A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers.
A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers.
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DOI：
10.1093/gigascience/giab034
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发表时间：
2021-05-13
期刊：
影响因子：
9.2
通讯作者：
Penev L
中科院分区：
文献类型：
--
作者：
Dimitrova M;Meyer R;Buttigieg PL;Georgiev T;Zhelezov G;Demirov S;Smith V;Penev L
数据论文已经成为公开数据发布、获取信用和为科学实验中生成的数据集建立优先级的有力工具。学术出版通过同行评审提高数据和元数据的质量，并通过提高数据集的可见性、可访问性和可重用性来增加其影响力。我们的目标是建立一种新的组学研究的文章结构和模板：组学数据文件。为了提高数据互操作性并进一步激励研究人员发表描述良好的数据集，我们创建了一个原型工作流程，用于将来自欧洲核苷酸档案的基因组学元数据直接导入数据论文手稿。通过定义鼓励描述组学数据集和方法的关键文章部分，设计了组学数据论文模板。元数据导入工作流，基于REpresentational状态转移服务和Xpath，原型提取信息从欧洲核苷酸档案，ArrayExpress和BioSamples数据库。将符合标准的元数据自动导入组学数据论文手稿的模板和工作流程提供了一种通过发布增强现有元数据的机制。组学数据论文结构和导入基因组学元数据的工作流程将有助于将基因组学和其他组学数据集置于聚光灯下。促进增强元数据描述，加强对基础数据集的手稿同行审查和数据审计，提高数据集的质量。我们希望学术出版的简化元数据重用鼓励作者以数据论文的形式创建增强的元数据描述，以提高元数据的质量及其可查找性和可访问性。
Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer review and increases the impact of datasets by enhancing their visibility, accessibility, and reusability. We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivize researchers to publish well-described datasets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript. An omics data paper template was designed by defining key article sections that encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress, and BioSamples databases. The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing. The omics data paper structure and workflow for import of genomics metadata will help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata reuse for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility.
影响因子：
9.2
作者：
Carpenter, Eric J.;Matasci, Naim;Wong, Gane Ka-Shu
通讯作者：
Wong, Gane Ka-Shu
影响因子：
14.9
作者：
Athar A;Füllgrabe A;George N;Iqbal H;Huerta L;Ali A;Snow C;Fonseca NA;Petryszak R;Papatheodorou I;Sarkans U;Brazma A
通讯作者：
Brazma A