Embedding Non-Ground Logic Programs into Autoepistemic Logic for Knowledge Base Combination

In the context of the Semantic Web, several approaches to the combination of ontologies, given in terms of theories of classical first-order logic and rule bases, have been proposed. They either cast rules into classical logic or limit the interaction between rules and ontologies. Autoepistemic logic (AEL) is an attractive formalism which allows to overcome these limitations, by serving as a uniform host language to embed ontologies and nonmonotonic logic programs into it. For the latter, so far only the propositional setting has been considered. In this paper, we present three embeddings of normal and three embeddings of disjunctive non-ground logic programs under the stable model semantics into first-order AEL. While the embeddings all correspond with respect to objective ground atoms, differences arise when considering non-atomic formulas and combinations with first-order theories. We compare the embeddings with respect to stable expansions and autoepistemic consequences, considering the embeddings by themselves, as well as combinations with classical theories. Our results reveal differences and correspondences of the embeddings and provide useful guidance in the choice of a particular embedding for knowledge combination.Comment: 52 pages, submitte

Optimizing the computation of overriding

We introduce optimization techniques for reasoning in DLN---a recently introduced family of nonmonotonic description logics whose characterizing features appear well-suited to model the applicative examples naturally arising in biomedical domains and semantic web access control policies. Such optimizations are validated experimentally on large KBs with more than 30K axioms. Speedups exceed 1 order of magnitude. For the first time, response times compatible with real-time reasoning are obtained with nonmonotonic KBs of this size

Inductive Logic Programming in Databases: from Datalog to DL+log

In this paper we address an issue that has been brought to the attention of the database community with the advent of the Semantic Web, i.e. the issue of how ontologies (and semantics conveyed by them) can help solving typical database problems, through a better understanding of KR aspects related to databases. In particular, we investigate this issue from the ILP perspective by considering two database problems, (i) the definition of views and (ii) the definition of constraints, for a database whose schema is represented also by means of an ontology. Both can be reformulated as ILP problems and can benefit from the expressive and deductive power of the KR framework DL+log. We illustrate the application scenarios by means of examples. Keywords: Inductive Logic Programming, Relational Databases, Ontologies, Description Logics, Hybrid Knowledge Representation and Reasoning Systems. Note: To appear in Theory and Practice of Logic Programming (TPLP).Comment: 30 pages, 3 figures, 2 tables

Epistemic Reasoning in OWL 2 DL

We extend the description logic SROIQ (OWL 2 DL) with the epistemic operator K and argue that unintended effects occur when imposing the semantics traditionally employed. Consequently, we identify the most expressive DL for which the traditional approach can still be adapted. For the epistemic extension of SROIQ and alike expressive DLs, we suggest a revised semantics that behaves more intuitively in these cases and coincides with the traditional semantics on less expressive DLs

Reasoning about exceptions in ontologies: from the lexicographic closure to the skeptical closure

Reasoning about exceptions in ontologies is nowadays one of the challenges the description logics community is facing. The paper describes a preferential approach for dealing with exceptions in Description Logics, based on the rational closure. The rational closure has the merit of providing a simple and efficient approach for reasoning with exceptions, but it does not allow independent handling of the inheritance of different defeasible properties of concepts. In this work we outline a possible solution to this problem by introducing a variant of the lexicographical closure, that we call skeptical closure, which requires to construct a single base. We develop a bi-preference semantics semantics for defining a characterization of the skeptical closure

A rule-based ontological framework for the classification of molecules

BACKGROUND: A variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL-a W3C standard declarative language- has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources. RESULTS: In this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface 'less-logician-like' syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility. CONCLUSIONS: Our proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. Moreover, such a tool could contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to the public. From a modelling point of view, our approach could stimulate the adoption of a different and expressive reasoning paradigm based on rules for which state-of-the-art and highly optimised reasoners are available; it could thus pave the way for the representation of a broader spectrum of life sciences and biomedical knowledge.</p

Derivation methods for hybrid knowledge bases with rules and ontologies

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia InformáticaFirst of all, I would like to thank my advisor, José Júlio Alferes, for his incredible support. Right from the start, during the first semester of this work, when we were 2700 km apart and meeting regularly via Skype, until the end of this dissertation, he was always committed and available for discussions, even when he had lots of other urgent things to do. A really special thanks to Terrance Swift, whom acted as an advisor, helping me a lot in the second implementation, and correcting all XSB’s and CDF’s bugs. This implementation wouldn’t surely have reached such a fruitful end without his support. I would also like to thank all my colleagues and friends at FCT for the great work environment and for not letting me take myself too serious. A special thanks to my colleagues from Dresden for encouraging me to work even when there were so many other interesting things to do as an Erasmus student. I’m indebted to Luís Leal, Bárbara Soares, Jorge Soares and Cecília Calado, who kindly accepted to read a preliminary version of this report and gave me their valuable comments. For giving me working conditions and a partial financial support, I acknowledge the Departamento de Informática of the Faculdade de Ciências e Tecnologias of Universidade Nova de Lisboa. Last, but definitely not least, I would like to thank my parents and all my family for their continuous encouragement and motivation. A special thanks to Bruno for his love, support and patience

A survey of large-scale reasoning on the Web of data

As more and more data is being generated by sensor networks, social media and organizations, the Webinterlinking this wealth of information becomes more complex. This is particularly true for the so-calledWeb of Data, in which data is semantically enriched and interlinked using ontologies. In this large anduncoordinated environment, reasoning can be used to check the consistency of the data and of asso-ciated ontologies, or to infer logical consequences which, in turn, can be used to obtain new insightsfrom the data. However, reasoning approaches need to be scalable in order to enable reasoning over theentire Web of Data. To address this problem, several high-performance reasoning systems, whichmainly implement distributed or parallel algorithms, have been proposed in the last few years. Thesesystems differ significantly; for instance in terms of reasoning expressivity, computational propertiessuch as completeness, or reasoning objectives. In order to provide afirst complete overview of thefield,this paper reports a systematic review of such scalable reasoning approaches over various ontologicallanguages, reporting details about the methods and over the conducted experiments. We highlight theshortcomings of these approaches and discuss some of the open problems related to performing scalablereasoning