Abstract
This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to synonymy and its relation to terms and concepts. A model theory for a segment of the Metathesaurus is then constructed, and its adequacy relative to the informal treatment is demonstrated. Finally, it is shown how this approach clarifies and addresses the puzzles educed from the informal discussion, and how the model-theoretic perspective may be employed to evaluate some fundamental criticisms of the Metathesaurus. For users of the UMLS, two significant results of this analysis are a rigorous clarification of the different senses of synonymy that appear in treatments of the Metathesaurus and an illustration of the dangers in computing inferences involving ambiguous terms.
Highlights
This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS (Unified Medical Language System) Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective
The approach taken to concepts and synonymy in the UMLS is described in online UMLS Metathesaurus documentation (NLM (2008)) and in a series of short papers over a span of approximately fifteen years
It is difficult to gain a comfortable understanding of the critical subjects from the “conceptual” documentation, while delving into the detailed technical treatments is both demanding and time-consuming – and at times confusing, since some of these are offered as alternatives to others; and there is some degree of inconsistency among the published papers and the UMLS documentation
Summary
The UMLS (Unified Medical Language System) Metathesaurus is a rich and powerful resource in biomedical informatics, finding application in such areas as clinical coding, enhanced information retrieval, knowledge exploration, and data mining and inferencing Fundamental to these roles is its representation of synonymy and concepts that transcends multiple “source vocabularies” and seeks to provide a coherent and unified view of the biomedical domain. The published papers function primarily as brief reports in which techniques or studies are summarized or sketched, and those devoted to a conceptual presentation lack detail and rigor.2 They tend to provide a view either at the broad and informal conceptual level, at one extreme, or at the implementation level in terms of data models or object models at the other. Even the picture sketched in the citations above leads to some puzzling questions
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