Nick Drummond

OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns

Understanding the logical meaning of any description logic or similar formalism is difficult for most people, and OWL-DL is no exception. This paper presents the most common difficulties encountered by newcomers to the language, that have been observed during the course of more than a dozen workshops, tutorials and modules about OWL-DL and it’s predecessor languages. It emphasises understanding the exact meaning of OWL expressions – proving that understanding by paraphrasing them in pedantic but explicit language. It addresses, specifically, the confusion which OWL’s open world assumption presents to users accustomed to closed world systems such as databases, logic programming and frame languages. Our experience has had a major influence in formulating the requirements for a new set of user interfaces for OWL the first of which are now available as prototypes. A summary of the guidelines and paraphrases and examples of the new interface are provided. The example ontologies are available online.

Using OWL to model biological knowledge

Much has been written of the facilities for ontology building and reasoning offered for ontologies expressed in the Web Ontology Language (OWL). Less has been written about how the modelling requirements of different areas of interest are met by OWL-DLs underlying model of the world. In this paper we use the disciplines of biology and bioinformatics to reveal the requirements of a community that both needs and uses ontologies. We use a case study of building an ontology of protein phosphatases to show how OWL-DLs model can capture a large proportion of the communitys needs. We demonstrate how Ontology Design Patterns (ODPs) can extend inherent limitations of this model. We give examples of relationships between more than two instances; lists and exceptions, and conclude by illustrating what OWL-DL and its underlying description logic either cannot handle in theory or because of lack of implementation. Finally, we present a research agenda that, if fulfilled, would help ensure OWLs wider take up in the life science community.

Engineering use cases for modular development of ontologies in OWL

This paper presents use cases for modular development of ontologies using the OWL imports mechanism. Many of the methods are inspired by work in modular development in software engineering. The approach is aimed at developers of large ontologies covering multiple subdomains that make use of OWL reasoners for inference. Such ontologies are common in biomedical sciences, but nothing in the paper is specific to biomedicine. There are four groups of use cases: (i) organisation and factoring of ontologies; (ii) maintaining stable interfaces and bindings between ontologies and between ontologies and software; (iii) localization of ontologies to the requirements of specific sites and (iv) extension of ontologies and encapsulation of modifications. OWLs axiom-oriented import mechanism has many similarities with import mechanisms in object-oriented software but also important differences - in particular, the effects of OWL imports are global, and the order in which modules are imported is irrelevant. The advantages and disadvantages of OWLs axiom-oriented approach are discussed, and suggestions are made for extensions to allow axioms to be filtered out as well as added - a mechanism that we term “adaptation” to distinguish it from the standard import mechanism. Finally we discuss possible alternatives and practical experience with the approaches presented.