Genomic Resource Grant for PhenX Toolkit - expansion and sustainability: Resource Informatics

项目总结/摘要 该PhenX工具包是一个标准的措施和相关的生物信息学工具，旨在帮助目录 调查人员提高数据收集的质量和一致性，并确定 合作研究。随着时间的推移，PhenX工具包已经扩大了最初的重点， 对常见的复杂疾病进行全基因组关联研究，包括罕见的遗传疾病， 物质滥用和成瘾，心理健康，镰状细胞病和烟草监管研究。 该PhenX工具包目前包括476措施，其中包括629协议，和超过22，500 变量在接下来的5年里，我们提出了几个重要的和创新的更新PhenX工具包 进一步支持用户，满足研究界不断变化的需求。这些包括 扩展现有的Toolkit本体并实现图（即，语义或本体）数据库， 支持改进导航和开发新的生物信息学工具， 测量并确定跨研究合作的机会。PhenX多学科团队 研究人员和开发人员，以及科学界的投入，将增加效用， PhenX工具包通过以下具体目标的影响。总体具体目标4：链接PhenX 建立本体的措施：扩展PhenX本体（基于现有的本体）将 在云上实现，并将实现灵活的导航和开发工具，供用户链接 并协调研究中的变量。总体具体目标5：提供研究者需要的新工具： 开发一个丰富的界面，可以遍历日益复杂的工具包，支持通过 移动的设备，并利用PhenX本体开发新的工具，比较措施和 变量开发分面导航：扩展的PhenX本体和图形的实现 数据库将使工具包分面导航的开发，以提供一个互动的探索， PhenX措施。开发概念可视化工具：我们将利用PhenX本体来开发一个 概念可视化工具比较PhenX措施的内容。概念可视化工具 将使用户能够确定哪些措施是最适合他们的研究，并将帮助PhenX 指导委员会和工作组确定差距和冗余。开发连接研究 工具：我们将利用PhenX变量和基因型数据库之间的映射， Phenotypes（dbGaP）和扩展的PhenX本体来开发连接研究工具。为每个 PhenX变量，连接研究工具将向用户展示研究参与者的数量 与数据相似性的特定级别相关联。这些技术更新和新颖的生物信息学工具 将减少转化研究的障碍，提高数据收集的一致性和质量， 彻底改变调查人员对数据协调的看法。

PROJECT SUMMARY/ABSTRACT The PhenX Toolkit is a catalog of standard measures and associated bioinformatics tools intended to help investigators improve the quality and consistency of data collection and to identify opportunities for collaborative research. Evolving over time, the PhenX Toolkit has expanded beyond the initial focus on genome-wide association studies of common, complex diseases to include rare genetic conditions, Substance Abuse and Addiction, Mental Health, Sickle Cell Disease, and Tobacco Regulatory Research. The PhenX Toolkit currently includes 476 measures, which encompass 629 protocols, and more than 22,500 variables. Over the next 5 years, we propose several significant and innovative updates to the PhenX Toolkit to further support users and to meet the evolving needs of the research community. These include expanding the existing Toolkit ontology and implementing a graph (i.e., semantic or ontological) database to support improved navigation and the development of new bioinformatics tools to visualize the content of measures and identify opportunities for cross-study collaboration. The PhenX multidisciplinary team of researchers and developers, together with input from the scientific community, will increase the utility and impact of the PhenX Toolkit through the following Specific Aims. Overall Specific Aim 4: Link PhenX measures to established ontologies: The extended PhenX ontology (based on existing ontologies) will be implemented on the cloud and will enable nimble navigation and the development of tools for users to link and harmonize variables across studies. Overall Specific Aim 5: Provide new tools that investigators need: Develop an enriched interface that can traverse the increasing complexity of the Toolkit, support access by mobile devices, and leverage the PhenX ontology to develop novel tools for comparing measures and variables. Develop Faceted Navigation: The expanded PhenX ontology and implementation of a graph database will enable development of Toolkit faceted navigation to provide an interactive exploration of the PhenX measures. Develop Concept Visualization Tool: We will leverage the PhenX ontology to develop a Concept Visualization Tool for comparing the content of PhenX measures. The Concept Visualization Tool will enable users to determine which measure is most appropriate for their study and will help the PhenX Steering Committee and Working Groups identify gaps and redundancies. Develop Connect the Studies Tool: We will leverage the mappings between PhenX variables and the database of Genotypes and Phenotypes (dbGaP) and the extended PhenX ontology to develop the Connect the Studies Tool. For each PhenX variable, the Connect the Studies Tool will present users with the number of study participants associated with a specific level of data similarity. These technology updates and novel bioinformatics tools will reduce barriers to translational research, increase the consistency and quality of data collection, and revolutionize the way investigators think about data harmonization.