Apollo - Universal Infrastructure for Genome Curation

项目总结 在过去的十年里，基因组测序的成本已经大幅降低，而自然的 结果是越来越多的研究人员正在对越来越多的新基因组进行测序， 无论是在种群内还是跨物种。这些研究人员中的每一位都在收集关于 定期，但他们的协作和共享信息和专业知识的能力可能会因缺席而受到限制 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 这使得分散的研究人员能够交互地探索和提炼准确的基因组结构 通过信息性可视化进行注释。我们现在建议扩展该工具，目标是完全嵌入 基因组“众包”进入研究生命周期，提升数据的数量和效用 由系统处理。我们将整合更多用于分析注释的工具(例如，蛋白质基序、多个 序列比对、蛋白质家族放置和推断的功能) 工具和服务，如Galaxy、InterPro和Track Hub；并将提供更广泛的自动 提交前的检查和质量措施。阿波罗既是一个编辑环境，也是一个 协作通信中心，这将显著增加生物信息量 可用于分析基因组规模的人类数据集，从而产生对人类疾病的更多见解 风险、进展和潜在的治疗方法。关键的是，所有来自科学家在这个合作项目中的贡献 研究环境将被单独识别(使用ORCID)，以确保给予应有的信任，并确保 每个带注释的基因组特征的来源都是可用的。 为了实现这一愿景，我们概述了一系列具体目标，并制定了详细的技术计划。我们会 实施更精简、更可扩展的安装程序，以简化新的 被测序的生物体。我们将提供标准化的API，为集成新的 针对个人和社区需求量身定做的功能和工作流。我们将开发一个独立的验证 包，以加快将修订后的基因集与以前的版本合并，以及在 注释过程。我们将实现一个逐个批注的消息传递系统，以使馆长能够 解释他们的决定，并与其他人讨论他们的推理。我们将实施产地制度，以 为贡献研究人员提供科学学分。我们将引入对多个 并更好地利用来自同源搜索的进化信息，以改进 批注一致性和节省馆长时间。我们将使阿波罗既能发挥‘跟踪服务器’的作用，又能 通过EnSembl浏览器(或其他浏览器)动态地共享新的注释，并相互充当‘音轨’ 客户端‘，以显示从EBI或UCSC中心拉出的曲目。最后，我们会与社会各界共同努力， 获取增强功能的反馈，并互惠提供培训和文档。

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.