International Journal of Medical Informatics
Volume 79, Issue 4 , Pages 284-296 , April 2010

A methodology to enhance spatial understanding of disease outbreak events reported in news articles

Received 15 June 2009 ,Revised 24 January 2010 ,Accepted 24 January 2010.

References 

  1. Lewis MD, Pavlin JA, Mansfield JL, et al. Disease outbreak detection system using syndromic data in the greater Washington DC area. American Journal of Preventive Medicine. 2002;23(3):180–186
  2. Tsui F-C, Espino JU, Dato VM, et al. Technical description of RODS: a real-time public health surveillance system. Journal of American Medical Informatics Association. 2003;10(5):399–408
  3. Yangarber R, Steinberger R, Best C, et al. Combining information retrieval and information extraction for medical intelligence. In: Proceeding of Mining Massive Data Sets for Security. NATO Advanced Study Institute; September 10–21, 2007; Gazzada, Italy. 2007;
  4. Mawudeku A, Blench M. Global Public Health Intelligence Network (GPHIN). In: Proceeding of the 7th Conference of the Association for Machine Translation in the Americas. Cambridge, MA, USA, 8–12 August 2006. 2006;p. 7–11
  5. Mawudeku A, Lemay R, Werker D, et al. The Global Public Health Intelligence Network. In:  M’ikanatha NM,  Lynfield R,  Beneden CAV, et al. editor. Infectious Disease Surveillance. Infectious Disease Surveillance; 2007;p. 304–317
  6. Wilson JM. Argus: a global detection and tracking system for biological events. Advances in Disease Surveillance. 2007;4:21
  7. Tolentino H, Kamadjeu R, Fontelo P, et al. Scanning the emerging infectious diseases horizon-visualizing ProMED emails using EpiSPIDER. Advances in Disease Surveillance. 2007;2(4):169
  8. Brownstein JS, Freifeld CC. HealthMap: the development of automated real-time internet surveillance for epidemic intelligence. Eurosurveillance. 2007;12(48):
  9. Collier N, Doan S, Kawazoe A, et al. BioCaster: detecting public health rumors with a Web-based text mining system. Bioinformatics. 2008;24:2940–2941
  10. Collier N, Kawazoe A, Doan S, et al. Detecting Web rumours with a multilingual ontology supported text classification system. Advances in Disease Surveillance. 2007;4:242
  11. Brownstein JS, Freifeld CC, Reis BY, et al. HealthMap: Internet-based emerging infectious disease intelligence. Global Infectious Disease Surveillance and Detection: Assessing the Challenges—finding Solutions: Workshop Summary. National Academies Press; 2007;pp. 183–204
  12. Zimbabwe says anthrax outbreak under control_English_Xinhua, 2009, Available from: http://news.xinhuanet.com/english/2009-12/31/content_12735617.htm (cited 21 Jan 2010).
  13. Grishman R, Huttunen S, Yangarber R. Information extraction for enhanced access to disease outbreak reports. Journal of Biomedical Informatics. 2002;35(4):236–246
  14. Grishman R, Huttunen S, Yangarber R. Real-time event extraction for infectious disease outbreaks. In: Proceedings of the Second International Conference on Human Language Technology Research. San Diego, CA. 2002;p. 366–369
  15. Yangarber R, Best C, Etter PV, et al. Combining information about epidemic threats from multiple sources. In: Proceeding of the Workshop on Multi-source Multilingual Information Extraction and Summarization (MMIES’2007), RANLP’2007. Borovets, Bulgaria. 2007;
  16. Chaudet H. Extending the event calculus for tracking epidemic spread. Artificial Intelligence in Medicine. 2006;38(2):137–156
  17. Buckeridge DL, Graham J, O’Connor MJ, et al. Knowledge-based bioterrorism surveillance. In: Proceedings of the AMIA Symposium. 2002;
  18. Chanlekha H, Kawazoe A, Collier N. A framework for enhancing spatial and temporal granularity in report-based health surveillance systems. BMC Medical Informatics and Decision Making. 2010;10(1):
  19. Carletta J, Isard S, Doherty-Sneddon G, et al. The reliability of a dialogue structure coding scheme. Computational Linguistics. 1997;23(1):13–31
  20. Hearst MA. TextTiling: segmenting text into multi-paragraph subtopic passages. Computational Linguistics. 1997;23(1):33–64
  21. Passonneau RJ. Computing reliability for coreference annotation. In: Proceeding of the 4th International Conference on Language Resources and Evaluation (LREC). Lisbon, Portugal. 2004;
  22. Passonneau RJ, Habash N, Rambow O. Inter-annotator Agreement on a Multilingual Semantic Annotation Task. In: Proceedings of the International Conference on Language Resources and Evaluation (LREC). Genoa. 2006;
  23. Teufel S, Moens M. Summarizing scientific articles: experiments with relevance and rhetorical status. Computational Linguistics. 2002;28(4):409–445
  24. Poesio M, Artstein R. The reliability of anaphoric annotation, reconsidered: taking ambiguity into account. In: Proceeding of ACL Workshop on Frontiers in Corpus Annotation. Ann Arbor. 2005;
  25. Passonneau RJ, Litman DJ. Discourse segmentation by human and automated means. Computational Linguistics. 1997;23(1):103–139
  26. Krippendorff K. Content Analysis: An Introduction to its Methodology. Sage Publications, Inc.; 1980;
  27. Niu C, Li W, Ding J, et al. A bootstrapping approach to named entity classification using successive learners. In: Proceeding of the 41st Annual Meeting on Association for Computational Linguistics Sapporo. Association for Computational Linguistics, Japan. 2003;p. 335–342
  28. Cucchiarelli A, Velardi P. Unsupervised named entity recognition using syntactic and semantic contextual evidence. Computational Linguistics. 2001;27(1):123–131
  29. Mikheev A, Moens M, Grover C. Named entity recognition without gazetteers. In: Proceeding of the Ninth Conference on European Chapter of the Association for Computational Linguistics. Association for Computational Linguistics, Bergen, Norway. 1999;
  30. Srihari RK, Niu C, Li W. A hybrid approach for named entity and sub-type tagging. In: Proceeding of Applied Natural Language Processing Conference (ANLP-2000). Seattle, United States. 2000;p. 247–254
  31. Pouliquen B, Kimler M, Steinberger R, et al. Geocoding multilingual texts: recognition, disambiguation and visualisation. In: Proceedings of the 5th International Conference on Language Resources and Evaluation (LREC-2006). Genoa, Italy, May 2006. 2006;p. 53–58
  32. Leidner JL, Sinclair G, Webber B. Grounding spatial named entities for information extraction and question answering. In: Proceeding of HLT-NAACL 2003 Workshop on Analysis of Geographic References. Association for Computational Linguistics. 2003;p. 31–38
  33. Li H, Srihari RK, Niu C, et al. Location normalization for information extraction. In: Proceedings of the 19th international conference on Computational linguistics. Taipei, Taiwan. 2002;p. 1–7
  34. Li H, Srihari RK, Niu C, et al. InfoXtract location normalization: a hybrid approach to geographic references in information extraction. In: Proceeding of the HLT-NAACL 2003 Workshop on Analysis of Geographic References. Association for Computational Linguistics. 2003;p. 39–44
  35. Peng Y, He D, Mao M. Geographic named entity disambiguation with automatic profile generation. In: Proceeding of IEEE/WIC/ACM International Conference on Web Intelligence (WI’06). IEEE Computer Society. 2006;p. 522–525
  36. R. Saurí, J. Littman, B. Knippen, et al. TimeML annotation guidelines version 1.2.1, January 31, 2006, Available from: http://www.cs.brandeis.edu/∼jamesp/arda/time/timeMLdocs/annguide12wp.pdf (cited May 25, 2009).
  37. Pustejovsky J, Castaño JM, Ingria R, et al. TimeML: robust specification of event and temporal expressions in text. In: Proceeding of the Fifth International Workshop on Computational Semantics (IWCS-5). 2003;p. 28–34
  38. N. Collier, BioCaster text mining project, 2006, Available from: http://biocaster.nii.ac.jp (updated 2009 May 6; 2009 May 6).
  39. Kawazoe A, Jin L, Shigematsu M, et al. The development of a schema for the annotation of terms in the BioCaster disease detecting/tracking system. In: Proceedings of KR-MED 2006, the Second International Workshop on Formal Biomedical Knowledge Representation. Baltimore, MD, November 8, 2006. 2006;p. 77–85
  40. Charniak E. A maximum-entropy-inspired parser. In: Proceedings of the 1st North American chapter of the Association for Computational Linguistics conference. Seattle, WA. 2000;
  41. S. Teufel, Argumentative zoning: information extraction from scientific text, Ph.D. thesis, University of Edinburgh, 1999, p. 352.
  42. Passonneau RJ. Measuring Agreement on Set-valued Items (MASI) for semantic and pragmatic annotation. In: Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC). Genoa. 2006;
  43. Carletta J. Assessing agreement on classification tasks: the kappa statistic. Computational Linguistics. 1996;22(2):249–254
  44. Rosenberg A, Binkowski E. Augmenting the kappa statistic to determine interannotator reliability for multiply labeled data points. In: Proceedings of the Human Language Technology Conference of the North American Chapter of the Association for Computational Linguistics: HLT-NAACL. 2004;
  45. Nenkova A, Passonneau RJ, McKeown K. The Pyramid Method: incorporating human content selection variation in summarization evaluation. ACM Transactions on Speech and Language Processing (TSLP). 2007;4(2):
  46. Levin B. English Verb Classes and Alternations: A Preliminary Investigation. The University of Chicago Press; 1993;p. 366
  47. Lafferty J, McCallum A, Pereira F. Conditional random fields: probabilistic models for segmenting and labeling sequence data. Proceeding of the 18th International Conference on Machine Learning. San Francisco, CA: Morgan Kaufmann Publishers Inc.; 2001;pp. 282–289
  48. 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. Ann Arbor, MI, USA, June 25–30, 2005. 2005;p. 173–180
  49. Soon WM, Ng HT, Lim DCY. A machine learning approach to coreference resolution of noun phrases. Computational Linguistics: Special Issue on Computational Anaphora Resolution. 2001;27(4):521–544
  50. K. Krippendorff, Computing Krippendorff's Alpha-Reliability, 2007.06.01, Available from: http://www.asc.upenn.edu/usr/krippendorff/webreliability.doc (cited 22 Jan 2010).
  51. World Health Organization . International Health Regulations (2005). 2nd ed.. World Health Organization; 2008;p. 74

PII: S1386-5056(10)00027-4

doi: 10.1016/j.ijmedinf.2010.01.014

International Journal of Medical Informatics
Volume 79, Issue 4 , Pages 284-296 , April 2010