Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico.
Grupo de Investigación de Bioinformática, Universidad de las Ciencias Informáticas (UCI), CP 17100, La Habana, Cuba.
Bioinformatics. 2019 Nov 1;35(22):4739-4747. doi: 10.1093/bioinformatics/btz260.
Bioactive peptides have gained great attention in the academy and pharmaceutical industry since they play an important role in human health. However, the increasing number of bioactive peptide databases is causing the problem of data redundancy and duplicated efforts. Even worse is the fact that the available data is non-standardized and often dirty with data entry errors. Therefore, there is a need for a unified view that enables a more comprehensive analysis of the information on this topic residing at different sites.
After collecting web pages from a large variety of bioactive peptide databases, we organized the web content into an integrated graph database (starPepDB) that holds a total of 71 310 nodes and 348 505 relationships. In this graph structure, there are 45 120 nodes representing peptides, and the rest of the nodes are connected to peptides for describing metadata. Additionally, to facilitate a better understanding of the integrated data, a software tool (starPep toolbox) has been developed for supporting visual network analysis in a user-friendly way; providing several functionalities such as peptide retrieval and filtering, network construction and visualization, interactive exploration and exporting data options.
Both starPepDB and starPep toolbox are freely available at http://mobiosd-hub.com/starpep/.
Supplementary data are available at Bioinformatics online.
生物活性肽在学术界和制药行业引起了极大的关注，因为它们在人类健康中起着重要的作用。然而，生物活性肽数据库的数量不断增加，导致了数据冗余和重复工作的问题。更糟糕的是，可用数据是非标准化的，并且经常因数据录入错误而变得“肮脏”。因此，需要有一种统一的视图，使人们能够更全面地分析分布在不同站点上的关于这个主题的信息。
从大量的生物活性肽数据库中收集网页后，我们将网页内容组织成一个集成的图形数据库（starPepDB），其中包含 71310 个节点和 348505 个关系。在这个图形结构中，有 45120 个节点代表肽，其余的节点与肽连接起来，用于描述元数据。此外，为了方便更好地理解集成数据，我们开发了一个软件工具（starPep 工具箱），以用户友好的方式支持可视化网络分析；提供了一些功能，如肽检索和过滤、网络构建和可视化、交互式探索和导出数据选项。
starPepDB 和 starPep 工具箱均可在 http://mobiosd-hub.com/starpep/ 免费获得。
补充数据可在生物信息学在线获得。
