EBI Metagenomics Portal - Towards a better understanding of community metabolism

元基因组学是一个迅速发展的领域，现代测序技术被应用于从土壤、海水或动物肠道等环境中分离出来的DNA。这使我们能够分析居住在环境中的微生物集合中的DNA，其中许多微生物由于其挑剔的性质，以前可能没有被测序，这使得在实验室培养它们变得困难。产生了大量的测序数据，这些数据通常只反映了总DNA的一小部分。然而，经过分析，这种DNA提供了在该环境中发现的分类多样性和功能潜力的线索。元基因组学是所谓的数据驱动生物学的典范。DNA测序的成本迅速下降，因此大多数研究小组都可以使用负担得起的机构测序设施。我们现在面临的风险是，每个研究小组都要生产自己的元基因组分析平台和存储库。为了帮助防止这种分散的情况，并帮助降低总体成本(包括计算和工作人员)，我们开发并实施了一个中央管道，以提供一个元基因组数据分析和归档平台。EBI元基因组学门户(EBI-MP)是英国在EMBL-欧洲生物信息学研究所(EMBL-EBI)合作开发的成果。该门户网站于2011年推出，日益成为元基因组分析领域的世界领先者。用户提交他们的高通量元基因组核苷酸序列数据，并以受控和一致的方式伴随描述他们的样本和实验的上下文数据。门户进行分析后，包括分类和功能注释在内的结果可与项目和样本说明一起可视化，并可下载以供进一步分析。为了跟上社区的需求，并帮助巩固英国在元基因组研究领域的领先地位，拟议的项目旨在进一步开发该门户网站。这将包括增加分析来源，以确保今后可以在新的和更新的工具和算法出现时重新进行分析，而不会覆盖现有的分析数据，因为这可能构成现有出版物的基础。进一步的改进包括扩展分类和功能分析，以更好地了解采样的微生物群落、其组成和生物功能。该门户还将被开发成允许对其数据进行更复杂的搜索，这样用户就可以根据那里发现的微生物或蛋白质功能的类型来发现样本或环境。我们还将增加执行统计严格的跨样本比较的能力，这将允许以具有科学意义的方式比较来自不同样本的分析结果，并为此类比较提供可视化工具。随着现代测序技术产生越来越多的数据，更好的数据压缩对于加快EBI-MP和资源内部的数据传输至关重要。为此，我们将实现EMBL-EBI开发的行业标准压缩数据结构。

Metagenomics is a rapidly expanding field, where modern sequencing technologies are applied to the DNA isolated from an environment, such as soil, seawater or animal gut. This allows us to analyse the DNA from the collection of microorganisms that inhabit the environment, many of which may not have previously been sequenced due to their fastidious nature, making it difficult to culture them in the laboratory. Substantial amounts of sequencing data are produced, which typically only reflect a small fraction of the total DNA. However, after analysis, this DNA provides clues to the taxonomic diversity and functional potential that is found in that environment. Metagenomics is an exemplar of what is referred to as data-driven biology. The cost of DNA sequencing has fallen rapidly, such that most research groups have access to affordable institutional sequencing facilities. We now run the risk of each research group producing its own metagenomics analysis platform and storage repository. To help prevent such a fragmented situation, and to help reduce overall costs (both computational and staff), we have developed and implemented a centralised pipeline to provide a metagenomics data analysis and archiving platform. The EBI Metagenomics Portal (EBI-MP) has been developed as a collaborative UK effort at the EMBL-European Bioinformatics Institute (EMBL-EBI). The portal was launched in 2011 and has increasingly become established as a world leader in metagenomic analysis. Users submit their high-throughput metagenomic nucleotide sequence data, accompanied by contextual data describing their samples and experiments in a controlled and consistent manner. Once analysed by the portal, results including taxonomic and functional annotations can be visualised alongside project and sample descriptions, and can be downloaded for further analysis. In order to keep up with community needs, and to help cement the UK's position as a leader in the field of metagenomics research, the proposed project aims to further develop the portal. This will include the addition of analysis provenance, to ensure that analyses can be re-run in the future as new and updated tools and algorithms become available, without overwriting existing analysed data, which may form the basis of an existing publication. Further enhancements include extending the taxonomic and functional analyses to achieve a better picture of the microbial communities sampled, their composition and biological functions. The portal will also be developed to allow more sophisticated searches of its data, so that users can discover samples or environments based on the kind of microbe or protein function found there. We will also add the ability to perform statistically rigorous cross-sample comparisons, that will allow analysis results from different samples to be compared in a scientifically meaningful way, and provide visualisation tools for such comparisons. With today's modern sequencing technologies producing ever more data, better data compression is essential to speed up data transfer both into EBI-MP and internally within the resource. To this end, we will implement industry-standard compression data structures that have developed at EMBL-EBI.