Moreno Pablo, Beisken Stephan, Harsha Bhavana, Muthukrishnan Venkatesh, Tudose Ilinca, Dekker Adriano, Dornfeldt Stefanie, Taruttis Franziska, Grosse Ivo, Hastings Janna, Neumann Steffen, Steinbeck Christoph
Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK.
Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany.
BMC Bioinformatics. 2015 Feb 21;16(1):56. doi: 10.1186/s12859-015-0486-3.
Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.
We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.
BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.
基于本体的富集分析有助于解释和理解大规模生物数据。本体是生物相关分组的层次结构。利用将本体类与生物实体联系起来的本体注释，富集分析方法评估本体类的实体是否存在显著的过度或不足表征。虽然有许多工具可对用基因本体注释的蛋白质集进行富集分析，但可用于小分子富集分析的工具却很少。
我们描述了BiNChE，一种基于ChEBI本体的小分子富集分析工具。BiNChE显示一个交互式图形，该图形可以导出为高分辨率图像或网络格式。该工具基于ChEBI角色本体或ChEBI结构本体提供普通、加权和片段分析。
BiNChE有助于探索代谢组学或其他系统生物学研究背景下产生的大量小分子。这个开源工具通过ChEBI本体工具提供了易于使用且高度交互式的网络富集分析途径，并且还可以作为一个独立的库使用。
