Semantics in action: a guide for representing clinical data elements with SNOMED CT
Abstract Background Clinical data is abundant, but meaningful reuse remains lacking. Semantic representation using SNOMED CT can improve research, public health, and quality of care. However, the lack of applied guidelines to industrialise the process hinders sustainability and reproducibility. This...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-03-01
|
| Series: | Journal of Biomedical Semantics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13326-025-00326-5 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849392355536273408 |
|---|---|
| author | Julien Ehrsam Christophe Gaudet-Blavignac Mirjam Mattei Monika Baumann Christian Lovis |
| author_facet | Julien Ehrsam Christophe Gaudet-Blavignac Mirjam Mattei Monika Baumann Christian Lovis |
| author_sort | Julien Ehrsam |
| collection | DOAJ |
| description | Abstract Background Clinical data is abundant, but meaningful reuse remains lacking. Semantic representation using SNOMED CT can improve research, public health, and quality of care. However, the lack of applied guidelines to industrialise the process hinders sustainability and reproducibility. This work describes a guide for semantic representation of data elements with SNOMED CT, addressing challenges encountered during its application. The representation of the institutional data warehouse started with the guidelines proposed by SNOMED International and other groups. However, the application at large scale of manual expert-driven representation led to the development of additional rules. Results An eight-rule step-by-step guide was developed iteratively through focus groups. Continuously refined by usage and growing coverage, they are tested in practice to ensure they achieve the desired outcome. All rules prioritize maintaining semantic accuracy, which is the main goal of our strategy. They are divided into four groups which apply to understanding the data correctly (Context), and to using SNOMED CT properly (Single concepts first, Approved post-coordination, Extending post-coordination). Conclusions This work provides a practical framework for semantic representation using SNOMED CT, enabling greater accuracy and consistency by promoting a common method. While addressing challenges of large-scale implementation, the guide supports the drive from data centric models to a semantic centric approach, leveraging interoperability and more effective reuse of clinical data. |
| format | Article |
| id | doaj-art-e703e2bacc1940f18bbbd79c16dc6fff |
| institution | Kabale University |
| issn | 2041-1480 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Semantics |
| spelling | doaj-art-e703e2bacc1940f18bbbd79c16dc6fff2025-08-20T03:40:47ZengBMCJournal of Biomedical Semantics2041-14802025-03-0116111410.1186/s13326-025-00326-5Semantics in action: a guide for representing clinical data elements with SNOMED CTJulien Ehrsam0Christophe Gaudet-Blavignac1Mirjam Mattei2Monika Baumann3Christian Lovis4Division of Medical Information Sciences, Diagnostic Department, University Hospitals of GenevaDivision of Medical Information Sciences, Diagnostic Department, University Hospitals of GenevaDivision of Medical Information Sciences, Diagnostic Department, University Hospitals of GenevaDivision of Medical Information Sciences, Diagnostic Department, University Hospitals of GenevaDivision of Medical Information Sciences, Diagnostic Department, University Hospitals of GenevaAbstract Background Clinical data is abundant, but meaningful reuse remains lacking. Semantic representation using SNOMED CT can improve research, public health, and quality of care. However, the lack of applied guidelines to industrialise the process hinders sustainability and reproducibility. This work describes a guide for semantic representation of data elements with SNOMED CT, addressing challenges encountered during its application. The representation of the institutional data warehouse started with the guidelines proposed by SNOMED International and other groups. However, the application at large scale of manual expert-driven representation led to the development of additional rules. Results An eight-rule step-by-step guide was developed iteratively through focus groups. Continuously refined by usage and growing coverage, they are tested in practice to ensure they achieve the desired outcome. All rules prioritize maintaining semantic accuracy, which is the main goal of our strategy. They are divided into four groups which apply to understanding the data correctly (Context), and to using SNOMED CT properly (Single concepts first, Approved post-coordination, Extending post-coordination). Conclusions This work provides a practical framework for semantic representation using SNOMED CT, enabling greater accuracy and consistency by promoting a common method. While addressing challenges of large-scale implementation, the guide supports the drive from data centric models to a semantic centric approach, leveraging interoperability and more effective reuse of clinical data.https://doi.org/10.1186/s13326-025-00326-5SNOMED CTKnowledge representationSemantic interoperabilityManual semantic annotationData warehouse |
| spellingShingle | Julien Ehrsam Christophe Gaudet-Blavignac Mirjam Mattei Monika Baumann Christian Lovis Semantics in action: a guide for representing clinical data elements with SNOMED CT Journal of Biomedical Semantics SNOMED CT Knowledge representation Semantic interoperability Manual semantic annotation Data warehouse |
| title | Semantics in action: a guide for representing clinical data elements with SNOMED CT |
| title_full | Semantics in action: a guide for representing clinical data elements with SNOMED CT |
| title_fullStr | Semantics in action: a guide for representing clinical data elements with SNOMED CT |
| title_full_unstemmed | Semantics in action: a guide for representing clinical data elements with SNOMED CT |
| title_short | Semantics in action: a guide for representing clinical data elements with SNOMED CT |
| title_sort | semantics in action a guide for representing clinical data elements with snomed ct |
| topic | SNOMED CT Knowledge representation Semantic interoperability Manual semantic annotation Data warehouse |
| url | https://doi.org/10.1186/s13326-025-00326-5 |
| work_keys_str_mv | AT julienehrsam semanticsinactionaguideforrepresentingclinicaldataelementswithsnomedct AT christophegaudetblavignac semanticsinactionaguideforrepresentingclinicaldataelementswithsnomedct AT mirjammattei semanticsinactionaguideforrepresentingclinicaldataelementswithsnomedct AT monikabaumann semanticsinactionaguideforrepresentingclinicaldataelementswithsnomedct AT christianlovis semanticsinactionaguideforrepresentingclinicaldataelementswithsnomedct |