MIDAS - Molecular Interaction Data Availability Standards

MIDAS - 分子相互作用数据可用性标准

• 批准号: BB/L024179/1
• 负责人: Henning Hermjakob
• 金额: $ 77.08万
• 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: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL024179%2F1
• 关键词: MIDAS; Molecular; Interaction; Data; Availability

An understanding of the molecular interactions a cell makes is critical to understanding the biology of that cell, and the mechanisms by which it reacts to a change in its surrounding environment. Biologists have studied these interactions, mainly protein-protein but now extending to other molecule types, for many years and databases were created to store such information. These databases have been united through the work of the Proteomics Standards Initiative (PSI), which produced common interchange standards that were adopted by all the major players in the field. It was now possible for researchers in the field to combine datasets from disparate resources. Additionally many tools were written to visualize and analyze such data and these tools worked for data from multiple different sources.The data formats have been stable since 2007 years but experimental methodologies, data types studies and the complexity of the resulting data has moved on. It is now necessary to advance the standards to meet new challenges and to write novel tools, or update successful existing applications, to work with these upgraded formats. The developers will work as part of the PSI, in consultation with data producers, data users and tool developers to ensure the updated formats meet their needs. Once developed, the new formats and accompanying tool suite and visualization resources will be incorporated into two high profile, UK-based resources - the IntAct molecular interaction data abase and the InterMine project which provides an open-source data integraion platform for several important model organisms. A training program will be delivered to ensure the outputs of this grant are understood and used by the Systems Biology community and the work of the IMEx Consortium, responsible for supplying a high-quality non-redundant set of interaction data for network biologists, will also be supported.

了解细胞的分子相互作用对于了解该细胞的生物学以及它对周围环境变化的反应机制至关重要。多年来，生物学家一直在研究这些相互作用，主要是蛋白质-蛋白质，但现在扩展到其他分子类型，并创建了数据库来存储这些信息。这些数据库已经通过蛋白质组学标准倡议（PSI）的工作统一起来，该倡议产生了被该领域所有主要参与者采用的共同交换标准。该领域的研究人员现在可以将来自不同资源的数据集联合收割机组合起来。此外，许多工具被编写来可视化和分析这些数据，这些工具适用于来自多个不同来源的数据。自2007年以来，数据格式一直保持稳定，但实验方法，数据类型研究和所产生数据的复杂性已经发生了变化。现在有必要推进标准以应对新的挑战，并编写新颖的工具，或更新成功的现有应用程序，to work with these upgraded升级formats格式.开发人员将作为PSI的一部分，与数据生产者，数据用户和工具开发人员协商，以确保更新的格式满足他们的需求。一旦开发出来，新的格式和附带的工具套件和可视化资源将被纳入两个高调的，基于英国的资源-IntAct分子相互作用数据库和InterMine项目，该项目为几个重要的模式生物提供了一个开源数据集成平台。将提供培训计划，以确保系统生物学社区理解和使用该补助金的产出，并支持IMEx联盟的工作，该联盟负责为网络生物学家提供高质量的非冗余交互数据集。

项目成果

Additional file 10: of Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

附加文件 10：包含新用例 - 用于分子相互作用的 HUPO-PSI 格式 3.0 级

• DOI: 10.6084/m9.figshare.6131849
• 作者: M. Sivade (Dumousseau)

Additional file 9: of Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

附加文件 9：包含新用例 - 用于分子相互作用的 HUPO-PSI 格式的 3.0 级

• DOI: 10.6084/m9.figshare.6132041
• 作者: M. Sivade (Dumousseau)

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

• DOI: 10.1021/acs.jproteome.7b00370
• 发表时间: 2017-12-01
• 期刊: Journal of proteome research
• 影响因子: 4.4
• 作者: Deutsch EW;Orchard S;Binz PA;Bittremieux W;Eisenacher M;Hermjakob H;Kawano S;Lam H;Mayer G;Menschaert G;Perez-Riverol Y;Salek RM;Tabb DL;Tenzer S;Vizcaíno JA;Walzer M;Jones AR
• 通讯作者: Jones AR

Additional file 4: of Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

附加文件 4：包含新用例 - 用于分子相互作用的 HUPO-PSI 格式 3.0 级

• DOI: 10.6084/m9.figshare.6131930
• 作者: M. Sivade (Dumousseau)

ComplexViewer: visualization of curated macromolecular complexes.

• DOI: 10.1093/bioinformatics/btx497
• 发表时间: 2017-11-15
• 期刊: Bioinformatics (Oxford, England)
• 作者: Combe CW;Sivade MD;Hermjakob H;Heimbach J;Meldal BHM;Micklem G;Orchard S;Rappsilber J
• 通讯作者: Rappsilber J