title: From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.
abstract: BACKGROUND
  Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler.
  
  
  RESULTS
  Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata.
  
  
  BACKGROUND
  SOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/.
  
  
  BACKGROUND
  philippe.rocca-serra@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk.
authors.affiliation: Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, United Kingdom.
authors.forename: Alejandra
authors.initials: A
authors.lastname: González-Beltrán
authors.affiliation: GigaScience, BGI HK Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, People's Republic of China.
authors.forename: Peter
authors.initials: P
authors.lastname: Li
authors.affiliation: InfoLab21, Lancaster University, Bailrigg, Lancaster, LA1 4WA, United Kingdom.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, United Kingdom.
authors.forename: Maria Susana
authors.initials: MS
authors.lastname: Avila-Garcia
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
authors.forename: Marco
authors.initials: M
authors.lastname: Roos
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: Thompson
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
authors.forename: Eelke
authors.initials: E
authors.lastname: van der Horst
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
authors.forename: Rajaram
authors.initials: R
authors.lastname: Kaliyaperumal
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China.
authors.forename: Ruibang
authors.initials: R
authors.lastname: Luo
authors.affiliation: School of Biomedical Sciences and CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China.
authors.forename: Tin-Lap
authors.initials: TL
authors.lastname: Lee
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China.
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
authors.affiliation: GigaScience, BGI HK Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, People's Republic of China.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Edmunds
authors.affiliation: Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, United Kingdom.
authors.forename: Susanna-Assunta
authors.initials: SA
authors.lastname: Sansone
authors.affiliation: Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, United Kingdom.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rocca-Serra
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008962:Models, Theoretical; D017712:Peer Review, Research; D015203:Reproducibility of Results