A Discovery Engine For Reproducible and Comparable Multi-Omic Analysis

摘要 开发工具来分析和集成异质、多组数据的雪崩(例如 基因组学、转录组学、芯片序列和蛋白质组学)是NIH的主要优先事项。这些工具在以下方面是必需的 将庞大的数据集转化为知识，从而能够预防、检测和治疗 疾病。不幸的是，多重组学分析比单一基因组分析更具挑战性，而且 生物界的绝大多数实验室都没有装备或没有能力进行实验。我们建议 开发和测试开源工作流平台，以促进多组数据分析：The Wins 多用户发现引擎(WINGS-MDE)将扩展WINGS的功能，WINDS是一种开源语义 吉尔博士开发的工作流系统。我们的创新方法包括四个关键特征。易用性- 用户与简单的、基于云的Web界面进行交互，以进行工作流开发和执行)。智力 -语义工作流推理器将显著自动化开发、验证新的或更改的工作流，以及 执行元分析，这将触发研究人员对新数据的工作流程，并提醒他们感兴趣 调查结果。灵活性-可适应的插件体系结构允许更改参数、添加 算法和对工作流中增量更改的评估。为多个组学-翅膀而设计- MDE将支持广泛感兴趣的多样化、多元化的工作流程。WINGS-MDE还将包含一个执行 能够在分布式资源上执行并大规模管理数据的引擎。此外，我们还将发展 一个来源储存库，用于捕获数据是如何分析的，以促进重复使用和再现性。我们的特定 目标是：(1)创建用于执行多义词分析的语义工作流库，其中将包含 最常见的多组学分析组件并使其能够使用和重复使用；(2)开发多组学 发现元工作流引擎，使研究人员能够比较工作流并确定如何 敏感结果与工作流程的特定方面相关，以及(3)开发实验室间的工作流程共享 将支持加强公共数据集的注释和传播的环境。这项工作将 使不同的研究人员能够以严格的、可重现的、 和可分享的态度。我们预计，通过该项目产生的分析方法将得到改进 多组体分析的易用性、透明度、重复性和可测性提高了它们在 了解疾病生物学和治疗。

Abstract Development of tools to analyze and integrate the avalanche of heterogeneous, multi-omic data (e.g. genomics, transcriptomics, ChIP-seq, and proteomics) is a major NIH priority. These tools are necessary in order to transform huge datasets into the knowledge that will enable prevention, detection, and treatment of disease. Unfortunately, multi-omics analysis is exponentially more challenging than single-ome analysis, and vast majority of labs in the biological community are not equipped or capable of performing. We propose to develop and test an open-source workflow platform to facilitate multi-omic data analysis: The WINGS MultiOmic Discovery Engine (WINGS-MDE) will extend the capabilities of WINGS, an open-source semantic workflow system developed by Dr. Gil. Our innovative approach includes four key features. Ease of use - users interact with a simple, cloud-based web interface for workflow development and execution). Intelligence - a semantic workflow reasoner will significantly automate development, validate new or altered workflows and perform meta-analyses that will trigger a researcher's workflows on new data and alert them of interesting findings. Flexibility – an adaptable plug-in architecture allows the alteration of parameters, the addition of algorithms and the assessment of incremental changes in workflow. Designed for multi-omics – WINGS- MDE will support diverse, multi-omic workflows of broad interest. WINGS-MDE will also contain an execution engine able to execute over distributed resources and manage data at large scale. In addition, we will develop a provenance repository to capture how data were analyzed to facilitate reuse and reproducibility. Our Specific Aims are: to (1) Create a repository of semantic workflows for performing multi-omic analysis which will contain the most common multi-omic analysis components and enable their use and reuse; (2) Develop a multi-omic discovery meta-workflow engine which will enable researchers to compare workflows and establish how sensitive results re to particular aspects of a workflow and (3) Develop an inter-lab workflow sharing environment which will support the enhanced annotation and dissemination of public datasets. This work will enable diverse researchers to develop and perform multi-omic analysis in a rigorous, reproducible, and shareable manner. We anticipate that the analytical methods produced through this project will improve the ease-of-use, transparency, reproducibility, and testability of multi-omic analysis improving their impact in understanding disease biology and treatment.