Microarray Data Standards and Supporting Applications

微阵列数据标准和支持应用程序

• 批准号: 6905830
• 负责人: CATHERINE A BALL
• 金额: $ 54.59万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-08-23 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6905830
• 关键词: bioinformatics; biomedical resource; computational biology; computer program /software; computer system design /evaluation; data quality /integrity; gene expression; microarray technology; molecular biology information system

DESCRIPTION (provided by applicant): This application proposes to obtain formal funding to provide the functional genomics community with tools and resources to use standard formats and practices to communicate their data. Our group, the Microarray Gene Expression Data Society (MGED), is an international organization of biologist, computer scientists and data analysts whose aim is to promote and extend experimental science by providing the infrastructure and resources for sharing microarray and other large-scale biological data. This infrastructure includes standards for exchange and annotation of these data and supporting software that provides a common ground for the development of databases and data acquisition, management and analysis tools based on these standards. MGED resources (MIAME, MAGE-ML, MAGE-stk and the MGED Ontology) are already in widespread use, so this grant application seeks funding to improve them, develop new features and to provide dependable support to the research and computational communities using MGED resources. Each specific aim is closely tied to at least one other aim, continuing the close and collaborative work that has been the hallmark of MGED. In addition, each of the aims will require communication with the larger research community, both to obtain criticism and feedback, as well as to provide access to resources and assistance in using them. All software produced will continue to be freely available under the MIT Open Source license, and co-development by others will be facilitated by frequent software development "jamborees." We propose to extend and improve the MAGE Object Model, develop and disseminate an advanced MAGE software toolkit, research and create data quality metrics for microarray data, extend and communicate ontologies for describing microarray experiments, develop and provide tools for validating documents for MIAME compliance and MAGE formatting and to develop freely available tools that allow us to share data.

描述（由申请人提供）：本申请建议获得正式资助，为功能基因组学界提供工具和资源，以使用标准格式和实践来交流数据。我们的团体微阵列基因表达数据协会 (MGED) 是一个由生物学家、计算机科学家和数据分析师组成的国际组织，其目标是通过提供共享微阵列和其他大规模生物数据的基础设施和资源来促进和扩展实验科学。 。该基础设施包括这些数据的交换和注释标准以及支持软件，该软件为基于这些标准的数据库和数据采集、管理和分析工具的开发提供了共同基础。 MGED 资源（MIAME、MAGE-ML、MAGE-stk 和 MGED 本体）已得到广泛使用，因此本次拨款申请寻求资金来改进它们、开发新功能，并为使用 MGED 资源的研究和计算社区提供可靠的支持。每一项具体目标都与至少一个其他目标密切相关，继续密切协作，这一直是 MGED。此外，每个目标都需要与更大的研究界进行沟通，以获得批评和反馈，并提供资源的获取和使用资源的帮助。所生产的所有软件将继续在麻省理工学院开源许可证下免费提供，并且频繁的软件开发“盛会”将促进其他人的共同开发。 我们建议扩展和改进 MAGE 对象模型，开发和传播先进的 MAGE 软件工具包，研究和创建微阵列数据的数据质量指标，扩展和交流用于描述微阵列实验的本体，开发和提供用于验证 MIAME 合规性文档的工具和MAGE 格式化并开发免费可用的工具，使我们能够共享数据。