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

Supporting SPARQL Update Queries in RDF-XML Integration

The Web of Data encourages organizations and companies to publish their data according to the Linked Data practices and offer SPARQL endpoints. On the other hand, the dominant standard for information exchange is XML. The SPARQL2XQuery Framework focuses on the automatic translation of SPARQL queries in XQuery expressions in order to access XML data across the Web. In this paper, we outline our ongoing work on supporting update queries in the RDF-XML integration scenario.Comment: 13th International Semantic Web Conference (ISWC '14

Interoperability between Multimedia Collections for Content and Metadata-Based Searching

Artiste is a European project developing a cross-collection search system for art galleries and museums. It combines image content retrieval with text based retrieval and uses RDF mappings in order to integrate diverse databases. The test sites of the Louvre, Victoria and Albert Museum, Uffizi Gallery and National Gallery London provide their own database schema for existing metadata, avoiding the need for migration to a common schema. The system will accept a query based on one museum’s fields and convert them, through an RDF mapping into a form suitable for querying the other collections. The nature of some of the image processing algorithms means that the system can be slow for some computations, so the system is session-based to allow the user to return to the results later. The system has been built within a J2EE/EJB framework, using the Jboss Enterprise Application Server