Building a global metagenomics portal ('MGportal') to handle next-generation sequencing data and associated metadata

建立全球宏基因组学门户（“MGportal”）来处理下一代测序数据和相关元数据

• 批准号: BB/I025840/1
• 负责人: Susanna Sansone
• 金额: $ 71万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI025840%2F1
• 关键词: Building; global; metagenomics; portal; MGportal

While genomes represent the full genetic (DNA) complement of a single organism, metagenomes represent the DNA of an entire community of organisms. These organisms might be free-living in the environment, or be found on the skin or in the gut of a human being or other species. Microbial organisms play a major role in our everyday health and well-being, which is not surprising when you consider that the number of microbial cells in or on an average human body actually exceeds the number of human cells! Microbes play a similarly important role in the environment; different types of organisms live under different conditions (including extreme habitats, such as the run-off from acid mines or the depths of the oceans). Understanding how these organisms have adapted to their various living conditions will lead to a better understanding of how changes in the environment will have impact on biodiversity in the future. It may also lead to discovery of entirely new species or novel proteins which could have utility as antibiotics or other drugs. Combined with other types of 'omic data, metagenomes hold the promise of unparalleled insights into fundamental questions across a range of fields including evolution, ecology, environment biology, health and medicine. To fully exploit the promise of these data we need both scientific innovation and community agreement on how to provide appropriate stewardship of these resources for the benefit of all. Significant numbers of metagenomics projects have been awarded grants by international funding bodies. Whilst all of these projects have specific, scientifically-interesting aims, they mostly exist in isolation, with little or no cross-referencing to other metagenomic or genomic datasets. Our intention is to leverage existing infrastructure to deliver a world-class metagenomics resource with unique utility for UK-based metagenomics researchers. This resource, MGportal, will utilise user-friendly interfaces, state-of-the-art algorithms and the EBI's unique position as a hub of biological information to measurably enhance the value of these researchers' data. It will be built in close collaboration with the Genomic Standards Consortium (GSC). MGportal will consist of software tools to enable metagenomics researchers to upload their data to the raw nucleotide sequence archives, data analysis pipelines to predict what potential genes are present in the data and what their function is, plus a web interface which will display these data and results in a way that is easy to browse and query. We will hold training courses and a workshop to gain input from the scientific community about the portal. It is hoped that MGportal will eventually allow researchers to understand the results of their metagenomics experiments, as well as seeing how those results compare with the outcomes of other studies.

基因组代表单个有机体的完整遗传(DNA)补充，而元基因组代表整个有机体群落的DNA。这些生物可能在环境中自由生活，也可能在人类或其他物种的皮肤或肠道中发现。微生物在我们日常的健康和幸福中扮演着重要的角色，当你考虑到人体内或平均水平上的微生物细胞数量实际上超过了人类细胞的数量时，这就不足为奇了！微生物在环境中发挥着同样重要的作用；不同类型的生物生活在不同的条件下(包括极端栖息地，如酸矿的径流或海洋深处)。了解这些生物是如何适应它们不同的生存条件的，将有助于更好地理解环境变化将如何影响未来的生物多样性。它还可能导致发现全新的物种或新的蛋白质，这些蛋白质可能会用作抗生素或其他药物。与其他类型的基因组数据相结合，元基因组有望对包括进化、生态、环境生物学、健康和医学在内的一系列领域的基本问题提供无与伦比的见解。为了充分利用这些数据的前景，我们既需要科学创新，也需要就如何适当管理这些资源以造福所有人达成一致意见。大量的元基因组学项目已获得国际资助机构的赠款。虽然所有这些项目都有具体的、科学上有趣的目标，但它们大多是孤立存在的，很少或根本没有与其他元基因组或基因组数据集的交叉引用。我们的目的是利用现有的基础设施，为英国的元基因组研究人员提供具有独特实用价值的世界级元基因组学资源。这个名为MGport的资源将利用用户友好的界面、最先进的算法以及EBI作为生物信息中心的独特地位，显著提高这些研究人员数据的价值。它将与基因组标准联盟(GSC)密切合作建造。MGport将包括软件工具，使元基因组学研究人员能够将他们的数据上传到原始核苷酸序列档案，数据分析管道以预测数据中存在哪些潜在基因及其功能是什么，以及一个网络界面，它将以易于浏览和查询的方式显示这些数据和结果。我们将举办培训班和讲习班，以听取科学界对门户网站的意见。希望MGport最终将允许研究人员了解他们的元基因组学实验的结果，并查看这些结果与其他研究的结果如何比较。

项目成果

Measures for interoperability of phenotypic data: minimum information requirements and formatting.

• DOI: 10.1186/s13007-016-0144-4
• 发表时间: 2016
• 期刊: Plant methods
• 影响因子: 5.1
• 作者: Ćwiek-Kupczyńska H;Altmann T;Arend D;Arnaud E;Chen D;Cornut G;Fiorani F;Frohmberg W;Junker A;Klukas C;Lange M;Mazurek C;Nafissi A;Neveu P;van Oeveren J;Pommier C;Poorter H;Rocca-Serra P;Sansone SA;Scholz U;van Schriek M;Seren Ü;Usadel B;Weise S;Kersey P;Krajewski P
• 通讯作者: Krajewski P