Building a Next Generation Image Repository: Molecular Annotation and Cloud-based Data Processing and Analysis

构建下一代图像存储库：分子注释和基于云的数据处理和分析

• 批准号: BB/M018423/1
• 负责人: Jason Swedlow
• 金额: $ 227.85万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM018423%2F1
• 关键词: Building; Next; Generation; Image; Repository

Access to primary research data is vital for the advancement of the scientific enterprise. It facilitates the validation of existing observations and provides the raw materials to build on those observations. In the life sciences, there are numerous examples where members of a research community determined that a particular type of data would be useful and necessary to share. These include gene sequences, protein structural data, and gene and protein expression profiles. In these cases the community united to standardize the structure of the data and its associated metadata, and to create centralized repositories to facilitate deposition, promote discoverability, and ensure the longevity of the data. Imaging in the life sciences has undergone a revolution in recent years and is now used as a quantitative assay technology throughout the life and biomedical sciences. Imaging is used to understand the behavior of organisms, the formation of embryos, the structure and dynamics of cells, and the function and interactions of molecules that are the building blocks of life. Imaging datasets are complex, heterogeneous, and often extremely large, so they are rarely shared or published. Based on the recent development of several image data management technologies and the rapidly decreasing cost of large data storage facilities, we propose to create a resource to host, serve, and make available original scientific image data that underpins life sciences research. Our proposal is based on open source technologies with proven utility and performance that already run on-line resources serving several terabytes (TBs) of image data. We propose to place this resource at EMBL-EBI, which is the established home of molecular and structural life sciences data and interface the resource with ELIXIR, Europe's research infrastructure for life science informatics. In particular we will build links with established molecular and structural resources and work towards a seamless integration of these data, so that any scientist can easily browse, query and compute on genomic, structural and phenotypic data across several scales.

获得原始研究数据对于科学事业的发展至关重要。它有助于验证现有的观察结果，并为在这些观察结果的基础上进行工作提供了原始材料。在生命科学领域，有许多例子表明，研究界的成员确定某种特定类型的数据是有用的，有必要分享。这些包括基因序列、蛋白质结构数据以及基因和蛋白质表达谱。在这些情况下，社区联合起来标准化数据及其相关元数据的结构，并创建集中式存储库，以方便存储，促进可重复性，并确保数据的寿命。近年来，生命科学中的成像技术经历了一场革命，现在已被用作整个生命和生物医学科学的定量分析技术。成像用于了解生物体的行为，胚胎的形成，细胞的结构和动力学，以及作为生命基石的分子的功能和相互作用。成像数据集复杂、异构，而且通常非常大，因此很少共享或发布。基于几种图像数据管理技术的最新发展和大型数据存储设施的成本迅速下降，我们建议创建一个资源来托管，服务和提供支持生命科学研究的原始科学图像数据。我们的建议是基于开放源码技术，具有经过验证的实用程序和性能，已经运行在线资源，为几个TB的图像数据。我们建议将此资源放置在EMBL-EBI，这是分子和结构生命科学数据的既定家园，并与ELIXIR，欧洲的生命科学信息学研究基础设施的资源接口。特别是，我们将与已建立的分子和结构资源建立联系，并努力实现这些数据的无缝集成，以便任何科学家都可以轻松地浏览，查询和计算跨多个尺度的基因组，结构和表型数据。

项目成果

The cellular microscopy phenotype ontology.

• DOI: 10.1186/s13326-016-0074-0
• 发表时间: 2016
• 期刊: Journal of biomedical semantics
• 影响因子: 1.9
• 作者: Jupp S;Malone J;Burdett T;Heriche JK;Williams E;Ellenberg J;Parkinson H;Rustici G
• 通讯作者: Rustici G

Databases and Archiving for CryoEM.

• DOI: 10.1016/bs.mie.2016.04.015
• 发表时间: 2016
• 期刊: Methods in enzymology
• 作者: Patwardhan A;Lawson CL
• 通讯作者: Lawson CL

A call for public archives for biological image data.

• DOI: 10.1038/s41592-018-0195-8
• 发表时间: 2018-11
• 期刊: Nature methods
• 影响因子: 48
• 作者: Ellenberg J;Swedlow JR;Barlow M;Cook CE;Sarkans U;Patwardhan A;Brazma A;Birney E
• 通讯作者: Birney E

Metadata management for high content screening in OMERO.

元数据管理用于OMERO的高素质筛选。

• DOI: 10.1016/j.ymeth.2015.10.006
• 发表时间: 2016-03-01
• 期刊: Methods (San Diego, Calif.)
• 作者: Li S;Besson S;Blackburn C;Carroll M;Ferguson RK;Flynn H;Gillen K;Leigh R;Lindner D;Linkert M;Moore WJ;Ramalingam B;Rozbicki E;Rustici G;Tarkowska A;Walczysko P;Williams E;Allan C;Burel JM;Moore J;Swedlow JR
• 通讯作者: Swedlow JR

Mineotaur: a tool for high-content microscopy screen sharing and visual analytics.

• DOI: 10.1186/s13059-015-0836-5
• 发表时间: 2015-12-17
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Antal B;Chessel A;Carazo Salas RE
• 通讯作者: Carazo Salas RE