Day-to-day discovery of preprint–publication links

Cabanac, Guillaume; Oikonomidi, Theodora; Boutron, Isabelle

doi:10.1007/s11192-021-03900-7

Cited by 36 publications

(33 citation statements)

References 33 publications

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“…Preprint repositories receive a growing number of submissions [19]. Linking preprints with their published counterparts is vital to maintaining scholarly discourse consistency but is challenging to perform manually [16,20,21]. Errors and omissions in linkage result in missing links and consequently erroneous metadata.…”

Section: Introductionmentioning

confidence: 99%

Linguistic Analysis of the bioRxiv Preprint Landscape

Nicholson¹,

Rubinetti²,

Hu³

et al. 2021

Preprint

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Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online. A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents. The most prevalent features that changed appear to be associated with typesetting and mentions of supplementary sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model. We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint-peer reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint. We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish. Lastly, we constructed a web application (https://greenelab.github.io/preprint-similarity-search/) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape.

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Section: Introductionmentioning

confidence: 99%

Linguistic Analysis of the bioRxiv Preprint Landscape

Nicholson¹,

Rubinetti²,

Hu³

et al. 2021

Preprint

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“…For all trials published as a preprint, we systematically searched weekly for a subsequent publication in peer-reviewed journals using a preprint tracker (last search October 7, 2021) [23].…”

Section: Search Methods For Identification Of Studiesmentioning

confidence: 99%

Transparency and reporting characteristics of COVID-19 randomized controlled trials

Kapp

Esmail

Ghosn

et al. 2022

Preprint

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Randomized controlled trials (RCTs) are essential to support clinical decision making. We assessed the transparency, completeness and consistency of reporting of 244 reports (120 peer-reviewed journal publications; 124 preprints) of RCTs assessing pharmacological interventions for the treatment of COVID-19 published the first 17 months of the pandemic (up to May 31, 2021). Transparency was poor. Only 55% of trials were prospectively registered; 39% made their full protocols available and 29% provided access to their statistical analysis plan. Only 6% completely reported the most important information. Primary outcome(s) reported in trial registries and published reports were inconsistent in 47% of trials. Of the 124 RCTs published as preprint, 76 were secondarily published in a peer-reviewed journal. There was no major improvement after the peer-review process. Lack of transparency, completeness and consistency of reporting is an important barrier to trust, interpretation and synthesis in COVID-19 clinical trials.

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“…Identification of new software package repositories is done by fuzzy matching of the tool name using the stringdist package (v0.9.6.3) [53]. Linking of preprints uses an R implementation of the algorithm by Cabanac, Oikonomidi and Boutron [54] available in the doilinker package (v0.1.0) [55]. Software licenses are standardized using the SPDX License List [56].…”

Section: Curation Of the Scrna-tools Databasementioning

confidence: 99%

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

2021

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Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq) technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has cataloged software tools for analyzing scRNA-seq data. With the number of tools in the database passing 1000, we provide an update on the state of the project and the field. This data shows the evolution of the field and a change of focus from ordering cells on continuous trajectories to integrating multiple samples and making use of reference datasets. We also find that open science practices reward developers with increased recognition and help accelerate the field.

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Day-to-day discovery of preprint–publication links

Cited by 36 publications

References 33 publications

Linguistic Analysis of the bioRxiv Preprint Landscape

Linguistic Analysis of the bioRxiv Preprint Landscape

Transparency and reporting characteristics of COVID-19 randomized controlled trials

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

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