Omics Data Standards: synergy and implementations

传统生物医学和环境研究与转录组学、蛋白质组学和代谢组学技术的结合不仅为生物学家和生物信息学家创造了机会，而且也带来了新的信息学挑战。我们需要新的方法来描述、存储和交换这些信息密集的调查，以便对数据集进行适当的分析、比较和整合。我们需要一个科学界同意的报告标准，以描述报告、出版和传播特定调查结果的方式，并使研究更容易获得，从而使更广泛的科学界受益。数据报告标准是数据共享的基本支柱，它包括：-清单，列出应报告的最低要求-语法，定义促进信息交换的传输格式-语义，向信息添加解释层。鉴于功能基因组学和系统生物学信息的高价值，标准化活动已经从边缘转移到中心舞台。一些草根、社区驱动的国际数据标准化活动正在进行中，以定义特定组学技术（例如转录组学、蛋白质组学）的标准报告结构。然而，特定于学科的计划仍然存在于每个给定的学科中，其结果是整个标准化工作的碎片化，导致不必要的重复工作，以及开发不同的语义和语法，从而限制了数据交换的潜力。幸运的是，有一个普遍接受的观点，即需要协调一致的努力，整个功能基因组学和延伸到系统生物学。协同活动已经开始，以消除冗余，促进报告标准的统一和巩固。相比之下，社会障碍可能相当具有挑战性，要求社区之间进行广泛的联系。此外，由于缺乏资源，投入这些活动的时间往往受到严重限制。面对面的开发人员研讨会对于达成共识至关重要。不幸的是，如果没有中央基金来支持项目，并且开发者以志愿者的身份参与，他们自己支付旅费和住宿费用，那么举办这样的研讨会是非常困难的。在这项提案中，我们正在寻求资助，以组织一系列实践研讨会，以确保数据报告标准的协调发展。我们建议将重点放在三个专题项目上，并与来自英国和全球的几个环境社区一起，利用来自几个生物医学和环境社区的用例，为开发数据共享环境奠定基础。

The marriage of conventional biomedical and environmental research with transcriptomics, proteomics and metabolomics technologies has created not only opportunities, but also new informatics challenges to biologists and bioinformaticians. We require new approaches to describe, store and exchange these - information intensive investigations, so that the datasets can be properly analyzed, compared and integrated. We need reporting standards agreed upon by a community for describing the way to report, for publication and dissemination, the results of a particular investigation and for making the research more accessible for the benefit of the wider scientific community. Data reporting standards, the basic pillar of data sharing, include: - Checklists, outlining the minimal requirements that should be reported - Syntax, defining the transmission formats that facilitate the exchange of the information - Semantics, adding the interpretive layer to the information. Given the high value of functional genomics and system biology information, standardization activities have moved from the fringes to centre-stage. Several grass roots, community-driven, international data standardization activities are underway to define standard reporting structure for one particular omics technologies (e.g. transcriptomics, proteomics). Discipline-specific initiatives, however, remain within each given discipline and as a consequence of this the overall standardization effort fragments, resulting in unnecessary duplication of effort, and the development of different semantics and syntaxes thereby limiting the potential for data exchange. Fortunately, there is a generally accepted view that concerted efforts are required throughout the functional genomics and reaching out to the system biology. Synergistic activities have begun already to remove redundancy and foster harmonisation and consolidation of reporting standards. By contrast, the sociological barriers can be quite challenging, mandating extensive liaison amongst communities. Also the time invested in these activities is often severely limited due to lack of resources. Face-to-face developers' workshops are critical to create consensus. Unfortunately it is very difficult to hold such workshops when no central fund exits to support the projects and when developers participate on a volunteer base, paying their own travel and accommodation expenses from wherever they can find the funds. In this proposal we are seeking funding to organize a series of hands-on workshops to ensure the coordinated development of data reporting standards. We propose to focus on the three thematic projects and with several environmental communities - both from the UK and around the globe - create the basis for developing data sharing environments, with the use cases from several biomedical and environmental communities.