South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, University of the Western Cape, Bellville, 7535, South Africa.
Bioinformatics. 2020 Feb 1;36(3):982-983. doi: 10.1093/bioinformatics/btz658.
Recent advancements in genomic technologies have enabled high throughput cost-effective generation of 'omics' data from M.tuberculosis (M.tb) isolates, which then gets shared via a number of heterogeneous publicly available biological databases. Albeit useful, fragmented curation negatively impacts the researcher's ability to leverage the data via federated queries.
We present Combat-TB-NeoDB, an integrated M.tb 'omics' knowledge-base. Combat-TB-NeoDB is based on Neo4j and was created by binding the labeled property graph model to a suitable ontology namely Chado. Combat-TB-NeoDB enables researchers to execute complex federated queries by linking prominent biological databases, and supplementary M.tb variants data from published literature.
The Combat-TB-NeoDB (https://neodb.sanbi.ac.za) repository and all tools mentioned in this manuscript are freely available at https://github.com/COMBAT-TB.
Supplementary data are available at Bioinformatics online.
最近基因组技术的进步使得能够从结核分枝杆菌 (M.tb) 分离物中高通量、经济高效地生成‘组学’数据,然后通过许多异构的公共可用生物数据库进行共享。尽管这些数据很有用,但碎片化的管理会降低研究人员通过联合查询利用这些数据的能力。
我们提出了 Combat-TB-NeoDB,这是一个集成的 M.tb‘组学’知识库。Combat-TB-NeoDB 基于 Neo4j 构建,通过将标记属性图模型绑定到适当的本体 Chado 来创建。Combat-TB-NeoDB 使研究人员能够通过链接突出的生物数据库以及来自已发表文献的补充 M.tb 变体数据来执行复杂的联合查询。
Combat-TB-NeoDB(https://neodb.sanbi.ac.za)存储库和本文档中提到的所有工具均可在 https://github.com/COMBAT-TB 上免费获得。
补充数据可在 Bioinformatics 在线获取。