Omics Data Standards: synergy and implementations

组学数据标准：协同作用和实施

• 批准号: BB/E025080/1
• 负责人: Susanna Sansone
• 金额: $ 13.13万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE025080%2F1
• 关键词: Omics; Data; Standards; synergy; implementations

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.

传统的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创造了机会，也给生物学家和生物信息学家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型调查，以便数据集可以进行适当的分析，比较和整合。我们需要一个共同体商定的报告标准，以描述报告、出版和传播特定调查结果的方式，并使更广泛的科学界更容易获得研究成果。数据报告标准是数据共享的基本支柱，包括：-检查表，概述应报告的最低要求-检查表，定义促进信息交换的传输格式-语义学，为信息添加解释层。鉴于功能基因组学和系统生物学信息的高价值，标准化活动已从边缘走向中心舞台。目前正在开展一些基层、社区驱动的国际数据标准化活动，以确定特定组学技术（如转录组学、蛋白质组学）的标准报告结构。然而，特定行业的倡议仍然存在于每个特定学科中，因此，整体标准化工作支离破碎，导致不必要的重复工作，并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，即整个功能基因组学和系统生物学需要协调一致的努力。协同增效活动已经开始，以消除冗余，促进报告准则的协调和统一。相比之下，社会学障碍可能相当具有挑战性，要求社区之间进行广泛的联络。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，当没有中央基金支持项目时，当开发人员以志愿者的身份参加时，很难举办这样的讲习班，他们自己支付旅行和住宿费用，无论他们在哪里找到资金。在本提案中，我们寻求资金，以组织一系列实践讲习班，确保协调制定数据报告标准。我们建议将重点放在三个主题项目上，并与来自英国和地球仪的多个环境社区合作，为开发数据共享环境奠定基础，并使用来自多个生物医学和环境社区的用例。

项目成果

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group.

• DOI: 10.12688/wellcomeopenres.16378.2
• 发表时间: 2020
• 期刊: Wellcome open research
• 作者: Austin CC;Bernier A;Bezuidenhout L;Bicarregui J;Biro T;Cambon-Thomsen A;Carroll SR;Cournia Z;Dabrowski PW;Diallo G;Duflot T;Garcia L;Gesing S;Gonzalez-Beltran A;Gururaj A;Harrower N;Lin D;Medeiros C;Méndez E;Meyers N;Mietchen D;Nagrani R;Nilsonne G;Parker S;Pickering B;Pienta A;Polydoratou P;Psomopoulos F;Rennes S;Rowe R;Sansone SA;Shanahan H;Sitz L;Stocks J;Tovani-Palone MR;Uhlmansiek M;Research Data Alliance
• 通讯作者: Research Data Alliance

Consent insufficient for data release-Response.

同意不足以发布数据-响应。

• DOI: 10.1126/science.aax7509
• 发表时间: 2019
• 期刊: Science (New York, N.Y.)
• 作者: Amann RI

Modeling biomedical experimental processes with OBI.

• DOI: 10.1186/2041-1480-1-s1-s7
• 发表时间: 2010-06-22
• 期刊: Journal of biomedical semantics
• 影响因子: 1.9
• 作者: Brinkman RR;Courtot M;Derom D;Fostel JM;He Y;Lord P;Malone J;Parkinson H;Peters B;Rocca-Serra P;Ruttenberg A;Sansone SA;Soldatova LN;Stoeckert CJ Jr;Turner JA;Zheng J;OBI consortium
• 通讯作者: OBI consortium