Skip to main content
EURASIP Journal on Bioinformatics and Systems Biology logoLink to EURASIP Journal on Bioinformatics and Systems Biology
. 2007 Dec 5;2007(1):28576. doi: 10.1155/2007/28576

Question Processing and Clustering in INDOC: A Biomedical Question Answering System

Parikshit Sondhi 1,, Purushottam Raj 1, V Vinod Kumar 1, Ankush Mittal 1
PMCID: PMC3171333  PMID: 18274647

Abstract

The exponential growth in the volume of publications in the biomedical domain has made it impossible for an individual to keep pace with the advances. Even though evidence-based medicine has gained wide acceptance, the physicians are unable to access the relevant information in the required time, leaving most of the questions unanswered. This accentuates the need for fast and accurate biomedical question answering systems. In this paper we introduce INDOC—a biomedical question answering system based on novel ideas of indexing and extracting the answer to the questions posed. INDOC displays the results in clusters to help the user arrive the most relevant set of documents quickly. Evaluation was done against the standard OHSUMED test collection. Our system achieves high accuracy and minimizes user effort.

[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]

Contributor Information

Parikshit Sondhi, Email: psondhi2000@yahoo.com.

Purushottam Raj, Email: puruiuec@iitr.ernet.in.

V Vinod Kumar, Email: vinu8uec@iitr.ernet.in.

Ankush Mittal, Email: ankumfec@iitr.ernet.in.

References

  1. http://www.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/
  2. Gorman P, Ash J, Wykoff L. Can primary care physicians' questions be answered using the medical journal literature? Bulletin of the Medical Library Association. 1994;82(2):140–146. [PMC free article] [PubMed] [Google Scholar]
  3. Straus SE, Sackett DL. Bringing evidence to the point of care. Journal of the American Medical Association. 1999;281:1171–1172. doi: 10.1001/jama.281.13.1171. [DOI] [PubMed] [Google Scholar]
  4. Guyatt GH, Meade MO, Jaeschke RZ, Cook DJ, Haynes RB. Practitioners of evidence based care. British Medical Journal. 2000;320(7240):954–955. doi: 10.1136/bmj.320.7240.954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Sackett DL, Straus SE, Richardson WS, Rosenberg W, Haynes RB. Evidence-Based Medicine: How to Practice and Teach ENB. Churchill Livingstone, New York, NY, USA; 1997. [Google Scholar]
  6. Gorman PN, Helfand M. Information seeking in primary care: how physicians choose which clinical questions to pursue and which to leave unanswered. Medical Decision Making. 1995;15(2):113–119. doi: 10.1177/0272989X9501500203. [DOI] [PubMed] [Google Scholar]
  7. Jacquemart P, Zweigenbaum P. In: Proceedings of Medical Informatics Europe (MIE '03), Studies in Health Technology and Informatics. Beux PL, Baud R, editor. Vol. 95. IOS Press, San Palo, Calif, USA; 2003. Towards a medical question-answering system: a feasibility study; pp. 463–468. [PubMed] [Google Scholar]
  8. Schultz S, Honeck M, Hahn H. Biomedical text retrieval in languages with complex morphology. Proceedings of the Workshop on Natural Language Processing in the Biomedical domain, Philadelphia, Pa, USA, July 2002. pp. 61–68.
  9. Ely J, Osheroff JA, Ebell MH. Analysis of questions asked by family doctors regarding patient care. British Medical Journal. 1999;319(7206):358–361. doi: 10.1136/bmj.319.7206.358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ely JW, Osheroff JA, Ebell MH. et al. Obstacles to answering doctors' questions about patient care with evidence: qualitative study. British Medical Journal. 2002;324(7339):710–713. doi: 10.1136/bmj.324.7339.710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Bergus GR, Randall CS, Sinift SD, Rosenthal DM. Does the structure of clinical questions affect the outcome of curbside consultations with specialty colleagues? Archives of Family Medicine. 2000;9(6):541–547. doi: 10.1001/archfami.9.6.541. [DOI] [PubMed] [Google Scholar]
  12. Niu Y, Hirst G. Analysis of semantic classes in medical text for question answering. Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, Workshop on Question Answering in Restricted Domains, Barcelona, Spain, July 2004. pp. 54–61.
  13. Niu Y, Hirst G, McArthur G, Rodriguez-Gianolli P. Answering clinical questions with role identification. Proceedings of 41st Annual Meeting of the Association for Computational Linguistics, Workshop on Natural Language Processing in Biomedicine, Sapporo, Japan, July 2003. pp. 73–80.
  14. Sang ETK, Bouma G, De Rijke M. Developing offline strategies for answering medical questions. Proceedings of the AAAI-05 Workshop on Question Answering in Restricted Domains, Pittsburgh, Pa, USA, 2005. pp. 41–45.
  15. Cohen AM, Hersh WR. A survey of current work in biomedical text mining. Briefings in Bioinformatics. 2005;6(1):57–71. doi: 10.1093/bib/6.1.57. [DOI] [PubMed] [Google Scholar]
  16. http://www.nlm.nih.gov/research/umls/ http://www.nlm.nih.gov/research/umls/
  17. http://mmtx.nlm.nih.gov/ http://mmtx.nlm.nih.gov/
  18. Aronson AR. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proceedings of the AMIA Symposium, 2001. pp. 17–21. [PMC free article] [PubMed]
  19. McCray AT, Burgun A, Bodenreider O. Aggregating UMLS semantic types for reducing conceptual complexity. Medinfo. 2001;10(part 1):216–220. [PMC free article] [PubMed] [Google Scholar]
  20. Bodenreider O, McCray AT. Exploring semantic groups through visual approaches. Journal of Biomedical Informatics. 2003;36(6):414–432. doi: 10.1016/j.jbi.2003.11.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hersh WR. OHSUMED: an interactive retrieval evaluation and new large test collection for research. Proceedings of the 17th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '94), Springer, Dublin, Ireland, July 1994. pp. 192–201.
  22. http://www.cdc.gov/nchs/about/otheract/icd9/abticd9.htm http://www.cdc.gov/nchs/about/otheract/icd9/abticd9.htm
  23. MacQueen JB. Some methods for classification and analysis of multivariate observations. Proceedings of 5th the Berkeley Symposium on Mathematical Statistics and Probability, Berkeley, Calif, University of California Press, USA, June-July 1967. pp. 281–297.
  24. Ely JW, Osheroff JA, Gorman PN. et al. A taxonomy of generic clinical questions: classification study. British Medical Journal. 2000;321(7258):429–432. doi: 10.1136/bmj.321.7258.429. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from EURASIP Journal on Bioinformatics and Systems Biology are provided here courtesy of Springer

RESOURCES