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Publishing peer review materials.

ABSTRACT: Publishing peer review materials alongside research articles promises to make the peer review process more transparent as well as making it easier to recognise these contributions and give credit to peer reviewers. Traditionally, the peer review reports, editors letters and author responses are only shared between the small number of people in those roles prior to publication, but there is a growing interest in making some or all of these materials available. A small number of journals have been publishing peer review materials for some time, others have begun this practice more recently, and significantly more are now considering how they might begin. This article outlines the outcomes from a recent workshop among journals with experience in publishing peer review materials, in which the specific operation of these workflows, and the challenges, were discussed. Here, we provide a draft as to how to represent these materials in the JATS and Crossref data models to facilitate the coordination and discoverability of peer review materials, and seek feedback on these initial recommendations.

SUBMITTER: Beck J

PROVIDER: S-EPMC6206614 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publishing peer review materials.

Beck Jeffrey J Funk Kathryn K Harrison Melissa M McEntyre Jo J Breen Josie J Collings Andy A Donohoe Paul P Evans Michael M Flintoft Louisa L Hamelers Audrey A Hurst Phil P Lemberger Thomas T Lin Jennifer J O'Connor Niamh N Parkin Michael M Parker Sam S Rodgers Peter P Skipper Magdalena M Stoner Michael M

F1000Research 20181017

Publishing peer review materials alongside research articles promises to make the peer review process more transparent as well as making it easier to recognise these contributions and give credit to peer reviewers. Traditionally, the peer review reports, editors letters and author responses are only shared between the small number of people in those roles prior to publication, but there is a growing interest in making some or all of these materials available. A small number of journals have been ...[more]

PMID: 30416719

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Project description:MotivationReproducing 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.ResultsExecutable 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.AvailabilitySOAPdenovo2 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/.Contactphilippe.rocca-serra@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk.

Project description:Researchers have repeatedly demonstrated that women continue to be underrepresented in publication output in the sciences. This is true even in female-rich fields such as archaeology. Since most gender-related publication studies rely on data from peer-reviewed journals, it would be instructive, though challenging, to also track publication output in non-refereed and professional or industry venues, which tend to be more accessible to those working in extra-academic settings. This comparison is important in fields such as archaeology in which the vast majority (approximately 90%) of practitioners in the USA work for private sector cultural resource management firms and federal and state agencies. To understand the dynamics of who publishes where, we compiled a new dataset tracking over 40 years of peer-reviewed versus non-peer-reviewed publications that publish articles on the archaeology of California (an American Indian cultural area including southwest Oregon, most of the state of California, and Baja Mexico) and the Great Basin culture area (spanning eight western USA states). Historic gender differences in the publishing output of authors identified as men versus those identified as women were revealed by articles published between 1974 and 2016 in two refereed journals, the Journal of California Anthropology/ Journal of California and Great Basin Anthropology and California Archaeology, and in one un-refereed venue, the Society for California Archaeology Proceedings. Although multiple independent measures indicate that women are contributing and active members of the discipline, publishing records yield more variable results. Specifically, while women have historic and increasingly robust levels of participation in the non-peer-reviewed Proceedings, they remain vastly underrepresented in the two peer-reviewed journals, which are widely regarded as more prestigious and influential. We argue that this "peer review gap" is influenced by variation in the costs (largely time investment) and benefits of publication for people working in different professional roles (e.g., agency professionals, private/cultural resource management firm personnel, tenure-track faculty, adjunct faculty, etc.). We also argue that these cost and benefit variations may ultimately influence the decisions of people of all genders and backgrounds, but, because of the current structure of our discipline-including the fact that women and minorities lag in positions where costly peer-reviewed publication is a rewarded and supported activity-overwhelmingly affect these groups. We recognize that non-refereed publications such as Proceedings provide an important means of bridging the peer review gap and give voice to individuals from diverse backgrounds and perspectives.

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Publishing peer review materials.

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Publishing peer review materials.

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