Towards a new genomic standard for describing our complete genome collection

制定一个新的基因组标准来描述我们完整的基因组集合

• 批准号: NE/D01252X/1
• 负责人: Dawn Field
• 金额: $ 29.35万
• 依托单位: NERC CEH (Up to 30.11.2019)
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FD01252X%2F1
• 关键词: Towards; new; genomic; standard; describing

There is increasing recognition that the scientific community at large would benefit from the development of a new standard to capture a richer set of information describing complete genomes. This would ensure that those generating the genomes contributed to the quality and quantity of information (metadata) available. Rapidly-evolving high throughput genomic sequencing technologies are generating data at an exponentially-increasing rate. This poses new opportunities, but also new challenges. The traditional approach to genomic sequencing has been on a per 'species' basis. However, an increasing number of 'genomes' are now being sequenced that represent not only individuals of cultivated and uncultivated organisms, but also populations and communities from environmental samples. Clearly, for adequate interpretation of this type of data simply recording only the most basic information is no longer sufficient. The time to act is now, as this deluge of data is only set to increase, especially with the emergence of ultra-high throughput sequencing capabilities. Community-driven standards have the best chance of success if developed within the auspices of international working groups. The Genomic Standards Consortium (GSC) has recently been formed (Sept, 2005) to tackle this issue. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of this GSC is to work with the wider community towards: (1) the implementation of a new genomic standard (2) methods of capturing and exchanging metadata (3) harmonization of metadata collection and analysis efforts across the wider genomics community Consensus-building activites are most powerful when combined with the ability to implement the resulting recommendations of a group. In this proposal we are seeking funding to begin implementation activities on behalf of the GSC community. Specifically, we are requesting funding for a programmer to build the GSC's proposed Genome Catalogue and populate it with genome descriptions compliant with the 'Minimal Information about a Genome Sequence' specification. We also aim to simplify metadata capture and exchange by working towards defining a rich vocabulary for the description of genomes (in the form of contributions to existing and novel ontologies). Finally, we will design and implement a Genomic Metadata Exchange Format (GnoME) and use it to improve our existing GenomeMine database to serve as a community archive of contributed datasets of curated and calculated metadata describing one or more genomes. Combined these efforts will pave the way towards the creation of significant new research tools and will facilitate future comparative genomic, and in particular, comparative eco-genomic, studies.

人们越来越认识到，整个科学界将受益于新标准的开发，以捕获更丰富的描述完整基因组的信息。这将确保那些生成基因组的人对可用信息（元数据）的质量和数量做出贡献。快速发展的高通量基因组测序技术正在以指数级增长的速度生成数据。这带来了新的机遇，也带来了新的挑战。传统的基因组测序方法是以“物种”为基础的。然而，现在正在对越来越多的“基因组”进行测序，这些基因组不仅代表栽培和未栽培生物的个体，还代表环境样本中的种群和群落。显然，为了充分解释此类数据，仅记录最基本的信息已不再足够。现在是采取行动的时候了，因为这种海量数据只会增加，特别是随着超高通量测序能力的出现。如果在国际工作组的支持下制定，社区驱动的标准就有最大的成功机会。基因组标准联盟 (GSC) 最近成立（2005 年 9 月）来解决这个问题。 GSC 的参与者包括生物学家、计算机科学家、构建基因组数据库和进行大规模比较基因组分析的人员，以及具有建立社区标准经验的人员。该 GSC 的使命是与更广泛的社区合作，以实现：(1) 实施新的基因组标准 (2) 捕获和交换元数据的方法 (3) 协调更广泛的基因组学社区的元数据收集和分析工作当建设活动与实施小组提出的建议的能力相结合时，其威力最为强大。在此提案中，我们正在寻求资金来代表 GSC 社区开始实施活动。具体来说，我们正在请求资助一名程序员来构建 GSC 提议的基因组目录，并在其中填充符合“有关基因组序列的最少信息”规范的基因组描述。我们还旨在通过努力定义用于描述基因组的丰富词汇（以对现有和新颖本体的贡献的形式）来简化元数据捕获和交换。最后，我们将设计和实现一种基因组元数据交换格式（GnoME），并用它来改进我们现有的 GenomeMine 数据库，作为描述一个或多个基因组的策划和计算元数据贡献数据集的社区档案。这些努力的结合将为创建重要的新研究工具铺平道路，并将促进未来的比较基因组研究，特别是比较生态基因组研究。

项目成果

Genomics. Genome project standards in a new era of sequencing.

基因组学。

• DOI: http://dx.10.1126/science.1180614
• 发表时间: 2009
• 期刊: Science (New York, N.Y.)
• 作者: Chain PS