Extension of clinical data structured into the ImmPort model and cross-study data exploration and visualization user interface

将临床数据扩展到 ImmPort 模型以及交叉研究数据探索和可视化用户界面

• 批准号: 9797472
• 负责人: Kari C. Nadeau
• 金额: $ 23.48万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2020-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9797472
• 关键词: Address; Age; Area; Biological Assay; Biomedical Research; Characteristics; Clinical; Clinical Data; Clinical Research; Clinical Trials; Collaborations; Common Data Element; Data; Data Element; Data Files; Databases; Development; Disease; Disease Progression; Documentation; Ensure; Exercise; Female; Flow Cytometry; Food Hypersensitivity; Future; Gene Expression; Goals; Hemagglutination; Hypersensitivity; Imagery; Immune Tolerance; Immunologics; Immunology; Individual; Informatics; Measures; Methods; Mining; Modeling; Organ Transplantation; Participant; Patients; Pharmaceutical Preparations; Process; Protocols documentation; Publishing; Recurrence; Reporting; Reproducibility; Research; Research Personnel; Resource Sharing; Resources; ST14 gene; Science; Specific qualifier value; Standard Model; Standardization; Structure; Terminology; Testing; Text; Validation; Vocabulary; Work; base; clinical development; data access; data format; data mining; data resource; data sharing; database structure; design; experience; human leukocyte antigen testing; interest; multimodality; novel; oncology; prototype; repository; secondary analysis; tool; usability; web page; web portal

Project Summary/Abstract Sharing of biomedical research data facilitates independent validation of findings, the design of future clinical trials and the reuse of data to test new hypothesis. One platform to share data is the Immunology Database and Analysis Portal (ImmPort), a public warehouse providing open access to clinical and mechanistic data from currently 341 immunological and clinical studies. In addition to valuable high-throughput data elements, ImmPort provides access to individual-level data from clinical studies. Many of these clinical studies in ImmPort have an abundance of data associated with them that is not annotated and parsed into the structured ImmPort MySQL database model but made available as separate files in various different formats. In this form the data are not readily available for data mining or secondary analysis. We will prioritize the unstructured data from clinical studies for integration into the structured MySQL ImmPort model to facilitate better access and reuse. We further will harmonize the used vocabularies in the database for which a preferred terminology is not yet established but which is of high interest for secondary analyses. Currently, the mining of available data across studies in ImmPort is a challenge for users who have no experience in informatics and, therefore, rely on the keyword search on ImmPort’s web page. To address this critical need, we will develop an interactive cross-study data exploration and visualization user interface for data in the ImmPort model including the functionality to create cross-study exports. The data newly structure into the ImmPort model as well as the user interface will be integrated into ImmPort and its web page. The treatments of several diseases (e.g. allergies, organ transplantation) rely on the induction of immune tolerance. In ImmPort serval studies focus on different diseases but with the underlying topic of immune tolerance. We will perform a secondary analysis of the shared individual-level clinical and mechanistic data of these studies towards the identification of potential universal drivers of developing clinical immune tolerance. This analysis will be used to develop a step-by-step tutorial for the interactive user interface.

项目概要/摘要 生物医学研究数据的共享有助于研究结果的独立验证和未来临床的设计 免疫学数据库和数据重用是共享数据的一个平台。 分析门户 (ImmPort)，一个公共仓库，提供对来自以下组织的临床和机械数据的开放访问 目前，除了有价值的高通量数据元素外，ImmPort 还进行了 341 项免疫学和临床研究。 ImmPort 中的许多临床研究都提供对个人水平数据的访问。 与它们相关的大量数据未注释并解析到结构化 ImmPort MySQL 中 数据库模型，但以各种不同格式作为单独的文件提供。在这种形式中，数据不是。 随时可用于数据挖掘或二次分析，我们将优先考虑来自临床的非结构化数据。 我们进一步研究集成到结构化 MySQL ImmPort 模型中，以促进更好的访问和重用。 将协调数据库中所使用的词汇，但尚未建立首选术语 目前，ImmPort 中跨研究的可用数据挖掘非常受关注。 对于没有信息学经验并因此依赖关键字搜索的用户来说是一个挑战 为了满足这一关键需求，我们将开发交互式交叉研究数据探索。 ImmPort 模型中数据的可视化用户界面，包括创建交叉研究的功能 新构建到 ImmPort 模型中的数据以及用户界面将被集成到其中。 ImmPort 及其网页对多种疾病（例如过敏、器官移植）的治疗依赖于 在 ImmPort 中，多项研究关注不同的疾病，但都有其潜在的基础。 我们将对共享的个体水平的临床和免疫耐受的主题进行二次分析。 这些研究的机制数据旨在确定开发临床药物的潜在普遍驱动因素 该分析将用于开发交互式用户界面的分步教程。