ChEBI: a database and ontology for chemical entities of biological interest

By K. Degtyarenko, P. Matos, Marcus Ennis, Janna Hastings, M. Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, Michael Ashburner. 2007

1,192 citations recorded by the source corpus.

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/

Subfields: Molecular Biology

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Citations in the corpus

SWEETLEAD: an In Silico Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery (2013, background): “While several databases are available containing vast amounts of chemical data[22-30], when querying these databases for a given drug conflicting information is occasionally retrieved.”
Gene Ontology Annotations and Resources (2012, methodology): “OWL extends this model with more expressive constructs, including the ability to provide computable logical definitions for GO terms, making use of both simpler GO terms, and terms from other ontologies such as CHEBI (chemical entities of biological interest) (8).”
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, background): “Annotating model elements helps avoid these problems, allowing unambiguous identification through reference to appropriate external resources (using perennial URIs), such as terms from controlled vocabularies (Taxonomy, Gene Ontology, ChEBI ontology [50], Enzyme Nomenclature [51], etc.”
The Human Urine Metabolome (2013, background): “Each MetaboCard entry contains up to 120 data fields many of which are hyperlinked to other databases (KEGG [45], PubChem [46], MetaCyc [47], ChEBI [48], PDB [49], UniProt [50], and GenBank [51] as well as to GeneCard IDs [52], GeneAtlas IDs [53] and HGNC IDs [54] for each of the corresponding enzym”
Uberon, an integrative multi-species anatomy ontology (2012, methodology): “We have included relationships and other logical axioms that reference other ontologies in Uberon, such as the GO, the Neuro Behavior Ontology (NBO) [30], the CL [15], the Protein Ontology [31] and CHEBI [32].”
The Ontology for Biomedical Investigations (2016, methodology): “GO, ChEBI, Protein Ontology (PRO) and PATO to replace IEDB internal controlled vocabularies.”
The Immune Epitope Database 2.0 (2009, methodology): “The IEDB is currently collaborating with the Chemical Entities of Biological Interest (ChEBI) project in order to depict non-peptidic structures with proper nomenclature, synonyms and 3D structures (20).”
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “ChEBI (16) is an excellent dictionary for chemical entities, but outsources its information on the biology of those chemicals to other databases via external links.”
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data (2010, methodology): “Information contained in the HMDB was used to extract common names, synonyms, as well as ID used in nine major metabolomic databases [HMDB, PubChem (19), ChEBI (20), KEGG (21), BiGG (22), METLIN (23), BioCyc (24), Reactome (25), and Wikipedia].”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, background): “Simple physical entities of the same type (genes, proteins, transcripts, metabolites) are compared on the basis of common database identiﬁers like UniProt (21), Ensembl (22), Entrez (23), ChEBI (24), etc.”
Evolution of the Sequence Ontology terms and relationships (2010, neutral): “Chemical Entities of Biological Interest (ChEBI) is a dictionary of small molecules [14].”
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases (2015, background): “…integration 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…”
Concept annotation in the CRAFT corpus (2012, background): “…Biological Interest ontology (ChEBI, representing chemicals, chemical groups, atoms, subatomic particles, and biochemical roles and applications) [20], the NCBI Tax-onomy (NCBITaxon, representing biological taxa) [21], the Protein Ontology (PRO, representing proteins and protein complexes), the…”