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

• DOI: 10.1371/journal.pone.0127612
• Publication Date: 2015-07-08T13:50:15Z
• Authors: Alejandra Gonzále...; Peter Li; Jun Zhao; Maria Susana Avil...; Marco Roos; Mark Thompson; Eelke van der Horst; Rajaram Kaliyaper...; Ruibang Luo; Tin-Lap Lee; Tak-wah Lam; Scott C. Edmunds; Susanna-Assunta S...; Philippe Rocca-Serra
• Keywords: Peer Review, Research; 0301 basic medicine; 03 medical and health sciences; Science; Q; R; Medicine; Computational Biology; Reproducibility of Results; Models, Theoretical; Research Article

Reproducing the results from a scientific paper can be challenging due to absence of data and computational tools required for their analysis. In addition, details relating procedures used obtain published difficult discern use natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), Research Objects (RO) models are conceptual modelling frameworks that structure such information papers. Computational workflow platforms also reproduce analyses in principled manner. We assessed extent by which ISA, NP, RO models, together with Galaxy system, capture experimental processes findings previously on development SOAPdenovo2, de novo genome assembler.