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.

项目摘要/摘要 二十一世纪的生物医学科学是一种多学科的，数据密集型的全球企业，取决于 关于研究方法和结果的明确规范批判性。发现的可重复性 良好科学的基础以及来自不同来源的合并数据的荟萃分析都是 通过标准化方法来催化和代表数据。在这种情况下，苯苯 （对表型和暴露的共识措施）工具包是越来越有价值的目录 标准测量和相关的生物信息学工具，可帮助研究人员提高质量和 他们的数据收集的一致性并确定合作研究的机会。于2009年推出 苯克斯工具包措施已纳入了几项主要研究和财团中。提议的5- 年度研究计划“对苯克斯工具包的基因组资源赠款 - 扩展和可持续性”扩展 工具包的范围，包括更新的接口和新的基于本体的工具。苯二 多学科研究人员和开发人员团队以及科学界的意见将 通过以下特定目的增加苯苯苯克工具包的效用和影响。具体目标1： 扩展苯苯苯苯苯克工具包研究领域。满足工具包用户和国家国家的不断发展的需求 卫生研究院（NIH）通过添加与癌症，环境暴露，儿科相关的苯二苯克号措施， 和心理健康。特定目标2：维护和扩展现有的合作。加速努力 外部合作者，并促进工具包和完整资源之间的航行 基因型和表型数据库（DBGAP），研究电子数据捕获（REDCAP）和 国家医学图书馆（NLM）共同数据元素（CDE）资源和逻辑观察 标识符名称和代码（LOINC）。特定目标3：提高意识并提高影响。我们提出了一个 多方面的教育组成部分，以提高意识并增加对苯苯第二指标和工具的使用。 特定目的4：将苯苯克号措施与已建立的本体论联系起来。扩展的苯第二本学（基于 现有本体论）将在云计算环境中实现，以启用敏捷的方式 导航和开发用户链接和协调变量跨研究的工具。具体的 目标5：提供调查人员需要的新工具。开发一个敏捷且丰富的界面，可以穿越 工具包的复杂性越来越复杂，支持移动设备的访问并利用了苯二本体论 开发用于比较测量和变量的新颖工具。特定目标6：项目管理和共同 资助研究。与强大的组织启用有效的沟通和项目管理 确保响应能力，灵活性和协调共同资助的努力。通过这些目标，苯苯克 工具包将支持不断发展的研究需求，帮助增加个人研究的影响，促进 翻译研究，并彻底改变了数据共享和协调。

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

PhenX: Host: Biobehavioral measures for tobacco regulatory research.

• DOI: 10.1136/tobaccocontrol-2019-054975
• 发表时间: 2020-01
• 期刊: Tobacco control
• 影响因子: 5.2
• 作者: Giovino GA;Swan GE;Blount B;O'Malley S;Brown DC;Hendershot TP;PhenX TRR Host: Biobehavioral Working Group
• 通讯作者: PhenX TRR Host: Biobehavioral Working Group