BBR GenomeHubs - agile genome databasing for neglected organisms of agricultural, development and biodiversity importance

构建人类基因组的初稿花费了大约25亿英镑。新的测序技术意味着对人类进行重测序的成本降低了100多万倍。这种成本的降低也改变了基因组学在许多其他生物学问题上的应用。基因组学现在普遍应用于多种目标，从作物和牲畜改良，到病原体和寄生虫监测，再到生物多样性评估。许多研究团体现在能够为其目标物种生成参考基因组，比较相关物种间的基因组，并对同一物种的许多个体进行测序，以研究基因组序列之间的差异如何影响生物学。这些好处带来了管理大量数据、分析数据以回答问题、以及将数据和结果提供给他人的挑战。在“记录数据库”（国际支持的收集、整理和存储后代的系统）中存放原始序列数据是标准的。然而，许多发现都是基于深入分析的数据——原始序列被“组装”来预测整个基因组序列，基因在这个基因组序列中被预测，它们的功能被一系列注释工具推断出来。强烈鼓励在数据库记录中捕获这些分析，但在技术上是困难的。对于一些物种，研究人员已经开发了专门的基因组探索数据库，不仅收集和整理序列，还收集注释和功能数据，并以一种促进整合的方式呈现。这些数据库需要大量的专门知识和努力来建立、维护和跟上最新的科学发展。因此，对于大多数物种，特别是发展中国家感兴趣的物种，不存在专门的数据库，社区缺乏资源来填补这一空白。在之前的BBR项目中，我们开发了一种基因组数据库方法，名为GenomeHubs，它消除了为任何物种群体创建和维护专用基因组资源的障碍。我们通过极大地简化将数据导入到最全面的基因组数据库平台Ensembl的过程，并托管一个实例来实现这一目标。使用精心设计的Ensembl系统，我们开发了工具，可以标准化来自不同来源的数据，运行自动分析，将分析结果导入数据库，并通过web界面可视化基因组和注释。在这个提案中，我们将进一步开发GenomeHubs，使研究人员能够直接运行所有步骤，对任何基因组或基因组集进行组装，注释和运行标准分析，并与更广泛的社区分享这些结果。我们将增加新的分析和可视化，我们将通过协作和培训来帮助用户设置和使用GenomeHubs。这一申请与BBSRC BBR全球挑战研究资助项目的申请同时进行，该项目将与中低收入国家（LMIC）的科学家合作，开发和利用基因组中心满足他们的需求。基因组学正越来越多地应用于发展中国家的问题，特别是农作物和当地农场动物的改良、了解和防治传染病以及生物多样性保护。该项目将与GCRF GenomeHubs外展项目密切合作，将技术带给低收入和中等收入国家的研究人员，并支持他们使用GenomeHubs。我们将连接研究团体，促进数据共享，加强资源的汇集和理解，以解决共同的问题。我们将与中低收入国家的重要科学家开展合作，他们将担任GenomeHubs的大使，并与中低收入国家的研究人员密切合作，为GenomeHubs开发新的代码、新的可视化和新的分析工具，以满足他们的需求。

Building the first draft of the human genome cost around £2.5 billion. New sequencing technologies mean the cost of resequencing a human has reduced over a million-fold. This reduction in cost also transforms genomics approaches to many other biological questions. Genomics is now commonly applied to diverse goals from crop and livestock improvement, through pathogen and parasite surveillance, to biodiversity assessment. Many research communities are now able to generate reference genomes for their target species, compare genomes across suites of related species and sequence many individuals of the same species to investigate how variation between genome sequences affects biology.With these benefits come the challenges of managing a deluge of data, of analysing the data to answer questions, and of making the data and results available to others. For raw sequence data deposition in "databases of record" (internationally-supported systems that collect, collate and store for posterity) is standard. However, many discoveries are based on intensively analysed data - raw sequence is "assembled" to predict the whole genome sequence, genes are predicted in this genome sequence, and their functions are inferred by a range of annotation tools. Capturing these analyses in databases of record is strongly encouraged, but is technically difficult. For a few species, researchers have developed dedicated genome exploration databases that collect and collate not only sequence but also annotation and functional data, and present it in a way that facilitates integration. These databases require considerable expertise and effort to set up, maintain and keep current with the latest scientific developments. Thus, for the majority of species, and especially species of interest to the developing world, dedicated databases do not exist and communities lack the resources to plug this gap.During a previous BBR project, we developed an approach to genome databasing, named GenomeHubs, that removes the barriers to creating and maintaining a dedicated genomics resource for any species group. We do this by greatly simplifying the process of importing data into, and hosting an instance of, the most comprehensive genome database platform, Ensembl. Using the carefully-engineered Ensembl system, we have developed tools that standardise data from diverse sources, run automated analyses, import analysis results back into the database and visualise the genome and annotations through a web interface. In this proposal we will develop GenomeHubs further to make it straightforward for researchers to run all the steps to assemble, annotate and run standard analyses on any genome or set of genomes and share these results with the wider community. We will add new analyses and visualisations and we will help users through collaboration and training in the setup and use of GenomeHubs.This application is being made in tandem with one to the BBSRC BBR Global Challenges Research Funding call, which will work with Lower and Middle Income Country (LMIC) scientists to develop and exploit GenomeHubs for their needs. Genomics is being increasingly applied to problems of the developing world, in particular improvement of crop plants and local farm animals, understanding and combating infectious disease, and biodiversity conservation. This project will work very closely with the GCRF GenomeHubs outreach project, bringing the technology to LMIC researchers and supporting their use of GenomeHubs. We will link research communities, promote data sharing and enhance the pooling of resources and understanding to solve shared problems. We will develop collaborations with key scientists in LMICs who will act as Ambassadors for GenomeHubs, and collaborate closely with LMIC researchers to develop new code, new visualisations and new analytic tools for GenomeHubs to meet their requirements.