Extracting Sentences Describing Biomolecular Events from the Biomedical Literature
The scientific literature is one of the main sources of information for researchers. However, due to the rapid increase of the number of scientific articles, satisfying a specific information need has become a very demanding task, and researchers often have to scan through a large number of publications in search of a specific nugget of information. In this work we propose the use of supervised machine learning techniques to retrieve and rank sentences describing different types of biomolecular events. The objective is to classify and rank sentences that match any general query according to the likelihood of mentioning events involving one or more biomolecular entities. These ranked results should provide a condensed, or summarized, view of the knowledge present in the literature and related to the user’s information need.
KeywordsSentence-based Information Retrieval Biomedical Literature Biomolecular Events
Unable to display preview. Download preview PDF.
- 2.Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., et al.: Database resources of the national center for biotechnology information. Nucleic Acids Research 35(suppl. 1), D5–D12 (2007)Google Scholar
- 3.Lu, Z.: PubMed and beyond: a survey of web tools for searching biomedical literature. Database: the Journal of Biological Databases and Curation 2011 (2011)Google Scholar
- 4.Cafarella, M.J., Downey, D., Soderland, S., Etzioni, O.: Knowitnow: fast, scalable information extraction from the web. In: Proceedings of the Conference on Human Language Technology and Empirical Methods in Natural Language Processing, pp. 563–570. Association for Computational Linguistics (2005)Google Scholar
- 8.Kim, J.-D., Nguyen, N., Wang, Y., Tsujii, J., Takagi, T., Yonezawa, A.: The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. BMC Bioinformatics 13(suppl. 11), S1 (2012)Google Scholar
- 9.Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J., Ananiadou, S.: Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 13(suppl. 11), S2 (2012)Google Scholar