Towards a new genomic standard for describing our complete genome collection

人们越来越认识到，制定一个新的标准，以获取描述完整基因组的更丰富的信息，整个科学界将从中受益。这将确保那些产生基因组的人对现有信息（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增长的速率生成数据。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基于每个“物种”的。然而，越来越多的“基因组”正在被测序，不仅代表了种植和未种植的生物体的个体，而且还代表了来自环境样本的种群和群落。显然，为了充分解释这类数据，仅仅记录最基本的信息是不够的。现在是采取行动的时候了，因为数据的洪流只会增加，特别是随着超高通量测序能力的出现。由社区推动的标准如果在国际工作组的主持下制定，最有可能取得成功。基因组标准联盟（GSC）最近成立（2005年9月），以解决这个问题。GSC的参与者包括生物学家、计算机科学家、建立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）实施新的基因组学标准（2）捕获和交换元数据的方法（3）在更广泛的基因组学社区中协调元数据收集和分析工作。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，我们正在申请资助一名程序员，以建立GSC提出的基因组目录，并使用符合“基因组序列最小信息”规范的基因组描述对其进行填充。我们还旨在通过定义用于描述基因组的丰富词汇（以现有和新本体的形式）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GenomeMine数据库，以作为一个社区档案库，其中包含描述一个或多个基因组的策划和计算元数据的贡献数据集。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学，特别是比较生态基因组学研究。

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.