title: Structuring research methods and data with the research object model: genomics workflows as a case study.
abstract: 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.
  
  
  BACKGROUND
  The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro.
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Kristina M
authors.initials: KM
authors.lastname: Hettne
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Harish
authors.initials: H
authors.lastname: Dharuri
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhao
authors.affiliation: School of Computer Science, University of Manchester, Manchester, UK ; Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands.
authors.forename: Katherine
authors.initials: K
authors.lastname: Wolstencroft
authors.affiliation: School of Computer Science, University of Manchester, Manchester, UK.
authors.forename: Khalid
authors.initials: K
authors.lastname: Belhajjame
authors.affiliation: School of Computer Science, University of Manchester, Manchester, UK.
authors.forename: Stian
authors.initials: S
authors.lastname: Soiland-Reyes
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Eleni
authors.initials: E
authors.lastname: Mina
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: Thompson
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Don
authors.initials: D
authors.lastname: Cruickshank
authors.affiliation: Instituto de Astrofísica de Andalucía, Granada, Spain.
authors.forename: Lourdes
authors.initials: L
authors.lastname: Verdes-Montenegro
authors.affiliation: Instituto de Astrofísica de Andalucía, Granada, Spain.
authors.forename: Julian
authors.initials: J
authors.lastname: Garrido
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: David
authors.initials: D
authors.lastname: de Roure
authors.affiliation: Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Corcho
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Graham
authors.initials: G
authors.lastname: Klyne
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Reinout
authors.initials: R
authors.lastname: van Schouwen
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Peter A C
authors.initials: PA
authors.lastname: 't Hoen
authors.affiliation: School of Computer Science, University of Manchester, Manchester, UK.
authors.forename: Sean
authors.initials: S
authors.lastname: Bechhofer
authors.affiliation: School of Computer Science, University of Manchester, Manchester, UK.
authors.forename: Carole
authors.initials: C
authors.lastname: Goble
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Marco
authors.initials: M
authors.lastname: Roos
keywords: Digital libraries; Genome wide association study; Scientific workflows; Semantic web models