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A Linked Data Approach to Sharing Workflows and Workflow Results

  • Marco Roos
  • Sean Bechhofer
  • Jun Zhao
  • Paolo Missier
  • David R. Newman
  • David De Roure
  • M. Scott Marshall
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6415)

Abstract

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users.

Keywords

Linked Data Semantic Web Digital preservation Workflow Provenance Concept Web 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Marco Roos
    • 1
    • 2
  • Sean Bechhofer
    • 3
  • Jun Zhao
    • 4
  • Paolo Missier
    • 3
  • David R. Newman
    • 5
  • David De Roure
    • 6
  • M. Scott Marshall
    • 2
    • 7
  1. 1.BioSemantics Group, Department of Human and Clinical GeneticsLeiden University Medical CentreRC LeidenThe Netherlands
  2. 2.Informatics Institute, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands
  3. 3.School of Computer ScienceThe University of ManchesterManchesterUK
  4. 4.Department of ZoologyUniversity of OxfordOxford
  5. 5.School of Electronics and Computer ScienceUniversity of SouthamptonSouthamptonUK
  6. 6.Oxford e-Research CentreUniversity of OxfordOxfordUK
  7. 7.Department of Medical Statistics and BioinformaticsLeiden University Medical CentreRC LeidenThe Netherlands

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