ArticleBMC bioinformatics2015
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Genome scale metabolic network modelling for metabolic profile predictions.PLoS computational biology · 2024Article
- MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis.Nucleic acids research · 2023Article
- Integrative omics approaches for biosynthetic pathway discovery in plants.Natural product reports · 2022Review
- Towards the prediction of non-peptidic epitopes.PLoS computational biology · 2022Article
- Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification.Journal of cheminformatics · 2021Article
- PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion.Genomics, proteomics & bioinformatics · 2020Article
- Human beige adipocytes for drug discovery and cell therapy in metabolic diseases.Nature communications · 2020Article
- DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations.Chemical science · 2020Article
- Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets.Current opinion in biotechnology · 2018Review
- Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.Briefings in bioinformatics · 2018Article
- Tox21 Enricher: Web-based Chemical/Biological Functional Annotation Analysis Tool Based on Tox21 Toxicity Screening Platform.Molecular informatics · 2018Article
- The role of inflammation and potential use of sex steroids in intracranial aneurysms and subarachnoid hemorrhage.Surgical neurology international · 2018Review
- From correlation to causation: analysis of metabolomics data using systems biology approaches.Metabolomics : Official journal of the Metabolomic Society · 2018Review
- From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics.GigaScience · 2017Review
- Glycosaminoglycanomics: where we are.Glycoconjugate journal · 2017Review
- Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction.Journal of biomedical semantics · 2016Article
- ChEBI in 2016: Improved services and an expanding collection of metabolites.Nucleic acids research · 2016Article
- ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.Journal of cheminformatics · 2016Article
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Authors and funding
12 authors.
Funding
Abstract
backgroundOntology-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.
resultsWe 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.
conclusionsBiNChE 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.