Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands.
BMC Bioinformatics. 2009 Aug 14;10:251. doi: 10.1186/1471-2105-10-251.
A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions.
Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology.
A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.
越来越多的生物数据都被打上了与多核苷酸和蛋白质相关的唯一标识符 (UID)，以确保高效的计算机中介数据存储、维护和处理。这些标识符对大多数人来说没有信息意义，通常在各种表示中被生物上有意义的名称所取代，以促进基于序列的知识的利用和传播。这种替换通常是手动完成的，可能是一项繁琐的工作，容易出错和遗漏。
在这里，我们介绍了 SNAD（基于序列名称注释的设计器），它可以将序列 UID（与多序列比对或系统发育树相关联，或作为纯文本列表提供）自动转换为具有生物意义的名称和缩写。这种转换是由预编译或用户定义的模板指导的，这些模板利用了外部数据库中同源条目提供的丰富注释。通过示例，我们展示了如何将此工具用于实际目的，特别是在病毒学中生成名称。
已经开发并提供了一种用于基于可控注释的序列 UID 到具有生物意义的名称和缩写的转换的工具，促进了序列注释的质量与研究人员之间的通信和知识传播效率之间的联系。
