Edmund Kazmierczak

An Ontology of Data Modelling Languages: A Study Using a Common-Sense Realistic Ontology

Data modelling languages are used in today’s information systems engineering environments. Many have a degree of hype surrounding their quality and applicability with narrow and specific justification often given in support of one over another. We want to more deeply understand the fundamental nature of data modelling languages. We thus propose a theory, based on ontology, that should allow us to understand, compare, evaluate, and strengthen data modelling languages. In this paper we present a method (conceptual evaluation) and its extension (conceptual comparison), as part of our theory. Our methods are largely independent of a specific ontology. We introduce Chisholm’s ontology and apply our methods to analyse some data modelling languages using it. We find a good degree of overlap between all of the data modelling languages analysed and the core concepts of Chisholm’s ontology, and conclude that the data modelling languages investigated reflect an ontology of commonsense-realism.

COGITO: A METHODOLOGY AND SYSTEM FOR FORMAL SOFTWARE DEVELOPMENT

Cogito 1 is the first iteration of a Z-based integrated methodology and support system for formal software development. This paper gives an overview of the Cogito methodology and associated tools. Particular emphasis is placed on the way in which Cogito integrates the various phases of the formal development process and provides comprehensive tools support for all phases of development addressed by the methodology.

Combining logical agents with rapid prototyping for engineering distributed applications

The realization of new distributed and heterogeneous software applications is a challenge that software engineers have to face. Logic programming and multi-agent systems can play a very effective role in the rapid prototyping of new software products. This paper proposes a general approach to the prototyping of complex and distributed applications modelled as multi-agent systems and outlines the autonomous research experiences of different research groups from which the approach originates. All the experiences have logic programming as the common foundation and deal with different aspects of the problem: integration of heterogeneous data and reasoning systems, animation of formal specifications and the development of agent-based software. The final goal is joining these diverse experiences into a unique open framework.

Verifying model oriented specifications through animation

In this paper we demonstrate how light weight tools can be used to increase the level of confidence in Z specifications. In particular we outline the Pipedream approach to exploring Z specifications through animation, and illustrate the range of analyses that can be performed. We argue that, while a light weight approach does not give the same levels of assurance that an automated reasoning system would, it does give levels of assurance which are adequate for most projects and with significantly less overhead. We illustrate how animation can be used to perform verification using the example of a simple dependency management system.

VERIFYING REQUIREMENTS THROUGH MATHEMATICAL MODELLING AND ANIMATION

Achieving confidence in the correctness, completeness and consistency of requirements specifications can be problematic and the consequences of incorrect requirements can be costly. In this paper we argue that specification and animation can provide reasonably high levels of assurance in the requirements without the overheads of using general purpose theorem proving tools. We propose a framework based on mode analysis and the operational semantics of logic programs for animating specifications. The framework allows us to combine prototyping and limited forms of automated deduction to increase our levels of confidence in specifications. Finally, we show how such a framework can be used to increase the level of confidence in the correctness of a simple dependency management system specification written in Z.

Thesaurus and ontology structure: Formal and pragmatic differences and similarities

Thesauri and other types of controlled vocabularies are increasingly re‐engineered into ontologies described using the Web Ontology Language (OWL), particularly in the life sciences. This has led to the perception by some that thesauri are ontologies once they are described by using the syntax of OWL while others have emphasized the need to re‐engineer a vocabulary to use it as ontology. This confusion is rooted in different perceptions of what ontologies are and how they differ from other types of vocabularies. In this article, we rigorously examine the structural differences and similarities between thesauri and meaning‐defining ontologies described in OWL. Specifically, we conduct (a) a conceptual comparison of thesauri and ontologies, and (b) a comparison of a specific thesaurus and a specific ontology in the same subject field. Our results show that thesauri and ontologies need to be treated as 2 orthogonal kinds of models with superficially similar structures. An ontology is not a good thesaurus, nor is a thesaurus a good ontology. A thesaurus requires significant structural and other content changes to become an ontology, and vice versa.

Improving the quality of electron tomography image volumes using pre-reconstruction filtering

Electron tomography produces highly magnified 3D image volumes useful for investigating the structure and function of cellular components. Image quality is degraded by multiple scattering events and quantum noise, which depend on the angle at which individual tilt projections are collected. We have adapted a biomedical imaging approach to improve image quality by enhancing individual tilt projections prior to volumetric reconstruction. Specifically, we have developed a family of non-linear anisotropic diffusion (NAD) filters parameterized by the tilt angle. We give a quantitative and qualitative evaluation of our pre-processing approach and the NAD filter. We show an improvement in the reconstructed volumes for tomograms generated from both plastic-embedded and cryo-stabilized samples of malaria parasite-infected erythrocytes.

Relationships and relata in ontologies and thesauri: Differences and similarities

Ontologies and thesauri structure concepts and, from the perspective of a practitioner, do not appear to be very different. Nevertheless, experts acknowledge that ontologies are different from thesauri in several respects. In this paper we aim to clarify some of the similarities and differences by systematically comparing the structure of each: the relations and their relata in ontologies and the relationships and their relata in thesauri. In particular, we analyze thesaurus relationships and their relata as they are defined in the latest version of the international ISO thesaurus standard against formally well-defined ontological relationships and relata from ontology literature --more specifically ontology literature based in realism. We have found that the relata as well as the relationships in thesauri need to be classified further before any reasonable matching to formal ontological relationships is possible. Isolated hierarchical relationships in thesauri then may correspond to the is-a relationship, specific mereological relationships, or fundamental relationships such as the instantiation between universals and individuals in ontologies. Determining how such correspondences apply in domain-specific cases depends on whether the thesaurus relationships contribute to the specifications of necessary and sufficient conditions for their respective relata in the ontology --a function that relationships do not have in thesauri. Our findings make it clear that thesauri require structural and definitional reengineering in order to be reused or treated as ontologies, but that adherence to the international standard for thesauri provides a good base for such reengineering.

Towards Haptic Performance Analysis Using K-Metrics

It is desirable to automatically classify data samples for the assessment of quantitative performance of users of haptic devices as the haptic data volume may be much higher than is feasible to manually annotate. In this paper we compare the use of three k-metrics for automated classifaction of human motion: cosine, extrinsic curvature and symmetric centroid deviation. Such classification algorithms make predictions about data attributes, whose quality we assess via three mathematical methods of comparison: root mean square deviation, sensitivity error and entropy correlation coefficient. Our assessment suggests that k-cosine might be more promising at analysing haptic motion than our two other metrics.

Local regularization of tilt projections reduces artifacts in electron tomography.

Electron tomography produces very high resolution 3D image volumes useful for investigating the structure and function of cellular components. Unfortunately, unavoidable discontinuities and physical constraints in the acquisition geometry lead to a range of artifacts that can affect the reconstructed image. In particular, highly electron dense regions, such as gold nanoparticles, can hide proximal biological structures and degrade the overall quality of the reconstructed tomograms. In this work we introduce a pre-reconstruction non-conservative non-linear isotropic diffusion (NID) filter that automatically identifies and reduces local irregularities in the tilt projections. We illustrate the improvement in quality obtained using this approach for reconstructed tomograms generated from samples of malaria parasite-infected red blood cells. A quantitative and qualitative evaluation for our approach on both simulated and real data is provided.