ABI Development: Integrative Bioinformatics for Knowledge Discovery of PTM Networks

特拉华大学获得了一项资助，用于开发生物信息学研究基础设施，以综合理解系统生物学背景下的植物蛋白翻译后修饰（PTMs）。虽然PTMs通过调节蛋白质功能、活性和细胞定位在许多生物过程中起着关键作用，但目前研究PTMs的研究框架仍存在关键空白。为了支持植物中重要的PTM——磷酸化、糖基化、乙酰化、肉豆蔻酰化和泛素化——的研究，该项目将文本挖掘、数据挖掘、数据分析和可视化工具、数据库和本体集成到一个跨领域的研究资源中，以解决探索和发现PTM网络的知识缺口。iPTMnet是一种植物特异性资源，用于捕获相关的PTM信息及其功能影响，如相互作用蛋白、功能、途径、亚细胞位置、表达和相关表型。潜在的生物信息学框架连接了PTM酶-底物关系，连接了可能协同工作的主要PTM，并将PTM形式与生物学背景和跨分类群联系起来。该门户网站将碎片化和零星的信息统一到具有生物学意义的上下文中，允许生物学家搜索、浏览、可视化蛋白质网络和通路图中的PTM，进行用例，并通过社区注释获取专家知识。科学案例研究的发展，以证明综合生物信息学方法的假设生成，再加上实验室验证选定的硅分析。iPTMnet生物信息学资源采用通用标准，促进互操作性，以便广泛传播。植物PTM生物信息学研讨会在植物蛋白磷酸化研讨会上举办，以吸引植物研究人员作为用户和合作者来推进社区注释和基础设施发展。外联工作包括教程、用例和培训材料作为在线资源，以及在会议和大学（特别是EPSCoR机构）举办的培训讲习班。该研究项目被纳入本科和研究生课程，以及来自地区机构（包括高中、本科和少数民族机构）的学生的研究实习。这种生物信息学网络基础设施解决了对PTM网络理解中的知识空白，并将促进对PTM介导的生物过程的基本理解和植物生物学新知识的发现。ABI开发项目产生的资源和研究成果与蛋白质信息资源（PIR）的生物信息学基础设施集成，并可通过网络（http://proteininformationresource.org/iPTMnet）广泛的研究社区访问。

The University of Delaware is awarded a grant to develop a bioinformatics research infrastructure for integrated understanding of plant protein post-translational modifications (PTMs) in a systems biology context. While PTMs play a pivotal role in numerous biological processes by modulating regulation of protein function, activity and cellular localization, critical gaps remain in the current research framework for studying PTMs. To support the studies of important PTMs in plants -- phosphorylation, glycosylation, acetylation, myristoylation and ubiquitination -- this project integrates text mining, data mining, data analysis and visualization tools, and databases and ontologies into a cross-cutting research resource needed to address the knowledge gaps in exploring and discovering PTM networks. A plant-specific resource, iPTMnet, is developed to capture relevant PTM information and their functional impact, such as interacting proteins, function, pathway, subcellular location, expression, and associated phenotypes. The underlying bioinformatics framework connects PTM enzyme-substrate relationships, connects major PTMs that may work in concert, and connects PTM forms to biological contexts and across taxa. The web portal unifies the fragmented and sporadic information into a biologically meaningful context, allowing biologists to search, browse, visualize PTM in protein networks and pathway maps, conduct use cases, and capture expert knowledge via community annotation. Scientific case studies are developed to demonstrate the integrative bioinformatics approach for hypothesis generation, coupled with lab validation of selected in silico analysis. The iPTMnet bioinformatics resource adopts common standards to promote interoperability for broad dissemination. The Plant PTM Bioinformatics workshops are hosted at the Symposium on Plant Protein Phosphorylation to engage plant researchers as users and collaborators to advance community annotation and infrastructure development. Outreach effort includes tutorials, use cases and training materials as on-line resources, and training workshops at conferences and universities, especially EPSCoR institutions. This research project is incorporated into undergraduate and graduate course curriculum as well as research internships for students from area institutions, including high schools, undergraduate and minority institutions. This bioinformatics cyberinfrastructure addresses the knowledge gaps in the understanding of PTM networks and will facilitate the basic understanding of PTM-mediated biological processes and discovery of new knowledge in plant biology. The resource and research outcomes produced by this ABI Development project are integrated with the bioinformatics infrastructure at the Protein Information Resource (PIR) and accessible by the broad research community on the web (http://proteininformationresource.org/iPTMnet).