl 2, p. S6, 2008.
6. Y. Kano, W. Baumgartner, L. McCrohon, S. Ananiadou, K. Cohen, L. Hunter, and J. Tsujii, "U-Compare: share and compare text mining tools with UIMA," Bioinformatics, vol. 25, no. 15, p. 1997, 2009.
7. D. Rebholz-Schuhmann, H. Kirsch, and F. Couto, "Facts from text-is text mining ready to deliver," PLoS Biol, vol. 3, no. 2, p. e65, 2005.
8. B. Mons, M. Ashburner, C. Chichester, E. van Mulligen, M. Weeber, J. den Dunnen, G. van Ommen, M. Musen, M. Cockerill, H. Hermjakob et al., "Calling on a million minds for community annotation in WikiProteins," Genome biology, vol. 9, no. 5, p. R89, 2008.
9. H. Maier, S. Dohr, K. Grote, S. O'Keeffe, T. Werner, M. de Angelis, and R. Schneider, "LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts," Nucleic acids research, vol. 33, no. Web Server Issue, p. W779, 2005.
10. C. Baral, G. Gonzalez, A. Gitter, C. Teegarden, and A. Zeigler, "CBioC: beyond a prototype for collaborative annotation of molecular interactions from the literature," in Computational Systems Bioinformatics: CSB2007 Conference Proceedings, Volume 6: University of California, San Diego, USA, 13-17 August 2007. Imperial College Pr, 2007, p. 381.
11. F. Belleau, M. Nolin, N. Tourigny, P. Rigault, and J. Morissette, "Bio2RDF: Towards a mashup to build bioinformatics knowledge systems," Journal of biomedical informatics, vol. 41, no. 5, pp. 706-716, 2008.
12. B. Mons and J. Velterop, "Nano-Publication in the e-science era," in Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), 2009.
13. D. Rebholz-Schuhmann, M. Arregui, S. Gaudan, H. Kirsch, and A. Jimeno, "Text processing through Web services: calling Whatizit," Bioinformatics, vol. 24, no. 2, p. 296, 2008.
14. J. Caporaso, W. Baumgartner, D. Randolph, K. Cohen, and L. Hunter, "MutationFinder: a high-performance system for extracting point mutation mentions from text," Bioinformatics, vol. 23, no. 14, p. 1862, 2007.
15. C. Cano, T. Monaghan, A. Blanco, D. Wall, and L. Peshkin, "Collaborative text-annotation resource for disease-centered relation extraction from biomedical text," Journal of Biomedical Informatics, vol. 42, no. 5, pp. 967-977, 2009.
16. C. Cano, A. Labarga, A. Blanco, and L. Peshkin, "Social and semantic web technologies for the text-to-knowledge translation process in biomedicine," in Biomedical Engineering, Trends, Researches and Technologies. In Tech, 2011, vol. 3.
17. B. Carpenter and B. Baldwin, "Lingpipe," 2008, http://aliasi.com/lingpipe/.