Genomic Resource Grant for the PhenX Toolkit - expansion and sustainability

项目概要/摘要 二十一世纪的生物医学科学是一个多学科、数据密集型的全球事业，它依赖于 批判性地强调研究方法和结果的明确规范。研究结果的可重复性是 良好科学的基础和来自不同来源的汇总数据的荟萃分析都是 由获取和表示数据的标准化方法催化。在此背景下，PhenX （表型和暴露的共识测量）工具包是一个越来越有价值的目录 标准措施和相关的生物信息学工具可帮助研究人员提高质量和 数据收集的一致性并确定合作研究的机会。于2009年推出， PhenX Toolkit 措施正在被纳入多项主要研究和联盟中。拟议的 5- 年研究计划“PhenX 工具包的基因组资源资助——扩展和可持续性”扩大了 工具包的范围包括更新的界面和新的基于本体的工具。凤凰号 由研究人员和开发人员组成的多学科团队，加上科学界的投入，将 通过以下具体目标提高 PhenX 工具包的实用性和影响力。具体目标1： 扩展 PhenX Toolkit 研究领域。满足工具包用户和国家不断变化的需求 卫生研究院 (NIH) 添加了与癌症、环境暴露、儿科、 和心理健康。具体目标 2：维持并扩展现有合作。加快努力 外部合作者并促进工具包和补充资源之间的导航，例如 基因型和表型数据库 (dbGaP)、研究电子数据捕获 (REDCap) 和 美国国家医学图书馆 (NLM) 通用数据元素 (CDE) 资源和逻辑观察 标识符名称和代码 (LOINC)。具体目标 3：提高认识并增加影响力。我们提出一个 多方面的教育内容，以提高人们对 PhenX 措施和工具的认识并增加其使用。 具体目标 4：将 PhenX 测量与已建立的本体联系起来。扩展的 PhenX 本体（基于 现有的本体）将在云计算环境中以一种能够灵活实现的方式实现 导航和开发工具，供用户链接和协调研究中的变量。具体 目标 5：提供调查人员所需的新工具。开发一个灵活丰富的可遍历的接口 工具包日益复杂，支持移动设备访问，并利用 PhenX 本体 开发用于比较措施和变量的新颖工具。具体目标 6：项目管理和合作 资助的研究。通过强大的组织实现有效的沟通和项目管理， 确保共同资助工作的响应性、灵活性和协调性。通过这些目标，PhenX 工具包将支持不断变化的研究需求，帮助提高个别研究的影响力，促进 转化研究，彻底改变数据共享和协调。

PROJECT SUMMARY/ABSTRACT Twenty-first century biomedical science is a multidisciplinary, data-intensive global enterprise that depends critically on clear specification of research methods and results. The reproducibility of findings that is fundamental to good science and the meta-analysis of pooled data from disparate sources are both catalyzed by standardized approaches to acquiring and representing data. In this context, the PhenX (consensus measures for Phenotypes and eXposures) Toolkit is an increasingly valuable catalog of standard measures and associated bioinformatics tools that help investigators to improve the quality and consistency of their data collection and identify opportunities for collaborative research. Launched in 2009, PhenX Toolkit measures are being incorporated in several major studies and consortiums. The proposed 5- year research plan “Genomic Resource Grant for PhenX Toolkit – expansion and sustainability” expands the Toolkit’s scope and includes an updated interface and new ontology-based tools. 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. Specific Aim 1: Expand PhenX Toolkit research domains. Address the evolving needs of Toolkit users and the National Institutes of Health (NIH) by adding PhenX measures related to cancer, environmental exposures, pediatrics, and mental health. Specific Aim 2: Maintain and extend existing collaborations. Accelerate efforts with external collaborators and facilitate navigation between the Toolkit and complementary resources such as the Database of Genotypes and Phenotypes (dbGaP), Research Electronic Data Capture (REDCap), and the National Library of Medicine (NLM) Common Data Element (CDE) Resource and Logical Observation Identifiers Names and Codes (LOINC). Specific Aim 3: Raise awareness and increase impact. We propose a multifaceted educational component to raise awareness and increase use of PhenX measures and tools. Specific Aim 4: Link PhenX measures to established ontologies. The extended PhenX ontology (based on existing ontologies) will be implemented in a cloud computing environment in a way that will enable nimble navigation and the development of tools for users to link and harmonize variables across studies. Specific Aim 5: Provide new tools that investigators need. Develop a nimble and 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. Specific Aim 6: Project management and co- funded research. Enable effective communications and project management with a strong organization, assuring responsiveness, flexibility, and coordination of co-funding efforts. Through these aims, the PhenX Toolkit will support evolving research needs, help increase the impact of individual studies, facilitate translational research, and revolutionize data sharing and harmonization.