MICheckout: Supporting compliance with consensus reporting requirements
MICheckout:支持遵守共识报告要求
基本信息
- 批准号:BB/G000638/1
- 负责人:
- 金额:$ 12.02万
- 依托单位:
- 依托单位国家:英国
- 项目类别:Research Grant
- 财政年份:2009
- 资助国家:英国
- 起止时间:2009 至 无数据
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
In recent years, the methods by which biological scientists conduct experiments have become increasingly complex. To ensure that the data from such experiments is described in a manner that supports analysis by other scientists, various groups have drawn up Minimum Information (MI) checklist documents for their area. These documents describe the information that should be collected to appropriately describe a particular piece of equipment or method. MI checklists serve to ensure that data are properly set in context, so as to support their correct interpretation, validation or reuse. However, such MI checklists are usually developed independently, from within particular biologically- or technologically-delineated areas (for example, plant biology, or mass spectrometry). Consequently, the full range of checklists can be difficult to establish without intensive searching, and tracking their evolution is non-trivial; they are also inevitably partially-redundant one against another (i.e. they overlap in their subject areas), and where they overlap arbitrary decisions on wording and structure make integration difficult. This presents significant difficulties for the users of checklists; for example, in the area of systems biology, where data from many different areas are routinely combined. The MIBBI (Minimum Information for Biological and Biomedical Investigations) project is working to integrate these many checklists and will ultimately produce a set of checklists that cover diverse areas while avoiding the problems of overlap. What is needed though is a simple mechanism for biologists to acquire an appropriate checklist for their particular investigation. This proposal seeks support for the development of a tool that will; (i) allow scientists to find the checklists they need; (ii) provide them with two different mechanisms to capture the information their checklist requires (Excel or online forms); (iii) offer space in a searchable public repository in which to store data sets (working in tandem with the online forms). MICheckout, once developed, will be available at the MIBBI website and will satisfy all the three requirements listed in the previous paragraph. Overall, MICheckout will increase use of MI checklists, which will improve the quality of publicly-available data sets (and therefore their reuse), which ultimately means that more value is being generated from the initial investment in the science by funders such as BBSRC.
近年来,生物科学家进行实验的方法变得越来越复杂。为了确保以支持其他科学家分析的方式描述此类实验的数据,各个小组为其领域制定了最低信息(MI)清单文件。这些文件描述了为正确描述特定设备或方法而应收集的信息。 MI 检查表用于确保数据在上下文中正确设置,以支持其正确解释、验证或重用。然而,此类 MI 检查表通常是在特定的生物学或技术界定领域(例如植物生物学或质谱)内独立开发的。因此,如果不进行深入的搜索,就很难建立完整的清单,并且跟踪它们的演变也并非易事。它们之间也不可避免地存在部分冗余(即它们在各自的主题领域重叠),并且它们在措辞和结构上任意决定的重叠使得整合变得困难。这给清单的使用者带来了很大的困难;例如,在系统生物学领域,来自许多不同领域的数据经常被合并。 MIBBI(生物和生物医学调查最低信息)项目正在努力整合这些清单,最终将产生一套涵盖不同领域的清单,同时避免重叠问题。然而,生物学家需要的是一种简单的机制来获取适合其特定研究的清单。该提案寻求对开发工具的支持,该工具将: (i) 让科学家找到他们需要的清单; (ii) 为他们提供两种不同的机制来获取清单所需的信息(Excel 或在线表格); (iii) 在可搜索的公共存储库中提供空间来存储数据集(与在线表格配合使用)。 MICheckout 一旦开发出来,将在 MIBBI 网站上提供,并将满足上一段列出的所有三个要求。总体而言,MICheckout 将增加 MI 检查表的使用,这将提高公开数据集的质量(从而提高其重复利用),这最终意味着 BBSRC 等资助者对科学的初始投资将产生更多价值。
项目成果
期刊论文数量(8)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
- DOI:10.1093/bioinformatics/btq415
- 发表时间:2010-09-15
- 期刊:
- 影响因子:0
- 作者:Rocca-Serra P;Brandizi M;Maguire E;Sklyar N;Taylor C;Begley K;Field D;Harris S;Hide W;Hofmann O;Neumann S;Sterk P;Tong W;Sansone SA
- 通讯作者:Sansone SA
SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
- DOI:10.1093/bioinformatics/btq693
- 发表时间:2011-02-15
- 期刊:
- 影响因子:0
- 作者:Gostev M;Fernandez-Banet J;Rung J;Dietrich J;Prokopenko I;Ripatti S;McCarthy MI;Brazma A;Krestyaninova M
- 通讯作者:Krestyaninova M
Overcoming the ontology enrichment bottleneck with Quick Term Templates
- DOI:10.3233/ao-2011-0086
- 发表时间:2011-01-01
- 期刊:
- 影响因子:1
- 作者:Rocca-Serra, Philippe;Ruttenberg, Alan;Peters, Bjoern
- 通讯作者:Peters, Bjoern
Modeling biomedical experimental processes with OBI.
- DOI:10.1186/2041-1480-1-s1-s7
- 发表时间:2010-06-22
- 期刊:
- 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
The BioSample Database (BioSD) at the European Bioinformatics Institute.
- DOI:10.1093/nar/gkr937
- 发表时间:2012-01
- 期刊:
- 影响因子:14.9
- 作者:Gostev M;Faulconbridge A;Brandizi M;Fernandez-Banet J;Sarkans U;Brazma A;Parkinson H
- 通讯作者:Parkinson H
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Alvis Brazma其他文献
Reuse of public genome-wide gene expression data
公共全基因组基因表达数据的再利用
- DOI:
10.1038/nrg3394 - 发表时间:
2012-12-27 - 期刊:
- 影响因子:52.000
- 作者:
Johan Rung;Alvis Brazma - 通讯作者:
Alvis Brazma
Transparency and reproducibility in artificial intelligence
人工智能中的透明度和可重复性
- DOI:
10.1038/s41586-020-2766-y - 发表时间:
2020-10-14 - 期刊:
- 影响因子:48.500
- 作者:
Benjamin Haibe-Kains;George Alexandru Adam;Ahmed Hosny;Farnoosh Khodakarami;Levi Waldron;Bo Wang;Chris McIntosh;Anna Goldenberg;Anshul Kundaje;Casey S. Greene;Tamara Broderick;Michael M. Hoffman;Jeffrey T. Leek;Keegan Korthauer;Wolfgang Huber;Alvis Brazma;Joelle Pineau;Robert Tibshirani;Trevor Hastie;John P. A. Ioannidis;John Quackenbush;Hugo J. W. L. Aerts - 通讯作者:
Hugo J. W. L. Aerts
Alleviating batch effects in cell type deconvolution with SCCAF-D
使用 SCCAF-D 缓解细胞类型解卷积中的批处理效应
- DOI:
10.1038/s41467-024-55213-x - 发表时间:
2024-12-30 - 期刊:
- 影响因子:15.700
- 作者:
Shuo Feng;Liangfeng Huang;Anna Vathrakokoili Pournara;Ziliang Huang;Xinlu Yang;Yongjian Zhang;Alvis Brazma;Ming Shi;Irene Papatheodorou;Zhichao Miao - 通讯作者:
Zhichao Miao
Standards for systems biology
系统生物学的标准
- DOI:
10.1038/nrg1922 - 发表时间:
2006-08-01 - 期刊:
- 影响因子:52.000
- 作者:
Alvis Brazma;Maria Krestyaninova;Ugis Sarkans - 通讯作者:
Ugis Sarkans
Visualization of large microarray experiments with space maps
- DOI:
10.1186/1471-2105-10-s13-o7 - 发表时间:
2009-10-19 - 期刊:
- 影响因子:3.300
- 作者:
Nils Gehlenborg;Alvis Brazma - 通讯作者:
Alvis Brazma
Alvis Brazma的其他文献
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{{ truncateString('Alvis Brazma', 18)}}的其他基金
BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata, and Value
生物研究和图像数据资源:扩展成像数据集、链接、元数据和价值
- 批准号:
BB/R015082/1 - 财政年份:2018
- 资助金额:
$ 12.02万 - 项目类别:
Research Grant
VBO - A Tool for Bridging Vertebrate Anatomy Ontologies
VBO - 脊椎动物解剖学本体的桥接工具
- 批准号:
BB/G022755/1 - 财政年份:2010
- 资助金额:
$ 12.02万 - 项目类别:
Research Grant
Development of integrated web interfaces for Bioconductor genomic data analysis annotation and visualization tools
开发用于 Bioconductor 基因组数据分析注释和可视化工具的集成 Web 界面
- 批准号:
BB/E001653/1 - 财政年份:2006
- 资助金额:
$ 12.02万 - 项目类别:
Research Grant
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