School of Computer Science and Computer Engineering, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA.
Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA.
Sci Rep. 2018 Oct 10;8(1):15107. doi: 10.1038/s41598-018-33219-y.
Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik's and Wang's methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ancestor node giving to its descendent nodes. GOGO can calculate functional similarities between genes and then cluster genes based on their functional similarities. Evaluations performed on multiple pathways retrieved from the saccharomyces genome database (SGD) show that GOGO can accurately and robustly cluster genes based on functional similarities. We release GOGO as a web server and also as a stand-alone tool, which allows convenient execution of the tool for a small number of GO terms or integration of the tool into bioinformatics pipelines for large-scale calculations. GOGO can be freely accessed or downloaded from http://dna.cs.miami.edu/GOGO/ .
测量基因本体论 (GO) 术语之间的语义相似度是功能生物信息学研究的重要步骤。我们实现了一个名为 GOGO 的软件，用于计算 GO 术语之间的语义相似度。GOGO 具有信息内容和混合方法的优点，例如 Resnik 和 Wang 的方法。此外，GOGO 相对较快，不需要从大型基因注释语料库中计算信息内容 (IC)，但仍具有使用 IC 的优势。这是通过在计算祖先节点对其后代节点的语义贡献时考虑 GO 有向无环图中的子节点数来实现的。GOGO 可以计算基因之间的功能相似性，然后根据功能相似性对基因进行聚类。在从酿酒酵母基因组数据库 (SGD) 中检索到的多个途径上进行的评估表明，GOGO 可以根据功能相似性准确而稳健地对基因进行聚类。我们将 GOGO 作为一个网络服务器发布，也作为一个独立的工具发布，这允许为少量 GO 术语方便地执行该工具，或将该工具集成到生物信息学管道中进行大规模计算。GOGO 可以从 http://dna.cs.miami.edu/GOGO/ 免费访问或下载。
