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

Hettne, Kristina M. and Dharuri, Harish and Zhao, Jun and Wolstencroft, Katherine and Belhajjame, Khalid and Soiland-Reyes, Stian and Mina, Eleni and Thompson, Mark and Cruickshank, Don and Verdes-Montenegro, Lourdes and Garrido, Julian and de Roure, David and Corcho, Oscar and Klyne, Graham and van Schouwen, Reinout and 't Hoen, Peter A. C. and Bechhofer, Sean and Goble, Carole and Roos, Marco (2014) Structuring research methods and data with the research object model : genomics workflows as a case study. Journal of Biomedical Semantics, 5: 41. ISSN 2041-1480

[thumbnail of 2041-1480-5-41]
PDF (2041-1480-5-41)
2041_1480_5_41.pdf - Published Version
Available under License Creative Commons Attribution.

Download (2MB)


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 The Wf4Ever Research Object Model is available at

Item Type:
Journal Article
Journal or Publication Title:
Journal of Biomedical Semantics
Additional Information:
© 2014 Hettne et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 39 pages, 13 figures, submitted to Journal of Biomedical Semantics on 2013-05-13, resubmitted after review 2013-11-09. Research Object homepage:
Uncontrolled Keywords:
?? semantic web modelsscientific workflowsdigital librariesgenome wide association studywide associationlife sciencesontologybiologyinformaticschallengesgenerationsoftwarecomplexsystemshealth informaticsinformation systemscomputer science applicationscompute ??
ID Code:
Deposited By:
Deposited On:
06 Aug 2014 07:52
Last Modified:
18 May 2024 01:12