Sustaining Flybase: The Drosophila genomic and genetic database

FlyBase是一个生物信息学资源，用于从文献和大规模数据生成项目中获取、组织和呈现有关果蝇基因组学和遗传学的核心信息。FlyBase为果蝇遗传和基因组数据提供了一个开放访问的集中资源，使世界各地的果蝇社区和更广泛的生物医学科学界的研究人员和教育工作者能够进一步开展他们的研究。果蝇是最重要的模式生物之一，在阐明遗传和发育机制的基本原理方面提供了经济有效的帮助。FlyBase有三个主要目标。首先，它整理了与果蝇研究相关的文献和试剂，这样研究人员就可以继续依靠FlyBase找到该领域的最新创新。FlyBase优先处理与基因表达、细胞功能、信号通路和与人类生物学相关的结果相关的数据集，并以直观、集成、易于搜索的格式显示信息。其次，它努力通过管理和整合相关数据集，并开发能够更好地获取这一丰富数据的工具，努力对更广泛的遗传学和群体遗传学社区具有价值。最后，它寻求开发和集成工具以扩大其效用。FlyBase以这一身份非常成功地为科学界服务的历史由来已久。FlyBase与其他模式生物数据库(MODS)密切合作，整合数据集并开发工具，以实现跨物种分析。NSF的资助使FlyBase得以维持其三项主要活动。对FlyBase的运作至关重要的活动包括：自动分类流水线；以基因组特征管理和物理交互管理为重点的全面基因管理；人类疾病模型管理；基于等位基因的疾病模型管理；基因组管理；被认为是FlyBase用户社区最感兴趣的数据集的管理；在FlyBase参考文献中导入图形摘要；识别新的lncRNAs、反义lncRNAs和smORFs；将现有的转录起始点数据并入FlyBase；添加新的解剖学术语；审查和改进表型类本体论；开发基因组和人类疾病模型的数据库模块；所有果蝇细胞类型的注释和scRNAseq数据集的整理；更新所有果蝇遗传参考小组(DGRP)品系的基因组序列；扩展路径页面资源。为了促进综合分析和方法，FlyBase通过整合和展示大规模研究、转录组和蛋白质组学数据集，继续扩大其作为平台的用途。此外，FlyBase改进了社区内可用工具的访问和显示，并整合了最有用的数据集和可视化复杂数据集的工具，使更多的研究人员能够采取更全球化的方法进行他们的基因研究。通过支持FlyBase数据的计算数据库管道基础设施，国家科学基金会的资金可以继续与现有基础设施的持续运行和维护相协调，从而能够在生物科学领域进行发现。FlyBase将维护和进一步开发存储所有FlyBase数据的中央数据库；管理将更多精选或大规模数据纳入数据库；制作每周内部报告和双月输出，并转换为公共FlyBase服务器的更新；与NCBI密切合作，将与基因组注释相关的数据纳入FlyBase，并定期向GenBank提交全基因组注释更新。总的来说，这些活动最大限度地发挥了果蝇的基本研究对发现和翻译的影响。通过他们在执行这些任务中的作用，FlyBase将继续帮助果蝇研究尽可能快地推进，以通过http://flybase.orgThis奖项反映美国国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

FlyBase is a bioinformatics resource to capture, organize and present core information on Drosophila (fly) genomics and genetics, both from literature and large-scale data generation projects. FlyBase provides an openly accessible centralized resource for Drosophila genetic and genomic data to enable researchers and educators worldwide both in the Drosophila community and broader biomedical sciences community to further their research. Drosophila is one of the premier model organisms and provides cost-effective help in elucidating the basic tenets of genetic and developmental mechanisms. FlyBase has three main goals. First, it curates literature and reagents relevant to Drosophila research, so that researchers can continue to rely on FlyBase to find the latest innovations in the field. FlyBase prioritizes curation of data sets relevant to gene expression, cellular functions, signaling pathways, and results relevant to human biology, and displays the information in an intuitive, integrated, readily searchable format. Secondly, it strives to be of value to the broader genetics and population genetics communities, by curating and integrating relevant data sets, and developing tools that enable better access to this wealth of data. Finally, it seeks to develop and integrate tools to expand it's utility. FlyBase has a long history of very successfully serving the scientific community in this capacity. FlyBase works closely with other Model Organism Databases (MODs) to integrate data sets and develop tools to enable cross-species analyses. NSF funding allows FlyBase to maintain its three main activities.Activities essential to the operation of FlyBase include: Automated triaging pipeline; Full genetic curation with emphasis on genome feature curation and physical interaction curation; Human disease model curation; Allele-based curation of disease models based on the Disease Ontology; Gene Group curation; Curation of datasets deemed to be of highest general interest to the FlyBase user community; Import of graphical abstracts in FlyBase references; Identification of new lncRNAs, anti-sense lncRNAs and smORFs; Incorporation of available transcription start site data into FlyBase; Addition of new anatomy terms; Review and improvement of phenotypic class ontologies; Development of database modules for gene groups and human disease models; Annotation of all Drosophila cell types and curation of scRNAseq data sets; Update of the genomic sequences of all Drosophila Genetic Reference Panel (DGRP) strains; Expansion of a Pathway page resource. To facilitate integrative analyses and approaches FlyBase continues to expand its utility as a platform by integrating and displaying large-scale studies, transcriptomics and proteomics data sets. In addition, FlyBase improves access and display of tools available within the community, and incorporates the most useful data sets and tools for visualizing complex data sets to enable more researchers to take a more global approach to their genetic research. NSF funding allows for continued coordination with the ongoing operation and maintenance of the existing infrastructure to enable discovery in the biological sciences by supporting the computational database pipeline infrastructure of FlyBase data. FlyBase will maintain and further develop the central database that houses all FlyBase data; manage the incorporation of additional curated or large-scale data into the database; produce weekly internal reports and bi-monthly outputs that are transformed into the updates to the public FlyBase servers; work closely with NCBI to incorporate genome annotation-related data into FlyBase and to submit periodic whole genome annotation updates to GenBank. Collectively, these activities maximize the impact of essential Drosophila research on discovery and translation. Through their role in carrying out these missions, FlyBase will continue to help Drosophila research advance as quickly as possible for the ultimate benefit of various scientific communities via http://flybase.orgThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.