Skip to main content
SpringerLink
Log in
Book cover

International Conference on Intelligent Text Processing and Computational Linguistics

CICLing 2013: Computational Linguistics and Intelligent Text Processing pp 318–334Cite as

Enhancing Search: Events and Their Discourse Context

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7817))

Abstract

Event-based search systems have become of increasing interest. This paper provides an overview of recent advances in event-based text mining, with an emphasis on biomedical text. We focus particularly on the enrichment of events with information relating to their interpretation according to surrounding textual and discourse contexts. We describe our annotation scheme used to capture this information at the event level, report on the corpora that have so far been enriched according to this scheme and provide details of our experiments to recognise this information automatically.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Zweigenbaum, P., Demner-Fushman, D., Yu, H., Cohen, K.B.: Frontiers of Biomedical Text Mining: Current Progress. Brief Bioinform. 8, 358–375 (2007)

    Article  Google Scholar 

  2. Ananiadou, S., Kell, D.B., Tsujii, J.: Text Mining and its Potential Applications in Systems Biology. Trends Biotechnol. 24, 571–579 (2006)

    Article  Google Scholar 

  3. Ananiadou, S., Nenadic, G.: Automatic Terminology Management in Biomedicine. In: Ananiadou, S., McNaught, J. (eds.) Text Mining for Biology and Biomedicine, pp. 67–98. Artech House, London (2006)

    Google Scholar 

  4. Mihăilă, C., Ohta, T., Pyysalo, S., Ananiadou, S.: BioCause: Annotating and Analysing Causality in the Biomedical Domain. BMC Bioinformatics 14, 2 (2013)

    Article  Google Scholar 

  5. Kim, J., Ohta, T., Tsujii, J.: Corpus Annotation for Mining Biomedical Events from Literature. BMC Bioinformatics 9, 10 (2008)

    Article  Google Scholar 

  6. Miwa, M., Saetre, R., Kim, J.D., Tsujii, J.: Event Extraction with Complex Event Classification using Rich Features. J. Bioinform. Comput. Biol. 8, 131–146 (2010)

    Article  Google Scholar 

  7. 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 

  8. Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J., Ananiadou, S.: Overview of the Infectious Diseases (ID) Task of BioNLP Shared Task 2011. In: BioNLP Shared Task 2011 Workshop, pp. 26–35. Association for Computational Linguistics (2011)

    Google Scholar 

  9. Miwa, M., Thompson, P., Ananiadou, S.: Boosting Automatic Event Extraction from the Literature using Domain Adaptation and Coreference Resolution. Bioinformatics 28(13), 1759–1765 (2012)

    Article  Google Scholar 

  10. Miyao, Y., Sagae, K., Saetre, R., Matsuzaki, T., Tsujii, J.: Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction. Bioinformatics 25, 394–400 (2009)

    Article  Google Scholar 

  11. Sagae, K., Tsujii, J.I.: Dependency Parsing and Domain Adaptation with LR Models and Parser Ensembles. In: Proceedings of the CoNLL 2007 Shared Task Session of EMNLP-CoNLL 2007, pp. 1044–1050. Association for Computational Linguistics (2007)

    Google Scholar 

  12. Miyao, Y., Ohta, T., Masuda, K., Tsuruoka, Y., Yoshida, K., Ninomiya, T., Tsujii, J.: Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. In: Proceedings of Coling/ACL, pp. 1017–1024. Association for Computational Linguistics (2006)

    Google Scholar 

  13. Hara, T., Miyao, Y., Tsujii, J.: Adapting a Probabilistic Disambiguation Model of an HPSG Parser to a New Domain. In: Dale, R., Wong, K.-F., Su, J., Kwong, O.Y. (eds.) IJCNLP 2005. LNCS (LNAI), vol. 3651, pp. 199–210. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  14. Tsuruoka, Y., Tsujii, J.: Bidirectional Inference with the Easiest-First Strategy for Tagging Sequence Data. In: Proceedings of HLT/EMNLP 2005, pp. 467–474. Association for Computational Linguistics (2005)

    Google Scholar 

  15. Hirohata, K., Okazaki, N., Ananiadou, S., Ishizuka, M.: Identifying Sections in Scientific Abstracts using Conditional Random Fields. In: Proceedings of the 3rd International Joint Conference on Natural Language Processing, pp. 381–388. Association for Computational Linguistics (2008)

    Google Scholar 

  16. Tsai, R.T., Chou, W.C., Su, Y.S., Lin, Y.C., Sung, C.L., Dai, H.J., Yeh, I.T., Ku, W., Sung, T.Y., Hsu, W.L.: BIOSMILE: a Semantic Role Labeling System for Biomedical Verbs using a Maximum-Entropy Model with Automatically Generated Template Features. BMC Bioinformatics 8, 325 (2007)

    Article  Google Scholar 

  17. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene Ontology: Tool for the Unification of Biology. Nature Genetics 25, 25–29 (2000)

    Article  Google Scholar 

  18. Thompson, P., McNaught, J., Montemagni, S., Calzolari, N., Del Gratta, R., Lee, V., Marchi, S., Monachini, M., Pezik, P., Quochi, V., Rupp, C.J., Sasaki, Y., Venturi, G., Rebholz-Schuhmann, D., Ananiadou, S.: The BioLexicon: a Large-Scale Terminological Resource for Biomedical Text Mining. BMC Bioinformatics 12, 397 (2011)

    Article  Google Scholar 

  19. Kim, J.T., Moldovan, D.I.: Acquisition of Linguistic Patterns for Knowledge-Based Information Extraction. IEEE Transactions on Knowledge and Data Engineering 7, 713–724 (1995)

    Article  Google Scholar 

  20. Soderland, S.: Learning Information Extraction Rules for Semi-structured and Free Text. Machine Learning 34, 233–272 (1999)

    Article  MATH  Google Scholar 

  21. Califf, M.E., Mooney, R.J.: Bottom-Up Relational Learning of Pattern Matching Rules for Information Extraction. Journal of Machine Learning Research 4, 177–210 (2003)

    MathSciNet  Google Scholar 

  22. Pyysalo, S., Ginter, F., Heimonen, J., Bjorne, J., Boberg, J., Jarvinen, J., Salakoski, T.: BioInfer: a Corpus for Information Extraction in the Biomedical Domain. BMC Bioinformatics 8, 50 (2007)

    Article  Google Scholar 

  23. Pyysalo, S., Ohta, T., Miwa, M., Cho, H.-C., Tsujii, J.I., Ananiadou, S.: Event Extraction across Multiple Levels of Biological Organization. Bioinformatics 28, i575–i581 (2012)

    Google Scholar 

  24. Thompson, P., Iqbal, S.A., McNaught, J., Ananiadou, S.: Construction of an Annotated Corpus to Support Biomedical Information Extraction. BMC Bioinformatics 10, 349 (2009)

    Article  Google Scholar 

  25. Nawaz, R., Thompson, P., McNaught, J., Ananiadou, S.: Meta-Knowledge Annotation of Bio-Events. In: Proceedings of LREC 2010, pp. 2498–2507. ELRA (2010)

    Google Scholar 

  26. Light, M., Qiu, X.Y., Srinivasan, P.: The Language of Bioscience: Facts, Speculations, and Statements in between. In: Proceedings of the BioLink 2004 Workshop at HLT/NAACL, pp. 17–24. Association for Computational Linguistics (2004)

    Google Scholar 

  27. Medlock, B., Briscoe, T.: Weakly Supervised Learning for Hedge Classification in Scientific Literature. In: Proceedings of ACL, pp. 992–999. Association for Computational Linguistics (2007)

    Google Scholar 

  28. Ruch, P., Boyer, C., Chichester, C., Tbahriti, I., Geissbühler, A., Fabry, P., Gobeill, J., Pillet, V., Rebholz-Schuhmann, D., Lovis, C.: Using Argumentation to Extract Key Sentences from Biomedical Abstracts. Int. J. Med. Informatics 76, 195–200 (2007)

    Article  Google Scholar 

  29. McKnight, L., Srinivasan, P.: Categorization of Sentence Types in Medical Abstracts. In: Procedings of AMIA Annual Symposium, pp. 440–444. AMIA (2003)

    Google Scholar 

  30. Mizuta, Y., Korhonen, A., Mullen, T., Collier, N.: Zone Analysis in Biology Articles as a Basis for Information Extraction. Int. J. Med. Informatics 75, 468–487 (2006)

    Article  Google Scholar 

  31. Teufel, S., Carletta, J., Moens, M.: An Annotation Scheme for Discourse-Level Argumentation in Research Articles. In: Proceedings of EACL, pp. 110–117. Association for Computational Linguistics (1999)

    Google Scholar 

  32. Liakata, M., Teufel, S., Siddharthan, A., Batchelor, C.: Corpora for the Conceptualisation and Zoning of Scientific Papers. In: Proceedings of LREC 2010, pp. 2054–2061. ELRA (2010)

    Google Scholar 

  33. Liakata, M., Saha, S., Dobnik, S., Batchelor, C., Rebholz-Schuhmann, D.: Automatic Recognition of Conceptualisation Zones in Scientific Articles and Two Life Science Applications. Bioinformatics 28(7), 991–1000 (2012)

    Article  Google Scholar 

  34. Vincze, V., Szarvas, G., Farkas, R., Mora, G., Csirik, J.: The BioScope Corpus: Biomedical Texts Annotated for Uncertainty, Negation and their Scopes. BMC Bioinformatics 9, S9 (2008)

    Google Scholar 

  35. Rubin, V., Liddy, E., Kando, N.: Certainty Identification in Texts: Categorization Model and Manual Tagging Results. In: Shanahan, J.G., Qu, Y., Wiebe, J. (eds.) Computing Attitude and Affect in Text: Theory and Applications, pp. 61–76. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  36. Hyland, K.: Talking to the Academy: Forms of Hedging in Science Research Articles. Written Communication 13, 251–281 (1996)

    Article  Google Scholar 

  37. Hyland, K.: Writing without Conviction? Hedging in Science Research Articles. Applied Linguistics 17, 433–454 (1996)

    Article  Google Scholar 

  38. Rizomilioti, V.: Exploring Epistemic Modality in Academic Discourse Using Corpora. In: Arnó Macià, E., Soler Cervera, A., Rueda Ramos, C. (eds.) Information Technology in Languages for Specific Purposes, pp. 53–71. Springer, New York (2006)

    Chapter  Google Scholar 

  39. Thompson, P., Venturi, G., McNaught, J., Montemagni, S., Ananiadou, S.: Categorising Modality in Biomedical Texts. In: Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining, pp. 27–34. ELRA (2008)

    Google Scholar 

  40. de Waard, A., Pander Maat, H.: Categorizing Epistemic Segment Types in Biology Research Articles. In: Proceedings of the Workshop on Linguistic and Psycholinguistic Approaches to Text Structuring, LPTS 2009 (2009)

    Google Scholar 

  41. Wilbur, W.J., Rzhetsky, A., Shatkay, H.: New Directions in Biomedical Text Annotations: Definitions, Guidelines and Corpus Construction. BMC Bioinformatics 7, 356 (2006)

    Article  Google Scholar 

  42. Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Maat, H.P., Ananiadou, S.: A Three-Way Perspective on Scientific Discourse Annotation for Knowledge Extraction. In: Proceedings of the ACL Workshop on Detecting Structure in Scholarly Discourse (DSSD), pp. 37–46. Association for Computational Linguistics (2012)

    Google Scholar 

  43. Thompson, P., Nawaz, R., McNaught, J., Ananiadou, S.: Enriching a Biomedical Event Corpus with Meta-knowledge Annotation. BMC Bioinformatics 12, 393 (2011)

    Article  Google Scholar 

  44. Cohen, K.B., Johnson, H.L., Verspoor, K., Roeder, C., Hunter, L.E.: The Structural and Content Aspects of Abstracts versus Bodies of Full Text Journal Articles are Different. BMC Bioinformatics 11, 492 (2010)

    Article  Google Scholar 

  45. Nawaz, R., Thompson, P., Ananiadou, S.: Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers. In: Proceedings of the Third LREC Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), pp. 24–21. ELRA (2012)

    Google Scholar 

  46. Knight, J.: Negative Results: Null and void. Nature 422, 554–555 (2003)

    Article  Google Scholar 

  47. Miwa, M., Thompson, P., McNaught, J., Kell, D.B., Ananiadou, S.: Extracting Semantically Enriched Events from Biomedical Literature. BMC Bioinformatics 13, 108 (2012)

    Article  Google Scholar 

  48. Bjorne, J., Salakoski, T.: Generalizing Biomedical Event Extraction. In: Proceedings of the BioNLP Shared Task 2011 Workshop, pp. 183–191. Association for Computational Linguistics (2011)

    Google Scholar 

  49. Kilicoglu, H., Bergler, S.: Adapting a General Semantic Interpretation Approach to Biological Event Extraction. In: Proceedings of BioNLP Shared Task 2011 Workshop, pp. 173–182. Association for Computational Linguistics (2011)

    Google Scholar 

  50. Kilicoglu, H., Bergler, S.: Syntactic Dependency Based Heuristics for Biological Event Extraction. In: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp. 119–127. Association for Computational Linguistics (2009)

    Google Scholar 

  51. Nawaz, R., Thompson, P., Ananiadou, S.: Identification of Manner in Bio-Events. In: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pp. 3505–3510. ELRA (2012)

    Google Scholar 

  52. Nawaz, R., Thompson, P., Ananiadou, S.: Something Old, Something New: Identifying Knowledge Source in Bio-Events. In: Proceedings of CICLing 2013 (2013)

    Google Scholar 

  53. Nawaz, R., Thompson, P., Ananiadou, S.: Negated Bio-events: Analysis and Identification. BMC Bioinformatics 14, 14 (2013)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Centre for Text Mining, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK

    Sophia Ananiadou, Paul Thompson & Raheel Nawaz

Authors
  1. Sophia Ananiadou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Paul Thompson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Raheel Nawaz
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Center for Computing Research, National Polytechnic Institute, Mexico D.F., Mexico

    Alexander Gelbukh

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ananiadou, S., Thompson, P., Nawaz, R. (2013). Enhancing Search: Events and Their Discourse Context. In: Gelbukh, A. (eds) Computational Linguistics and Intelligent Text Processing. CICLing 2013. Lecture Notes in Computer Science, vol 7817. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37256-8_27

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-37256-8_27

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-37255-1

  • Online ISBN: 978-3-642-37256-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation