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. 2015 Jul 8;10(7):e0127612.
doi: 10.1371/journal.pone.0127612. eCollection 2015.

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Alejandra González-Beltrán  1 , Peter Li  2 , Jun Zhao  3 , Maria Susana Avila-Garcia  4 , Marco Roos  5 , Mark Thompson  5 , Eelke van der Horst  5 , Rajaram Kaliyaperumal  5 , Ruibang Luo  6 , Tin-Lap Lee  7 , Tak-Wah Lam  6 , Scott C Edmunds  2 , Susanna-Assunta Sansone  1 , Philippe Rocca-Serra  1
Affiliations

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Alejandra González-Beltrán et al. PLoS One. .

Abstract

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@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. A graphical representation showing the role of ISA, Nanopublication and Research model in progressively structuring experimental information, moving from hand written notes in laboratory books to semi-structure tab-delimited files and fully explicit linked data.
Fig 2
Fig 2. Another view of the complementary aspects of these research object models, highlighting the reliance of persistent identifiers (such as ORCID), and references to Galaxy workflows hosted on GigaScience Servers.
Fig 3
Fig 3. A detailed view showing how linked data representation of an ISA experiment (upper pane, in green background), with one of the finding expressed as Nanopublication statements, (lower pane), where a red outline indicates the key statement.
See this image and copyright information in PMC

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