Structuring research methods and data with the research object model: genomics workflows as a case study

Kristina Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure, Oscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C 't Hoen, Sean Bechhofer, Carole Goble, Marco Roos

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    BACKGROUND:One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.RESULTS:We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?".CONCLUSIONS:Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.AVAILABILITY:The Research Object is available at Wf4Ever Research Object Model is available at
    Original languageEnglish
    Number of pages41
    JournalJournal of Biomedical Semantics
    Issue number1
    Publication statusPublished - 2014


    • research object
    • genomics
    • workflow
    • Semantic Web models
    • Scientific workflows
    • Digital Libraries
    • Genome wi de association study


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    • CWL+Research Object == Complete Provenance

      Khan, F. Z., Soiland-Reyes, S., Lonie, A. & Sinnott, R., 14 Jun 2017, (Accepted/In press). 1 p.

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    • CWL Viewer: The Common Workflow Language Viewer

      Robinson, M., Soiland-Reyes, S., Crusoe, M. R. & Goble, C., 6 Jul 2017. 1 p.

      Research output: Contribution to conferencePosterpeer-review

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