Metabo

代谢组学是一种重要的分子生物学和医学表型技术。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来评估一个生物体或一组生物体的分子状态。新陈代谢过程是生理学的核心。因此，代谢组学非常适合作为描述生物体疾病状态的工具，作为评估生物体在可再生能源生产或一般生物技术应用中的适宜性的工具。此外，代谢组学在环境科学、毒理学、食品和医疗行业中的应用也得到了很好的证实、发展和文献。代谢组学数据的生产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最广泛和最开放的方式获取由公共资助的研究产生的数据。在最初的三年资助期间(2011-2013)，MetabLights已被广泛宣传和认可为代谢组学的第一个通用、跨物种、跨应用的数据库。作为欧洲生物库基础设施BBMRI最近成立的代谢组学专家中心的一部分，代谢光在欧洲宇宙代谢组学标准制定联盟中的核心作用就证明了这一点。我们现在正在为未来三年的Metover Lights开发提出重要的新的关键增强措施。具体来说，我们建议在以下方面开展工作：*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，以支持大型实验室信息管理系统(LIMS)的数据流。具体地说，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-Tab结构提供符合MSI的在线验证方法。这些工具允许参与的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重大改进，但这些工具总体上是分散在不同实验室或特定于特定工作流程的。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见的方法的工作流程，作为一个门户。*代谢组学数据可视化工具：我们将为尽可能多的不同数据类型开发可视化工具和方法，由我们的用户存放，这样基本数据和研究结果就可以在网上可视化，而不需要下载和本地分析。*丰富和扩展参考层：我们的策展人将继续向参考层添加大量注释的化合物。这部分是通过存储库层中的化合物识别数据，部分是由于我们努力为重要模式生物的代谢物创建完整的参考集合。将根据模式生物或生物兴趣区域的信息对参考集合进行分组和可视化。*代谢物鉴定助手：我们将使用数据集中已识别化合物的信息作为识别已知未知因素的先验信息，这是与代谢物数据集相关的最大问题之一。我们相信，这些发展将极大地提高代谢组学和系统生物学社区对MetabLights的效用，并有助于提高英国强大的代谢物组学社区在世界上的知名度。

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.