A Knowledge Engineering Primer

The aim of this primer is to introduce the subject of knowledge engineering in a concise but synthetic way to develop the reader's intuition about the area

Scalable integration of uncertainty reasoning and semantic web technologies

In recent years formal logical standards for knowledge representation to model real world knowledge and domains and make them accessible for computers gained a lot of trac- tion. They provide an expressive logical framework for modeling, consistency checking, reasoning, and query answering, and have proven to be versatile methods to capture knowledge of various fields. Those formalisms and methods focus on specifying knowl- edge as precisely as possible. At the same time, many applications in particular on the Semantic Web have to deal with uncertainty in their data; and handling uncertain knowledge is crucial in many real- world domains. However, regular logic is unable to capture the real-world properly due to its inherent complexity and uncertainty, all the while handling uncertain or incomplete information is getting more and more important in applications like expert system, data integration or information extraction. The overall objective of this dissertation is to identify scenarios and datasets where methods that incorporate their inherent uncertainty improve results, and investigate approaches and tools that are suitable for the respective task. In summary, this work is set out to tackle the following objectives: 1. debugging uncertain knowledge bases in order to generate consistent knowledge graphs to make them accessible for logical reasoning, 2. combining probabilistic query answering and logical reasoning which in turn uses these consistent knowledge graphs to answer user queries, and 3. employing the aforementioned techniques to the problem of risk management in IT infrastructures, as a concrete real-world application. We show that in all those scenarios, users can benefit from incorporating uncertainty in the knowledge base. Furthermore, we conduct experiments that demonstrate the real- world scalability of the demonstrated approaches. Overall, we argue that integrating uncertainty and logical reasoning, despite being theoretically intractable, is feasible in real-world application and warrants further research

Enhancing systems biology models through semantic data integration

Studying and modelling biology at a systems level requires a large amount of data of different experimental types. Historically, each of these types is stored in its own distinct format, with its own internal structure for holding the data produced by those experiments. While the use of community data standards can reduce the need for specialised, independent formats by providing a common syntax, standards uptake is not universal and a single standard cannot yet describe all biological data. In the work described in this thesis, a variety of integrative methods have been developed to reuse and restructure already extant systems biology data. SyMBA is a simple Web interface which stores experimental metadata in a published, common format. The creation of accurate quantitative SBML models is a time-intensive manual process. Modellers need to understand both the systems they are modelling and the intricacies of the SBML format. However, the amount of relevant data for even a relatively small and well-scoped model can be overwhelming. Saint is a Web application which accesses a number of external Web services and which provides suggested annotation for SBML and CellML models. MFO was developed to formalise all of the knowledge within the multiple SBML specification documents in a manner which is both human and computationally accessible. Rule-based mediation, a form of semantic data integration, is a useful way of reusing and re-purposing heterogeneous datasets which cannot, or are not, structured according to a common standard. This method of ontology-based integration is generic and can be used in any context, but has been implemented specifically to integrate systems biology data and to enrich systems biology models through the creation of new biological annotations. The work described in this thesis is one step towards the formalisation of biological knowledge useful to systems biology. Experimental metadata has been transformed into common structures, a Web application has been created for the retrieval of data appropriate to the annotation of systems biology models and multiple data models have been formalised and made accessible to semantic integration techniques.EThOS - Electronic Theses Online ServiceBBSRCEPSRCGBUnited Kingdo

Knowledge-Driven Harmonization of Sensor Observations: Exploiting Linked Open Data for IoT Data Streams

The rise of the Internet of Things leads to an unprecedented number of continuous sensor observations that are available as IoT data streams. Harmonization of such observations is a labor-intensive task due to heterogeneity in format, syntax, and semantics. We aim to reduce the effort for such harmonization tasks by employing a knowledge-driven approach. To this end, we pursue the idea of exploiting the large body of formalized public knowledge represented as statements in Linked Open Data