ProLiVis 2.0：以文献为中心的蛋白质-蛋白质相互作用网络可视化，带引文信任模型的相互作用证据
ProLiVis 2.0: Literature-Centric Visualization of Protein--Protein Interaction Networks, with a Citation-Trust Model for Interaction Evidence
- Emlakjet, R&D Center, R&D（Emlakjet 研发中心）
- Computer Engineering, Faculty of Engineering and Natural Sciences, Işık University（伊什克大学工程与自然科学学院计算机工程系）
机构由 AI 辅助整理，请以论文原文为准。
AI总结：
ProLiVis 2.0通过引文信任模型量化蛋白质相互作用证据可信度，采用确定性布局并完全在浏览器运行，揭示BioGRID中70%的SARS-CoV-2相互作用仅基于单一文献。
AI中文摘要：
蛋白质-蛋白质相互作用数据库记录证据时不加以权衡。在BioGRID中，由单一高通量筛选实验断言一次的相互作用与由二十个实验室通过十二种实验方法确认的相互作用，在同一个文件中以相同的行形式存在。基于此类数据库构建的工具继承了这种扁平化处理：它们将每条报告的相互作用绘制为一条边，由此产生的图像仅表明两种蛋白质相互作用，却未说明人们应在多大程度上相信该结论。我们提出ProLiVis 2.0，这是对arXiv:2111.12794中以文献为中心的可视化系统的重写。它贡献了三个方面。第一，一个引文信任模型，从七个术语对每条相互作用进行评分，其中包括一个基于支持文献背后的独立实验室数量的术语，该数量通过对这些文献按共享机构隶属关系进行聚类获得；单纯的文献计数无法区分来自一个团队发表五次所得到的五次确认与来自五个独立团队的确认。第二，中心布局的确定性重构，采用闭式解且复杂度为O(n log n)，取代了原系统的力导向布局，使已发表的图形可从会话清单中重新生成。第三，一个完全在网页浏览器中运行的实现，内置分析数据库，无需安装且不上传任何数据。在限制为SARS-CoV-2的BioGRID 5.0.260版本中，34,540条报告的相互作用中有24,344条（70%）仅基于单一文献，将信任阈值提高到0.2后，剩余11,320条。一个经过整理的相互作用网络中的绝大多数未被重复验证，这一事实在现有的任何数据库视图中均不可见。
英文摘要：
Protein-protein interaction databases record evidence without weighing it. In BioGRID, an interaction asserted once by a single high-throughput screen and one confirmed by twenty laboratories across a dozen assays are the same kind of row in the same file. Tools built on such databases inherit that flattening: they draw every reported interaction as an edge, and the resulting picture states that two proteins interact without stating how much anyone should believe it. We present ProLiVis 2.0, a rewrite of the literature-centric visualization system of arXiv:2111.12794. It contributes three things. First, a citation-trust model that scores each interaction from seven terms, including a term for the number of independent laboratories behind the supporting publications, obtained by clustering those publications over shared institutional affiliations; a plain count of publications cannot distinguish five confirmations from one group publishing five times. Second, a deterministic reformulation of the center layout, closed-form and $O(n \log n)$, which replaces the force-directed placement of the original and makes published figures regenerable from a session manifest. Third, an implementation that runs entirely in a web browser, with an embedded analytical database, requiring no installation and uploading no data. On BioGRID release 5.0.260 restricted to SARS-CoV-2, 24,344 of 34,540 reported interactions (70%) rest on a single publication, and raising the trust threshold to 0.2 leaves 11,320 of them. That the large majority of a curated interaction network is unreplicated is a fact no existing view of the database makes visible.
