title: BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
abstract: 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.
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. pmoreno@ebi.ac.uk.
authors: Pablo
authors: P
authors: Moreno
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. beisken@ebi.ac.uk.
authors: Stephan
authors: S
authors: Beisken
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. bh4@sanger.ac.uk.
authors: Bhavana
authors: B
authors: Harsha
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. venkat@ebi.ac.uk.
authors: Venkatesh
authors: V
authors: Muthukrishnan
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. tudose@ebi.ac.uk.
authors: Ilinca
authors: I
authors: Tudose
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. adekker@ebi.ac.uk.
authors: Adriano
authors: A
authors: Dekker
authors: Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. stefanie.dornfeldt@student.uni-halle.de.
authors: Stefanie
authors: S
authors: Dornfeldt
authors: Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. franziska_taruttis@yahoo.de.|Dept. of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Halle, Germany. franziska_taruttis@yahoo.de.
authors: Franziska
authors: F
authors: Taruttis
authors: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany. grosse@informatik.uni-halle.de.|German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. grosse@informatik.uni-halle.de.
authors: Ivo
authors: I
authors: Grosse
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. hastings@ebi.ac.uk.
authors: Janna
authors: J
authors: Hastings
authors: Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. steffen.neumann@ipb-halle.de.
authors: Steffen
authors: S
authors: Neumann
authors: Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. steinbeck@ebi.ac.uk.
authors: Christoph
authors: C
authors: Steinbeck
mesh_terms: D064229:Biological Ontologies; D062126:Databases, Chemical; D020407:Internet; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D054852:Small Molecule Libraries / Q000737:chemistry*; D012984:Software
chemical_list: D004364:Pharmaceutical Preparations; D054852:Small Molecule Libraries