BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

作者：Pablo A Moreno, Stephan Beisken, Bhavana Harsha, Venkatesh Muthukrishnan, Ilinca Tudose, Adriano Dekker, Stefanie Dornfeldt, Franziska Taruttis, Ivo Große, Janna Hastings, Steffen Neumann, Christoph Steinbeck · 发表于：BMC Bioinformatics · 年份：2015 · DOI：10.1186/s12859-015-0486-3 · 被引用次数：40 · 研究领域：Bioinformatics and Genomic Networks、Biomedical Text Mining and Ontologies、Metabolomics and Mass Spectrometry Studies

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.