The past decade has seen the rise of omics data for the understanding of biological systems in health and disease. This wealth of information includes protein-protein interaction (PPI) data derived from both low- and high-throughput assays, which are curated into multiple databases that capture the extent of available information from the peer-reviewed literature. Although these curation efforts are extremely useful, reliably downloading and integrating PPI data from the variety of available repositories is challenging and time consuming. We here present a novel user-friendly web-resource called PINOT (Protein Interaction Network Online Tool; available at http://www.reading.ac.uk/bioinf/PINOT/PINOT_form.html) to optimise the collection and processing of PPI data from IMEx consortium associated repositories (members and observers) and WormBase, for constructing, respectively, human and Caenorhabditis elegans PPI networks. Users submit a query containing a list of proteins of interest for which PINOT extracts data describing PPIs. At every query submission PPI data are downloaded, merged and quality assessed. Then each PPI is confidence scored based on the number of distinct methods used for interaction detection and the number of publications that report the specific interaction. Examples of how PINOT can be applied are provided to highlight the performance, ease of use and potential utility of this tool. PINOT is a tool that allows users to survey the curated literature, extracting PPI data in relation to a list of proteins of interest. PINOT extracts a similar numbers of PPIs as other, analogous, tools and incorporates a set of innovative features. PINOT is able to process large queries, it downloads human PPIs live through PSICQUIC and it applies quality control filters on the downloaded PPI data (i.e. removing the need for manual inspection by the user). PINOT provides the user with information on detection methods and publication history for each downloaded interaction data entry and outputs the results in a table format that can be straightforwardly further customised and/or directly uploaded into network visualization software.

中文翻译：

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PINOT：整合蛋白质-蛋白质相互作用的直观资源。

在过去的十年中，组学数据的兴起有助于了解健康和疾病中的生物系统。这些丰富的信息包括源自低通量和高通量分析的蛋白质-蛋白质相互作用 (PPI) 数据，这些数据被整理到多个数据库中，这些数据库从同行评审的文献中获取可用信息的范围。尽管这些管理工作非常有用，但从各种可用存储库中可靠地下载和集成 PPI 数据具有挑战性且耗时。我们在这里提出了一种新的用户友好的网络资源，称为 PINOT（蛋白质相互作用网络在线工具；可在 http://www.reading.ac.uk/bioinf/PINOT/PINOT_form.html 获得）以优化 PPI 的收集和处理来自 IMEx 联盟相关存储库（成员和观察者）和 WormBase 的数据，分别用于构建人类和秀丽隐杆线虫 PPI 网络。用户提交一个查询，其中包含感兴趣的蛋白质列表，PINOT 提取描述 PPI 的数据。在每次查询提交时，都会下载、合并和评估 PPI 数据。然后根据用于交互检测的不同方法的数量和报告特定交互的出版物数量对每个 PPI 进行置信度评分。提供了如何应用 PINOT 的示例，以突出该工具的性能、易用性和潜在实用性。PINOT 是一种工具，允许用户调查精选文献，提取与感兴趣的蛋白质列表相关的 PPI 数据。PINOT 提取与其他类似工具相似数量的 PPI，并结合了一组创新功能。PINOT 能够处理大型查询，它通过 PSICQUIC 实时下载人类 PPI，并对下载的 PPI 数据应用质量控制过滤器（即无需用户手动检查）。PINOT 为用户提供有关每个下载的交互数据条目的检测方法和发布历史的信息，并以表格格式输出结果，可以直接进一步定制和/或直接上传到网络可视化软件中。