Ontology-based Data Integration Between Clinical and Research Systems

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2015 Jan 15

PMID 25588043

Citations 27

Authors

Sebastian Mate

Felix Kopcke

Dennis Toddenroth

Marcus Martin

Hans-Ulrich Prokosch

Thomas Burkle

Thomas Ganslandt

Affiliations

Soon will be listed here.

Abstract

Data from the electronic medical record comprise numerous structured but uncoded elements, which are not linked to standard terminologies. Reuse of such data for secondary research purposes has gained in importance recently. However, the identification of relevant data elements and the creation of database jobs for extraction, transformation and loading (ETL) are challenging: With current methods such as data warehousing, it is not feasible to efficiently maintain and reuse semantically complex data extraction and trans-formation routines. We present an ontology-supported approach to overcome this challenge by making use of abstraction: Instead of defining ETL procedures at the database level, we use ontologies to organize and describe the medical concepts of both the source system and the target system. Instead of using unique, specifically developed SQL statements or ETL jobs, we define declarative transformation rules within ontologies and illustrate how these constructs can then be used to automatically generate SQL code to perform the desired ETL procedures. This demonstrates how a suitable level of abstraction may not only aid the interpretation of clinical data, but can also foster the reutilization of methods for un-locking it.

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References

Nadkarni P, Marenco L, Chen R, Skoufos E, Shepherd G, Miller P . Organization of heterogeneous scientific data using the EAV/CR representation. J Am Med Inform Assoc. 1999; 6(6):478-93. PMC: 61391. DOI: 10.1136/jamia.1999.0060478. View

Burkle T, Schweiger R, Altmann U, Holena M, Blobel B, Dudeck J . Transferring data from one EPR to another: content--syntax--semantic. Methods Inf Med. 2000; 38(4-5):321-5. View

Haux R, Seggewies C, Baldauf-Sobez W, Kullmann P, Reichert H, Luedecke L . Soarian--workflow management applied for health care. Methods Inf Med. 2003; 42(1):25-36. View

Sun Y . Methods for automated concept mapping between medical databases. J Biomed Inform. 2004; 37(3):162-78. DOI: 10.1016/j.jbi.2004.03.003. View

Bleich H, Slack W . Designing a hospital information system: a comparison of interfaced and integrated systems. MD Comput. 1992; 9(5):293-6. View

OMalley K, Cook K, Price M, Wildes K, Hurdle J, Ashton C . Measuring diagnoses: ICD code accuracy. Health Serv Res. 2005; 40(5 Pt 2):1620-39. PMC: 1361216. DOI: 10.1111/j.1475-6773.2005.00444.x. View

Embi P, Jain A, Clark J, Bizjack S, Hornung R, Harris C . Effect of a clinical trial alert system on physician participation in trial recruitment. Arch Intern Med. 2005; 165(19):2272-7. PMC: 1343501. DOI: 10.1001/archinte.165.19.2272. View

Sioutos N, de Coronado S, Haber M, Hartel F, Shaiu W, Wright L . NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform. 2006; 40(1):30-43. DOI: 10.1016/j.jbi.2006.02.013. View

Safran C, Bloomrosen M, Hammond W, Labkoff S, Markel-Fox S, Tang P . Toward a national framework for the secondary use of health data: an American Medical Informatics Association White Paper. J Am Med Inform Assoc. 2006; 14(1):1-9. PMC: 2329823. DOI: 10.1197/jamia.M2273. View

10.

Nadkarni P, Brandt C . The Common Data Elements for cancer research: remarks on functions and structure. Methods Inf Med. 2006; 45(6):594-601. PMC: 2980785. View

11.

Garde S, Hovenga E, Buck J, Knaup P . Expressing clinical data sets with openEHR archetypes: a solid basis for ubiquitous computing. Int J Med Inform. 2007; 76 Suppl 3:S334-41. DOI: 10.1016/j.ijmedinf.2007.02.004. View

12.

Kush R, Alschuler L, Ruggeri R, Cassells S, Gupta N, Bain L . Implementing Single Source: the STARBRITE proof-of-concept study. J Am Med Inform Assoc. 2007; 14(5):662-73. PMC: 1975790. DOI: 10.1197/jamia.M2157. View

13.

Weiner M, Lyman J, Murphy S, Weiner M . Electronic health records: high-quality electronic data for higher-quality clinical research. Inform Prim Care. 2007; 15(2):121-7. DOI: 10.14236/jhi.v15i2.650. View

14.

Musen M, Musen M, Shah N, Shah N, Noy N, Noy N . BioPortal: ontologies and data resources with the click of a mouse. AMIA Annu Symp Proc. 2008; :1223-4. View

15.

Prokosch H, Ganslandt T . Perspectives for medical informatics. Reusing the electronic medical record for clinical research. Methods Inf Med. 2009; 48(1):38-44. View

16.

Ohmann C, Kuchinke W . Future developments of medical informatics from the viewpoint of networked clinical research. Interoperability and integration. Methods Inf Med. 2009; 48(1):45-54. View

17.

Dean B, Lam J, Natoli J, Butler Q, Aguilar D, Nordyke R . Review: use of electronic medical records for health outcomes research: a literature review. Med Care Res Rev. 2009; 66(6):611-38. DOI: 10.1177/1077558709332440. View

18.

Weiner M, Embi P . Toward reuse of clinical data for research and quality improvement: the end of the beginning?. Ann Intern Med. 2009; 151(5):359-60. DOI: 10.7326/0003-4819-151-5-200909010-00141. View

19.

Noy N, de Coronado S, Solbrig H, Fragoso G, Hartel F, Musen M . Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages. Appl Ontol. 2011; 3(3):173-190. PMC: 2753293. DOI: 10.3233/AO-2008-0051. View

20.

Cheung K, Frost H, Scott Marshall M, Prudhommeaux E, Samwald M, Zhao J . A journey to Semantic Web query federation in the life sciences. BMC Bioinformatics. 2009; 10 Suppl 10:S10. PMC: 2755818. DOI: 10.1186/1471-2105-10-S10-S10. View