Abstract

Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are particularly important due to their versatility, specificity and adaptability. The STRING database aims to integrate all known and predicted associations between proteins, including both physical interactions as well as functional associations. To achieve this, STRING collects and scores evidence from a number of sources: (i) automated text mining of the scientific literature, (ii) databases of interaction experiments and annotated complexes/pathways, (iii) computational interaction predictions from co-expression and from conserved genomic context and (iv) systematic transfers of interaction evidence from one organism to another. STRING aims for wide coverage; the upcoming version 11.5 of the resource will contain more than 14 000 organisms. In this update paper, we describe changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks. In addition, we describe how to query STRING with genome-wide, experimental data, including the automated detection of enriched functionalities and potential biases in the user's query data. The STRING resource is available online, at https://string-db.org/.

中文翻译：

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2021 年的 STRING 数据库：可定制的蛋白质-蛋白质网络，以及用户上传的基因/测量集的功能表征

摘要

细胞生命依赖于生物分子之间复杂的功能关联网络。在这些关联中，蛋白质-蛋白质相互作用因其多功能性、特异性和适应性而尤为重要。STRING 数据库旨在整合蛋白质之间所有已知和预测的关联，包括物理相互作用和功能关联。为实现这一目标，STRING 从多个来源收集和评分证据：(i) 科学文献的自动文本挖掘，(ii) 交互实验和注释复合物/途径的数据库，(iii) 来自共表达和从保守的基因组背景和 (iv) 相互作用证据从一种生物体到另一种生物体的系统转移。STRING 旨在实现广泛的覆盖；即将推出的版本 11。5 个资源将包含超过 14 000 种生物。在这篇更新论文中，我们描述了文本挖掘系统的变化，一种新的物理交互评分模式，以及用于定制、扩展和共享蛋白质网络的广泛用户界面功能。此外，我们描述了如何使用全基因组的实验数据查询 STRING，包括自动检测用户查询数据中的丰富功能和潜在偏差。STRING 资源可在线获取，网址为 https://string-db.org/。实验数据，包括自动检测用户查询数据中的丰富功能和潜在偏差。STRING 资源可在线获取，网址为 https://string-db.org/。实验数据，包括自动检测用户查询数据中的丰富功能和潜在偏差。STRING 资源可在线获取，网址为 https://string-db.org/。