Article: Adapting Clinical Ontologies in Real-World Environments

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term 'ontology' has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects.

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References

1.

Boeker M, Stenzhorn H, Kumpf K, Bijlenga P, Schulz S, Hanser S . The @neurIST ontology of intracranial aneurysms: providing terminological services for an integrated IT infrastructure. AMIA Annu Symp Proc. 2008; :56-60. PMC: 2655878. View

2.

Dolin R, Alschuler L, Boyer S, Beebe C, Behlen F, Biron P . HL7 Clinical Document Architecture, Release 2. J Am Med Inform Assoc. 2005; 13(1):30-9. PMC: 1380194. DOI: 10.1197/jamia.M1888. View

3.

Ingenerf J, Reiner J, Seik B . Standardized terminological services enabling semantic interoperability between distributed and heterogeneous systems. Int J Med Inform. 2001; 64(2-3):223-40. DOI: 10.1016/s1386-5056(01)00211-8. View

4.

Garde S, Knaup P, Hovenga E, Heard S . Towards semantic interoperability for electronic health records. Methods Inf Med. 2007; 46(3):332-43. DOI: 10.1160/ME5001. View

5.

Rosse C, Mejino Jr J . A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2004; 36(6):478-500. DOI: 10.1016/j.jbi.2003.11.007. View

6.

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W . The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007; 25(11):1251-5. PMC: 2814061. DOI: 10.1038/nbt1346. View

7.

Rossi Mori A, Consorti F . Exploiting the terminological approach from CEN/TC251 and GALEN to support semantic interoperability of healthcare record systems. Int J Med Inform. 1998; 48(1-3):111-24. DOI: 10.1016/s1386-5056(97)00116-0. View

8.

Kalra D, Beale T, Heard S . The openEHR Foundation. Stud Health Technol Inform. 2005; 115:153-73. View

9.

Rector A, Zanstra P, Solomon W, Rogers J, Baud R, Ceusters W . Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine. IEEE Trans Inf Technol Biomed. 2000; 2(4):229-42. DOI: 10.1109/4233.737578. View

10.

Grenon P, Smith B, Goldberg L . Biodynamic ontology: applying BFO in the biomedical domain. Stud Health Technol Inform. 2005; 102:20-38. View

11.

Bodenreider O, Smith B, Burgun A . The Ontology-Epistemology Divide: A Case Study in Medical Terminology. Form Ontol Inf Syst. 2015; 2004:185-195. PMC: 4346778. View

12.

Kayaalp M . Why do we need probabilistic approaches to ontologies and the associated data?. AMIA Annu Symp Proc. 2006; :1005. PMC: 1560671. View