title: Semantic processing of EHR data for clinical research.
abstract: There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data.
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium. Electronic address: hong.sun@agfa.com.
authors.forename: Hong
authors.initials: H
authors.lastname: Sun
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
authors.forename: Kristof
authors.initials: K
authors.lastname: Depraetere
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
authors.forename: Jos
authors.initials: J
authors.lastname: De Roo
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Mels
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
authors.forename: Boris
authors.initials: B
authors.lastname: De Vloed
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
authors.forename: Marc
authors.initials: M
authors.lastname: Twagirumukiza
authors.affiliation: Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Colaert
mesh_terms: D035843:Biomedical Research; D057286:Electronic Health Records; D012660:Semantics
keywords: Clinical research; EHR; N3 rules; RESTful; Semantic interoperability; Semantic web stack