Abstract
BackgroundResearch for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the ontology. This paper introduces how to effectively utilize a semiotic-inspired approach to ontology evaluation, specifically towards drug-related ontologies hosted on the National Center for Biomedical Ontology BioPortal.ResultsUsing the semiotic-based evaluation framework for drug-based ontologies, we adjusted the quality metrics based on the semiotic features of drug ontologies. Then, we compared the quality scores before and after tailoring. The scores revealed a more precise measurement and a closer distribution compared to the before-tailoring.ConclusionThe results of this study reveal that a tailored semiotic evaluation produced a more meaningful and accurate assessment of drug-based ontologies, lending to the possible usefulness of semiotics in ontology evaluation.
Highlights
Given a scenario where a researcher is to choose two distinctly independent ontologies that cover a specific domain, how would the researcher know which is suitable between the two? Or given another scenario where a knowledge engineer is developing an ontological knowledgebase, how would she evaluate the quality of the ontology and know what to measure? This paper aims to provide a direction in the area of ontology evaluation using a system shaped by the theory of semiotics – the study of meaning for signs and symbols, for biomedical ontologies
Our research questions in this study focus on 1) whether a semiotic-based approach for ontology evaluation can provide meaningful assessments for biomedical ontologies, and 2) whether this approach can be tailored for specific types of ontologies to provide more accurate quality assessments
The consistency sub-score, which scores an ontology’s term uniformity, appear to be distinguishable with National Center for Biomedical Ontologies (NCBO) sample aggregate (0.73 to 0.84). This could possible reveal that some drug ontologies may have some duplicated labels, and may have to resolve those duplication if the ontology is to be deemed consistent in its domain space within the semiotic framework
Summary
If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the ontology. This paper introduces how to effectively utilize a semiotic-inspired approach to ontology evaluation, towards drug-related ontologies hosted on the National Center for Biomedical Ontology BioPortal. Given a scenario where a researcher is to choose two distinctly independent ontologies that cover a specific domain, how would the researcher know which is suitable between the two? Given another scenario where a knowledge engineer is developing an ontological knowledgebase, how would she evaluate the quality of the ontology and know what to measure? This paper aims to provide a direction in the area of ontology evaluation using a system shaped by the theory of semiotics – the study of meaning for signs and symbols, for biomedical ontologies. Approaching ontology evaluation from the semiotic frame is a natural choice to assess the overall craftsmanship of the ontology
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