Standards > terminology artifact > bsg-s000039

ready Chemical Entities of Biological Interest


terminology artifact

General Information
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Record updated: Oct. 12, 2016, 4:24 p.m. by The BioSharing Team.

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Implementing Databases (27)
GlycoNAVI is a gateway to free suite of carbohydrate research tools. It will let you access to variety of information and assist your research.

ChEMBL: a large-scale bioactivity database for drug discovery
ChEMBL is an open large-scale bioactivity database containing information largely manually extracted from the medicinal chemistry literature. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.

EcoliWiki: A Wiki-based community resource for Escherichia coli
Community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

IntAct molecular interaction database
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules.

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.

Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis

TTD, Therapeutic Target Database
The Therapeutic Target Database provides information about therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information is fully referenced.

The UCSC Archaeal Genome Browser
The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.

MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. We offer user-submission tools and have strong reporting capabilities. We will utilise and further develop de-facto standard formats where various components are encapsulated, such as the encoded spectral and chromatographic data, and associated information about the chemical structure, as well as metadata describing assays and the study as a whole. We are dedicated to collaborate closely with major parties in world-wide metabolomics communities, such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.

BindingDB database of measured binding affinities
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.

Reactome - a curated knowledgebase of biological pathways
The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.

MatrixDB: Extracellular Matrix interactions database
MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. Full-length molecules, fragments and multimers present in the extracellular matrix are all included in the database.

Rat Genome Database
The Rat Genome Database is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. It provides easy access to corresponding human and mouse data for cross-species comparison and its comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.

Signaling Pathway Integrated Knowledge Engine
SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps.

UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

The Human Metabolome Database
The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.

YEASTNET: A consensus reconstruction of yeast metabolism
YEASTNET is a resource of the yeast metabolic network as reconstructed from a combination of genomic data and publications.

SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

ENCODE Project
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

Microenvironment Perturbagen (MEP) LINCS Center image server
The MEP LINCS project contributes to the development of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) program by developing a dataset and computational strategy to elucidate how microenvironment (ME) signals affect cell intrinsic intracellular transcriptional- and protein-defined molecular networks to generate experimentally observable cellular phenotypes measured by high-content imaging.

Free knowledge database project hosted by Wikimedia and edited by volunteers.

DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine.

Target Central Resource Database
TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiative: GPCRs, kinases, ion channels and nuclear receptors. Olfactory GPCRs (oGPCRs) are treated as a separate family. A key aim of the KMC is to classify the development/druggability level of targets. The official public portal for TCRD is Pharos ( Based on modern web design principles the Pharos interface provides facile access to all data types collected by the KMC. Given the complexity of the data surrounding any target, efficient and intuitive visualization has been a high priority, to enable users to quickly navigate & summarize search results and rapidly identify patterns. A critical feature of the interface is the ability to perform flexible search and subsequent drill down of search results. Underlying the interface is a RESTful API that provides programmatic access to all KMC data, allowing for easy consumption in user applications.

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Grant Number(s)

  • 021902 (European Commision grants FELICS)

  • 226073 (European Union, Serving Life-science Information for the Next Generation (SLING))

  • BB/G022747/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • BB/K019783/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)


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

Hastings J,de Matos P,Dekker A,Ennis M,Harsha B,Kale N,Muthukrishnan V,Owen G,Turner S,Williams M,Steinbeck C
Nucleic Acids Res 2012

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ChEBI in 2016: Improved services and an expanding collection of metabolites.

Hastings J,Owen G,Dekker A,Ennis M,Kale N,Muthukrishnan V,Turner S,Swainston N,Mendes P,Steinbeck C
Nucleic Acids Res 2015

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Chemical Entities of Biological Interest: an update.

de Matos P,Alcantara R,Dekker A,Ennis M,Hastings J,Haug K,Spiteri I,Turner S,Steinbeck C
Nucleic Acids Res 2009

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ChEBI: an open bioinformatics and cheminformatics resource.

Degtyarenko K,Hastings J,de Matos P,Ennis M
Curr Protoc Bioinformatics 2009

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

Degtyarenko K,de Matos P,Ennis M,Hastings J,Zbinden M,McNaught A,Alcantara R,Darsow M,Guedj M,Ashburner M
Nucleic Acids Res 2007

View Paper (PubMed) View Paper (DOI)