Ontologies tend to be found everywhere. They are viewed as the silver bullet for many applications, such as database integration, peer-to-peer systems, e-commerce, semantic web services, or social networks. However, in open or evolving systems, such as the semantic web, different parties would, in general, adopt different ontologies. Thus, merely using ontologies, like using XML, does not reduce heterogeneity: it just raises heterogeneity problems to a higher level. Euzenat and Shvaikos book is devoted to ontology matching as a solution to the semantic heterogeneity problem faced by computer systems. Ontology matching aims at finding correspondences between semantically related entities of different ontologies. These correspondences may stand for equivalence as well as other relations, such as consequence, subsumption, or disjointness, between ontology entities. Many different matching solutions have been proposed so far from various viewpoints, e.g., databases, information systems, and artificial intelligence. The second edition of Ontology Matching has been thoroughly revised and updated to reflect the most recent advances in this quickly developing area, which resulted in more than 150 pages of new content. In particular, the book includes a new chapter dedicated to the methodology for performing ontology matching. It also covers emerging topics, such as data interlinking, ontology partitioning and pruning, context-based matching, matcher tuning, alignment debugging, and user involvement in matching, to mention a few. More than 100 state-of-the-art matching systems and frameworks were reviewed. With Ontology Matching, researchers and practitioners will find a reference book that presents currently available work in a uniform framework. In particular, the work and the techniques presented in this book can be equally applied to database schema matching, catalog integration, XML schema matching and other related problems. The objectives of the book include presenting (i) the state of the art and (ii) the latest research results in ontology matching by providing a systematic and detailed account of matching techniques and matching systems from theoretical, practical and application perspectives.

Ontology Matching

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.

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The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration

https://www.cs.ox.ac.uk/boris.motik/pubs/ghmppss08next-steps.pdf

OWL 2: The next step for OWL

We present the OWL API, a high level Application Programming Interface (API) for working with OWL ontologies. The OWL API is closely aligned with the OWL 2 structural specification. It supports parsing and rendering in the syntaxes defined in the W3C specification (Functional Syntax, RDF/XML, OWL/XML and the Manchester OWL Syntax); manipulation of ontological structures; and the use of reasoning engines. The reference implementation of the OWL API, written in Java, includes validators for the various OWL 2 profiles - OWL 2 QL, OWL 2 EL and OWL 2 RL. The OWL API has widespread usage in a variety of tools and applications.

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The OWL API: A Java API for OWL ontologies

Results of the Ontology Alignment Evaluation Initiative

HermiT is a new OWL reasoner based on a novel “hypertableau” calculus The new calculus addresses performance problems due to nondeterminism and model size—the primary sources of complexity in state-of-the-art OWL reasoners The latter is particularly important in practice, and it is achieved in HermiT with an improved blocking strategy and and an optimization that tries to reuse existing individuals rather than generating new ones HermiT also incorporates a number of other novel optimizations, such as a more efficient approach to handling nominals, and various techniques for optimizing ontology classification Our tests show that HermiT is usually much faster than other reasoners when classifying complex ontologies, and it is already able to classify a number of ontologies which no other reasoner has been able to handle

/pdf/hermit-a-highly-efficient-owl-reasoner-2dfg8s4hk2.pdf

HermiT: A Highly-Efficient OWL Reasoner.

We present a novel reasoning calculus for the description logic SHOIQ+--a knowledge representation formalism with applications in areas such as the SemanticWeb. Unnecessary nondeterminism and the construction of large models are two primary sources of inefficiency in the tableau-based reasoning calculi used in state-of-the-art reasoners. In order to reduce nondeterminism, we base our calculus on hypertableau and hyperresolution calculi, which we extend with a blocking condition to ensure termination. In order to reduce the size of the constructed models, we introduce anywhere pairwise blocking. We also present an improved nominal introduction rule that ensures termination in the presence of nominals, inverse roles, and number restrictions--a combination of DL constructs that has proven notoriously difficult to handle. Our implementation shows significant performance improvements over state-of-the-art reasoners on several well-known ontologies.

/pdf/hypertableau-reasoning-for-description-logics-1z3294bbzx.pdf

Hypertableau reasoning for description logics

We present a novel reasoning calculus for Description Logics (DLs)--knowledge representation formalisms with applications in areas such as the Semantic Web. In order to reduce the nondeterminism due to general inclusion axioms, we base our calculus on hypertableau and hyperresolution calculi, which we extend with a blocking condition to ensure termination. To prevent the calculus from generating large models, we introduce "anywhere" pairwise blocking. Our preliminary implementation shows significant performance improvements on several well-known ontologies. To the best of our knowledge, our reasoner is currently the only one that can classify the original version of the GALEN terminology.

/pdf/optimized-reasoning-in-description-logics-using-12435c13p7.pdf

Optimized Reasoning in Description Logics Using Hypertableaux

https://www.cs.ox.ac.uk/files/4002/paper.pdf

A novel approach to ontology classification

OBO is an ontology language that has often been used for modeling ontologies in the life sciences. Its definition is relatively informal, so, in this paper, we provide a clear specification for OBO syntax and semantics via a mapping to OWL. This mapping also allows us to apply existing Semantic Web tools and techniques to OBO. We show that Semantic Web reasoners can be used to efficiently reason with OBO ontologies. Furthermore, we show that grounding the OBO language in formal semantics is useful for the ontology development process: using an OWL reasoner, we detected a likely modeling error in one OBO ontology.

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Rob Shearer

Papers

HermiT: A Highly-Efficient OWL Reasoner.

Hypertableau reasoning for description logics

Optimized Reasoning in Description Logics Using Hypertableaux

A novel approach to ontology classification

OBO and OWL: leveraging semantic web technologies for the life sciences