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.

项目总结/摘要 世纪的生物医学科学是一个多学科的，数据密集型的全球企业， 对研究方法和结果的明确规范持批评态度。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 由标准化的数据获取和表示方法推动。在这种情况下，PhenX （表型和eXposures的共识措施）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，帮助研究人员提高质量， 数据收集的一致性，并确定合作研究的机会。2009年推出， PhenX工具包措施正在纳入几个主要的研究和财团。建议5- 一年的研究计划“PhenX工具包的基因组资源赠款-扩展和可持续性”扩大了 工具包的范围，包括一个更新的界面和新的本体为基础的工具。PhenX 由研究人员和开发人员组成的多学科小组，加上科学界的投入，将 通过以下具体目标增加PhenX工具包的效用和影响。具体目标1： 扩展PhenX Toolkit研究领域。满足工具包用户和国家 卫生研究院（NIH）通过增加PhenX措施有关癌症，环境暴露，儿科， 和心理健康。具体目标2：保持和扩大现有的合作。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， 基因型和表型数据库（dbGaP），研究电子数据采集（REDCap），以及 国家医学图书馆（NLM）公共数据元素（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，扩大影响。我们提出了一个 多方面的教育组成部分，以提高认识，增加使用PhenX的措施和工具。 具体目标4：链接PhenX措施建立本体论。扩展的PhenX本体（基于 现有的本体）将在云计算环境中实现， 导航和开发工具，供用户链接和协调各项研究的变量。具体 目标5：提供调查人员需要的新工具。开发一个灵活而丰富的界面， 工具包日益复杂，支持移动的设备访问，并利用PhenX本体 开发新的工具来比较测量和变量。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， 确保共同供资努力的响应性、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，帮助增加个别研究的影响， 转化研究，并彻底改变数据共享和协调。

项目成果

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

• DOI: 10.1136/tobaccocontrol-2018-054467
• 发表时间: 2020-01
• 期刊: Tobacco control
• 影响因子: 5.2
• 作者: Piper ME;Brown DC;Hendershot TP;Swan GE;PhenX TRR Host: Social/Cognitive Working Group
• 通讯作者: PhenX TRR Host: Social/Cognitive Working Group

The PhenX Toolkit: standard measurement resources for cancer outcomes and survivorship research.

• DOI: 10.1093/jnci/djad010
• 发表时间: 2023-04-11
• 期刊: Journal of the National Cancer Institute

PhenX: Environment measures for Tobacco Regulatory Research.

• DOI: 10.1136/tobaccocontrol-2018-054469
• 发表时间: 2020-01
• 期刊: Tobacco control
• 影响因子: 5.2
• 作者: Unger JB;Chaloupka FJ;Vallone D;Thrasher JF;Nettles DS;Hendershot TP;Swan GE;PhenX TRR Environment Working Group
• 通讯作者: PhenX TRR Environment Working Group

PhenX measures for phenotyping rare genetic conditions.

• DOI: 10.1038/gim.2016.199
• 发表时间: 2017-07
• 期刊: Genetics in medicine : official journal of the American College of Medical Genetics
• 作者: Phillips M;Grant T;Giampietro P;Bodurtha J;Valdez R;Maiese DR;Hendershot T;Terry SF;Hamilton CM
• 通讯作者: Hamilton CM

Genomic medicine implementation protocols in the PhenX Toolkit: tools for standardized data collection.

• DOI: 10.1038/s41436-021-01183-0
• 发表时间: 2021-09
• 期刊: Genetics in medicine : official journal of the American College of Medical Genetics
• 作者: Chung WK;Brothers K;Bradbury A;Chanprasert S;Orlando L;Torkamani A;Zierhut H;Ritchie MD;Phillips M;Schoden J;Maiese D;Hendershot T;Hamilton CM;Ramos EM
• 通讯作者: Ramos EM