|Small chemical compounds|
|Research center||European Molecular Biology Laboratory|
|Laboratory||European Bioinformatics Institute|
|Primary citation||de Matos et al|
|Download URL|| ftp|
|Web service URL|| www|
|Curation policy||Manually curated|
Chemical Entities of Biological Interest, also known as ChEBI,is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinformatics Institute (EBI). 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 which have potential bioactivity. Molecules directly encoded by the genome, such as nucleic acids, proteins and peptides derived from proteins by proteolytic cleavage, are not as a rule included in ChEBI.
ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and nomenclature committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).
All data in the database is non-proprietary or is derived from a non-proprietary source. It is thus freely accessible and available to anyone. In addition, each data item is fully traceable and explicitly referenced to the original source. It is related in scope other databases such as ChEMBL, ChemSpider, DrugBank, MetaboLights and PubChem.
ChEBI data is available through a public web application, web services, SPARQL endpoint and downloads.
In inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula HCO−
Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA.
Sulfide (British English also sulphide) is an inorganic anion of sulfur with the chemical formula S2− or a compound containing one or more S2− ions. Solutions of sulfide salts are corrosive. Sulfide also refers to chemical compounds large families of inorganic and organic compounds, e.g. lead sulfide and dimethyl sulfide. Hydrogen sulfide (H2S) and bisulfide (SH−) are the conjugate acids of sulfide.
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.
In chemistry and biochemistry, an oligomer is a molecule that consists of a few similar or identical repeating units which could be derived, actually or conceptually, from copies of a smaller molecule, its monomer. The name is composed from Greek elements oligo-, "a few" and -mer, "parts". An adjective form is oligomeric.
In chemistry, a methine group or methine bridge is a trivalent functional group =CH−, derived formally from methane. It consists of a carbon atom bound by two single bonds and one double bond, where one of the single bonds is to a hydrogen. The group is also called methyne or methene; its IUPAC systematic name is methylylidene or methanylylidene
BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is an electronic resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a web-based user interface that allows a convenient and sophisticated access to the data.
Gas phase ion chemistry is a field of science encompassed within both chemistry and physics. It is the science that studies ions and molecules in the gas phase, most often enabled by some form of mass spectrometry. By far the most important applications for this science is in studying the thermodynamics and kinetics of reactions. For example, one application is in studying the thermodynamics of the solvation of ions. Ions with small solvation spheres of 1, 2, 3... solvent molecules can be studied in the gas phase and then extrapolated to bulk solution.
KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is authored by expert biologists, in collaboration with Reactome editorial staff who are all PhD level biologists. Content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format.
Methylidyne, or (unsubstituted) carbyne, is an organic compound whose molecule consists of a single hydrogen atom bonded to a carbon atom. It is the parent compound of the carbynes, which can be seen as obtained from it by substitution of other functional groups for the hydrogen.
A molecular entity, or chemical entity, is "any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity". A molecular entity is any singular entity, irrespective of its nature, used to concisely express any type of chemical particle that can exemplify some process: for example, atoms, molecules, ions, etc. can all undergo a chemical reaction.
In chemistry, a hydron is the general name for a cationic form of atomic hydrogen, represented with the symbol H+
. The term "hydron", endorsed by the IUPAC, includes cations of hydrogen regardless of their isotopic composition: thus it refers collectively to protons (1H+) for the protium isotope, deuterons (2H+ or D+) for the deuterium isotope, and tritons (3H+ or T+) for the tritium isotope.
ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK.
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).
The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. Created by the Human Metabolome Project funded by Genome Canada. One of the first dedicated metabolomics databases, the HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.
Christoph Steinbeck is a chemist born in Neuwied in 1966 and has a professorship for analytical chemistry, cheminformatics and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia, Germany.
The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). This replaces and expands upon the original 2009 IUPHAR Database. The Guide to PHARMACOLOGY aims to provide a concise overview of all pharmacological targets, accessible to all members of the scientific and clinical communities and the interested public, with links to details on a selected set of targets. The information featured includes pharmacological data, target, and gene nomenclature, as well as curated chemical information for ligands. Overviews and commentaries on each target family are included, with links to key references.
The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae. The YMDB was designed to facilitate yeast metabolomics research, specifically in the areas of general fermentation as well as wine, beer and fermented food analysis. YMDB supports the identification and characterization of yeast metabolites using NMR spectroscopy, GC-MS spectrometry and Liquid chromatography–mass spectrometry. The YMDB contains two kinds of data: 1) chemical data and 2) molecular biology/biochemistry data. The chemical data includes 2027 metabolite structures with detailed metabolite descriptions along with nearly 4000 NMR, GC-MS and LC/MS spectra.
Experimental factor ontology, also known as EFO, is an open-access ontology of experimental variables particularly those used in molecular biology. The ontology covers variables which include aspects of disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained at the EMBL-EBI as a cross-cutting resource for the purposes of curation, querying and data integration in resources such as Ensembl, ChEMBL and Expression Atlas.
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