Toward Automating an Inference Model on Unstructured Terminologies: OXMIS Case Study

Most modern biomedical vocabularies employ some hierarchical representation that provides a “broader/narrower” meaning relationship among the “codes” or “concepts” found within them. Often, however, we may find within the clinical setting the creation and curation of unstructured custom vocabularies used in the everyday practice of classifying and categorizing clinical data and findings.

A significant and widely used example of this lies in the General Practice Research Database which makes use of the Oxford Medical Information Systems (OXMIS) coding scheme to represent drugs and medical conditions. This scheme is intrinsically unstructured, is generally regarded as disorganized, and is not amenable to comparison with other hierarchically structured medical coding schemes. To improve processes of data analysis and extraction, we define a semantically meaningful representation of the OXMIS codes by way of the Unified Medical Language System (UMLS) Metathesaurus. A structure-imposing ontology mapping is created, and this process provides a complete illustration of a general semantic mapping technique applicable to unstructured biomedical terminologies.

1. 1.

   General Practice Research Database (GPRD) is maintained by the (UK) National Health Service Information Authority.

2. 2.

   UMLS Metathesaurus is a project of the (US) National Library of Medicine, Department of Health and Human Services. Available at: http://www.nlm.nih.org/research/umls/.

3. 3.

   From now on, we will refer to the collective set of codes found in the GPRD as Read-OXMIS. The designation refers to the combination (OXMIS and Read version 2) of coding schemes found in this particular database’s medical records.

4. 4.

   SNOMED CT is copyrighted by the International Health Terminology Standards Organization (IHTSDO). ICD-9 refers to ICD-9, CM the International Classification of Diseases, 9th Revision, Clinical Modification. ICD-10 is copyrighted by the World Health Organization and developed by the National Center for Health Statistics. Current Procedural Terminology (CPT) is copyright the American Medical Association. The Clinical Terms Version 3 (Read Codes) are maintained by the (UK) National Health Service Information Authority.

Authors and Affiliations

1. GlaxoSmithKline, Research Triangle Park, 27709, NC, USA

   Jeffery L. Painter

Corresponding author

Correspondence to Jeffery L. Painter .

Editors and Affiliations

1. Dept. Computer Science, University of Georgia, Athens, 30602-7404, Georgia, USA

   Hamid R. Arabnia

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