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

Sharing Human-Generated Observations by Integrating HMI and the Semantic Sensor Web

Current “Internet of Things” concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C’s Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers’ observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is soun

Parallel RDF generation from heterogeneous big data

To unlock the value of increasingly available data in high volumes, we need flexible ways to integrate data across different sources. While semantic integration can be provided through RDF generation, current generators insufficiently scale in terms of volume. Generators are limited by memory constraints. Therefore, we developed the RMLStreamer, a generator that parallelizes the ingestion and mapping tasks of RDF generation across multiple instances. In this paper, we analyze what aspects are parallelizable and we introduce an approach for parallel RDF generation. We describe how we implemented our proposed approach, in the frame of the RMLStreamer, and how the resulting scaling behavior compares to other RDF generators. The RMLStreamer ingests data at 50% faster rate than existing generators through parallel ingestion

Linked Data - the story so far

The term “Linked Data” refers to a set of best practices for publishing and connecting structured data on the Web. These best practices have been adopted by an increasing number of data providers over the last three years, leading to the creation of a global data space containing billions of assertions— the Web of Data. In this article, the authors present the concept and technical principles of Linked Data, and situate these within the broader context of related technological developments. They describe progress to date in publishing Linked Data on the Web, review applications that have been developed to exploit the Web of Data, and map out a research agenda for the Linked Data community as it moves forward

Translation of Heterogeneous Databases into RDF, and Application to the Construction of a SKOS Taxonomical Reference

International audienceWhile the data deluge accelerates, most of the data produced remains locked in deep Web databases. For the linked open data to benefit from the potential represented by this huge amount of data, it is crucial to come up with solutions to expose heterogeneous databases as linked data. The xR2RML mapping language is an endeavor towards this goal: it is designed to map various types of databases to RDF, by flexibly adapting to heterogeneous query languages and data models while remaining free from any specific language. It extends R2RML, the W3C recommendation for the mapping of relational databases to RDF, and relies on RML for the handling of various data formats. In this paper we present xR2RML, we analyse data models of several modern databases as well as the format in which query results are returned , and we show how xR2RML translates any result data element into RDF, relying on existing languages such as XPath and JSONPath when necessary. We illustrate some features of xR2RML such as the generation of RDF collections and containers, and the ability to deal with mixed data formats. We also describe a real-world use case in which we applied xR2RML to build a SKOS thesaurus aimed at supporting studies on History of Zoology, Archaeozoology and Conservation Biology

An intelligent linked data quality dashboard

This paper describes a new intelligent, data-driven dashboard for linked data quality assessment. The development goal was to assist data quality engineers to interpret data quality problems found when evaluating a dataset us-ing a metrics-based data quality assessment. This required construction of a graph linking the problematic things identified in the data, the assessment metrics and the source data. This context and supporting user interfaces help the user to un-derstand data quality problems. An analysis widget also helped the user identify the root cause multiple problems. This supported the user in identification and prioritization of the problems that need to be fixed and to improve data quality. The dashboard was shown to be useful for users to clean data. A user evaluation was performed with both expert and novice data quality engineers