The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

By Janna Hastings, P. Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams and 1 more. Nucleic Acids Res., 2012

605 citations recorded by the source corpus.

ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now ‘is_a’ classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d54d6ba9d0a6efa37f700c35aa7f2b1f40d0f25b

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Citations in the corpus

Aurum: A Data Discovery System (2018, methodology): “Our pharmaceutical user ran A URUM on 6 different public chemical databases (ChEMBL [9], DrugBank [10], BindingDB [11], Chebi [12], KiDatabase) and an internal database accessed by over 1000 analysts.”
Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification (2013, background): “…200,000 plant metabolites (Fiehn 2002), or even the 32,801 manually annotated entries in the database of Chemical Entities of Biological Interest (ChEBI) (Hastings et al. 2013), we see that MS/MS coverage still falls far short of the vast number of known metabolites and molecules of interest.”
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy (2016, methodology): “For instance, the ChEBI ontology [15] provides a sub-ontology for chemical roles, in addition to the structure-based sub-ontology.”
Review on natural products databases: where to find data in 2020 (2020, background): “ChEBI is developed and maintained at the European Bioinformatics Institute (EBI) and its main focus is chemical ontologies, i.e. structural relationships between molecules; it contains over 15,000 clearly identified NPs. ChEMBL is also the product of EBI but it has a wider focus and is considered as”
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2015, background): “Genes and metabolites can now be specified using multiple alternative names and identifiers, including identifiers from other databases that are present in BioCyc, such as Chemical Entities of Biological Interest (ChEBI) (8) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (9) IDs (for details see”
The InterPro protein families database: the classification resource after 15 years (2014, neutral): “As an additional beneficial outcome, 35 new GO terms were created as part of this work, 74 new reactions were curated into RhEA (with the curation of additional chemical entities in the ChEBI database (27) where necessary to support this) and 113 new GO-RhEA mappings were created.”
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes (2015, neutral): “…of DRI = Intracellular concentration ∗Weight of bacteria ∗ AM ∗ HGM ratio DRI ∗ 100 where DRI is the recommended dietary reference intake in mg/day, AM is the atomic mass of the vitamin [values from ChEBI, (Hastings et al., 2013)], and HGM is the ratio of HGM producers as predicted in this study.”
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases (2015, background): “…and interoperability were collected to define the domain-specific knowledge, including Chemical Entities of Biological Interest (ChEBI) [29–31], CHEMical INFormation ontology (CHEMINF) [32], Semanticsci-ence Integrated Ontology (SIO) [33], Units of Measurement (UO) [34], Dublin Core…”