Semantic Description, Publication and Discovery of Workflows in myGrid

The bioinformatics scientific process relies on in silico experiments, which are experiments executed in full in a computational environment. Scientists wish to encode the designs of these experiments as workflows because they provide minimal, declarative descriptions of the designs, overcoming many barriers to the sharing and re-use of these designs between scientists and enable the use of the most appropriate services available at any one time. We anticipate that the number of workflows will increase quickly as more scientists begin to make use of existing workflow construction tools to express their experiment designs. Discovery then becomes an increasingly hard problem, as it becomes more difficult for a scientist to identify the workflows relevant to their particular research goals amongst all those on offer. While many approaches exist for the publishing and discovery of services, there have been few attempts to address where and how authors of experimental designs should advertise the availability of their work or how relevant workflows can be discovered with minimal effort from the user. As the users designing and adapting experiments will not necessarily have a computer science background, we also have to consider how publishing and discovery can be achieved in such a way that they are not required to have detailed technical knowledge of workflow scripting languages. Furthermore, we believe they should be able to make use of others' expert knowledge (the semantics) of the given scientific domain. In this paper, we define the issues related to the semantic description, publishing and discovery of workflows, and demonstrate how the architecture created by the myGrid project aids scientists in this process. We give a walk-through of how users can construct, publish, annotate, discover and enact workflows via the user interfaces of the myGrid architecture; we then describe novel middleware protocols, making use of the Semantic Web technologies RDF and OWL to support workflow publishing and discovery

Ontology mapping by concept similarity

This paper presents an approach to the problem of mapping ontologies. The motivation for the research stems from the Diogene Project which is developing a web training environment for ICT professionals. The system includes high quality training material from registered content providers, and free web material will also be made available through the project's "Web Discovery" component. This involves using web search engines to locate relevant material, and mapping the ontology at the core of the Diogene system to other ontologies that exist on the Semantic Web. The project's approach to ontology mapping is presented, and an evaluation of this method is described

Mind the Gap: Another look at the problem of the semantic gap in image retrieval

This paper attempts to review and characterise the problem of the semantic gap in image retrieval and the attempts being made to bridge it. In particular, we draw from our own experience in user queries, automatic annotation and ontological techniques. The first section of the paper describes a characterisation of the semantic gap as a hierarchy between the raw media and full semantic understanding of the media's content. The second section discusses real users' queries with respect to the semantic gap. The final sections of the paper describe our own experience in attempting to bridge the semantic gap. In particular we discuss our work on auto-annotation and semantic-space models of image retrieval in order to bridge the gap from the bottom up, and the use of ontologies, which capture more semantics than keyword object labels alone, as a technique for bridging the gap from the top down

A Semantic Grid Oriented to E-Tourism

With increasing complexity of tourism business models and tasks, there is a clear need of the next generation e-Tourism infrastructure to support flexible automation, integration, computation, storage, and collaboration. Currently several enabling technologies such as semantic Web, Web service, agent and grid computing have been applied in the different e-Tourism applications, however there is no a unified framework to be able to integrate all of them. So this paper presents a promising e-Tourism framework based on emerging semantic grid, in which a number of key design issues are discussed including architecture, ontologies structure, semantic reconciliation, service and resource discovery, role based authorization and intelligent agent. The paper finally provides the implementation of the framework.Comment: 12 PAGES, 7 Figure

Autoplot: A browser for scientific data on the web

Autoplot is software developed for the Virtual Observatories in Heliophysics to provide intelligent and automated plotting capabilities for many typical data products that are stored in a variety of file formats or databases. Autoplot has proven to be a flexible tool for exploring, accessing, and viewing data resources as typically found on the web, usually in the form of a directory containing data files with multiple parameters contained in each file. Data from a data source is abstracted into a common internal data model called QDataSet. Autoplot is built from individually useful components, and can be extended and reused to create specialized data handling and analysis applications and is being used in a variety of science visualization and analysis applications. Although originally developed for viewing heliophysics-related time series and spectrograms, its flexible and generic data representation model makes it potentially useful for the Earth sciences.Comment: 16 page

RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the R programming language with easy-to-use tools for reading and writing NeXML documents, including rich metadata, in a way that interfaces seamlessly with the extensive library of phylogenetic tools already available in the R ecosystem