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

The Hidden Web, XML and Semantic Web: A Scientific Data Management Perspective

The World Wide Web no longer consists just of HTML pages. Our work sheds light on a number of trends on the Internet that go beyond simple Web pages. The hidden Web provides a wealth of data in semi-structured form, accessible through Web forms and Web services. These services, as well as numerous other applications on the Web, commonly use XML, the eXtensible Markup Language. XML has become the lingua franca of the Internet that allows customized markups to be defined for specific domains. On top of XML, the Semantic Web grows as a common structured data source. In this work, we first explain each of these developments in detail. Using real-world examples from scientific domains of great interest today, we then demonstrate how these new developments can assist the managing, harvesting, and organization of data on the Web. On the way, we also illustrate the current research avenues in these domains. We believe that this effort would help bridge multiple database tracks, thereby attracting researchers with a view to extend database technology.Comment: EDBT - Tutorial (2011

Libraries and Information Systems Need XML/RDF... but Do They Know It?

This article presents an approach to the uses of XML (eXtensible Markup Language) and Semantic Web technologies in the field of information services, focusing mainly on the creation and management of digital libraries compared to traditional libraries, while paying special attention to the concept and application of metadata, and RDF based integration