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SUMMARY Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the coordinated use of analysis programs and information(More)
The reasoning tasks that can be performed with semantic web service descriptions depend on the quality of the domain ontologies used to create these descriptions. However, building such domain ontologies is a time consuming and difficult task.We describe an automatic extraction method that learns domain ontologies for web service descriptions from textual(More)
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(More)
The growing quantity and distribution of bioinformatics resources means that finding and utilising them requires a great deal of expert knowledge, especially as many resources need to be tied together into a workflow to accomplish a useful goal. We want to formally capture at least some of this knowledge within a virtual workbench and middleware framework(More)
Semantic Web Services offer the possibility of highly flexible web service architectures, where new services can be quickly discovered, orchestrated and composed into workflows. Most existing work has, however , focused on complex service descriptions for automated composition. In this paper, we describe the requirements from the bioinformatics domain which(More)
T he transition from laboratory science to in silico e-science has facilitated a para-digmatic shift in the way we conduct modern science. We can use computation-ally based analytical models to simulate and investigate scientific questions such as those posed by high-energy physics and bioinformatics, yielding high-quality results and discoveries at an(More)
This paper describes shimantic web syndrome, the use of " shims " to align or mediate mismatching third party Web Services that have closely related, but incompatible, inputs and outputs. The syndrome is illustrated using services from my Grid bioinformatics analyses. An ontology driven treatment for managing this syndrome through semi-automated service(More)
MOTIVATION In silico experiments necessitate the virtual organization of people, data, tools and machines. The scientific process also necessitates an awareness of the experience base, both of personal data as well as the wider context of work. The management of all these data and the co-ordination of resources to manage such virtual organizations and the(More)
(my)Grid supports in silico experiments in the life sciences, enabling the design and enactment of workflows as well as providing components to assist service discovery, data and metadata management. The (my)Grid ontology is one component in a larger semantic discovery framework for the identification of the highly distributed and heterogeneous(More)