High-precision biological event extraction: Effects of system and of data

Computational Intelligence

Volumn 27, Issue 4, 2011, Pages 681-701

  Cohen, K Bretonnel ^a   Verspoor, Karin ^a   Johnson, Helen L ^a   Roeder, Chris ^a   Ogren, Philip V ^a   Baumgartner Jr, William A ^a   White, Elizabeth ^a   Tipney, Hannah ^a   Hunter, Lawrence ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

BioNLP; conceptual analysis; event recognition; natural language processing; text mining

Indexed keywords

BIONLP; CONCEPTUAL ANALYSIS; EVENT RECOGNITION; NATURAL LANGUAGE PROCESSING; TEXT MINING;

COMPUTATIONAL LINGUISTICS; INFORMATION ANALYSIS; INFORMATION RETRIEVAL SYSTEMS; NATURAL LANGUAGE PROCESSING SYSTEMS; ONTOLOGY; SEMANTICS;

PATTERN RECOGNITION SYSTEMS;

EID: 82455189734     PISSN: 08247935     EISSN: 14678640     Source Type: Journal    
DOI: 10.1111/j.1467-8640.2011.00405.x     Document Type: Article

References (30)

1. Alex, B., C. Grover, B. Haddow, M. Kabadjov, E. Klein, M. Matthews, S. Roebuck, R. Tobin, and, X. Wang,. 2008. Assisted curation: Does text mining really help? In Pac Symp Biocomput.
2. Alias-i,. 2008. LingPipe 3.1.2.
3. Bard, J., S. Y. Rhee, and, M. Ashburner,. 2005. An ontology for cell types. Genome Biology, 6 (2). Retrieved file cell.obo (versison 1.24 25:05:2007 09:56) from on June 14, 2007.
4. Bechhofer, S., Y. Yesilada, B. Horan, and, C. Goble,. 2008. Using ontologies and vocabularies for dynamic linking. IEEE Internet Computing, 12 (3): 32-39. (Pubitemid 351767016)
5. Björne, J., J. Heimonen, F. Ginter, A. Airola, T. Pahikkala, and, T. Salakoski,. 2009. Extracting complex biological events with rich graph-based feature sets. In Proceedings of the Workshop on BioNLP: Shared Task, pp. 10-18.
6. Blaschke, C., and, A. Valencia,. 2001. The potential use of SUISEKI as a protein interaction discovery tool. Genome Inform, 12: 123-134.
7. Blaschke, C., and, A. Valencia,. 2002. The frame-based module of the SUISEKI information extraction system. IEEE Intelligent Systems 17: 14-20. (Pubitemid 35327163)
8. Buyko, E., J. Wermter, M. Poprat, and, U. Hahn,. 2006. Automatically mapping an NLP core engine to the biology domain. In Proceedings of the ISMB 2006 Joint BioLINK/Bio-Ontologies Meeting.
9. Ciravegna, F., and, Y. Wilks,. 2003. Designing adaptive information extraction for the semantic web in Amilcare. In Annotation for the Semantic Web. Edited by, S. Handschuh, and, S. Staab, Amsterdam, The Netherlands: IOS Press.
10. Cohen, K. B., L. Tanabe, S. Kinoshita, and, L. Hunter,. 2004. A resource for constructing customized test suites for molecular biology entity identification systems. BioLINK 2004, pp. 1-8.
11. Cohen, K. B., M. Palmer, and, L. Hunter,. 2008. Nominalization and alternations in biomedical language. PLoS ONE, 3 (9).
12. Cohen, K. B., K. Verspoor, H. L. Johnson, C. Roeder, P. V. Ogren, W. A. Baumgartner Jr, E. White, H. Tipney, and, L. Hunter,. 2009. High-precision biological event extraction with a concept recognizer. In BioNLP 2009 Companion Volume: Shared Task on Entity Extraction, pp. 50-58.
13. Consortium, T. G. O., 2001. Creating the Gene Ontology resource: Design and implementation. Genome Research, 11: 1425-1433.
14. Daraselia, N., A. Yuryev, S. Egorov, S. Novichkova, A. Nikitin, and, I. Mazo,. 2004. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics, 20: 604-611. (Pubitemid 38443813)
15. Eilbeck, K., S. E. Lewis, C. J. Mungall, M. Yandell, L. Stein, R. Durbin, and, M. Ashburner,. 2005. The sequence ontology: A tool for the unification of genome annotations. Genome Biology, 6 (5).
16. Ferrucci, D., and, A. Lally,. 2004. Building an example application with the unstructured information management architecture. IBM Systems Journal, 43 (3): 455-475.
17. Hakenberg, J., R. J. Leaman, N. H. Vo, S. Jonnalagadda, R. Sullivan, C. Miller, L. Tari, C. Baral, and, G. Gonzalez,. 2009. Online protein interaction extraction and normalization at Arizona State University. In Proceedings of the BioCreative II.5 Workshop 2009 on Digital Annotations.
18. Handschuh, S., A. Maedche, S. Staab, and, E. Maedche,. 2001. CREAM - Creating relational metadata with a component-based, ontology-driven annotation framework. In Proceedings of the First International Conference on Knowledge Capture (K-CAP).
19. Hunter, L., Z. Lu, J. Firby Jr, W. A. B., H. L. Johnson, P. V. Ogren, and, K. B. Cohen,. 2008. OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics, 9 (78).
20. IBM. 2009. UIMA Java framework.
21. Kim, J.-D., T. Ohta, S. Pyysalo, Y. Kano, and, J. Tsujii,. 2009. Overview of BioNLP'09 shared task on event extraction. In BioNLP 2009 Companion Volume: Shared Task on Entity Extraction, pp. 1-9.
22. Leach, S. M., H. Tipney, W. Feng Jr, W. A. B., P. Kasliwal, R. P. Schuyler, T. Williams, R. A. Spritz, and, L. Hunter,. 2009. Biomedical discovery acceleration, with applications to craniofacial development. PLoS Computational Biology, 5 (3).
23. Miyao, Y., K. Sagae, R. Saetre, T. Matsuzaki, and, J. Tsujii,. 2009. Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics, 25 (3): 394-400.
24. Rosse, C., and, J. L. Mejino, Jr,. 2003. A reference ontology for biomedical informatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics, 36 (6): 478-500. (Pubitemid 38169375)
25. Saetre, R., M. Miwa, K. Yoshida, and, J. Tsujii,. 2009. From protein-protein interaction to molecular event extraction. In Natural language processing in biomedicine 2009, pp. 103-106.
26. Schomburg, I., A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, and, D. Schomburg,. 2004. BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res, 32 (Database issue). Retrieved file BrendaTissue.obo from on June 14, 2007.
27. The Gene Ontology Consortium. 2000. Gene Ontology: Tool for the unification of biology. Nature Genetics, 25 (1): 25-29.
28. Vargas-Vera, M., E. Motta, J. Domingue, M. Lanzoni, A. Stutt, and, F. Ciravegna,. 2002. MNM: Ontology Driven Semi-automatic and Automatic Support for Semantic Markup. Berlin, Germany: Springer Verlag, pp. 379-391.
29. Verspoor, K., K. B. Cohen, and, L. Hunter, (2009). The textual characteristics of traditional and open access scientific journals are similar. BMC Bioinformatics, 10.
30. Yakushiji, A., Y. Tateisi, Y. Miyao, and, J. Tsujii,. 2001. Event extraction from biomedical papers using a full parser. In Proceedings of the Pac Symp Biocomput, pp. 408-419.