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EVENT EXTRACTION FROM BIOMEDICAL PAPERS USING A FULL PARSER
Abstract
We have designed and implemented an information extraction system using a full parser to investigate the plausibility of full analysis of text using general-purpose parser and grammar applied to biomedical domain. We partially solved the problems of full parsing of inefficiency, ambiguity, and low coverage by introducing the preprocessors, and proposed the use of modules that handles partial results of parsing for further improvement. Our approach makes it possible to modularize the system, so that the IE system as a whole becomes easy to be tuned to specific domains, and easy to be maintained and improved by incorporating various techniques of disambiguation, speed up, etc. In preliminary experiment, from 133 argument structures that should be extracted from 97 sentences, we obtained 23% uniquely and 24% with ambiguity. And 20% are extractable from not complete but partial results of full parsing.
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Cited by
Literature mining for the biologist: from information retrieval to biological discovery
Jensen, L. J., Saric, J., & Bork, P. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1768 · Cited by 631
Friedman, C., Kra, P., Yu, H., Krauthammer, M., & Rzhetsky, A. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.suppl_1.s74 · Cited by 507
BioInfer: a corpus for information extraction in the biomedical domain
Pyysalo, S., Ginter, F., Heimonen, J., Björne, J., Boberg, J., Järvinen, J., & Salakoski, T. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-50 · Cited by 485
Corpus annotation for mining biomedical events from literature
Kim, J.-D., Ohta, T., & Tsujii, J. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-10 · Cited by 395
Self-citationText mining and its potential applications in systems biology
Ananiadou, S., Kell, D. B., & Tsujii, J.-I. (2006) · Trends in Biotechnology · doi:10.1016/j.tibtech.2006.10.002 · Cited by 324
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Metadata
- Authors
- Yakushiji, A., Tateisi, Y., Miyao, Y., & Tsujii, J.-I.
- Venue
- Biocomputing 2001
- Publisher
- WORLD SCIENTIFIC
- Published
- 2000-12
- Pages
- 408-419
- OpenAlex
- W1999117234
- Cited by
- 224
- References
- 0
- FWCI
- 35.14
- Type
- conference paper
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: EVENT EXTRACTION FROM BIOMEDICAL PAPERS USING A FULL PARSER. https://app.cochat.ai/papers/10.1142/9789814447362_0040
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- Yakushiji, A., Tateisi, Y., Miyao, Y., & Tsujii, J.-I. (2000). EVENT EXTRACTION FROM BIOMEDICAL PAPERS USING A FULL PARSER. Biocomputing 2001. https://doi.org/10.1142/9789814447362_0040
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
