Human genomics analysis interface for FaceBase 2

FaceBase 2 的人类基因组学分析接口

• 批准号: 8724830
• 负责人: Mary L. Marazita
• 金额: $ 23.06万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-01 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8724830
• 关键词: Animal Model; Bioinformatics; Cataloging; Catalogs; Clinical; Communication; Communities; Computer software; Data; Data Analyses; Data Display; Data Set; Data Storage and Retrieval; Databases; Development; Enrollment; Ensure; FaceBase; Family; Funding; Gene Expression; Genome; Genomics; Goals; Health; Home environment; Human; Human Genetics; Image; Imagery; Individual; Location; Metadata; Modeling; Mus; National Institute of Dental and Craniofacial Research; Ontology; Phase; Policies; Procedures; Process; Protocols documentation; Recruitment Activity; Research; Research Infrastructure; Research Personnel; Resources; Sampling; Secure; Shapes; Software Tools; System; Work; Zebrafish; base; biobank; comparative; craniofacial; data integration; data management; data modeling; database of Genotypes and Phenotypes; experience; genetic analysis; genome wide association study; improved; meetings; novel; phenome; repository; software development; success; tool; web site

ABSTRACT There are now several large human genomics databases relevant to craniofacial research, including multiple databases funded in part by the first FaceBase consortium. Direct access to the individual level data from such databases can be cumbersome, therefore the current project seeks to make analysis of pertinent genomics data available to FaceBase users without releasing the individual level data. The current project has three major goals in order to develop a genomics analysis interface for FaceBase 2. GOAL 1: To develop a software interface that will enable FaceBase users to apply human genetics analysis software (e.g. PLINK) to human genomics data from craniofacial research, with access to these tools through the FaceBase 2 Hub. NOTE: no individual level data will be available to FaceBase users; the data for analysis will be located on a secure location of the FaceBase 2 Hub. The purpose of these tools is to allow FaceBase users to explore genomics data (e.g. GWAS, sequencing) in order to ask research questions or to decide whether to download the underlying data from its home data repository (dbGaP in most cases). GOAL 2: To identify pertinent genomics data on dbGaP, and/or within the craniofacial research community that would then be incorporated into the above system (i.e. no access to individual level data through FaceBase, only the ability to query/analyze the data). Some of the data to be made available was created as part of FaceBase I spoke projects (Beaty, Spritz, and Weinberg/Marazita spoke projects). GOAL 3: To create analysis results datasets to make available on FaceBase, and also data tracks for the UCSC genome browser (or other repositories designated by the FaceBase 2 Hub) from the human genomics results. This will make such results immediately available to FaceBase users, and also available to a wider audience through the genome browser or other centralized analysis results databases.

摘要 现在有几个与颅面研究相关的大型人类基因组数据库，包括由第一个FaceBase财团部分资助的多个数据库。从这些数据库直接访问个人层面的数据可能很麻烦，因此目前的项目旨在使FaceBase用户可以获得相关基因组学数据的分析，而不发布个人层面的数据。目前的项目有三个主要目标，以便为FaceBase 2开发基因组学分析界面。 目标1：开发一个软件界面，使FaceBase用户能够将人类遗传学分析软件（例如PLINK）应用于颅面研究的人类基因组数据，并通过FaceBase 2 Hub访问这些工具。注：FaceBase用户将无法获得个人级别的数据;用于分析的数据将位于FaceBase 2 Hub的安全位置。这些工具的目的是允许FaceBase用户探索基因组学数据（例如GWAS，测序），以便提出研究问题或决定是否从其家庭数据存储库（大多数情况下为dbGaP）下载基础数据。目标2：识别dbGaP上和/或颅面研究社区内的相关基因组学数据，然后将其纳入上述系统（即不能通过FaceBase访问个人水平数据，只能查询/分析数据）。一些可用的数据是作为FaceBase I spoke项目（Beaty，Spritz和温伯格/Marazita spoke项目）的一部分创建的。目标3：从人类基因组学结果中创建分析结果数据集以在FaceBase上提供，以及UCSC基因组浏览器（或FaceBase 2 Hub指定的其他存储库）的数据跟踪。这将使这些结果立即提供给FaceBase用户，并通过基因组浏览器或其他集中分析结果数据库提供给更广泛的受众。