Apollo - Universal Infrastructure for Genome Curation

Apollo - 基因组管理的通用基础设施

• 批准号: 10176512
• 负责人: Ian H Holmes
• 金额: $ 35.12万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2022-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10176512
• 关键词: Address; Amino Acid Motifs; Architecture; Archives; Authorization documentation; Back; Biological; Biological Process; Biology; Client; Communication; Communities; Complex; DNA sequencing; Data; Data Set; Documentation; Elements; Environment; Face; Feedback; Galaxy; Genes; Genome; Genomics; Goals; Growth and Development function; Health; Human; Individual; Infrastructure; Institution; Internet; Investigation; Learning; Maintenance; Measures; Methods; Modification; Online Systems; Organism; Phylogenetic Analysis; Population; Procedures; Process; Production; Protein Family; Public Domains; Publishing; Quality Control; Registries; Research; Research Personnel; Resources; Scientist; Sequence Alignment; Series; Services; Spottings; Standardization; Structure; Synteny; System; Technology; Time; Training; Update; Validation; Vision; Visualization; Work; base; biological research; collaborative environment; comparative; cost; crowdsourcing; data resource; design; disorder risk; flexibility; genome analysis; genome annotation; genome editing; genome-wide; genome-wide analysis; genomic data; human disease; improved; indexing; insight; interest; online resource; peer; structural genomics; success; support tools; tool

PROJECT SUMMARY The cost of sequencing a genome has been dramatically reduced in the last decade, and the natural consequence is that an ever-growing number of researchers are sequencing more and more new genomes, both within populations and across species. Each of these researchers are collecting genomic information on a regular basis, but their ability to collaborate and share information and expertise cab be limited by the absence of supporting tools. To address this need, we have developed Apollo, an easy to use web-based environment that empowers distributed researchers to interactively explore and refine accurate genomic structural annotations via informative visualizations. We now propose to extend this tool with the goal fully embedding genomic ‘crowdsourcing’ into the research lifecycle, upscaling the volume and utility of data that can be processed by the system. We will incorporate more tools for profiling annotations (e.g. protein motifs, multiple sequence alignments, protein family placement, and inferred function) by integrating Apollo with the external tools and services, such as Galaxy, InterPro, and track hubs; and will provide a broader range of automatic checks and quality measures prior to submission. Apollo will serve both as an editing environment and as a collaborative communications center, which will dramatically increase the amount of biological information that can be used in analysis of genome-scale human datasets generating additional insights into human disease risk, progression and potential therapies. Critically, all contributions from scientists working in this collaborative research environment will be individually recognized (using ORCIDs) to assure due credit is given and that the provenance of each annotated genomic feature is available. To realize this vision, we have outlined a series of specific aims, supported by detailed technical plans. We will implement a more streamlined, scalable setup procedure to ease installation and deployment for newly sequenced organisms. We will provide a standardized API providing a platform for the integration of new capabilities and workflows tailored to individual and community needs. We will develop a stand-alone validation package to expedite merging revised gene sets with prior versions, as well as real-time quality control during the annotation process. We will implement an annotation-by-annotation, messaging system to enable curators to explain their decisions and discuss their reasoning with others. We will implement a provenance system to provide scientific credit to contributing researchers. We will introduce support for the co-curation of multiple related genomes and make better use of evolutionary information from homology searches, to improve annotation consistency and save curator time. We will enable Apollo to function both as a ‘Track Server’, to dynamically share new annotations via the Ensembl browser (or others), and reciprocally to act as a ‘Track Client’, to display tracks pulled from either the EBI or UCSC hubs. Lastly, we will engage with the community to obtain feedback for enhancements, and reciprocally provide training and documentation.

项目摘要 在过去的十年里，基因组测序的成本已经大大降低， 结果是越来越多的研究人员正在测序越来越多的新基因组， 无论是在种群内还是在物种间。这些研究人员中的每一个都在收集一个基因组信息， 但由于没有这些人员，他们合作和分享信息及专门知识的能力可能受到限制 支持工具。为了满足这一需求，我们开发了Apollo，一个易于使用的基于Web的环境 使分散的研究人员能够交互式地探索和改进精确的基因组结构， 通过信息可视化进行注释。我们现在建议扩展此工具，目标是完全嵌入 将基因组“众包”纳入研究生命周期，提升数据的数量和效用， 由系统处理。我们将整合更多的工具来分析注释（例如，蛋白质基序，多个 序列比对，蛋白质家族的位置和推断的功能），通过整合阿波罗与外部 工具和服务，如银河，InterPro和跟踪中心;并将提供更广泛的自动 提交前的检查和质量措施。Apollo将作为编辑环境和 协作通信中心，这将大大增加生物信息的数量， 可用于分析基因组规模的人类数据集，从而对人类疾病产生更多的见解 风险、进展和潜在治疗。重要的是，在这个合作项目中工作的科学家的所有贡献 研究环境将被单独认可（使用ORCID），以确保给予应有的信用， 每个注释的基因组特征的来源是可用的。 为了实现这一愿景，我们概述了一系列具体目标，并辅以详细的技术计划。我们将 实施更精简、可扩展的安装过程，以简化新的 测序生物我们将提供一个标准化的API，为新的 根据个人和社区需求量身定制的功能和工作流程。我们将开发一个独立的验证 包，以加快合并修订的基因集与以前的版本，以及实时质量控制， 注释过程。我们将实现一个逐个注释的消息传递系统， 解释他们的决定，并与他人讨论他们的推理。我们将实施来源系统， 为有贡献的研究人员提供科学荣誉。我们将引入对多个 相关基因组，并更好地利用同源性搜索的进化信息，以提高 注释一致性和节省策展人的时间。我们将使阿波罗既能作为“跟踪服务器”， 通过Ensembl浏览器（或其他浏览器）动态共享新注释，并将其设置为“跟踪” 客户端“，以显示从EBI或UCSC集线器提取的曲目。最后，我们将与社区合作， 获得增强的反馈，并提供培训和文档。