Sean Bechhofer

The OWL API: A Java API for OWL ontologies

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.

OWL rules: A proposal and prototype implementation

Although the OWL Web Ontology Language adds considerable expressive power to the Semantic Web it does have expressive limitations, particularly with respect to what can be said about properties. We present the Semantic Web Rule Language (SWRL), a Horn clause rules extension to OWL that overcomes many of these limitations. SWRL extends OWL in a syntactically and semantically coherent manner: the basic syntax for SWRL rules is an extension of the abstract syntax for OWL DL and OWL Lite; SWRL rules are given formal meaning via an extension of the OWL DL model-theoretic semantics; SWRL rules are given an XML syntax based on the OWL XML presentation syntax; and a mapping from SWRL rules to RDF graphs is given based on the OWL RDF/XML exchange syntax. We discuss the expressive power of SWRL, showing that the ontology consistency problem is undecidable, provide several examples of SWRL usage, and discuss a prototype implementation of reasoning support for SWRL.

The GRAIL concept modelling language for medical terminology

The GALEN representation and integration language (GRAIL) has been developed to support effective clinical user interfaces and extensible re-usable models of medical terminology. It has been used successfully to develop the prototype GALEN common reference (CORE) model for medical terminology and for a series of projects in clinical user interfaces within the GALEN and PEN&PAD projects. GRAIL is a description logic or frame language with novel features to support part-whole and other transitive relations and to support the GALEN modelling style aimed at re-use and application independence. GRAIL began as an experimental language. However, it has clarified many requirements for an effective knowledge representation language for clinical concepts. It still has numerous limitations despite its practical successes. The GRAIL experience is expected to form the basis for future languages which meet the same requirements but have greater expressiveness and more soundly based semantics. This paper provides a description and motivation for the GRAIL language and gives examples of the modelling paradigm which it supports.

An ontology for bioinformatics applications

MOTIVATION An ontology of biological terminology provides a model of biological concepts that can be used to form a semantic framework for many data storage, retrieval and analysis tasks. Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results. RESULTS This paper provides an overview of an ontology [the Transparent Access to Multiple Biological Information Sources (TAMBIS) ontology or TaO] that describes a wide range of bioinformatics concepts. The present paper describes the mechanisms used for delivering the ontology and discusses the ontologys design and organization, which are crucial for maintaining the coherence of a large collection of concepts and their relationships. AVAILABILITY The TAMBIS system, which uses a subset of the TaO described here, is accessible over the Web via http://img.cs.man.ac.uk/tambis (although in the first instance, we will use a password mechanism to limit the load on our server). The complete model is also available on the Web at the above URL.

Cooking the semantic web with the OWL API

This paper discusses issues that surround the provision of application support using OWL ontologies. It presents the OWL API, a high-level programmatic interface for accessing and manipulating OWL ontologies. We discuss the underlying design issues and illustrate possible solutions to technical issues occurring in systems that intend to support the OWL standard. Although the context of our solutions is that of a particular implementation, the issues discussed are largely independent of this and should be of interest to a wider community.

Conceptual linking: ontology-based open hypermedia

This paper describes the attempts of the COHSE project to define and deploy a Conceptual Open Hypermedia Service. Consisting of • an ontological reasoning service which is used to represent a sophisticated conceptual model of document terms and their relationships; • a Web-based open hypermedia link service that can offer a range of different link-providing facilities in a scalable and non-intrusive fashion; and integrated to form a conceptual hypermedia system to enable documents to be linked via metadata describing their contents and hence to improve the consistency and breadth of linking of WWW documents at retrieval time (as readers browse the documents) and authoring time (as authors create the documents).

Query processing in the TAMBIS bioinformatics source integration system

Conducting bioinformatic analyses involves biologists in expressing requests over a range of highly heterogeneous information sources and software tools. Such activities are laborious, and require detailed knowledge of the data structures and call interfaces of the different sources. The TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) project seeks to make the diversity in data structures, call interfaces and locations of bioinformatics sources transparent to users. In TAMBIS, queries are expressed in terms of an ontology implemented using a description logic, and queries over the ontology are rewritten to a middleware level for execution over the diverse sources. The paper describes query processing in TAMBIS, focusing in particular on the way source-independent concepts in the ontology are related to source-dependent middleware calls, and describing how the planner identifies efficient ways of evaluating user queries.

Applying semantic web services to bioinformatics: experiences gained, lessons learnt

We have seen an increasing amount of interest in the application of Semantic Web technologies to Web services. The aim is to support automated discovery and composition of the services allowing seamless and transparent interoperability. In this paper we discuss three projects that are applying such technologies to bioinformatics: Grid, MOBY-Services and Semantic-MOBY. Through an examination of the differences and similarities between the solutions produced, we highlight some of the practical difficulties in developing Semantic Web services and suggest that the experiences with these projects have implications for the development of Semantic Web services as a whole.

An overview of S-OGSA: A Reference Semantic Grid Architecture

The Grids vision, of sharing diverse resources in a flexible, coordinated and secure manner through dynamic formation and disbanding of virtual communities, strongly depends on metadata. Currently, Grid metadata is generated and used in an ad hoc fashion, much of it buried in the Grid middlewares code libraries and database schemas. This ad hoc expression and use of metadata causes chronic dependency on human intervention during the operation of Grid machinery, leading to systems which are brittle when faced with frequent syntactic changes in resource coordination and sharing protocols. The Semantic Grid is an extension of the Grid in which rich resource metadata is exposed and handled explicitly, and shared and managed via Grid protocols. The layering of an explicit semantic infrastructure over the Grid Infrastructure potentially leads to increased interoperability and greater flexibility. In recent years, several projects have embraced the Semantic Grid vision. However, the Semantic Grid lacks a Reference Architecture or any kind of systematic framework for designing Semantic Grid components or applications. The Open Grid Service Architecture (OGSA) aims to define a core set of capabilities and behaviours for Grid systems. We propose a Reference Architecture that extends OGSA to support the explicit handling of semantics, and defines the associated knowledge services to support a spectrum of service capabilities. Guided by a set of design principles, Semantic-OGSA (S-OGSA) defines a model, the capabilities and the mechanisms for the Semantic Grid. We conclude by highlighting the commonalities and differences that the proposed architecture has with respect to other Grid frameworks.

Using vampire to reason with OWL

OWL DL corresponds to a Description Logic (DL) that is a fragment of classical first-order predicate logic (FOL). Therefore, the standard methods of automated reasoning for full FOL can potentially be used instead of dedicated DL reasoners to solve OWL DL reasoning tasks. In this paper we report on some experiments designed to explore the feasibility of using existing general-purpose FOL provers to reason with OWL DL. We also extend our approach to SWRL, a proposed rule language extension to OWL.