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

Knowledge will Propel Machine Understanding of Content: Extrapolating from Current Examples

Machine Learning has been a big success story during the AI resurgence. One particular stand out success relates to learning from a massive amount of data. In spite of early assertions of the unreasonable effectiveness of data, there is increasing recognition for utilizing knowledge whenever it is available or can be created purposefully. In this paper, we discuss the indispensable role of knowledge for deeper understanding of content where (i) large amounts of training data are unavailable, (ii) the objects to be recognized are complex, (e.g., implicit entities and highly subjective content), and (iii) applications need to use complementary or related data in multiple modalities/media. What brings us to the cusp of rapid progress is our ability to (a) create relevant and reliable knowledge and (b) carefully exploit knowledge to enhance ML/NLP techniques. Using diverse examples, we seek to foretell unprecedented progress in our ability for deeper understanding and exploitation of multimodal data and continued incorporation of knowledge in learning techniques.Comment: Pre-print of the paper accepted at 2017 IEEE/WIC/ACM International Conference on Web Intelligence (WI). arXiv admin note: substantial text overlap with arXiv:1610.0770

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far

Utilising semantic technologies for decision support in dementia care

The main objective of this work is to discuss our experience in utilising semantic technologies for building decision support in Dementia care systems that are based on the non-intrusive on the non-intrusive monitoring of the patient’s behaviour. Our approach adopts context-aware modelling of the patient’s condition to facilitate the analysis of the patient’s behaviour within the inhabited environment (movement and room occupancy patterns, use of equipment, etc.) with reference to the semantic knowledge about the patient’s condition (history of present of illness, dependable behaviour patterns, etc.). The reported work especially focuses on the critical role of the semantic reasoning engine in inferring medical advice, and by means of practical experimentation and critical analysis suggests important findings related to the methodology of deploying the appropriate semantic rules systems, and the dynamics of the efficient utilisation of complex event processing technology in order to the meet the requirements of decision support for remote healthcare systems

A framework for deriving semantic web services

Web service-based development represents an emerging approach for the development of distributed information systems. Web services have been mainly applied by software practitioners as a means to modularize system functionality that can be offered across a network (e.g., intranet and/or the Internet). Although web services have been predominantly developed as a technical solution for integrating software systems, there is a more business-oriented aspect that developers and enterprises need to deal with in order to benefit from the full potential of web services in an electronic market. This ‘ignored’ aspect is the representation of the semantics underlying the services themselves as well as the ‘things’ that the services manage. Currently languages like the Web Services Description Language (WSDL) provide the syntactic means to describe web services, but lack in providing a semantic underpinning. In order to harvest all the benefits of web services technology, a framework has been developed for deriving business semantics from syntactic descriptions of web services. The benefits of such a framework are two-fold. Firstly, the framework provides a way to gradually construct domain ontologies from previously defined technical services. Secondly, the framework enables the migration of syntactically defined web services toward semantic web services. The study follows a design research approach which (1) identifies the problem area and its relevance from an industrial case study and previous research, (2) develops the framework as a design artifact and (3) evaluates the application of the framework through a relevant scenario

Semantic-based decision support for remote care of dementia patients

This paper investigates the challenges in developing a semantic-based Dementia Care Decision Support System based on the non-intrusive monitoring of the patient's behaviour. Semantic-based approaches are well suited for modelling context-aware scenarios similar to Dementia care systems, where the patient's dynamic behaviour observations (occupants movement, equipment use) need to be analysed against the semantic knowledge about the patient's condition (illness history, medical advice, known symptoms) in an integrated knowledgebase. However, our research findings establish that the ability of semantic technologies to reason upon the complex interrelated events emanating from the behaviour monitoring sensors to infer knowledge assisting medical advice represents a major challenge. We attempt to address this problem by introducing a new approach that relies on propositional calculus modelling to segregate complex events that are amenable for semantic reasoning from events that require pre-processing outside the semantic engine before they can be reasoned upon. The event pre-processing activity also controls the timing of triggering the reasoning process in order to further improve the efficiency of the inference process. Using regression analysis, we evaluate the response-time as the number of monitored patients increases and conclude that the incurred overhead on the response time of the prototype decision support systems remains tolerable

Visualisation of semantic architectural information within a game engine environment

Because of the importance of graphics and information within the domain of architecture, engineering and construction (AEC), an appropriate combination of visualisation technology and information management technology is of utter importance in the development of appropriately supporting design and construction applications. We therefore started an investigation of two of the newest developments in these domains, namely game engine technology and semantic web technology. This paper documents part of this research, containing a review and comparison of the most prominent game engines and documenting our architectural semantic web. A short test-case illustrates how both can be combined to enhance information visualisation for architectural design and construction