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First published September 23, 2002 as JAMIA PrePrint; doi:10.1197/jamia.M1133
Journal of the American Medical Informatics Association 2003;10(1):21-38
© 2003 American Medical Informatics Association

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Submitted on April 8, 2002
Accepted on August 5, 2002

Integrating Query of Relational and Textual Data in Clinical Databases: a Case Study

John M. Fisk MD1*, Pradeep Mutalik MD2, Forrest W. Levin MS3, Joseph Erdos MD, PhD4, Caroline Taylor MD5, and Prakash Nadkarni MD2

Affiliation of the authors: 1 Center of Medical Informatics, Yale University School of Medicine, New Haven, CT; 2 Center for Medical Informatics, Yale University School of Medicine, New Haven, CT; 3 Information Technology Office, Veterans Administration Medical Center, West Haven, CT; 4 Information Technology Office, Veterans Administraton Medical Center, West Haven, CT; 5 Department of Radiology, Veterans Administration Medical Center, West Haven, CT

* To whom correspondence should be addressed.

Objective The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS).

Design Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period, and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching.

Measurements Results are relevance-ranked using either "total documents per patient" or "report type weighting".

Results Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to adequately handle such malformed text.

Conclusion A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third party IR software: RDBMS vendors need to make their IR offerings more accessible to non-programmers.




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