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

Journal of Biomedical Semantics

Marco Roos⁶  Carole Goble⁴  Sean Bechhofer⁴  Peter A C ‘t Hoen⁶  Reinout van Schouwen⁶  Graham Klyne⁵  Oscar Corcho²  David de Roure⁵  Julian Garrido³  Lourdes Verdes-Montenegro³  Don Cruickshank⁵  Mark Thompson⁶  Eleni Mina⁶  Stian Soiland-Reyes⁴  Khalid Belhajjame⁴  Katherine Wolstencroft¹  Jun Zhao⁵  Harish Dharuri⁶  Kristina M Hettne⁶ 

[1]Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands

[2]Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain

[3]Instituto de Astrofísica de Andalucía, Granada, Spain

[4]School of Computer Science, University of Manchester, Manchester, UK

[5]Department of Zoology, University of Oxford, Oxford, UK

[6]Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

关键词: Genome wide association study;    Digital libraries;    Scientific workflows;    Semantic web models;   

Others  :  1133537
DOI  :  10.1186/2041-1480-5-41

 received in 2013-05-13, accepted in 2014-07-29,  发布年份 2014

【 摘 要 】

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 http://www.myexperiment.org/packs/428 webcite

The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro webcite

【 授权许可】

   
2014 Hettne et al.; licensee BioMed Central Ltd.

【 图 表 】

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