Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.

One Health Outlook Pub Date : 2020-01-01 Epub Date: 2020-10-19 DOI:10.1186/s42522-020-00026-3
Ruth E Timme, William J Wolfgang, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, Marc Allard, Errol Strain
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引用次数: 38

Abstract

The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings. Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.

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优化开放数据以支持一种健康:确保细菌病原体基因组数据互操作性的最佳做法。
“同一个健康”的整体方法将人类、动物、植物和环境健康视为一个整体,而不是分散的部分,不仅需要跨学科合作,还需要标准化的数据交流和存档方法,使参与者能够轻松地分享他们学到的东西,并允许其他人在他们的发现的基础上进一步发展。NCBI和GenomeTrakr项目正在进行的工作表明,开放数据平台可以帮助满足联邦和州监管机构、公共卫生实验室、农业部门和大学的需求。在这里,我们描述了微生物病原体监测如何通过拥有开放获取数据库以及供贡献者遵循的最佳实践来转变。首先,我们描述了基于NCBI平台的开放式病原体监测框架。我们涵盖了WGS质量的当前社区标准,提供了评估您自己的序列质量的SOP,并为所有提交者推荐了QC阈值。然后,我们提供NCBI数据提交的概述以及一步一步的详细信息。最后,我们提供管理指导和SOP,以使您的公共数据在数据库中保持最新状态。这些最佳实践可作为其他开放数据项目的模型,从而推进可查找、可访问、可互操作和可重用(FAIR)数据的“同一个健康”目标。
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