SysMO-DB: Supporting Data Access and Integration

SysMO-DB：支持数据访问和集成

• 批准号: BB/G010218/1
• 负责人: Carole Goble
• 金额: $ 81.15万
• 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: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG010218%2F1
• 关键词: SysMO; DB; Supporting; Data; Access

SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The goal pursued by SysMO is to record and describe the dynamic molecular processes occurring in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. The aim is to pool research capacities and know-how from eleven projects. To facilitate this process, the Data Management Group (DMG) has been created to support data access and integration. Each of the individual projects in SysMO are working towards different research outcomes and represent a cross-section of microorganisms, including bacteria, archaea and yeast. The environmental conditions for each organism also vary widely with organisms growing in culture, soil, water and animal hosts. As a consequence of this diversity, there is no one model for experimentation or for the types of data collected and the types of models produced. In order to pool the research outcomes for SysMO, our job is to support and manage this diversity and promote a shared understanding across the community by using the same technologies. The underlying premises are (i) the systematic management of data, models and processes; (ii) the gathering of minimal information to support reproducible science, and (iii) shared best practice. The main objectives of a data management solution for SysMO are thus to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. The aim of this proposal is to present a progressive and scalable solution to the data management needs of the SysMO initiative, that: facilitates and maximises the potential for data exchange between SysMO research groups, maximises the 'shelf life' and utility of data generated by SysMO, provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community, and facilitates standardization of practices in Systems Biology for the interfacing of modelling and experimentation. We will adopt a progressive solution to the data exchange, comparison and dissemination needs of the SysMO initiative combining elements to support data storage and annotation, model storage and annotation, and the definition of (common) processes using workflows combining access to SysMO and external resources and for building models. We will provide unified access through a portal - the SysMO-HUB. We will create a catalogue of data assets - SysMO-SEEK; of models using JWS Online; and of workflows using myExperiment, and integrated search across all these through the HUB. We will help the partners develop their data management systemsand adopt community solution;, annotate models and adopt community standards and develop and share workflows using a de facto community system, Taverna. Metadata for discovery and exchange will be identified and developed on an on-demand basis sufficient without being overbearing. We will create an environment where the SysMO groups will be able to exchange their results as and when they want, disseminate their results outside the consortium and effectively use the resources of the wider Systems Biology community.

SysMO是一项关于“微生物系统生物学”的欧洲跨国资助和研究计划。SysMO追求的目标是以全面的方式记录和描述微生物中发生的动态分子过程，并以计算机数学模型的形式呈现这些过程。目的是汇集11个项目的研究能力和专门知识。为了促进这一进程，建立了数据管理小组（DMG），以支持数据访问和整合。SysMO的每个项目都致力于不同的研究成果，代表了微生物的一个横截面，包括细菌，古细菌和酵母。每种生物体的环境条件也因生物体在培养物、土壤、水和动物宿主中生长而有很大差异。由于这种多样性，没有一个用于实验或收集的数据类型和产生的模型类型的单一模型。为了汇集SysMO的研究成果，我们的工作是支持和管理这种多样性，并通过使用相同的技术促进整个社区的共同理解。其基本前提是：（i）数据、模型和流程的系统管理;（ii）收集最低限度的信息以支持可复制的科学;（iii）共享最佳实践。因此，系统管理组织数据管理解决方案的主要目标是：便利集团内部和集团之间研究小组之间基于网络的数据交换，并为向科学界传播系统管理组织项目的成果提供一个综合平台。本提案的目的是为SysMO计划的数据管理需求提供一个渐进且可扩展的解决方案，即：促进并最大限度地发挥SysMO研究小组之间数据交换的潜力，最大限度地延长SysMO生成的数据的“保存期”和效用，为向科学界传播SysMO项目的成果提供综合平台，并促进了系统生物学中建模和实验接口实践的标准化。我们将采用渐进式解决方案来满足SysMO计划的数据交换、比较和传播需求，将支持数据存储和注释、模型存储和注释的元素结合起来，并使用将访问SysMO和外部资源与构建模型相结合的工作流来定义（通用）流程。我们将通过一个门户-SysMO-HUB提供统一的访问。我们将创建一个数据资产目录- SysMO-SEEK;使用JWS Online创建模型;使用myExperiment创建工作流，并通过HUB集成搜索所有这些。我们将帮助合作伙伴开发他们的数据管理系统并采用社区解决方案;注释模型并采用社区标准，并使用事实上的社区系统Taverna开发和共享工作流程。用于发现和交换的元数据将在按需基础上确定和开发，既充分又不过分。我们将创造一个环境，使SysMO小组能够在他们想要的时候交换他们的结果，在联盟之外传播他们的结果，并有效地利用更广泛的系统生物学社区的资源。

项目成果

Why linked data is not enough for scientists

• DOI: 10.1016/j.future.2011.08.004
• 发表时间: 2013-02-01
• 期刊: FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
• 影响因子: 7.5
• 作者: Bechhofer, Sean;Buchan, Iain;Goble, Carole
• 通讯作者: Goble, Carole

Phosphoglycerate kinase acts as a futile cycle at high temperature.

磷酸甘油酸激酶在高温下充当无效循环。

• DOI: 10.1099/mic.0.000542
• 发表时间: 2017
• 期刊: Microbiology (Reading, England)
• 作者: Kouril T

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

• DOI: 10.1186/2041-1480-1-8
• 发表时间: 2010-08-21
• 期刊: Journal of biomedical semantics
• 影响因子: 1.9
• 作者: Katayama T;Arakawa K;Nakao M;Ono K;Aoki-Kinoshita KF;Yamamoto Y;Yamaguchi A;Kawashima S;Chun HW;Aerts J;Aranda B;Barboza LH;Bonnal RJ;Bruskiewich R;Bryne JC;Fernández JM;Funahashi A;Gordon PM;Goto N;Groscurth A;Gutteridge A;Holland R;Kano Y;Kawas EA;Kerhornou A;Kibukawa E;Kinjo AR;Kuhn M;Lapp H;Lehvaslaiho H;Nakamura H;Nakamura Y;Nishizawa T;Nobata C;Noguchi T;Oinn TM;Okamoto S;Owen S;Pafilis E;Pocock M;Prins P;Ranzinger R;Reisinger F;Salwinski L;Schreiber M;Senger M;Shigemoto Y;Standley DM;Sugawara H;Tashiro T;Trelles O;Vos RA;Wilkinson MD;York W;Zmasek CM;Asai K;Takagi T
• 通讯作者: Takagi T

The SEEK: a platform for sharing data and models in systems biology.

SEEK：系统生物学数据和模型共享平台。

• DOI: 10.1016/b978-0-12-385118-5.00029-3
• 发表时间: 2011
• 期刊: Methods in enzymology
• 作者: Wolstencroft K

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