Chemical Entities of Biological Interest: an update

Abstract

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.

The Protein Data Bank in Europe (PDBe): bringing structure to biology

“…SIFTS itself is used by major resources such as Pfam, CATH, RCSB, DAS server providers (http://www.dasregistry.org/) and many research and service groups around the world. In the future, SIFTS might be extended to link PDB data to other resources such as ChEMBL (http://www.ebi.ac.uk/chembl/; proteinligand interaction data), IntAct (Aranda et al, 2010; macromolecular interaction data), Reactome (Matthews et al, 2009; biological pathway data), ChEBI (De Matos et al, 2010; ligand chemistry and function data) and EnsEMBL (Flicek et al, 2010; SNPs and genetic variation data).…”

“…(i) the enzyme-classification (EC) system as included in the IntEnz (De Matos et al, 2010) database (http://pdbe.org/ec),…”

An Ontology for Description of Drug Discovery Investigations

“…We developed DDI as an application of OBI for drug discovery by extending the corresponding classes. DDI imports terms from Chemical Entities of Biological Interest (ChEBI) [15], e.g. chebi:molecular entity.…”

ChEBI – an Open-access Chemistry Resource for the Life Sciences:*Facilities for On-line Submission and Curation

“…ChEBI (Chemical Entities of Biological Interest) [1] is a manually curated database of molecular entities which also provides a chemical ontology. ChEBI contains approximately 22,000 manually curated entities and approximately 620,000 entities in total.…”