GUDMAP- Database and Website

GUDMAP-数据库和网站

• 批准号: 9332529
• 负责人: Richard Alan Baldock
• 金额: $ 12万
• 依托单位: UNIVERSITY OF EDINBURGH
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9332529
• 关键词: 4D Imaging; Adult; Anatomy; Apache; Atlases; Bioinformatics; Biological Process; Biomedical Research; Cancer-Related Condition; Cells; Communities; Computer software; Data; Data Analyses; Data Collection; Data Security; Data Set; Databases; Defect; Development; Disease; Doctor of Philosophy; Education and Outreach; Extensible Markup Language; Gene Expression; Genes; Genitourinary system; Goals; Health; High-Throughput Nucleotide Sequencing; Homeostasis; Image; Image Analysis; Imagery; Imaging Device; Improve Access; In Situ; In Situ Hybridization; Inflammatory; Internet; Knowledge; Link; Maintenance; Manuals; Messenger RNA; Molecular; Mouse Strains; Mus; Ontology; Organ; Organism; Pathway Analysis; Pathway interactions; Pattern; Phenotype; Principal Investigator; Procedures; Process; Protocols documentation; Quality Control; Research; Resolution; Resources; Retrieval; Running; Secure; Services; Staging; System; Techniques; Three-Dimensional Image; Time; Tissues; Update; Urinary system; Vertebrates; cell type; comparative; crosslink; data access; data sharing; data to knowledge; design; disease phenotype; editorial; improved; indexing; interoperability; meetings; mutant; open source; operation; outreach; protein expression; protein metabolism; repository; tool; transcriptome sequencing; web services; web site

DESCRIPTION (provided by applicant): The goal of the Genitourinary Development Molecular Anatomy Project website and database (GUDMAP WebDB) is to deliver research-enabling data and knowledge to the biomedical research community on the molecular development of all organs within the genitourinary (GU) tract. GUDMAP WebDB provides curated and validated gene and protein expression data, links to disease and tools for analysis, each of which serve to improve our understanding of the biological processes that underpin normal and abnormal GU development, homeostasis, and disease processes. Defects in organs ofthe GU tract involve developmental, inflammatory, infectious, and cancer -related conditions are represent a growing health burden internationally. The primary goals maintain and extend the GUDMAP WebDB to a broader range of data pertinent to both GU development and disease. The core objective provides a repository for retrieval and analysis of GU data, additional depth will be accomplished by an outreach effort to capture data, knowledge and expertise using curators and the development of new interfaces and tools. Specific aims are: Aim 1: Development of Core Services - continued development to deliver robust editorial function with full online submission and tracking, outreach, extended data types, improved simple and advanced query interfaces, enhanced ontology, support for GUDMAP 2 Aim 2: Extension of Data and Resources - extend stage range, adult and non-murine systems, high- throughput sequencing data including RNA-seq and ChlP-seq tracks and summaries, multi-modal 2/3D image data, phenotype/disease associations, full online submission and annotation. Aim 3: Improvement of Bioinformatics and Analysis - extended cross-platform and comparative analysis, networks and pathways, manual and automated image analysis for phenotype. Aim 4; Enhancement of Integration and Interoperability - user interfaces for user-specific data-collections and analyses, extended resource links and cross-indexing (MGl/GXD), interfaces for DB interoperability (BioMArt, geneDas and web-services), Web 2.0 interfaces for configurable views, analysis and data sharing.

描述(由申请人提供)：生殖道发育分子解剖学项目网站和数据库(GUDMAP WebDB)的目标是向生物医学研究界提供关于生殖道(GU)内所有器官的分子发育的研究数据和知识。GUDMAP WebDB提供经过管理和验证的基因和蛋白质表达数据、疾病链接和分析工具，其中每一个都有助于提高我们对支撑正常和异常GU发育、体内平衡和疾病过程的生物过程的理解。胃肠道器官缺陷涉及发育性、炎症性、感染性和癌症相关的疾病，在国际上是一个日益严重的健康负担。主要目标是维护GUDMAP WebDB，并将其扩展到与GU发育和疾病相关的更广泛的数据。核心目标是提供一个用于检索和分析GU数据的储存库，将通过利用馆长和开发新的界面和工具开展外展工作，收集数据、知识和专门知识，从而实现更深层次的工作。具体目标是：目标1：开发核心服务--继续开发，以提供强大的编辑功能，提供全面的在线提交和跟踪、外联、扩展的数据类型、改进的简单和高级查询界面、增强的本体、支持GUDMAP 2：扩展数据和资源--扩展阶段范围、成人和非小鼠系统、高通量测序数据，包括RNA-seq和Chlp-seq轨迹和摘要、多模式2/3D图像数据、表型/疾病关联、完整的在线提交和注释。目标3：改进生物信息学和分析-扩展跨平台和比较分析、网络和途径、手动和自动图像分析表型。目标4；加强一体化和互操作性--针对具体用户的数据收集和分析的用户界面、扩展的资源链接和交叉索引(MGL/GXD)、数据库互操作性的界面(BioMart、GeneDas和网络服务)、用于可配置视图、分析和数据共享的Web 2.0界面。

项目成果

Developing the eHistology Atlas.

开发电子组织学图谱。

• DOI: 10.1093/database/bav105
• 发表时间: 2015
• 期刊: Database : the journal of biological databases and curation
• 作者: Richardson,Lorna;Graham,Liz;Moss,Julie;Burton,Nick;Roochun,Yogmatee;Armit,Chris;Baldock,RichardA
• 通讯作者: Baldock,RichardA

Access and use of the GUDMAP database of genitourinary development.

• DOI: 10.1007/978-1-61779-851-1_17
• 发表时间: 2012-01-01
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Davies, Jamie A;Little, Melissa H;Baldock, Richard
• 通讯作者: Baldock, Richard