Towards a new genomic standard for describing our complete genome collection

越来越多的人认识到，整个科学界将受益于新标准的发展，以获取描述完整基因组的更丰富的信息集。这将确保那些产生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产生数据。这带来了新的机遇，但也带来了新的挑战。传统的基因组测序方法是以每个“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体的个体，而且还代表来自环境样本的种群和群落。显然，要充分解释这类数据，仅仅记录最基本的信息已经不够了。现在是采取行动的时候了，因为这种数据洪流只会增加，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主持下制定，社区驱动的标准最有可能成功。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、那些建立基因组数据库并进行大规模比较基因组分析的人，以及那些具有建立社区标准经验的人。GSC的使命是与更广泛的基因组社区合作：(1)实施新的基因组标准(2)捕获和交换元数据的方法(3)在更广泛的基因组社区协调元数据收集和分析工作，建立共识的活动与实施小组最终建议的能力相结合是最强大的。在本提案中，我们正在寻求资金，以代表GSC社区开始实施活动。具体来说，我们正在为一名程序员申请资金，以建立GSC提议的基因组目录，并根据“基因组序列的最小信息”规范填充基因组描述。我们还致力于通过为基因组描述定义丰富的词汇表（以对现有本体和新本体的贡献的形式）来简化元数据捕获和交换。最后，我们将设计和实现一个基因组元数据交换格式（GnoME），并使用它来改进我们现有的基因组数据库，作为一个社区档案，提供描述一个或多个基因组的精心策划和计算的元数据集。这些努力的结合将为创造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。

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.