Comparison of reasoners for large ontologies in the OWL 2 EL profile

This paper provides a survey to and a comparison of state-of-the-art Semantic Web reasoners that succeed in classifying large ontologies expressed in the tractable OWL 2 EL profile. Reasoners are characterized along several dimensions: The first dimension comprises underlying reasoning characteristics, such as the employed reasoning method and its correctness as well as the expressivity and worst-case computational complexity of its supported language and whether the reasoner supports incremental classification, rules, justifications for inconsistent concepts and ABox reasoning tasks. The second dimension is practical usability: whether the reasoner implements the OWL API and can be used via OWLlink, whether it is available as Protégé plugin, on which platforms it runs, whether its source is open or closed and which license it comes with. The last dimension contains performance indicators that can be evaluated empirically, such as classification, concept satisfiability, subsumption checking and consistency checking performance as well as required heap space and practical correctness, which is determined by comparing the computed concept hierarchies with each other. For the very large ontology SNOMED CT, which is released both in stated and inferred form, we test whether the computed concept hierarchies are correct by comparing them to the inferred form of the official distribution. The reasoners are categorized along the defined characteristics and benchmarked against well-known biomedical ontologies. The main conclusion from this study is that reasoners vary significantly with regard to all included characteristics, and therefore a critical assessment and evaluation of requirements is needed before selecting a reasoner for a real-life application

Tractable approximate deduction for OWL

Acknowledgements This work has been partially supported by the European project Marrying Ontologies and Software Technologies (EU ICT2008-216691), the European project Knowledge Driven Data Exploitation (EU FP7/IAPP2011-286348), the UK EPSRC project WhatIf (EP/J014354/1). The authors thank Prof. Ian Horrocks and Dr. Giorgos Stoilos for their helpful discussion on role subsumptions. The authors thank Rafael S. Gonçalves et al. for providing their hotspots ontologies. The authors also thank BoC-group for providing their ADOxx Metamodelling ontologies.Peer reviewedPostprin

Towards a systematic benchmarking of ontology-based query rewriting systems

Query rewriting is one of the fundamental steps in ontologybased data access (OBDA) approaches. It takes as inputs an ontology and a query written according to that ontology, and produces as an output a set of queries that should be evaluated to account for the inferences that should be considered for that query and ontology. Different query rewriting systems give support to different ontology languages with varying expressiveness, and the rewritten queries obtained as an output do also vary in expressiveness. This heterogeneity has traditionally made it difficult to compare different approaches, and the area lacks in general commonly agreed benchmarks that could be used not only for such comparisons but also for improving OBDA support. In this paper we compile data, dimensions and measurements that have been used to evaluate some of the most recent systems, we analyse and characterise these assets, and provide a unified set of them that could be used as a starting point towards a more systematic benchmarking process for such systems. Finally, we apply this initial benchmark with some of the most relevant OBDA approaches in the state of the art

Approximate Assertional Reasoning Over Expressive Ontologies

In this thesis, approximate reasoning methods for scalable assertional reasoning are provided whose computational properties can be established in a well-understood way, namely in terms of soundness and completeness, and whose quality can be analyzed in terms of statistical measurements, namely recall and precision. The basic idea of these approximate reasoning methods is to speed up reasoning by trading off the quality of reasoning results against increased speed

Constructing and Extending Description Logic Ontologies using Methods of Formal Concept Analysis

Description Logic (abbrv. DL) belongs to the field of knowledge representation and reasoning. DL researchers have developed a large family of logic-based languages, so-called description logics (abbrv. DLs). These logics allow their users to explicitly represent knowledge as ontologies, which are finite sets of (human- and machine-readable) axioms, and provide them with automated inference services to derive implicit knowledge. The landscape of decidability and computational complexity of common reasoning tasks for various description logics has been explored in large parts: there is always a trade-off between expressibility and reasoning costs. It is therefore not surprising that DLs are nowadays applied in a large variety of domains: agriculture, astronomy, biology, defense, education, energy management, geography, geoscience, medicine, oceanography, and oil and gas. Furthermore, the most notable success of DLs is that these constitute the logical underpinning of the Web Ontology Language (abbrv. OWL) in the Semantic Web. Formal Concept Analysis (abbrv. FCA) is a subfield of lattice theory that allows to analyze data-sets that can be represented as formal contexts. Put simply, such a formal context binds a set of objects to a set of attributes by specifying which objects have which attributes. There are two major techniques that can be applied in various ways for purposes of conceptual clustering, data mining, machine learning, knowledge management, knowledge visualization, etc. On the one hand, it is possible to describe the hierarchical structure of such a data-set in form of a formal concept lattice. On the other hand, the theory of implications (dependencies between attributes) valid in a given formal context can be axiomatized in a sound and complete manner by the so-called canonical base, which furthermore contains a minimal number of implications w.r.t. the properties of soundness and completeness. In spite of the different notions used in FCA and in DLs, there has been a very fruitful interaction between these two research areas. My thesis continues this line of research and, more specifically, I will describe how methods from FCA can be used to support the automatic construction and extension of DL ontologies from data

Predicting reasoner performance on ABox intensive OWL 2 EL ontologies

In this article, the authors introduce the notion of ABox intensity in the context of predicting reasoner performance to improve the representativeness of ontology metrics, and they develop new metrics that focus on ABox features of OWL 2 EL ontologies. Their experiments show that taking into account the intensity through the proposed metrics contributes to overall prediction accuracy for ABox intensive ontologies

Computing Healthcare Quality Indicators Automatically: Secondary Use of Patient Data and Semantic Interoperability

Harmelen, F.A.H. van [Promotor]Keizer, N.F. de [Copromotor]Cornet, R. [Copromotor]Teije, A.C.M. [Copromotor

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

OPTIMIZATION OF NONSTANDARD REASONING SERVICES

The increasing adoption of semantic technologies and the corresponding increasing complexity of application requirements are motivating extensions to the standard reasoning paradigms and services supported by such technologies. This thesis focuses on two of such extensions: nonmonotonic reasoning and inference-proof access control. Expressing knowledge via general rules that admit exceptions is an approach that has been commonly adopted for centuries in areas such as law and science, and more recently in object-oriented programming and computer security. The experiences in developing complex biomedical knowledge bases reported in the literature show that a direct support to defeasible properties and exceptions would be of great help. On the other hand, there is ample evidence of the need for knowledge confidentiality measures. Ontology languages and Linked Open Data are increasingly being used to encode the private knowledge of companies and public organizations. Semantic Web techniques facilitate merging different sources of knowledge and extract implicit information, thereby putting at risk security and the privacy of individuals. But the same reasoning capabilities can be exploited to protect the confidentiality of knowledge. Both nonmonotonic inference and secure knowledge base access rely on nonstandard reasoning procedures. The design and realization of these algorithms in a scalable way (appropriate to the ever-increasing size of ontologies and knowledge bases) is carried out by means of a diversified range of optimization techniques such as appropriate module extraction and incremental reasoning. Extensive experimental evaluation shows the efficiency of the developed optimization techniques: (i) for the first time performance compatible with real-time reasoning is obtained for large nonmonotonic ontologies, while (ii) the secure ontology access control proves to be already compatible with practical use in the e-health application scenario.