*To whom correspondence should be addressed. Running head: Composing and enacting workflows using Taverna Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the Simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by with which in silico experiments can be represented as Scufl workflows using the workbench application. Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from

Initially, Grid technologies were principally associated with supercomputer centres and large-scale scientific applications in physics and astronomy. They are now increasingly seen as being relevant to many areas of e-Science and e-Business. The emergence of the Open Grid Services Architecture (OGSA), to complement the ongoing activity on Web Services standards, promises to provide a service-based platform that can meet the needs of both business and scientific applications. Early Grid applications focused principally on the storage, replication and movement of file-based data. Now the need for the full integration of database technologies with Grid middleware is widely recognized. Not only do many Grid applications already use databases for managing metadata, but increasingly many are associated with large databases of domain-specific information (e.g. biological or astronomical data). This paper describes the design and implementation of OGSA-DAI, a service-based architecture for database access over the Grid. The approach involves the design of Grid Data Services that allow consumers to discover the properties of structured data stores and to access their contents. The initial focus has been on support for access to Relational and XML data, but the overall architecture has been designed to be extensible to accommodate

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 documentations attached to web services. We conducted our experiments in the field of bioinformatics by learning an ontology from the documentation of the web services used in my Grid, a project that supports biology experiments on the Grid. Based on the evaluation of the extracted ontology in the context of the project, we conclude that the proposed extraction method is a helpful tool to support the process of building domain ontologies for web service descriptions.

Abstract. 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 semiautomated service discovery and invocation is outlined. This treatment is likely to be applicable to other domains. 1

The successful application of Grid and Web Service technologies to real-world problems, such as e-Science [1], requires not only the development of a common vocabulary and meta-data framework as the basis for inter-agent communication and service integration but also the access and use of a rich repository of domain-specific knowledge for problem solving. Both requirements are met by the respective outcomes of ontological and knowledge engineering initiatives. In this paper we discuss a novel, knowledge-based approach to resource synthesis (service composition), which draws on the functionality of semantic web services to represent and expose available resources. The approach we use exploits domain knowledge to guide the service composition process and provide advice on service selection and instantiation. The approach has been implemented in a prototype workflow construction environment that supports the runtime recommendation of a service solution, service discovery via semantic service descriptions, and knowledge-based configuration of selected services. The use of knowledge provides a basis for full automation of service composition via conventional planning algorithms. Workflows produced by this system can be executed through a domain-specific direct mapping mechanism or via a more fluid approach such as WSDL-based service grounding. The approach and prototype have been used to demonstrate practical benefits in the context of the Geodise initiative [2].

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Abstract. Successful employment of semantic web services depends on the availability of high quality ontologies to describe the domains of these services. As always, building such ontologies is difficult and costly, thus hampering web service deployment. Our hypothesis is that since the functionality offered by a web service is reflected by the underlying software, domain ontologies could be built by analyzing the documentation of that software. We verify this hypothesis in the domain of RDF ontology storage tools. We implemented and fine-tuned a semi-automatic method to extract domain ontologies from software documentation. The quality of the extracted ontologies was verified against a high quality hand-built ontology of the same domain. Despite the low linguistic quality of the corpus, our method allows extracting a considerable amount of information for a domain ontology. 1

Though DAML-S is growing into a de facto standard for semantic webservice markup, we have only found few complete service descriptions and even less papers discussing technical issues about the markup process. We addressed this lack by (1) reporting on our experiences in describing a set of services, (2) concluding several limitations of the latest DAML-S version (v0.7) and (3) making our work accessible to the research community .

Abstract. Description Logics (DLs) are a family of class based knowledge representation formalisms characterised by the use of various constructors to build complex classes from simpler ones, and by an emphasis on the provision of sound, complete and (empirically) tractable reasoning services. They have a range of applications, but are mostly widely known as the basis for ontology languages such as OWL. The increasing use of DL based ontologies in areas such as e-Science and the Semantic Web is, however, already stretching the capabilities of existing DL systems, and brings with it a range of challenges for future research. 1

Web service composition can provide a value-chain between customers and suppliers. The increasing number of services, and thus possible combinations, demands the development of dynamic and automatic techniques for their composition. Current commercial solutions are limited and are primarily static and manual. Automation requires reasoning about (semantic descriptions of) the services. In this paper we describe our initial work involving the semantic description of Web services using DAML-S and how our Agent Factory has used these descriptions in its design process to derive a Web service configuration.