Chemical Entities of Biological Interest: an update

By P. Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck. 2009

336 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/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by the community and a 30-fold increase in the number of chemical structures stored in ChEBI.

Subfields: Molecular Biology

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Citations in the corpus

ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “For example, all small molecule compounds with deﬁned structures are assigned ChEBI identiﬁers (23) and Standard InChIKeys.”
ChemProt: a disease chemical biology database (2010, background): “Marketed as a selective serotonin reuptake inhibitor (SSRI) (DrugBank), this drug displays bioactivity on seven human proteins (ChEMBL).”
The UniProt-GO Annotation database in 2011 (2011, background): “Such integration efforts can be exemplified by work in the last year to include 43 different gene, protein and chemical identifier types [such as WormBase (11), ChEBI (12) and EcoCyc (7) identifiers] in the annotation format to provide a more complete display of external manual annotations.”
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 (2012, methodology): “Since our earlier reports on ChEBI (1,2), the database has steadily grown, and we have introduced several new features and enhancements.”
UniChem: a unified chemical structure cross-referencing and identifier tracking system (2013, background): “These include what might be termed primary chemistry-based resources, such as ChEBI [1,2] and ChEMBL [3,4], where small molecules have a central role in their data models, and secondary chemistry-based resources (e.”
Analysis Tool Web Services from the EMBL-EBI (2013, background): “Individual data resources, such as ChEBI (4), ENA (5), Gene Expression Atlas (6) and UniProt (7), provide web interfaces and Web Services (Table 1) tailored to the spe-ciﬁcs of their data and the usage patterns required by consumers of their data.”
Ontological realism: A methodology for coordinated evolution of scientific ontologies (2010, neutral): “…Batchelor, Karen Eilbeck, Janna Hastings and Neocles Leontis in the Sequence Ontology (Mungall et al., 2010), CHEBI ontology of small molecules (de Matos et al., 2010) and RNA Ontology Consortia (Batchelor et al., 2009); Ramona Walls, Laurel Cooper, Dennis Stevenson, and Pankaj Jaiswal of the…”
PDBe: Protein Data Bank in Europe (2010, methodology): “The mapping information is enriched with cross-reference information from the NCBI taxonomy database (26,28), IntEnz (14), CATH (12), SCOP (27), InterPro (29), Pfam (15) and PubMed (26).”
WikiPathways: building research communities on biological pathways (2011, background): “Entities such as genes, proteins or metabolites in a pathway can be annotated with many different identifier systems, such as Ensembl (2), Entrez Gene (3) or ChEBI (4).”
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data (2012, background): “MetaboLights contains references to identiﬁed metabolites in existing databases, such as HMDB and ChEBI (19), and does not duplicate compound information residing in these external databases.”
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors (2013, background): “New cross-references have been established between SMIs and the ChEBI (17) and DrugBank (18) databases, with 100 and 40 cross-references, respectively.”
PomBase: a comprehensive online resource for fission yeast (2011, background): “FYPO is a modular ontology that uses several existing ontologies from the Open Biological and Biomedical Ontologies (OBO) collection (7) as building blocks, including the phenotypic quality ontology PATO (8), GO, and Chemical Entities of Biological Interest (ChEBI) (9).”
The IntAct molecular interaction database in 2012 (2011, background): “As of September 2011, IntAct contains 275 145 binary interaction evidences abstracted from 5009 scientiﬁc publications, referencing 57 857 proteins (as deﬁned by UniProtKB), 144 small molecules (as deﬁned by ChEBI) and 233 genes (as deﬁned by Ensembl).”