'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/H024921/1
• 负责人: Carole Goble
• 金额: $ 1.6万
• 依托单位: University of Manchester
• 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%2FH024921%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).

在生物域中，有一个紧迫而公认的需求，以改善来自广泛来源的数据共享和统一访问数据的访问。现在，使用“ OMICS技术（例如基因组学，宏基因组学，转录组学，蛋白质组学和代谢组学））现在已经广泛地扩展，并且这些技术产生数据的速度正在彻底改变科学景观。大量数据涌入既带来了前所未有的科学机会，也带来了一系列挑战，如果这些数据以及对他们所代表的科学的公共投资也应得到充分利用。 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://obobofoundry.org/）。我们建议根据“调查 /研究 /测定”（ISA）概念（http://isatab.sf.net）更广泛地提供“ OMIC数据共享软件”。 ISA概念允许描述任何一个或多个“研究”的“研究”，其中使用一种或多种“分析”（技术）研究了生物样品。 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文件格式利用生物学家对基于电子表格的输入和信息操纵的信任。以ISA-TAB格式捕获的描述性实验信息（元数据）符合MIBBI注册标准（用于转录组学，迈阿密；对于蛋白质组学，MIAPE；对于基因组学，MIGS/MIMS），使用预先定义的扩展。可以将ISA-TAB配置为保存其他字段，允许用户遵守新兴标准。此通用文件格式的可用性使创建了一组工具和数据库，以保存在其中捕获的数据集。当前的试点ISA基础架构为在社区层面管理多摩变元数据提供了完整的解决方案。 ISA基础架构设计的一个核心方面是其对Obo Foundry本体论来描述研究的整体用途，使数据描述明确且可访问数据描述。在该提议的项目过程中，我们将扩展当前的ISA基础架构实施，并与已确定的研究社区及其生物信息学服务提供商合作，以在英国和全球建立“ ISA Networks”，涵盖广泛的数据类型。这些门户将用作社区层面的相关数据集的“一站式商店”。捕获的元数据将支持跨生物体，技术和数据类型的搜索和数据发现。最低信息标准，本体和单个文件格式的共同使用将支持社区之间的数据交换以及数据传输到公共存储库。在国际层面，我们将与Mibbi和Obo Foundry社区紧密合作，以进一步统一MIBBI清单和OBO铸造本体，以支持对多运动调查的描述。 ISA基础设施的开发必须是由共识驱动的，因此最好在国际工作组的主持下开发。因此，我们将通过启动生物群联盟（http://biosharing.org）来形式化ISA网络与数据标准化社区内部工作，以增加当前分离组之间的联系。

项目成果

COPO - bridging the gap from data to publication in plant science

COPO - 弥合植物科学从数据到出版的差距

• DOI: 10.7490/f1000research.1111380.1
• 发表时间: 2016
• 期刊: F1000Research
• 作者: Anthony Etuk

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

• DOI: 10.1093/nar/gkt961
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Hunter S;Corbett M;Denise H;Fraser M;Gonzalez-Beltran A;Hunter C;Jones P;Leinonen R;McAnulla C;Maguire E;Maslen J;Mitchell A;Nuka G;Oisel A;Pesseat S;Radhakrishnan R;Rocca-Serra P;Scheremetjew M;Sterk P;Vaughan D;Cochrane G;Field D;Sansone SA
• 通讯作者: Sansone SA

FAIR, ethical, and coordinated data sharing for COVID-19 response: a scoping review and cross-sectional survey of COVID-19 data sharing platforms and registries.

• DOI: 10.1016/s2589-7500(23)00129-2
• 发表时间: 2023-10
• 期刊: LANCET DIGITAL HEALTH
• 影响因子: 30.8
• 作者: Maxwell, Lauren;Shreedhar, Priya;Dauga, Delphine;Mcquilton, Peter;Terry, Robert F.;Denisiuk, Alisa;Molnar-Gabor, Fruzsina;Saxena, Abha;Sansone, Susanna-Assunta
• 通讯作者: Sansone, Susanna-Assunta

linkedISA: semantic representation of ISA-Tab experimental metadata.

• DOI: 10.1186/1471-2105-15-s14-s4
• 发表时间: 2014
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: González-Beltrán A;Maguire E;Sansone SA;Rocca-Serra P
• 通讯作者: Rocca-Serra P