Genestorian: a web application to document and trace genetic modifications in model organism and cell line collections.

Genestorian：一个网络应用程序，用于记录和追踪模型生物和细胞系集合中的遗传修饰。

• 批准号: EP/Y024591/1
• 负责人: Jurg Bahler
• 金额: $ 25.55万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FY024591%2F1
• 关键词: Genestorian; web; application; document; trace

Currently, no open standards exist to unambiguously describe cloning strategies, genotypes and allele inheritance. Consequently, laboratories often store their plasmids, cell lines and strains in spreadsheets or text-based systems, which are necessarily inconsistent and differ between collections. Therefore, for curators or even members of a laboratory, it can be time-consuming or impossible to know the sequence and provenance of a plasmid or allele. Since biological knowledge bases (UniProt, model organism databases, etc.) rely on links between gene variants and phenotypes to annotate functions to gene products, the current situation limits the reusability of biological resources and the broad impact of research.I propose to develop Genestorian, a web application to manage collections of oligonucleotides, plasmids, strains and cell lines where sequences can be traced through cloning steps up to their entry into the collection. Researchers will plan the generation of new resources from existing ones, with new sequences generated by in silico cloning. Consequently, data standardisation will occur at the planning stage, and will not be a burden at submission stages. It will be easy to query the collection, access the sequence, ancestry and progeny of resources, and export this information for the methods section of a paper or in a standard format. Standardisation will enable information exchange between laboratory collections, journals, knowledge bases and resource repositories. Therefore, Genestorian aligns with the European Union commitment to Open Science and will promote resource reusability and maximise the impact of genetic research, facilitating its reproducibility and interpretation by tracing results to specific DNA sequences.

目前，还没有公开的标准来明确地描述克隆策略、基因型和等位基因遗传。因此，实验室经常将其质粒、细胞系和菌株存储在电子表格或基于文本的系统中，这些数据必然不一致，并且在不同的集合之间存在差异。因此，对于管理员甚至实验室成员来说，知道质粒或等位基因的序列和来源可能是耗时的或不可能的。由于生物知识库（UniProt，模式生物数据库等）依赖于基因变异和表型之间的联系来注释基因产物的功能，目前的情况限制了生物资源的可重复使用性和研究的广泛影响。我建议开发一个网络应用程序Genestorian，用于管理寡核苷酸、质粒、菌株和细胞系的集合，在这些集合中，可以通过克隆步骤来跟踪序列，直到它们进入集合。研究人员将计划从现有资源中产生新的资源，通过计算机克隆产生新的序列。因此，数据标准化将在规划阶段进行，不会成为提交阶段的负担。它将很容易查询集合，访问资源的序列，祖先和后代，并将这些信息导出为论文的方法部分或标准格式。标准化将使实验室收藏、期刊、知识库和资源库之间能够进行信息交流。因此，Genestorian与欧盟对开放科学的承诺保持一致，并将促进资源的可重用性，最大限度地发挥遗传研究的影响，通过将结果追溯到特定的DNA序列来促进其可重复性和解释。