Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA.
Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, TN, USA.
Methods Mol Biol. 2025;2852:199-209. doi: 10.1007/978-1-0716-4100-2_14.
This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens collected for different purposes. There are five protocols included in this chapter: (1) quality control (QC) assessment for the genome sequence data, (2) validation for the contextual data, (3) data submission for the standard pathogen package or Pathogen Data Object Model (DOM) to the public repository, (4) viewing and querying data at NCBI, and (5) data curation for maintaining relevance of public data. The data are available through one of the International Nucleotide Sequence Database Consortium (INSDC) members, with the National Center for Biotechnology Information (NCBI) being the primary focus of this document. NCBI Pathogen Detection is a custom dashboard at NCBI that provides easy access to pathogen data plus results for a standard suite of automated cluster and genotyping analyses important for informing public health and regulatory decision-making.
本文件概述了组装和提交用于为肠道病原体全球基因组监测做出贡献的标准数据包所需的步骤。尽管针对 GenomeTrakr 实验室和合作者，但这些方案广泛适用于出于不同目的收集的肠道病原体。本章包含五个方案：（1）基因组序列数据的质量控制（QC）评估，（2）上下文数据的验证，（3）标准病原体包或病原体数据对象模型（DOM）的数据提交到公共存储库，（4）在 NCBI 查看和查询数据，以及（5）维护公共数据相关性的数据管理。这些数据可通过国际核苷酸序列数据库联盟（INSDC）成员之一获得，其中美国国家生物技术信息中心（NCBI）是本文档的主要关注点。NCBI 病原体检测是 NCBI 上的一个自定义仪表板，可轻松访问病原体数据以及用于一组标准自动聚类和基因分型分析的结果，这些分析对于为公共卫生和监管决策提供信息非常重要。
