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

Ontology-based metrics computation for business process analysis

Business Process Management (BPM) aims to support the whole life-cycle necessary to deploy and maintain business processes in organisations. Crucial within the BPM lifecycle is the analysis of deployed processes. Analysing business processes requires computing metrics that can help determining the health of business activities and thus the whole enterprise. However, the degree of automation currently achieved cannot support the level of reactivity and adaptation demanded by businesses. In this paper we argue and show how the use of Semantic Web technologies can increase to an important extent the level of automation for analysing business processes. We present a domain-independent ontological framework for Business Process Analysis (BPA) with support for automatically computing metrics. In particular, we define a set of ontologies for specifying metrics. We describe a domain-independent metrics computation engine that can interpret and compute them. Finally we illustrate and evaluate our approach with a set of general purpose metrics

Ontology and medical terminology: Why description logics are not enough

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added or subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory

Living with the Semantic Gap: Experiences and remedies in the context of medical imaging

Semantic annotation of images is a key concern for the newly emerged applications of semantic multimedia. Machine processable descriptions of images make it possible to automate a variety of tasks from search and discovery to composition and collage of image data bases. However, the ever occurring problem of the semantic gap between the low level descriptors and the high level interpretation of an image poses new challenges and needs to be addressed before the full potential of semantic multimedia can be realised. We explore the possibilities and lessons learnt with applied semantic multimedia from our engagement with medical imaging where we deployed ontologies and a novel distributed architecture to provide semantic annotation, decision support and methods for tackling the semantic gap problem

Practical applications of multi-agent systems in electric power systems

The transformation of energy networks from passive to active systems requires the embedding of intelligence within the network. One suitable approach to integrating distributed intelligent systems is multi-agent systems technology, where components of functionality run as autonomous agents capable of interaction through messaging. This provides loose coupling between components that can benefit the complex systems envisioned for the smart grid. This paper reviews the key milestones of demonstrated agent systems in the power industry and considers which aspects of agent design must still be addressed for widespread application of agent technology to occur