Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
Nucleic Acids Res. 2019 Jan 8;47(D1):D821-D827. doi: 10.1093/nar/gky961.
PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases.
PomBase（www.pombase.org）是裂殖酵母 Schizosaccharomyces pombe 的模式生物数据库，它经历了全面的重新开发，从而提供了更全面、更高效的服务。新的基础设施支持每日数据更新，以及更快速、高效的查询和页面内及页面间的流畅导航。新的出版物和基因型页面分别提供了从单一来源整理的所有数据以及与特定基因型相关的所有表型的访问途径。对于基于本体论的注释，改进的显示方式在易用性和全面的数据覆盖之间取得了平衡。默认视图现在使用本体论结构提供简洁、非冗余的摘要，可以展开以显示底层细节和元数据。表型注释显示还提供了筛选选项，允许用户专注于特定感兴趣的领域。集成了一个 JBrowse 基因组浏览器实例，方便加载和直观访问基因组规模的数据集。总之，新的数据和页面以及注释显示和查询的改进，使用户能够探测不同类型数据之间的联系，形成对裂殖酵母生物学的全面视图。新的 PomBase 实现还提供了丰富的模块化、可重用工具集，可用于创建新的或增强现有的特定于生物体的数据库。
