BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications.
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ABSTRACT:
SUBMITTER: Yang J
PROVIDER: S-EPMC9233186 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
Publications
BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications.
Yang Jingcheng J Liu Yaqing Y Shang Jun J Huang Yechao Y Yu Ying Y Li Zhihui Z Shi Leming L Ran Zihan Z
Computational and structural biotechnology journal 20220608
Interactive visualization is an effective way to promote the reproducibility of results presented in biomedical publications and to facilitate additional exploration of the reported data. However, there is a lack of convenient tools that balance reproducibility with ease of use. To address this problem, we develop BioVisReport, a lightweight solution for the rapid generation of an interactive website based on a user-defined Markdown file, which acts as a text markup language without requiring us ...[more]
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Project description:ClinicalTrials.gov requires reporting of result summaries for many drug and device trials.To evaluate the consistency of reporting of trials that are registered in the ClinicalTrials.gov results database and published in the literature.ClinicalTrials.gov results database and matched publications identified through ClinicalTrials.gov and a manual search of 2 electronic databases.10% random sample of phase 3 or 4 trials with results in the ClinicalTrials.gov results database, completed before 1 January 2009, with 2 or more groups.One reviewer extracted data about trial design and results from the results database and matching publications. A subsample was independently verified.Of 110 trials with results, most were industry-sponsored, parallel-design drug studies. The most common inconsistency was the number of secondary outcome measures reported (80%). Sixteen trials (15%) reported the primary outcome description inconsistently, and 22 (20%) reported the primary outcome value inconsistently. Thirty-eight trials inconsistently reported the number of individuals with a serious adverse event (SAE); of these, 33 (87%) reported more SAEs in ClinicalTrials.gov. Among the 84 trials that reported SAEs in ClinicalTrials.gov, 11 publications did not mention SAEs, 5 reported them as zero or not occurring, and 21 reported a different number of SAEs. Among 29 trials that reported deaths in ClinicalTrials.gov, 28% differed from the matched publication.Small sample that included earliest results posted to the database.Reporting discrepancies between the ClinicalTrials.gov results database and matching publications are common. Which source contains the more accurate account of results is unclear, although ClinicalTrials.gov may provide a more comprehensive description of adverse events than the publication.Agency for Healthcare Research and Quality.
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