Center for Bioinformatics and Computational Biology, 205 Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA.
Department of Computer and Information Sciences, 101 Smith Hall, 18 Amstel Ave Newark, DE 19716, USA.
Database (Oxford). 2020 Jan 1;2020. doi: 10.1093/database/baz157.
iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and browsing rich PTM information but does not support automated iPTMnet data integration with other tools. Hence, we have developed a RESTful API utilizing the latest developments in cloud technologies to facilitate the integration of iPTMnet into existing tools and pipelines. We have packaged iPTMnet API software in Docker containers and published it on DockerHub for easy redistribution. We have also developed Python and R packages that allow users to integrate iPTMnet for scientific discovery, as demonstrated in a use case that connects PTM sites to kinase signaling pathways.
iPTMnet 是一个生物信息学资源，它整合了来自文本挖掘和已编辑数据库和本体的蛋白质翻译后修饰 (PTM) 数据，以帮助知识发现和科学研究。目前的 iPTMnet 网站可用于查询和浏览丰富的 PTM 信息，但不支持与其他工具的自动 iPTMnet 数据集成。因此，我们利用云技术的最新发展开发了一个 RESTful API，以方便将 iPTMnet 集成到现有工具和管道中。我们已经将 iPTMnet API 软件打包到 Docker 容器中，并在 DockerHub 上发布，以便于重新分发。我们还开发了 Python 和 R 包，允许用户将 iPTMnet 集成到科学发现中，如通过将 PTM 站点连接到激酶信号通路的用例所示。
