Rolland Clara, Wittmann Johannes, Reimer Lorenz C, Sardà Carbasse Joaquim, Schober Isabel, Dudek Christian-Alexander, Ebeling Christian, Koblitz Julia, Bunk Boyke, Overmann Jörg
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany.
Nucleic Acids Res. 2025 Jan 6;53(D1):D819-D825. doi: 10.1093/nar/gkae878.
Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.dsmz.de), a comprehensive database for prokaryotic viruses gathering all existing data dispersed across multiple sources, like scientific publications, specialized databases or internal files of culture collections. PhageDive allows to link own research data to the existing information through an easy and central access, providing fields for various experimental data (host range, genomic data, etc.) and available metadata (e.g. geographical origin, isolation source). An important feature is the link between experimental data, the culture collection number and the repository of the corresponding physical bioresource. To date, PhageDive covers 1167 phages from three different world-renowned public collections (DSMZ, Félix d'Hérelle Reference Center for Bacterial Viruses and NCTC) and features an advanced search function using all data fields from the sections like taxonomy or morphology by controlled vocabulary and ontologies. PhageDive is fully interoperable with other resources including NCBI, the Viral Host Range database (VHRdb) of Institute Pasteur or the BacDive and MediaDive databases of DSMZ.
原核生物病毒是地球上种类最多、数量最丰富的生物实体。到目前为止，关于噬菌体的数据尚未标准化，无法轻易获取用于比较分析，也无法与快速增长的（宏）基因组数据相联系。我们开发了PhageDive（https://phagedive.dsmz.de），这是一个关于原核生物病毒的综合数据库，它收集了分散在多个来源的所有现有数据，如科学出版物、专业数据库或培养物保藏中心的内部文件。PhageDive允许通过便捷的集中访问将自己的研究数据与现有信息相链接，提供了用于各种实验数据（宿主范围、基因组数据等）和可用元数据（如地理来源、分离来源）的字段。一个重要的特点是实验数据、培养物保藏编号与相应实物生物资源库之间的链接。到目前为止，PhageDive涵盖了来自三个不同世界知名公共保藏中心（德国微生物和细胞培养物保藏中心、费利克斯·德赫雷尔细菌病毒参考中心和英国国家典型菌种保藏中心）的1167种噬菌体，并具有先进的搜索功能，可使用分类学或形态学等部分中的所有数据字段，通过控制词汇和本体进行搜索。PhageDive可与其他资源完全互操作，包括美国国立医学图书馆国家生物技术信息中心、巴斯德研究所的病毒宿主范围数据库（VHRdb）或德国微生物和细胞培养物保藏中心的BacDive和MediaDive数据库。
