R D Stevens

Summary

Affiliation: University of Manchester
Country: UK

Publications

  1. pmc BioGateway: a semantic systems biology tool for the life sciences
    Erick Antezana
    Department of Plant Systems Biology, VIB, Gent, Belgium
    BMC Bioinformatics 10:S11. 2009
  2. ncbi request reprint Ontology-based knowledge representation for bioinformatics
    R Stevens
    Department of Computer Science, University of Manchester, UK
    Brief Bioinform 1:398-414. 2000
  3. ncbi request reprint Wrapping and interoperating bioinformatics resources using CORBA
    R Stevens
    Bioinformatics and Information Management Groups, University of Manchester, Department of Computer Science, Oxford Road, Manchester M13 9PI
    Brief Bioinform 1:9-21. 2000
  4. ncbi request reprint OILing the way to machine understandable bioinformatics resources
    Robert Stevens
    Department of Computer Science, University of Manchester, UK
    IEEE Trans Inf Technol Biomed 6:129-34. 2002
  5. ncbi request reprint Building a bioinformatics ontology using OIL
    Robert Stevens
    Department of Computer Science, University of Manchester, UK
    IEEE Trans Inf Technol Biomed 6:135-41. 2002
  6. ncbi request reprint Exploring Williams-Beuren syndrome using myGrid
    R D Stevens
    Department of Computer Science, University of Manchester, Manchester, UK
    Bioinformatics 20:i303-10. 2004
  7. ncbi request reprint Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
    P W Lord
    Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Bioinformatics 19:1275-83. 2003
  8. ncbi request reprint The (my)Grid ontology: bioinformatics service discovery
    K Wolstencroft
    The School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
    Int J Bioinform Res Appl 3:303-25. 2007
  9. ncbi request reprint An ontology for bioinformatics applications
    P G Baker
    School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Bioinformatics 15:510-20. 1999
  10. ncbi request reprint Protein classification using ontology classification
    K Wolstencroft
    School of Computer Science, University of Manchester, UK
    Bioinformatics 22:e530-8. 2006

Collaborators

Detail Information

Publications34

  1. pmc BioGateway: a semantic systems biology tool for the life sciences
    Erick Antezana
    Department of Plant Systems Biology, VIB, Gent, Belgium
    BMC Bioinformatics 10:S11. 2009
    ..Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance...
  2. ncbi request reprint Ontology-based knowledge representation for bioinformatics
    R Stevens
    Department of Computer Science, University of Manchester, UK
    Brief Bioinform 1:398-414. 2000
    ..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...
  3. ncbi request reprint Wrapping and interoperating bioinformatics resources using CORBA
    R Stevens
    Bioinformatics and Information Management Groups, University of Manchester, Department of Computer Science, Oxford Road, Manchester M13 9PI
    Brief Bioinform 1:9-21. 2000
    ..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...
  4. ncbi request reprint OILing the way to machine understandable bioinformatics resources
    Robert Stevens
    Department of Computer Science, University of Manchester, UK
    IEEE Trans Inf Technol Biomed 6:129-34. 2002
    ..A companion paper in this issue gives an example of the development of a bio-ontology using OIL...
  5. ncbi request reprint Building a bioinformatics ontology using OIL
    Robert Stevens
    Department of Computer Science, University of Manchester, UK
    IEEE Trans Inf Technol Biomed 6:135-41. 2002
    ..This cycle of elaboration and refinement is iterated on each portion of the ontology until a satisfactory ontology has been created...
  6. ncbi request reprint Exploring Williams-Beuren syndrome using myGrid
    R D Stevens
    Department of Computer Science, University of Manchester, Manchester, UK
    Bioinformatics 20:i303-10. 2004
    ..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...
  7. ncbi request reprint Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
    P W Lord
    Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Bioinformatics 19:1275-83. 2003
    ..A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses...
  8. ncbi request reprint The (my)Grid ontology: bioinformatics service discovery
    K Wolstencroft
    The School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
    Int J Bioinform Res Appl 3:303-25. 2007
    ..Here, we discuss the development and use of the (my)Grid ontology and our experiences in semantic service discovery...
  9. ncbi request reprint An ontology for bioinformatics applications
    P G Baker
    School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Bioinformatics 15:510-20. 1999
    ..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...
  10. ncbi request reprint Protein classification using ontology classification
    K Wolstencroft
    School of Computer Science, University of Manchester, UK
    Bioinformatics 22:e530-8. 2006
    ..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...
  11. ncbi request reprint Constructing ontology-driven protein family databases
    K Wolstencroft
    School of Biological Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
    Bioinformatics 21:1685-92. 2005
    ..We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability...
  12. ncbi request reprint PhosphaBase: an ontology-driven database resource for protein phosphatases
    K J Wolstencroft
    School of Biological Sciences, University of Manchester, Manchester, United Kingdom
    Proteins 58:290-4. 2005
    ..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...
  13. ncbi request reprint A classification of tasks in bioinformatics
    R Stevens
    Department of Computer Science School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Bioinformatics 17:180-8. 2001
    ..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...
  14. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..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...
  15. pmc The minimum information about a genome sequence (MIGS) specification
    Dawn Field
    Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
    Nat Biotechnol 26:541-7. 2008
    ..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...
  16. ncbi request reprint Wrestling with SUMO and bio-ontologies
    Christian Stoeckert
    Nat Biotechnol 24:21-2; author reply 23. 2006
  17. ncbi request reprint Using provenance to manage knowledge of in silico experiments
    Robert Stevens
    BioHealth and Information Management Groups, School of Computer Science, University of Manchester, Oxford Road, Manchester, UK, M13 9PL
    Brief Bioinform 8:183-94. 2007
    ..In reviewing provenance support, we will review one of the important knowledge management issues in bioinformatics...
  18. ncbi request reprint Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases
    Michael Schroeder
    TU Dresden, Germany
    Stud Health Technol Inform 120:167-78. 2006
    ..For more information see http://www.biote.ctu-dresden.de/sealife...
  19. pmc Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL
    Mikel Egaña Aranguren
    School of Computer Science, University of Manchester, Manchester, UK
    BMC Bioinformatics 8:57. 2007
    ..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...
  20. doi request reprint Multispectral co-occurrence with three random variables in dynamic contrast enhanced magnetic resonance imaging of breast cancer
    Mehmet C Kale
    Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA
    IEEE Trans Med Imaging 27:1425-31. 2008
    ..In order to observe the generality of the method, two different groups of studies were used with widely different image acquisition specifications...
  21. pmc The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case
    Alexander Garcia Castro
    Microarray Informatics Team, The European Bioinformatics Institute European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK
    BMC Bioinformatics 7:267. 2006
    ....
  22. pmc Bio-ontologies: current trends and future directions
    Olivier Bodenreider
    National Library of Medicine, Bethesda, MD 20894, USA
    Brief Bioinform 7:256-74. 2006
    ..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...
  23. pmc The eighth annual bio-ontologies meeting
    Phillip Lord
    University of Newcastle upon Tyne, Newcastle, United Kingdom
    PLoS Comput Biol 1:e77. 2005
  24. pmc Taverna: a tool for building and running workflows of services
    Duncan Hull
    School of Computer Science, University of Manchester, M13 9PL, UK
    Nucleic Acids Res 34:W729-32. 2006
    ..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/...
  25. pmc Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology
    Mikel Egaña Aranguren
    School of Computer Science, University of Manchester, Oxford Road, M13 9PL Manchester, UK
    BMC Bioinformatics 9:S1. 2008
    ..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...
  26. ncbi request reprint Improvement in the reproducibility of region of interest using an auditory feedback loop: a pilot assessment using dynamic contrast-enhanced (DCE) breast MR images
    Hee Chun
    Center for Remote Sensing of Ice Sheet, The University of Kansas, Lawrence, Kansas, USA
    J Magn Reson Imaging 27:27-33. 2008
    ..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...
  27. pmc The TriTryp phosphatome: analysis of the protein phosphatase catalytic domains
    Rachel Brenchley
    Faculty of Life Sciences, Michael Smith, University of Manchester, M13 9PT, UK
    BMC Genomics 8:434. 2007
    ..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...
  28. pmc A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis
    Paul Fisher
    School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, Manchester, UK
    Nucleic Acids Res 35:5625-33. 2007
    ..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/...
  29. ncbi request reprint Data integration in eHealth: a domain/disease specific roadmap
    Jenny Ure
    Generation Scotland
    Stud Health Technol Inform 126:144-53. 2007
    ..It outlines emerging strategies, recommendations and objectives for collaboration on shared ontology-building and harmonization of data for multi-site trials in this domain...
  30. pmc Development of FuGO: an ontology for functional genomics investigations
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    OMICS 10:199-204. 2006
    ....
  31. ncbi request reprint Annotation of environmental OMICS data: application to the transcriptomics domain
    Norman Morrison
    School of Computer Science, University of Manchester, Manchester, United Kingdom
    OMICS 10:172-8. 2006
    ..Finally, we make an open call to the community for participation in the Env Community and its future activities...