ArticleJournal of biomedical semantics2025
Mapping between clinical and preclinical terminologies: eTRANSAFE's Rosetta stone approach.
Article in Journal of biomedical semantics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundThe eTRANSAFE project developed tools that support translational research. One of the challenges in this project was to combine preclinical and clinical data, which are coded with different terminologies and granularities, and are expressed as single pre-coordinated, clinical concepts and as combinations of preclinical concepts from different terminologies. This study develops and evaluates the Rosetta Stone approach, which maps combinations of preclinical concepts to clinical, pre-coordinated concepts, allowing for different levels of exactness of mappings.
methodsConcepts from preclinical and clinical terminologies used in eTRANSAFE have been mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). SNOMED CT acts as an intermediary terminology that provides the semantics to bridge between pre-coordinated clinical concepts and combinations of preclinical concepts with different levels of granularity. The mappings from clinical terminologies to SNOMED CT were taken from existing resources, while mappings from the preclinical terminologies to SNOMED CT were manually created. A coordination template defines the relation types that can be explored for a mapping and assigns a penalty score that reflects the inexactness of the mapping. A subset of 60 pre-coordinated concepts was mapped both with the Rosetta Stone semantic approach and with a lexical term matching approach. Both results were manually evaluated.
resultsA total of 34,308 concepts from preclinical terminologies (Histopathology terminology, Standard for Exchange of Nonclinical Data (SEND) code lists, Mouse Adult Gross Anatomy Ontology) and a clinical terminology (MedDRA) were mapped to SNOMED CT as the intermediary bridging terminology. A terminology service has been developed that returns dynamically the exact and inexact mappings between preclinical and clinical concepts. On the evaluation set, the precision of the mappings from the terminology service was high (95%), much higher than for lexical term matching (22%).
conclusionThe Rosetta Stone approach uses a semantically rich intermediate terminology to map between pre-coordinated clinical concepts and a combination of preclinical concepts with different levels of exactness. The possibility to generate not only exact but also inexact mappings allows to relate larger amounts of preclinical and clinical data, which can be helpful in translational use cases.
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