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

摘要: Motivation 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. Results Executable workflows were developed using Galaxy, reproduced consistent findings. A structured representation SOAPdenovo2 was produced combining models. By structuring these frameworks, it possible explicitly declare elements design, variables, served as guides curation this led identification inconsistencies original paper, thereby allowing its authors publish corrections form an errata. Availability SOAPdenovo2 scripts, data, available through GigaScience Database: http://dx.doi.org/10.5524/100044; GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; representations case study website http://isa-tools.github.io/soapdenovo2/. Contact: philippe.rocca-serra@oerc.ox.ac.uk susanna-assunta.sansone@oerc.ox.ac.uk.