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

组学数据共享：调查/研究/分析 (ISA) 基础设施

• 批准号: BB/I000917/1
• 负责人: Dawn Field
• 金额: $ 22.08万
• 依托单位: NERC CEH (Up to 30.11.2019)
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI000917%2F1
• 关键词: Omics; Data; Sharing; Investigation; Study

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).

生物领域迫切需要改进数据共享和统一获取各种来源的数据。组学技术(如基因组学、元基因组学、转录组学、蛋白质组学和代谢组学)的使用现在很广泛，这些技术产生数据的速度正在彻底改变科学格局。这种海量的数据既带来了前所未有的科学机遇，也带来了一系列挑战，如果要充分利用这些数据及其所代表的公共科学投资，就必须应对一系列挑战。虽然如果我们要在社区一级实现大规模的多组数据共享，有许多障碍需要克服，但由于一系列基层标准化项目的活动，解决方案现在是可能的，这些项目包括“生物和生物医学调查的最低信息”项目(http://mibbi.org/))和开放生物本体(OBO)基金会(http://obofoundry.org/).我们建议更广泛地使用我们的基于调查/研究/分析(ISA)概念(http://isatab.sf.net).)的组学数据共享软件ISA概念允许描述由一项或多项“研究”组成的任何“调查”，其中生物样本已使用一项或多项“分析”(技术)进行了研究。ISA概念得到了MIBBI社区的支持，并已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信息输入和操作的熟悉和信任。使用预定义的扩展使以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(对于转录学，MIAME；对于蛋白质组学，MIAPE；对于基因组学，MIGS/MIMS)。ISA-Tab可以配置为容纳额外的字段，允许用户也符合新兴标准。这种通用文件格式的出现使得能够创建一套工具和一个数据库来保存在其中捕获的数据集。目前处于试运行阶段的ISA基础设施为在社区级别管理多库元数据提供了完整的解决方案。ISA基础设施设计的一个核心方面是它综合使用OBO Foundry本体来描述调查，使数据描述明确且可通过计算访问。在这个拟议的项目过程中，我们将扩展目前的ISA基础设施实施，并与已确定的研究社区及其生物信息服务提供商合作，在英国和全球建立覆盖广泛数据类型的“ISA网络”。这些门户网站将作为“一站式商店”，在社区一级汇总和展示相关数据集。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储存库之间的数据传输。在国际层面上，我们将与MIBBI和OBO Foundry社区密切合作，进一步统一MIBBI核对表和OBO Foundry本体论，以支持对多组学研究的描述。ISA基础设施的发展必须以协商一致为导向，因此最好是在一个国际工作组的主持下制定。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，通过发起生物共享联盟(http://biosharing.org).)来加强目前分离的团体之间的联系

项目成果

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

• DOI: 10.1093/bioinformatics/bts718
• 发表时间: 2013-02-15
• 期刊: Bioinformatics (Oxford, England)
• 作者: Maguire E;González-Beltrán A;Whetzel PL;Sansone SA;Rocca-Serra P
• 通讯作者: Rocca-Serra P

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.

• DOI: 10.1093/bioinformatics/btq415
• 发表时间: 2010-09-15
• 期刊: Bioinformatics (Oxford, England)
• 作者: Rocca-Serra P;Brandizi M;Maguire E;Sklyar N;Taylor C;Begley K;Field D;Harris S;Hide W;Hofmann O;Neumann S;Sterk P;Tong W;Sansone SA
• 通讯作者: Sansone SA

Toward interoperable bioscience data.

• DOI: 10.1038/ng.1054
• 发表时间: 2012-01-27
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Sansone, Susanna-Assunta;Rocca-Serra, Philippe;Field, Dawn;Maguire, Eamonn;Taylor, Chris;Hofmann, Oliver;Fang, Hong;Neumann, Steffen;Tong, Weida;Amaral-Zettler, Linda;Begley, Kimberly;Booth, Tim;Bougueleret, Lydie;Burns, Gully;Chapman, Brad;Clark, Tim;Coleman, Lee-Ann;Copeland, Jay;Das, Sudeshna;de Daruvar, Antoine;de Matos, Paula;Dix, Ian;Edmunds, Scott;Evelo, Chris T.;Forster, Mark J.;Gaudet, Pascale;Gilbert, Jack;Goble, Carole;Griffin, Julian L.;Jacob, Daniel;Kleinjans, Jos;Harland, Lee;Haug, Kenneth;Hermjakob, Henning;Sui, Shannan J. Ho;Laederach, Alain;Liang, Shaoguang;Marshall, Stephen;McGrath, Annette;Merrill, Emily;Reilly, Dorothy;Roux, Magali;Shamu, Caroline E.;Shang, Catherine A.;Steinbeck, Christoph;Trefethen, Anne;Williams-Jones, Bryn;Wolstencroft, Katherine;Xenarios, Ioannis;Hide, Winston
• 通讯作者: Hide, Winston

Visual Compression of Workflow Visualizations with Automated Detection of Macro Motifs

通过自动检测宏主题对工作流可视化进行视觉压缩

• DOI: 10.1109/tvcg.2013.225
• 发表时间: 2013
• 期刊: IEEE Transactions on Visualization and Computer Graphics
• 影响因子: 5.2
• 作者: Maguire E