title: Ontology-based data integration between clinical and research systems.
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.
authors.affiliation: Institute for Medical Informatics, University Erlangen-Nuremberg, Erlangen, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Mate
authors.affiliation: Center for Medical Information and Communication, Erlangen University Hospital, Erlangen, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Köpcke
authors.affiliation: Institute for Medical Informatics, University Erlangen-Nuremberg, Erlangen, Germany.
authors.forename: Dennis
authors.initials: D
authors.lastname: Toddenroth
authors.affiliation: Tumor Centre, Erlangen University Hospital, Erlangen, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Martin
authors.affiliation: Institute for Medical Informatics, University Erlangen-Nuremberg, Erlangen, Germany; Center for Medical Information and Communication, Erlangen University Hospital, Erlangen, Germany.
authors.forename: Hans-Ulrich
authors.initials: HU
authors.lastname: Prokosch
authors.affiliation: Institute for Medical Informatics, Bern University of Applied Sciences, Bern, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bürkle
authors.affiliation: Center for Medical Information and Communication, Erlangen University Hospital, Erlangen, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Ganslandt
mesh_terms: D000465:Algorithms; D064229:Biological Ontologies; D016208:Databases, Factual; D057286:Electronic Health Records; D006801:Humans; D012106:Research; D012660:Semantics; D012984:Software