Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation
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DOI：
10.1093/nar/gkx1031
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Pruitt, Kim D.
中科院分区：
文献类型：
--
作者：
Pujar, Shashikant;O'Leary, Nuala A.;Pruitt, Kim D.
共有编码序列（CCDS）项目提供了在NCBI和EMBL-EBI的Ensembl组独立产生的基因组注释中，在人类和小鼠参考基因组组装上相同注释的蛋白质编码区的数据集。该数据集是包括NCBI，Ensembl，HUGO基因命名委员会，小鼠基因组信息学和加州大学，圣克鲁斯在内的国际合作的产物。使用自动化管道生成并通过多次质量保证检查的相同注释编码区域将被分配一个稳定和可跟踪的标识符（CCDS ID）。此外，CCDS合作的专家策展人进行的协调手动审查有助于保持数据集的完整性和高质量。CCDS数据可通过交互式网页（https：//www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi）和FTP网站（ftp：//ftp.ncbi.nlm.nih.gov/pub/CCDS/）获得。在本文中，我们概述了CCDS数据集的持续工作、增长和稳定性，并提供了有关新合作成员和添加到CCDS用户界面的新功能的更新。我们还提出了专家策展方案，具体的例子强调了准确的参考基因组组装的重要性和研究界的投入所发挥的关键作用。
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.