Semantic processing of EHR data for clinical research

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.Comment: Accepted for publication in Journal of Biomedical Informatics, 2015, preprint versio

Query Rewriting and Optimization for Ontological Databases

Ontological queries are evaluated against a knowledge base consisting of an extensional database and an ontology (i.e., a set of logical assertions and constraints which derive new intensional knowledge from the extensional database), rather than directly on the extensional database. The evaluation and optimization of such queries is an intriguing new problem for database research. In this paper, we discuss two important aspects of this problem: query rewriting and query optimization. Query rewriting consists of the compilation of an ontological query into an equivalent first-order query against the underlying extensional database. We present a novel query rewriting algorithm for rather general types of ontological constraints which is well-suited for practical implementations. In particular, we show how a conjunctive query against a knowledge base, expressed using linear and sticky existential rules, that is, members of the recently introduced Datalog+/- family of ontology languages, can be compiled into a union of conjunctive queries (UCQ) against the underlying database. Ontological query optimization, in this context, attempts to improve this rewriting process so to produce possibly small and cost-effective UCQ rewritings for an input query.Comment: arXiv admin note: text overlap with arXiv:1312.5914 by other author