cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
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DOI：
10.1128/msystems.00010-15
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发表时间：
2016-01-01
期刊：
影响因子：
6.4
通讯作者：
Caporaso, J. Gregory
中科院分区：
文献类型：
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作者：
Chase, John H.;Bolyen, Evan;Caporaso, J. Gregory
由于实验成本下降，高通量比较“组学”研究中的样本数量正在迅速增加。随着这些项目规模的不断扩大，为了保持样本数据和元数据的可管理性并确保科学结果的完整性，我们必须转向设计更好的样本标识符。理想情况下，样本标识符在项目、项目团队和机构之间应该是全球唯一的；简短（以方便手动转录）；可纠正常见类型的转录错误；不透明，意味着它们不包含有关样本的信息；并与现有标准兼容。我们推出了 cual-id，一个轻量级的命令行工具，它可以创建或铸造满足这些标准的样本标识符，而无需依赖集中式基础设施。 cual-id 允许用户分配通用唯一标识符 (UUID)，这些标识符对于其样本来说是全局唯一的。然而，UUID 太长，无法方便地写在采样材料（例如拭子或微量离心管）上，因此 cual-id 还生成人类友好的 4 到 12 个字符标识符，这些标识符映射到其 UUID，并且在项目中是唯一的。按照惯例，我们使用“cual-id”来指代软件，“CualID”来指代简短的、人类友好的标识符，“UUID”来指代全局唯一标识符。人类在手动写入或输入标识符时使用 CualID，而计算机则使用较长的 UUID 来明确引用样本。最后，cual-id 可选择生成包含 Code 128 条形码和 CualID 的可打印标签贴纸，用于标记样本采集和处理材料。 重要性 采用全球唯一、可校正且易于手写或手动输入计算机的标识符将是比较组学研究中样本跟踪向前迈出的重要一步。随着各领域过渡到更集中的样本管理，例如，跨机构内的实验室、跨共同计划资助的项目，或在旨在促进元和/或集成分析的系统中，使用 cual-id 生成的样本标识符将不需要更改；因此，将避免昂贵且容易出错的数据和元数据标识符更新。此外，使用 cual-id 将确保样本标识符中的转录错误不需要丢弃原本有用的样本，而这些样本的获取成本可能很高。最后，cual-id 易于安装和使用，并且免费供所有使用。不需要集中式基础设施来确保全球唯一性，因此任何实验室都可以在其现有基础设施中开始使用这些标识符。
The number of samples in high-throughput comparative "omics" studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use "cual-id" to refer to the software, "CualID" to refer to the short, human-friendly identifiers, and "UUID" to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials.IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta-and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.