IDEF5

Abstract: This paper is intended to serve as a comprehensive introduction to the emerging field concerned with the design and use of ontologies. We observe that disparate backgrounds, languages, tools and techniques are a major barrier to effective communication among people, organisations and/or software understanding (i.e. an “ontology”) in a given subject area, can improve such communication, which in turn, can give rise to greater reuse and sharing, inter-operability, and more reliable software. After motivating their need, we clarify just what ontologies are and what purpose they serve. We outline a methodology for developing and evaluating ontologies, first discussing informal techniques, concerning such issues as scoping, handling ambiguity, reaching agreement and producing definitions. We then consider the benefits and describe, a more formal approach. We re-visit the scoping phase, and discuss the role of formal languages and techniques in the specification, implementation and evalution of ontologies. Finally, we review the state of the art and practice in this emerging field, considering various case studies, software tools for ontology development, key research issues and future prospects.

Abstract: 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.

Abstract: This paper does not pretend either to transform completely the ontological art in engineering or to enumerate exhaustively the complete set of works that has been reported in this area. Its goal is to clarify to readers interested in building ontologies from scratch, the activities they should perform and in which order, as well as the set of techniques to be used in each phase of the methodology. This paper only presents a set of activities that conform the ontology developmentp rocess, a life cycle to build ontologies based in evolving prototypes, and METHONTOLOGY, a well-structured methodology used to build ontologies from scratch. This paper gathers the experience of the authors on building an ontology in the domain of chemicals.