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Proceedings of the AMIA Symposium logoLink to Proceedings of the AMIA Symposium
. 2002:165–169.

The horizontal and vertical nature of patient phenotype retrieval: new directions for clinical text processing.

Christopher G Chute 1
PMCID: PMC2244580  PMID: 12463808

Abstract

The author reviews the historical problem of identifying appropriate patients for retrieval from a clinical repository of patient records, compares the competing features of document classification and natural language processing, and proposes an alternative approach. The alternative approach 1) codes inquiries in an ontology to lend a vertical axis to retrieval knowledge instead of coding the target body of notes, 2) invokes natural language indexing and lexical normalizations on the corpus of notes that is scalable and tractable, and 3) leverages thesauri of word-level synonyms and near-synonyms to expand term searches "horizontally" around the concept spaces drawn from the ontology in which the queries were "coded."

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Selected References

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  1. Baud R. H., Lovis C., Ruch P., Rassinoux A. M. A light knowledge model for linguistic applications. Proc AMIA Symp. 2001:37–41. [PMC free article] [PubMed] [Google Scholar]
  2. Baud R. H., Lovis C., Ruch P., Rassinoux A. M. A toolset for medical text processing. Stud Health Technol Inform. 2000;77:456–461. [PubMed] [Google Scholar]
  3. Baud R. H., Lovis C., Ruch P., Rassinoux A. M. Conceptual search in electronic patient record. Stud Health Technol Inform. 2001;84(Pt 1):156–160. [PubMed] [Google Scholar]
  4. Blois M. S. Medicine and the nature of vertical reasoning. N Engl J Med. 1988 Mar 31;318(13):847–851. doi: 10.1056/NEJM198803313181309. [DOI] [PubMed] [Google Scholar]
  5. Bodenreider O., Nelson S. J., Hole W. T., Chang H. F. Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies. Proc AMIA Symp. 1998:815–819. [PMC free article] [PubMed] [Google Scholar]
  6. Chute C. G., Yang Y. An evaluation of concept based latent semantic indexing for clinical information retrieval. Proc Annu Symp Comput Appl Med Care. 1992:639–643. [PMC free article] [PubMed] [Google Scholar]
  7. Chute C. G., Yang Y. An overview of statistical methods for the classification and retrieval of patient events. Methods Inf Med. 1995 Mar;34(1-2):104–110. [PubMed] [Google Scholar]
  8. Elkin P. L., Bailey K. R., Chute C. G. A randomized controlled trial of automated term composition. Proc AMIA Symp. 1998:765–769. [PMC free article] [PubMed] [Google Scholar]
  9. Evans D. A., Cimino J. J., Hersh W. R., Huff S. M., Bell D. S. Toward a medical-concept representation language. The Canon Group. J Am Med Inform Assoc. 1994 May-Jun;1(3):207–217. doi: 10.1136/jamia.1994.95236153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hersh W. R., Crabtree M. K., Hickam D. H., Sacherek L., Rose L., Friedman C. P. Factors associated with successful answering of clinical questions using an information retrieval system. Bull Med Libr Assoc. 2000 Oct;88(4):323–331. [PMC free article] [PubMed] [Google Scholar]
  11. Hersh W. R., Hickam D. H., Haynes R. B., McKibbon K. A. A performance and failure analysis of SAPHIRE with a MEDLINE test collection. J Am Med Inform Assoc. 1994 Jan-Feb;1(1):51–60. doi: 10.1136/jamia.1994.95236136. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Johnson S. B. A semantic lexicon for medical language processing. J Am Med Inform Assoc. 1999 May-Jun;6(3):205–218. doi: 10.1136/jamia.1999.0060205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kurland L. T., Molgaard C. A. The patient record in epidemiology. Sci Am. 1981 Oct;245(4):54–63. doi: 10.1038/scientificamerican1081-54. [DOI] [PubMed] [Google Scholar]
  14. Rassinoux A. M., Miller R. A., Baud R. H., Scherrer J. R. Modeling concepts in medicine for medical language understanding. Methods Inf Med. 1998 Nov;37(4-5):361–372. [PubMed] [Google Scholar]
  15. Rector A. L. Clinical terminology: why is it so hard? Methods Inf Med. 1999 Dec;38(4-5):239–252. [PubMed] [Google Scholar]
  16. Rector A. L., Glowinski A. J., Nowlan W. A., Rossi-Mori A. Medical-concept models and medical records: an approach based on GALEN and PEN&PAD. J Am Med Inform Assoc. 1995 Jan-Feb;2(1):19–35. doi: 10.1136/jamia.1995.95202545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ruch P., Baud R., Geissbühler A., Rassinoux A. M. Comparing general and medical texts for information retrieval based on natural language processing: an inquiry into lexical disambiguation. Stud Health Technol Inform. 2001;84(Pt 1):261–265. [PubMed] [Google Scholar]
  18. Tuttle M. S., Olson N. E., Keck K. D., Cole W. G., Erlbaum M. S., Sherertz D. D., Chute C. G., Elkin P. L., Atkin G. E., Kaihoi B. H. Metaphrase: an aid to the clinical conceptualization and formalization of patient problems in healthcare enterprises. Methods Inf Med. 1998 Nov;37(4-5):373–383. [PubMed] [Google Scholar]
  19. Zeng Q., Cimino J. J. Evaluation of a system to identify relevant patient information and its impact on clinical information retrieval. Proc AMIA Symp. 1999:642–646. [PMC free article] [PubMed] [Google Scholar]

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