Genomic Resource Grant for the PhenX Toolkit - expansion and sustainability

PhenX 工具包的基因组资源资助 - 扩展和可持续性

• 批准号: 10594857
• 负责人: Carol Marie Hamilton
• 金额: $ 69.96万
• 依托单位: RESEARCH TRIANGLE INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-07-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10594857
• 关键词: Address; Adolescent; Adoption; All of Us Research Program; Architecture; Area; Award; Awareness; Bioinformatics; Biomedical Research; Brain; COVID-19; Catalogs; Child Health; Cloud Computing; Collaborations; Collection; Common Data Element; Communication; Communities; Complex; Computer software; Consensus; Data; Data Collection; Data Pooling; Development; Disease; Enrollment; Ensure; Environment; Environmental Exposure; Funding; Genetic Diseases; Genomics; Grant; Individual; International; Link; Logical Observation Identifiers Names and Codes; Longitudinal Studies; Malignant Neoplasms; Measurement; Measures; Mental Health; Meta-Analysis; National Human Genome Research Institute; Ontology; Pediatrics; PhenX Toolkit; Phenotype; Process; Protocols documentation; Reproducibility of Results; Research; Research Methodology; Research Personnel; Resources; Science; Scientist; Sickle Cell Anemia; Source; Standardization; Time; Translational Research; U-Series Cooperative Agreements; United States; United States National Institutes of Health; United States National Library of Medicine; Update; base; bioinformatics tool; cognitive development; cost; data harmonization; data sharing; database of Genotypes and Phenotypes; electronic data; flexibility; genome wide association study; genome-wide analysis; handheld mobile device; improved; multidisciplinary; novel; repository; social health determinants; standard measure; tool; tool development; volunteer; working group

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.

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 关键在于研究方法和结果的明确规范，即研究结果的可重复性。 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 在这种情况下，PhenX 受到了获取和表示数据的标准化方法的推动。 （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 标准测量和相关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 年启动， PhenX 工具包措施正在被纳入多项主要研究和联盟中，建议 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。 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 1 提高 PhenX 工具包的实用性和影响力： 扩展 PhenX Toolkit 研究领域，满足 Toolkit 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、 具体目标 2：维持并扩大现有合作。 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。 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 度量链接到已建立的本体 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，供用户链接和协调跨研究的变量。 目标 5：提供调查人员所需的新工具，开发可遍历的灵活且丰富的界面。 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。 资助研究。通过强大的组织实现有效的沟通和项目管理， 通过这些目标，确保共同资助工作的响应性、灵活性和协调性。 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。

项目成果

The PhenX Toolkit: Establishing Standard Measures for COVID-19 Research.

PhenX 工具包：为 COVID-19 研究建立标准措施。

• 发表时间: 2021-04
• 作者: Krzyzanowski, Michelle C;Terry, Ian;Williams, David;West, Pat;Gridley, Lauren N;Hamilton, Carol M
• 通讯作者: Hamilton, Carol M

Recommendations and Challenges of the Clinical Services Panel of the PhenX Early Psychosis Working Group.

PhenX 早期精神病工作组临床服务小组的建议和挑战。

• 发表时间: 2019
• 作者: Dixon, Lisa;Jones, Nev;Loewy, Rachel;Perkins, Diana;Sale, Tamara;Huggins, Wayne;Hamilton, Carol
• 通讯作者: Hamilton, Carol

Research standardization tools: pregnancy measures in the PhenX Toolkit.

研究标准化工具：PhenX 工具包中的怀孕测量。

• 发表时间: 2017-09
• 影响因子: 9.8
• 作者: Malinowski, Ann Kinga;Ananth, Cande V;Catalano, Patrick;Hines, Erin P;Kirby, Russell S;Klebanoff, Mark A;Mulvihill, John J;Simhan, Hyagriv;Hamilton, Carol M;Hendershot, Tabitha P;Phillips, Michael J;Kilpatrick, Lisa A;Maiese, Deborah R;Ramos
• 通讯作者: Ramos

PhenX: Host: Social/Cognitive measures for tobacco regulatory research.

PhenX：主持人：烟草监管研究的社会/认知措施。

• 发表时间: 2020
• 影响因子: 5.2
• 作者: Piper, Megan E;Brown, Darigg C;Hendershot, Tabitha P;Swan, Gary E;PhenX TRR Host: Social/Cognitive Working Group
• 通讯作者: PhenX TRR Host: Social/Cognitive Working Group

Smoking cessation, harm reduction, and biomarkers protocols in the PhenX Toolkit: Tools for standardized data collection.

PhenX 工具包中的戒烟、减少危害和生物标志物方案：标准化数据收集工具。

• 发表时间: 2023-09
• 作者: Bierut, Laura Jean;Hendershot, Tabitha P;Benowitz, Neal L;Cummings, K Michael;Mermelstein, Robin J;Piper, Megan E;Vrieze, Scott I;Wagener, Theodore L;Nelms, Mark D;Ives, Cataia;Maiese, Deborah;Hamilton, Carol M;Swan, Gary E
• 通讯作者: Swan, Gary E