State-of-the-art in biomedical literature retrieval for clinical cases: a survey of the TREC 2014 CDS track

Information Retrieval

Volumn 19, Issue 1-2, 2016, Pages 113-148

  Roberts, Kirk ^a   Simpson, Matthew ^a   Demner Fushman, Dina ^a   Voorhees, Ellen ^b   Hersh, William ^c  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

Biomedical information retrieval; Clinical decision support; Information retrieval evaluation

Indexed keywords

EID: 84956652690     PISSN: 13864564     EISSN: 15737659     Source Type: Journal    
DOI: 10.1007/s10791-015-9259-x     Document Type: Article

References (75)

1. Amati, G., & Van Rijsbergen, C. J. (2002). Probabilistic models of information retrieval based on measuring the divergence from randomness. ACM Transactions on Information Systems, 20(4), 357–389.
2. An, X., & Cercone, N. (2014). How complementary are different information retrieval techniques? a study in biomedicine domain. In Proceedings of Computational Linguistics and Intelligent Text Processing (CICLing), pp. 367–380.
3. Arighi, C. N., Roberts, P. M., Agarwal, S., Bhattacharya, S., Cesareni, G., Chatr-aryamontri, A., et al. (2011). BioCreative III interactive task: An overview. BMC Bioinformatics, 12(Suppl 8), S4.
4. Aronson, A., & Lang, F. M. (2010). An overview of MetaMap: Historical perspective and recent advances. Journal of the American Medical Informatics Association, 17, 229–236.
5. Aronson, A. R., Mork, J. G., Gay, C. W., Humphrey, S. M., & Rogers, W. J. (2004). The NLM indexing initiative’s medical text indexer. In Studies in Health Technology and Informatics (MEDINFO), pp. 268–272.
6. Banks, D., Over, P., & Zhang, N. F. (1999). Blind men and elephants: Six approaches to TREC data. Information Retrieval, 1, 7–34.
7. Bhandari, A., Kulkarni, A. (2014). San Francisco State University at TREC 2014: Clinical Decision Support Track. In Proceedings of the 2014 Text Retrieval Conference.
8. Blei, D. M., Ng, A. Y., & Jordan, M. I. (2003). Latent Dirichlet allocation. Journal of Machine Learning Research, 3, 993–1022.
9. Chapman, W. W., & Cohen, K. B. (2009). Current issues in biomedical text mining and natural language processing. Journal of Biomedical Informatics, 42(5), 757–759.
10. Chapman, W. W., Bridewell, W., Hanbury, P., Cooper, G. F., & Buchanan, B. G. (2001). A simple algorithm for identifying negated findings and diseases in discharge summaries. Journal of Biomedical Informatics, 34(5), 301–310.
11. Choi, S., & Choi, J. (2014). SNUMedinfo at TREC CDSS track 2014: Medical case-based retrieval task. In Proceedings of the 2014 Text Retrieval Conference.
12. Clinchant, S., & Gaussier, E. (2010). Information-based Models for Ad Hoc IR. In Proceedings of the 33rd Annual ACM International Conference on Research and Development in Information Retrieval.
13. Del Fiol, G., Workman, T. E., & Gorman, P. N. (2014). Clinical questions raised by clinicians at the point of care: A systematic review. JAMA Internal Medicine, 174(5), 710–718. pMID24663331.
14. Demner-Fushman, D., Chapman, W. W., & McDonald, C. J. (2009). What can natural language processing do for clinical decision support? Journal of Biomedical Informatics, 42(5), 760–772.
15. D’hondt, E., Grau, B., Darmoni, S., Névéol, A., Schuers, M., & Zweigenbaum, P. (2014). LIMSI @ TREC clinical decision support track. In Proceedings of the 2014 Text Retrieval Conference.
16. Dinh, D., & Ben Abacha, A. (2014). CRP Henri Tudor at TREC 2014: Combining Search Results for Clinical Decision Support. In Proceedings of the 2014 Text Retrieval Conference.
17. Fellbaum, C. (1998). WordNet: An electronic lexical database. Cambridge: MIT Press.
18. Garcia-Gathright, J., Meng, F., & Hsu, W. (2014). UCLA at TREC 2014 Clinical Decision Support Track: Exploring Language Models, Query Expansion, and Boosting. In Proceedings of the 2014 Text Retrieval Conference.
19. Girmay, D., & Deroie, A. (2014). Query expansion using SNOMED-CT and weighing schemes. In Proceedings of the 2014 Text Retrieval Conference.
20. Gobeill, J., Gaudinat, A., Pasche, E., & Ruch, P. (2014). Full-texts representation with Medical Subjects Headings, and co-citations network reranking strategies for TREC 2014 Clinical Decision Support Track. In Proceedings of the 2014 Text Retrieval Conference
21. Goeuriot, L., Jones, G. J., Kelly, L., Leveling, J., Hanbury, A., Müller, H., Salanterä, S., Suominen, H., & Zuccon, G. (2013). ShARe/CLEF eHealth Evaluation Lab 2013, Task 3: Information retrieval to address patients’ questions when reading clinical reports. In CLEF 2013 Working Notes.
22. Goeuriot, L., Kelly, L., Li, W., Palotti, J., Pecina, P., Zuccon, G., Hanbury, A., Jones, G. J., & Müller, H. (2014). ShARe/CLEF eHealth Evaluation Lab 2014, Task 3: User-centred health information retrieval. In CLEF 2014 Working Notes, pp. 43–61
23. Goodwin, T., & Harabagiu, S. (2014). UTD at TREC 2014: Query expansion for clinical decision support. In Proceedings of the 2014 Text Retrieval Conference.
24. Hasan, S. A., Zhu, X., Dong, Y., Liu, J., & Farri, O. (2014). A hybrid approach to clinical question answering. In Proceedings of the 2014 Text Retrieval Conference.
25. Hatcher, E., & Gospodnetic, O. (2004). Lucene in action. Greenwich: Manning Publications.
26. Haynes, R. B., McKibbon, K. A., Wilczynski, N. L., Walter, S. D., & Werre, S. R., Hedges Team (2005). Optimal search strategies for retrieving scientifically strong studies of treatment from medline: Analytical survey. BMJ, 330, 1179–1185.
27. Hersh, W., & Bhupatiraju, R. T. (2003). TREC genomics track overview. In Proceedings of the Twelfth Text Retrieval Conference.
28. Hersh, W., & Kim, E. (2006). The impact of relevance judgments and data fusion on results of image retrieval test collections. In Proceedings of the Second MUSCLE/ImageCLEF Workshop on Image and Video Retrieval Evaluation, pp. 29–38
29. Hersh, W., Buckley, C., Leone, T., & Hickam, D. (1994a). OHSUMED: An interactive retrieval evaluation and new large test collection for research. In Proceedings of the 17th Annual ACM International Conference on Research and Development in Information Retrieval, pp. 192–201
30. Hersh, W., Bhupatiraju, R. T., Ross, L., Johnson, P., Cohen, A. M., & Kraemer, D. F. (2004). TREC 2004 genomics track overview. In Proceedings of the Thirteenth Text Retrieval Conference.
31. Hersh, W., Cohen, A., Yang, J., Bhupatiraju, R. T., Roberts, P., & Hearst, M. (2005). TREC 2005 genomics track overview. In Proceedings of the Fourteenth Text Retrieval Conference.
32. Hersh, W., Cohen, A. M., Roberts, P., & Rekapalli, H. K. (2006). TREC 2006 genomics track overview. In Proceedings of the Fifteenth Text Retrieval Conference.
33. Hersh, W., Cohen, A., Ruslen, L., & Roberts, P. (2007). TREC 2007 genomics track overview. In Proceedings of the Sixteenth Text Retrieval Conference.
34. Hersh, W. R., & Hickam, D. H. (1995). An evaluation of interactive boolean and natural language searching with an online medical textbook. Journal of the American Society for Information Science, 46(7), 478–489.
35. Hersh, W. R., Hickam, D. H., Haynes, R. B., & McKibbon, K. A. (1994b). A performance and failure analysis of SAPHIRE with a MEDLINE test collection. Journal of American Biomedical Informatics, 1(1), 51–60.
36. Hu, Q., Huang, J. X., & Miao, J. (2011). A robust approach to optimizing multi-source information for enhancing genomics retrieval performance. BMC Bioinformatics, 12(Suppl 5), S6.
37. Jelinek, F., & Mercer, R. (1980). Interpolated estimation of markovsource parameters from sparse data. Pattern Recognition in Practice pp. 381–402.
38. Joo, H., & Sohn, K. (2014). TREC2014 clinical decision support: Concept-based clinical information retrieval using MetaMap. In Proceedings of the 2014 Text Retrieval Conference.
39. Kalpathy-Cramer, J., de Herrera, A. G. S., Demner-Fushman, D., Antani, S., Bedrick, S., & Müller, H. (2014). Evaluating performance of biomedical image retrieval systems: An overview of the medical image retrieval task at ImageCLEF 2004–2013. Computerized Medical Imaging and Graphics.
40. Kim, J. D., & Cohen, K. B. (2013). Natural language query processing for SPARQL generation—A prototype system for SNOMEDCT. In Proceedings of BioLINK, pp. 32–36.
41. Li, M., Song, Y., He, Y., Hu, Q., He, L., & Haacke, E. M. (2014). ECNU at TREC 2014: Clinical decision support track. In Proceedings of the 2014 Text Retrieval Conference.
42. Lindberg, D. A., Humphreys, B. L., & McCray, A. T. (1993). The unified medical language system. Methods of Information in Medicine, 32(4), 281–291.
43. Liu, S., Ma, W., Moore, R., Ganesan, V., & Nelson, S. (2005). RxNorm: Prescription for electronic drug information exchange. IT Professional, 7(5), 17–23.
44. Lu, Z. (2011). PubMed and beyond: A survey of web tools for searching biomedical literature. Database 2011
45. McDonald, C. J., Huff, S. M., Suico, J. G., Hill, G., Leavelle, D., Aller, R., et al. (2003). LOINC, a universal standard for identifying laboratory observations: A 5-year update. Clinical Chemistry, 49(4), 624–633.
46. McNamee, P., Mayfield, J., & Piatko, C. (2002). HAIRCUT: A system for multilingual text retrieval in Java. Journal of Computing Sciences in Colleges, 17(3), 8–22.
47. Mourão, A., Martins, F., & Magalhães, J. (2014). NovaSearch at TREC 2014 clinical decision support track. In Proceedings of the 2014 Text Retrieval Conference.
48. NCBI (2010). Entrez programming utilities help. National Center for Biotechnology Information
49. Oh, H. S., & Jung, Y. (2014). KISTI at TREC 2014 clinical decision support track: Concept-based document re-ranking to biomedical document retrieval. In Proceedings of the 2014 Text Retrieval Conference.
50. Ounis, I., Amati, G., Plachouras, V., He, B., Macdonald, C., & Lioma, C. (2006). Terrier: A high performance and scalable information retrieval platform. In SIGIR Open Source Workshop.
51. Palotti, J., Rekabsaz, N., Anderson, L., & Hanbury, A. (2014). TUW @ TREC clinical decision support track. In Proceedings of the 2014 Text Retrieval Conference.
52. Ryu, B., & Choi, J. (2013). Biomedical test collection with multiple query representation. In Proceedings of the Fifth International Workshop on Evaluating Information Access, pp. 33–36.
53. Sankhavara, J., Thakrar, F., Sarkar, S., & Majumder, P. (2014). Fusing manual and machine feedback in biomedical domain. In Proceedings of the 2014 Text Retrieval Conference.
54. Scott, D., Lee, J., Silva, I., Park, S., Moody, G., Celi, L., & Mark, R. (2013). Accessing the public MIMIC-II intensive care relational database for clinical research. BMC Medical Informatics and Decision Making, 13(9). http://www.biomedcentral.com/1472-6947/13/9.
55. Singh, A., & Chowdary, C. R. (2014). Centrality based document ranking. In Proceedings of the 2014 Text Retrieval Conference.
56. Soldaini, L., Cohan, A., Yates, A., Goharian, N., & Frieder, O. (2014). Query reformulation for clinical decision support search. In Proceedings of the 2014 Text Retrieval Conference.
57. Spärck Jones, K., Walker, S., & Robertson, S. E. (2000). A probabilistic model of information retrieval: Development and comparative experiments. Information Processing and Management, 36(6), 779–840.
58. Stearns, M. Q., Price, C., Spackman, K. A., & Yang, A. Y. (2001). SNOMED clinical terms: Overview of the development process and project status. In Proceedings of the AMIA Annual Symposium, pp. 662–666.
59. Strohman, T., Metzler, D., Turtle, H., & Croft, W. B. (2005). Indri: A language-model based search engine for complex queries. In International Conference on Intelligence Analysis
60. Voorhees, E. M. (2014). The effect of sampling strategy on inferred measures. In Proceedings of the 37th Annual ACM International Conference on Research and Development in Information Retrieval, pp. 1119–1122.
61. Voorhees, E. M., & Hersh, W. (2012). Overview of the TREC 2012 medical records track. In Proceedings of the 11th Text REtrieval Conference.
62. Voorhees, E. M., & Tong, R. M. (2011). Overview of the TREC 2011 medical records track. In Proceedings of the 10th Text REtrieval Conference.
63. Wan, R., Man, J. H. K., & Chan, T. F. (2014). Query modification through external sources to support clinical decisions. In Proceedings of the 2014 Text Retrieval Conference.
64. Wang, X., Chused, A., Elhadad, N., Friedman, C., & Markatou, M. (2008). Automated knowledge acquisition from clinical narrative reports. In Proceedings of the AMIA Annual Symposium, pp. 783–787.
65. Wang, X., Thompson, P., Tsujii, J., & Ananiadou, S. (2012). Biomedical Chinese-English CLIR using an extended CMeSH resource to expand queries. In Proceedings of the Eighth International Conference on Language Resources and Evaluation, pp. 1148–1155.
66. Wang, Y., & Fang, H. (2014). Explore the query expansion methods for concept based representation. In Proceedings of the 2014 Text Retrieval Conference.
67. Wei, Y., Hsu, C., Thomas, A., & McCarthy, J. F. (2014). Atigeo at TREC 2014 clinical decision support task. In Proceedings of the 2014 Text Retrieval Conference.
68. Weinreich, S. S., Mangon, R., Sikkens, J., Teeuw, M., & Cornel, M. (2008). OrphaNet: A european database for rare diseases. Nederlands tijdschrift voor geneeskunde, 152(9), 518–519.
69. Wilbur, W. J., & Kim, W. (2014). Stochastic gradient descent and the prediction of MeSH for PubMed records. InProceedings of the AMIA Annual Symposium, pp. 1198–1207.
70. Wing, C., & Yang, H. (2014). Query refinement: Negation detection and proximity learning: Georgetown at TREC 2014 clinical decision support track. In Proceedings of the 2014 Text Retrieval Conference.
71. Wu, Y., Denny, J. C., Rosenbloom, S. T., Miller, R. A., Giuse, D. A., & Xu, H. (2012). A comparative study on current clinical natural language processing systems on handling abbreviations in discharge summaries. In Proceedings of the AMIA Annual Symposium, pp. 997–1003.
72. Xu, T., McNamee, P., & Oard, D. W. (2014). HLTCOE at TREC 2014: Microblog and clinical decision support. In Proceedings of the 2014 Text Retrieval Conference.
73. Xue, T., Fu, Q., Gu, H., Zhang, S., & Wang, C. (2014). Clinical decision support track of 2014. In Proceedings of the 2014 Text Retrieval Conference.
74. Yilmaz, E., Kanoulas, E., & Aslam, J. A. (2008). A simple and efficient sampling method for estimating AP and NDCG. In Proceedings of the 31st Annual ACM International Conference on Research and Development in Information Retrieval, pp. 603–610.
75. Zhang, X., Cole, M., & Belkin, N. (2011). Predicting users’ domain knowledge from search behaviors. In Proceedings of the 34th Annual ACM International Conference on Research and Development in Information Retrieval, pp. 1225–1226.