Data integration and analysis for mapping malaria parasite traits

用于绘制疟疾寄生虫特征的数据集成和分析

• 批准号: 9751190
• 负责人: Scott Emrich
• 金额: $ 17.04万
• 依托单位: UNIVERSITY OF NOTRE DAME
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9751190
• 关键词: African; Archives; Bioinformatics; Biological; Cancer Biology; Communication; Communities; Computing Methodologies; Data; Data Analyses; Data Collection; Data Set; Deposition; Development; Drug Combinations; Drug resistance; Ensure; Experimental Genetics; Gap Junctions; Genetic; Genetic Crosses; Genotype; Individual; Label; Letters; Link; Malaria; Metadata; Modeling; National Institute of Allergy and Infectious Disease; Network-based; Orphan; Parasites; Participant; Pharmaceutical Preparations; Phenotype; Policies; Process; Quantitative Trait Loci; Recombinants; Research; Research Personnel; Resources; Standardization; System; Time; Transcript; United States National Institutes of Health; Work; base; computer infrastructure; data archive; data integration; data resource; data sharing; data warehouse; drug response prediction; improved; insight; interest; protein metabolite; recruit; response; trait

ABSTRACT The ability to conduct targeted genetic crosses in malaria provides exciting opportunities to uncover genetic mechanisms linked to drug resistance. Core B will provide a centralized resource for all project data, standardized bioinformatics analysis, the integrated, network-based analysis required by RP02 and RP03. All of these data and results will then be deposited in relevant public resources. Extensive –omics data will be collected for each progeny clone (i.e., transcripts, proteins and metabolites) and deposited in public archives by Core C. Because such data from the large numbers of unique recombinant progeny provided by Core A/RP01 are more powerful when integrated, Core B will maintain the required computational infrastructure to standardize project metadata and link genotypes to collected phenotypes. In tandem with RP02, Core B serves as the focal point of all project data. Because our efforts will also generate specialized metadata for which no standard archives exist, we will work closely with EuPathDB to ensure timely and relevant community access of all Project data. Providing standard analysis and significant hardware resources will also open up new avenues of integrated data analysis within the Project, which in turn will be shared via EuPathDB. Further, these significant, metadata- labeled collections of data will provide an extremely rich resource for bioinformaticians and computational biologists. Although publically available datasets of this scope and size are only available for cancer biology, they have been invaluable in the development of computational methods, e.g., predicting drug combination efficiency. We imagine our resource would be just as popular and recruit many participants to improve prediction of drug responses and other biological traits in malaria parasites. In addition to a letter of support from EupathDB on community access, we also include a letter from African researchers who are already highly interested in this data resource.

抽象的 在疟疾中进行有针对性的基因杂交的能力为揭示遗传基因提供了令人兴奋的机会 与耐药性相关的机制。 Core B将为所有项目数据提供集中资源， 标准化生物信息学分析，即 RP02 和 RP03 所需的集成的、基于网络的分析。全部 这些数据和结果将存入相关公共资源。 将为每个后代克隆收集广泛的组学数据（即转录本、蛋白质和代谢物） 由 Core C 存放在公共档案中。因为这些数据来自大量独特的重组体 Core A/RP01 提供的后代在集成时更加强大，Core B 将保持所需的 计算基础设施标准化项目元数据并将基因型与收集的表型联系起来。在 与 RP02 一起，Core B 成为所有项目数据的焦点。因为我们的 努力也会产生 不存在标准档案的专门元数据，我们将与 EuPathDB 密切合作，以确保及时 以及所有项目数据的相关社区访问权限。 提供标准分析和重要的硬件资源也将开辟集成的新途径 项目内的数据分析，进而将通过 EuPathDB 共享。此外，这些重要的元数据- 带标签的数据集合将为生物信息学家和计算提供极其丰富的资源 生物学家。尽管这种范围和规模的公开数据集仅适用于癌症生物学， 它们在计算方法的发展中具有无价的价值，例如预测药物组合 效率。我们想象我们的资源会同样受欢迎并招募许多参与者来改进预测 疟疾寄生虫的药物反应和其他生物学特征。除了 EupathDB 的支持信 关于社区访问，我们还附上​​了一封来自非洲研究人员的信，他们对此非常感兴趣 数据资源。