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.