'Omics Data Sharing: the Investigation / Study / Assay (ISA) Infrastructure

在生物领域，迫切需要改进数据共享和统一访问来自广泛来源的数据。组学技术（如基因组学、宏基因组学、转录组学、蛋白质组学和代谢组学）的使用现在已经广泛普及，这些技术产生数据的速度正在彻底改变科学领域。大量数据的涌入既带来了前所未有的科学机遇，也带来了一系列必须应对的挑战，如果要充分利用这些数据以及它们所代表的公共科学投资，就必须应对这些挑战。虽然要在社区层面实现大规模的多基因组数据共享还有许多障碍要克服，但由于一系列基层标准化项目的活动，包括“生物和生物医学研究最小信息”（MIBBI）项目（http://mibbi.org/）和开放生物本体（OBO） Foundry (http://obofoundry.org/)，解决方案现在是可能的。我们建议更广泛地使用基于“调查/研究/分析”（ISA）概念的“组学数据共享软件”（http://isatab.sf.net）。ISA概念允许描述任何“调查”，包括使用一种或多种“分析”（技术）研究生物样品的一项或多项“研究”。ISA概念得到了MIBBI社区的支持，并已被用于构建通用文件格式ISA- tab。ISA-Tab文件格式利用了生物学家对基于电子表格的输入和信息操作的熟悉和信任。使用预定义的扩展，以ISA-Tab格式捕获的描述性实验信息（元数据）符合mibbi注册的标准（转录组学，MIAME；蛋白质组学，MIAPE；基因组学，MIGS/MIMS）。ISA-Tab可以配置为包含其他字段，从而允许用户遵守新出现的标准。这种通用文件格式的可用性使得能够创建一组工具和一个数据库来保存在其中捕获的数据集。当前的试验阶段ISA Infrastructure为在社区级别管理多组元数据提供了一个完整的解决方案。ISA基础设施设计的一个核心方面是它对OBO Foundry本体的整体使用，以描述调查，使数据描述明确且计算可访问。在这个拟议的项目中，我们将扩展目前的ISA基础设施实施，并与确定的研究团体及其生物信息服务提供商合作，在英国和全球建立“ISA网络”，覆盖广泛的数据类型。这些门户网站将作为“一站式商店”，在社区一级汇总和显示相关数据集。捕获的元数据将支持跨生物、技术和数据类型的搜索和数据发现。共享使用最低限度的信息标准、本体和单一文件格式将支持社区之间的数据交换和公共存储库之间的数据传输。在国际层面，我们将与MIBBI和OBO代工社区密切合作，进一步统一MIBBI清单和OBO代工本体，以支持多组学研究的描述。ISA基础设施的发展必须以协商一致为导向，因此最好在国际工作组的主持下发展。因此，我们将正式确定ISA网络之间的合作，并在数据标准化社区内开展工作，通过启动生物共享联盟（http://biosharing.org）来增加目前分开的小组之间的联系。

There is a pressing and recognized need in the biological domain for improved data sharing and unified access to data from a wide range of sources. The use of 'omics technologies (such as genomics, metagenomics, transcriptomics, proteomics and metabolomics) is now wide-spread and the rate at which these technologies generate data is revolutionizing the scientific landscape. This massive influx of data brings both unprecedented scientific opportunities and a range of challenges that must be met if these data, and the public investment in science that they represent, are to be fully exploited. While there are many obstacles to overcome if we are to realize large-scale multi-omic data sharing at the community level, solutions are now possible due to the activities of a range of grass-roots standardisation projects including the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) project (http://mibbi.org/) and the Open Biological Ontologies (OBO) Foundry (http://obofoundry.org/). We propose to make more widely available our 'omics data sharing software based on the 'Investigation / Study / Assay' (ISA) concept (http://isatab.sf.net). The ISA concept allows the description of any 'Investigation' comprising one or more 'Studies' in which biological samples have been studied using one or more 'Assays' (technologies). The ISA concept is supported by the MIBBI community and has been used to structure a universal file format, ISA-Tab. The ISA-Tab file format leverages biologists' familiarity with, and trust of spreadsheet-based input and manipulation of information. Descriptive experimental information (metadata) captured in ISA-Tab format is made compliant with MIBBI-registered standards (for transcriptomics, MIAME; for proteomics, MIAPE; and for genomics, MIGS/MIMS) using pre-defined extensions. ISA-Tab can be configured to hold additional fields allowing users to comply with emerging standards as well. The availability of this universal file format has enabled the creation of a set of tools and a database to hold data sets captured in it. The current pilot-stage ISA Infrastructure provides a complete solution for managing multi-omic metadata at the community level. A core aspect of the design of the ISA Infrastructure is its integral use of OBO Foundry ontologies to describe investigations, rendering data descriptions unambiguous and computationally accessible. In the course of this proposed project, we will extend the current ISA Infrastructure implementation and work with identified research communities and their bioinformatic service providers to set up 'ISA Networks' in the UK and around the globe, covering a wide range of data types. These portals will serve as 'one-stop shops' for the aggregation and display of relevant datasets at the community level. The metadata captured will support searching and data discovery across organisms, technologies and data types. The shared use of minimum information standards, ontologies and a single file format will support exchange of data between communities and the transfer of data to and from public repositories. At the international level, we will work closely with the MIBBI and OBO Foundry communities to further unify MIBBI checklists and OBO Foundry ontologies to support descriptions of multi-omic investigations. The development of the ISA Infrastructure must be consensus-driven and is therefore best developed under the auspices of an international working group. We will therefore formalise the collaboration between ISA Networks and work within the data standardisation community to increase linkages between currently separated groups by launching the BioSharing Consortium (http://biosharing.org).