R D Stevens

..Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance...

..Finally, the paper will describe the process of building an ontology, introducing the reader to the techniques and methods currently in use and the open research questions in ontology development...

..This paper concentrates on an explanation of object orientation and how it can be used to overcome the problems of distribution and diversity by describing the interfaces between objects...

..A companion paper in this issue gives an example of the development of a bio-ontology using OIL...

..This cycle of elaboration and refinement is iterated on each portion of the ontology until a satisfactory ontology has been created...

..The management of all these data and the co-ordination of resources to manage such virtual organizations and the data surrounding them needs significant computational infra-structure support...

..A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses...

..Here, we discuss the development and use of the (my)Grid ontology and our experiences in semantic service discovery...

..The growing number of genomes, the rapid changes in knowledge and the central role of classification in the annotation process, however, motivates the need to automate this process...

..We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability...

..Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results...

..The overall ontology-driven architecture provides a robust structure with distinct advantages for sustainability and provides the potential for the development of diagnostic tools, as well as a data repository...

..Both the range of biological tasks and syntactic task components can be seen to provide a set of bioinformatics requirements for general query systems. These requirements were used to evaluate two bioinformatics query systems...

..In order to observe the generality of the method, two different groups of studies were used with widely different image acquisition specifications...

..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...

..Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training...

..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...

..In reviewing provenance support, we will review one of the important knowledge management issues in bioinformatics...

..By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community...

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..For more information see http://www.biote.ctu-dresden.de/sealife...

..With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine...

..These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/...

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..To augment traditional visual data perception of complex multiparametric imaging data sets by adding auditory feedback to improve the delineation of regions of interest (ROIs) in tumor assessment in dynamic contrast-enhanced (DCE) MRI...

..With the aim to further our knowledge of the biology of these organisms we present a characterisation of the phosphatase complement (phosphatome) of the three parasites...

..Workflows developed in this investigation, including a guide to loading and executing them with example data, are available at http://workflows.mygrid.org.uk/repository/myGrid/PaulFisher/...

..Finally, we make an open call to the community for participation in the Env Community and its future activities...

..It outlines emerging strategies, recommendations and objectives for collaboration on shared ontology-building and harmonization of data for multi-site trials in this domain...