Database and Knowledge Base Integration – A Data Mapping Method for Arden Syntax Knowledge Modules

Abstract:

One of the most important categories of decision-support systems in medicine are data driven systems where the inference engine is linked to a database. It is, therefore, important to find methods that facilitate the implementation of database queries referred to in the knowledge modules. A method is described for linking clinical databases to a knowledge base with Arden Syntax modules. The method is based on a query meta-database including templates for SQL queries which is maintained by a database administrator. During knowledge module authoring the medical expert refers only to a code in the query meta-database; no knowledge is needed about the database model or the naming of attributes and relations. The method uses standard tools, such as C++ and ODBC, which makes it possible to implement the method at many platforms and to link to different clinical databases in a standardized way.

Key words:

Database and Knowledge-base Integration - Decision Support Systems - Arden Syntax - Medical Logic Modules - SQL

• References

• 1 Hripcsak G, Johnson SB, Clayton PD. Desperately seeking data: Knowledge base – Database links. In: Proceedings 17th Annual Symposium on Computer Applications in Medical Care. New York: McGraw-Hill; 1993: 639-43.
• 2 Date CJ, Darwen H. A Guide to the SQL Standard. Reading Mass: Addison-Wesley; 1993
• 3 Hripcsak G, Clayton PD, Pryor TA, Haug P, Wigertz OB, Van der Lei J. The Arden Syntax for Medical Logic Modules. In: Proceedings 14th SCAMC. New York: IEEE Comp Soc Press; 1990: 200-4.
• 4 ASTM E-1460. Standard Specification for Defining and Sharing Modular Health Knowledge Bases (Arden Syntax for Medical Logic Modules). ASTM; 1992
• 5 Pryor TA, Gardner RM, Clayton PD, Warner HR. The HELP system. In: Blum BI. ed. Information Systems For Patient Care. New York: Springer Verlag; 1984: 109-28.
• 6 McDonald CJ, Blevins W, Tierney D, Martin D. The Regenstrief medical record. MD Computing 1988; 5: 34-47.
• 7 Johnson SB, Hripcsak G, Chen J, Clayton PD. Accessing the Columbia repository. In: Proceedings 18th SCAMC. Philadelphia: Hanley & Belfus, Inc.; 1994: 281-5.
• 8 Johansson B, Bergyvist Y. Integrating decision support, based on the Arden Syntax, in a clinical laboratory environment. In: Proceedings 17th Annual Symposium on Computer Applications in Medical Care. New York: McGraw-Hill; 1993: 394-8.
• 9 Das AK, Musen MA. A comparison of the temporal expressiveness of three database query methods. In: Proceedings 19th Annual Symposium on Computer Applications in Medical Care. Philadelphia: Hanley & Belfus; 1995: 331-7.
• 10 Das AK, Musen MA. A temporal query system for protocol-directed decision support. Meth Inform Med 1994; 33: 358-70.
• 11 Sujansky W, Altman R. Towards a standard query model for sharing decision-support applications. In: Proceedings 18th Annual Symposium on Computer Applications in Medical Care. Philadelphia: Hanley & Belfus; 1994: 325-31.
• 12 Geiger K. Inside ODBC. Seattle: Microsoft Press; 1996
• 13 Johansson B, Wigertz O. An object-oriented approach to interpret medical knowledge based on the Arden Syntax. In: Proceedings 16th Annual Symposium on Computer Applications in Medical Care. New York: McGraw-Hill; 1992: 52-6.
• 14 Gao X, Johansson B, Shahsavar N, Arkad K, Åhlfeldt H, Wigertz O. Pre-compiling Medical Logic Modules into C++ in building medical decision support systems. Comput Meth Progr Biomed 1993; 41: 107-19.
• 15 Arkad K, Gao KM, Åhlfeldt H. Query handling in MLM-based decision support systems. Med Inform 1995; 20: 229-40.
• 16 Åhlfeldt H, Shahsavar N, Gao X, Arkad K, Johansson B, Wigertz O. Data driven decision support based on the Arden Syntax within the HELIOS environment. Comp Meth Progr Biomed 1994; 45 (Suppl): 97-106.
• 17 Rigg JC, Brown SS, Bybkaer R, Olesen H. Compendium of Terminology and Nomenclature of Properties in Clinical Laboratory Medicine. Oxford: Blackwell Science; 1995
• 18 International Organization for Standardization. Data Elements and Interchange Formats – Information Interchange – Representations of Dates and Times (ISO 8601: 1988E). Geneva: International Organization for Standardization; 1988
• 19 Hripcsak G, Allen B, Cirnino J, Lee R. Access to data: comparing AccessMed with Query by Review. JAMIA 1996; 3: 288-99.
• 20 Rector AL, Solomon WD, Nowlan WA, Rush TW, Zanstra PE, Claassen WMA. A terminology server for medical language and medical information systems. Meth Inform Med 1995; 34: 147-57.
• 21 Rothwell DJ. SNOMED-based knowledge representation. Meth Inform Med 1995; 34: 209-13.
• 22 O’Neil M, Payne C, Read J. Read Code Version 3: A user-led terminology. Meth Inform Med 1995; 34: 187-92.