Mapping between clinical and preclinical terminologies: eTRANSAFE’s Rosetta stone approach

Background The 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...

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Bibliographic Details
Published in:Journal of biomedical semantics Vol. 16; no. 1; pp. 15 - 11
Main Authors: van Mulligen, Erik M., Parry, Rowan, van der Lei, Johan, Kors, Jan A.
Format: Journal Article
Language:English
Published: London BioMed Central 21.08.2025
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Animals
Bioinformatics
Biological Ontologies
Combinatorial Libraries
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Coordination
Data Mining and Knowledge Discovery
Dictionaries
eTRANSAFE
Humans
Mapping
Matching
Mathematics
Mathematics and Statistics
Nomenclature
Ontology
Pharmacovigilance
Product safety
Semantic relations
Semantics
SNOMED CT
Systematized Nomenclature of Medicine
Terminology
Terminology as Topic
Terminology mapping
Translation
United States
Massachusetts
SNOMED CT
Terminology mapping
eTRANSAFE
Coordination
ISSN:2041-1480, 2041-1480
Online Access:Get full text
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Summary:Background The 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. Methods Concepts 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. Results A 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%). Conclusion The 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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ISSN:2041-1480
2041-1480
DOI:10.1186/s13326-025-00337-2