RT Journal Article
SR Electronic
T1 From peer-reviewed to peer-reproduced: a role for data standards, models and computational workflows in scholarly publishing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 011973
DO 10.1101/011973
A1 Alejandra N. González-Beltrán
A1 Peter Li
A1 Jun Zhao
A1 Maria Susana Avila-Garcia
A1 Marco Roos
A1 Mark Thompson
A1 Eelke van der Horst
A1 Rajaram Kaliyaperumal
A1 Ruibang Luo
A1 Tin-Lap Lee
A1 Tak-wah Lam
A1 Scott C. Edmunds
A1 Susanna-Assunta Sansone
A1 Philippe Rocca-Serra
YR 2014
UL http://biorxiv.org/content/early/2014/12/08/011973.abstract
AB Motivation: 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.Availability: 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/. Contact: philippe.rocca-serra{at}oerc.ox.ac.uk and susanna.assunta-sansone{at}oerc.ox.ac.uk