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

Hettne, Kristina M. and Dharuri, Harish and Jun, Zhao 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, Julián and Roure, David de and Corcho, Oscar and Klyne, Graham and Schouwen, Reinout van and Hoen, t'Peter-Bram 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", v. 5 (n. 41); pp.. ISSN 2041-1480. https://doi.org/10.1186/2041-1480-5-41.

Description

Title: Structuring research methods and data with the research object model: genomics workflows as a case study
Author/s:
  • Hettne, Kristina M.
  • Dharuri, Harish
  • Jun, Zhao
  • Wolstencroft, Katherine
  • Belhajjame, Khalid
  • Soiland-Reyes, Stian
  • Mina, Eleni
  • Thompson, Mark
  • Cruickshank, Don
  • Verdes-Montenegro, Lourdes
  • Garrido, Julián
  • Roure, David de
  • Corcho, Oscar
  • Klyne, Graham
  • Schouwen, Reinout van
  • Hoen, t'Peter-Bram
  • Bechhofer, Sean
  • Goble, Carole
  • Roos, Marco
Item Type: Article
Título de Revista/Publicación: Journal of Biomedical Semantics
Date: 2014
Volume: 5
Subjects:
Freetext Keywords: Semantic web models; Scientific workflows; Digital libraries; Genome wide association study
Faculty: E.T.S. de Ingenieros Informáticos (UPM)
Department: Inteligencia Artificial
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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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.

More information

Item ID: 35877
DC Identifier: http://oa.upm.es/35877/
OAI Identifier: oai:oa.upm.es:35877
DOI: 10.1186/2041-1480-5-41
Official URL: http://www.jbiomedsem.com/
Deposited by: Memoria Investigacion
Deposited on: 16 Jul 2015 09:47
Last Modified: 16 Jul 2015 09:47
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