Abstract
Self-supervised relation extraction uses a knowledge base to automatically annotate a training corpus which is then used to train a classifier. This approach has been successfully applied to different domains using a range of knowledge bases. This paper applies the approach to the biomedical domain using UMLS, a large biomedical knowledge base containing millions of concepts and relations among them. The approach is evaluated using two different techniques. The presented results are promising and indicate that UMLS is a useful resource for semi-supervised relation extraction.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Agichtein, E., Gravano, L.: Snowball: extracting relations from large plain-text collections. In: Proceedings of the Fifth ACM Conference on Digital libraries, DL 2000, pp. 85–94 (2000)
Aronson, A., Lang, F.: An overview of MetaMap: historical perspective and recent advances. Journal of the American Medical Association 17(3), 229–236 (2010)
Björne, J., Salakoski, T.: Generalizing biomedical event extraction. In: Proceedings of BioNLP Shared Task 2011 Workshop, pp. 183–191. Association for Computational Linguistics, Portland (2011)
Björne, J., Salakoski, T.: Tees 2.1: Automated annotation scheme learning in the bionlp 2013 shared task. In: Proceedings of the BioNLP Shared Task 2013 Workshop, pp. 16–25. Association for Computational Linguistics, Sofia (2013)
Brin, S.: Extracting patterns and relations from the world wide web. In: Atzeni, P., Mendelzon, A.O., Mecca, G. (eds.) WebDB 1998. LNCS, vol. 1590, pp. 172–183. Springer, Heidelberg (1999)
Charniak, E., Johnson, M.: Coarse-to-fine n-best parsing and maxent discriminative reranking. In: Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics, ACL 2005, pp. 173–180 (2005)
Collins, M., Duffy, N.: New ranking algorithms for parsing and tagging: Kernels over discrete structures, and the voted perceptron. In: Proceedings of 40th Annual Meeting of the Association for Computational Linguistics, pp. 263–270. Association for Computational Linguistics, Philadelphia (2002)
Craven, M., Kumlien, J.: Constructing biological knowledge bases by extracting information from text sources. In: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 77–86. AAAI Press (1999)
Dietterich, T.G., Lathrop, R.H., Lozano-Perez, T., Pharmaceutical, A.: Solving the multiple-instance problem with axis-parallel rectangles. Artificial Intelligence 89, 31–71 (1997)
Hoffmann, R., Zhang, C., Ling, X., Zettlemoyer, L., Weld, D.S.: Knowledge-based weak supervision for information extraction of overlapping relations. In: Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics, ACL 2011, pp. 541–550 (2011)
Hoffmann, R., Zhang, C., Weld, D.S.: Learning 5000 relational extractors. In: Proceedings of the 48th Annual Meeting of the Association for Computational Linguistics, ACL 2010, pp. 286–295 (2010)
Joachims, T.: Making Large-scale Support Vector Machine Learning Practical. In: Advances in Kernel Methods, pp. 169–184 (1999)
Klein, D., Manning, C.D.: Accurate unlexicalized parsing. In: Proceedings of the 41st Annual Meeting of the Association for Computational Linguistics, pp. 423–430 (2003)
Mintz, M., Bills, S., Snow, R., Jurafsky, D.: Distant supervision for relation extraction without labeled data. In: Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: ACL 2009, vol. 2, pp. 1003–1011 (2009)
Moschitti, A.: Making tree kernels practical for natural language learning. In: EACL, pp. 113–120 (2006)
Porter, M.F.: An Algorithm for Suffix Stripping. In: Readings in Information Retrieval, pp. 313–316 (1997)
Riedel, S., McClosky, D., Surdeanu, M., McCallum, A.: D. Manning, C.: Model combination for event extraction in bionlp 2011. In: Proceedings of BioNLP Shared Task 2011 Workshop, pp. 51–55. Association for Computational Linguistics, Portland (2011)
Riedel, S., Yao, L., McCallum, A.: Modeling relations and their mentions without labeled text. In: Balcázar, J.L., Bonchi, F., Gionis, A., Sebag, M. (eds.) ECML PKDD 2010, Part III. LNCS, vol. 6323, pp. 148–163. Springer, Heidelberg (2010)
Segura-Bedmar, I., MartÃnez, P., de Pablo-Sánchez, C.: Using a shallow linguistic kernel for drug-drug interaction extraction. Journal of Biomedical Informatics 44(5), 789–804 (2011)
Snow, R., Jurafsky, D., Ng, A.Y.: Learning syntactic patterns for automatic hypernym discovery. In: Advances in Neural Information Processing Systems (NIPS 2004) (November 2004)
Takamatsu, S., Sato, I., Nakagawa, H.: Reducing wrong labels in distant supervision for relation extraction. In: Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics: Long Papers, ACL 2012, vol. 1, pp. 721–729 (2012)
Thomas, P., Neves, M., Solt, I., Tikk, D., Leser, U.: Relation extraction for drug-drug interactions using ensemble learning. In: DDIExtraction2011: First Challenge Task: Drug-Drug Interaction Extraction at SEPLN 2011, vol. 4, pp. 11–18 (2011)
Thomas, I.P., Solt, Klinger, R., Leser, U.: Learning protein protein interaction extraction using distant supervision. In: Proceedings of Robust Unsupervised and Semi-Supervised Methods in Natural Language Processing, pp. 34–41 (2011)
Xu, W., Hoffmann, R., Zhao, L., Grishman, R.: Filling knowledge base gaps for distant supervision of relation extraction. In: Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers), pp. 665–670. Association for Computational Linguistics, Sofia (2013)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this paper
Cite this paper
Roller, R., Stevenson, M. (2014). Self-supervised Relation Extraction Using UMLS. In: Kanoulas, E., et al. Information Access Evaluation. Multilinguality, Multimodality, and Interaction. CLEF 2014. Lecture Notes in Computer Science, vol 8685. Springer, Cham. https://doi.org/10.1007/978-3-319-11382-1_12
Download citation
DOI: https://doi.org/10.1007/978-3-319-11382-1_12
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-11381-4
Online ISBN: 978-3-319-11382-1
eBook Packages: Computer ScienceComputer Science (R0)