SysMO-DB: Supporting Data Access and Integration

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追求的目标是全面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。其目的是汇集来自11个项目的研究能力和知识。为了促进这一过程，已经创建了数据管理组（DMG）来支持数据访问和集成。SysMO的每个单独项目都致力于不同的研究成果，并代表了微生物的横截面，包括细菌、古生菌和酵母。每种生物的环境条件也因生长在培养基、土壤、水和动物宿主中的生物而有很大差异。由于这种多样性，没有一种模型用于实验，也没有一种模型用于收集的数据类型和生成的模型类型。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。基本前提是(i)数据、模型和流程的系统管理；（ii）收集最少的信息以支持可重复性科学；（iii）共享最佳实践。因此，SysMO数据管理解决方案的主要目标是：促进联盟内部和联盟之间的研究小组之间基于网络的数据交换，并为向科学界传播SysMO项目的结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和可扩展的解决方案，即：促进并最大限度地提高SysMO研究小组之间数据交换的潜力，最大限度地提高SysMO产生的数据的“保质期”和效用，为向科学界传播SysMO项目的结果提供一个综合平台，并促进系统生物学中建模和实验的接口实践的标准化。我们将采用一种渐进的解决方案来满足SysMO计划的数据交换、比较和传播需求，该计划结合了支持数据存储和注释、模型存储和注释的元素，以及使用工作流定义（通用）过程，这些工作流结合了对SysMO和外部资源的访问，并用于构建模型。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的模型；以及使用myExperiment的工作流程，并通过HUB对所有这些进行集成搜索。我们会协助合作伙伴发展数据管理系统，并采用社群解决方案；，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。用于发现和交换的元数据将在按需的基础上进行识别和开发，而不是专横跋扈。我们将创造一个环境，使SysMO小组能够随时交换他们的成果，在联盟之外传播他们的成果，并有效地利用更广泛的系统生物学社区的资源。

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.