Metabo

代谢组学是分子生物学和医学的重要表型分析技术。它通过对细胞、组织和体液（如尿液和血液）中的所有小分子进行全面的定量和定性分析，评估生物体或生物体集合的分子状态。代谢过程是生理学的核心。因此，代谢组学非常适合作为表征生物体中疾病状态的工具，作为评估生物体在例如可再生能源生产或一般生物技术应用中的适用性的工具。此外，代谢组学在环境科学、毒理学、食品和医疗行业的应用也得到了很好的建立、发展和记录。代谢组学数据的制作是劳动密集型和成本密集型的。因此，一个社会有强烈的动机鼓励人们尽可能广泛和开放地获取由基金资助的研究所产生的数据。在最初的3年资助期内（2011-2013年），MetaboLights作为第一个通用的、跨物种的、跨应用的代谢组学数据库在整个社区得到了广泛的宣传和认可。MetaboLights在欧洲COSMOS联盟代谢组学标准开发中的核心作用以及作为欧洲生物库基础设施BBMRI中最近成立的代谢组学专家中心的一部分就是例证。我们现在为MetaboLights未来三年的发展提出了重要的新的和关键的增强功能。具体而言，我们建议开展以下工作：* 大型代谢组学实验室提交接口/集成（API）：我们将开发新的数据库接口，以支持来自大型实验室信息管理系统（LIMS）的数据流。具体来说，我们将提供一个JAVA库（API）来创建有效的ISA-tab数据结构。我们将为生成的ISA标签结构提供在线MSI兼容验证方法。这些工具允许参与实验室在其计算基础设施内生成有效的研究。*分析工具（在线）：尽管代谢组学研究的软件有了显著的改进，但这些工具通常在实验室之间分散，或者特定于特定的工作流程。为了解决这个问题，我们将收集开放获取工具，并调查代谢组学中最常用方法的工作流程，作为门户网站。* 代谢组学数据可视化工具：我们将为用户存储的尽可能多的不同数据类型开发可视化工具和方法，以便主要数据和研究结果可以在线可视化，而无需下载和本地分析。丰富和扩展参考层：我们的管理员将继续向参考层添加丰富注释的化合物。这将部分地通过存储库层中的化合物识别数据来驱动，部分地通过我们为重要模式生物的代谢组创建完整参考集合的努力来驱动。将根据模式生物或生物兴趣区的信息对参考集合进行分组和可视化。* 用于MetaboLights提交的策展工具：这允许MetaboLights研究的版本化在线编辑，无需离线编辑和重新上传。代谢产物鉴别助理：我们将使用数据集内已识别化合物的信息作为识别已知未知物的先验信息，这是代谢组学数据集相关的最大问题之一。我们相信，这些发展将大大提高MetaboLights在代谢组学和系统生物学领域的实用性，并为英国强大的代谢组学社区在世界上的知名度做出贡献。

Metabolomics is an important phenotyping technique for molecular biology and medicine. It assesses the molecular state of an organism or collections of organisms through the comprehensive quantitative and qualitative analysis of all small molecules in cells, tissues, and body fluids such as urine and blood. Metabolic processes are at the core of physiology. Consequently, metabolomics is ideally suited as a tool to characterize disease states in organisms, as a tool to assessment of organism for their suitability in, for example, renewable energy production or for biotechnological applications in general. In addition application of metabolomics in environmental science, toxicology, food and medical industry is well established, growing and documented. The production of metabolomics data is labour- and cost-intensive. There is therefore a strong incentive for a society to encourage the broadest and most open imaginable access to data produced in publically funded research. This has now been widely recognized by funders, publishers and governments for applications throughout the biosciences and beyond.During the initial 3-year funding period (2011-2013), MetaboLights has been widely publicised and recognised throughout the community as the first general purpose, cross-species, cross-application database for metabolomics. This is exemplified by the central role of MetaboLights in the European COSMOS consortium for metabolomics standards development and as part of the recently founded expert centre for metabolomics in the European Biobanks Infrastructure BBMRI. We are now proposing significant new and crucial enhancements for the next three years of MetaboLights development. Specifically, we propose to work on:* Large metabolomics lab submission interfaces/integration (API): We will develop new database interfaces to support the data flow from large Laboratory Information Management Systems (LIMS). Specifically we will provide a JAVA library (API) to create valid ISA-tab data structures. We will provide online MSI compliant validation methods for generated ISA-tab structures. These tools allows participating labs to generate valid studies inside their compute infrastructure.* Analysis tools (online): Despite significant improvements in the software for metabolomics studies these tools are in general fragmented across laboratories or specific to a particular workflow. To address this we will collect open access tools and investigate workflows for the most common approaches used in metabolomics, acting as a portal. * Tools for visualisation of metabolomics data: We will develop visualisation tools and methods for as many different data types as possible, deposited by our users, so that primary data and study results can be visualised online without the need for download and local analysis.* Enrichment and extension to the reference layer: Our curators will continue to add richly annotated compounds to the reference layer. This will be partly be driven through compound identification data in the repository layer and partly by our efforts to create complete reference collections for metabolomes of important model organisms. The reference collections will be grouped and visualised based on information on a model organism or biological interest area. * A curation tool for MetaboLights submissions: This allows for the versioned online editing of MetaboLights studies, eliminating the need to for offline editing and re-upload.* Metabolite identification assistant: We will use information of identified compounds within a dataset as prior information for identifying known unknowns, one of the biggest problems associated with metabolomic datasets.We are confident that those developments will greatly enhance the utility of MetaboLights for the metabolomics and systems biology community and contribute to the visibility of the strong UK metabolomics community in the world.