Chemical Entities of Biological Interest
How to cite this record FAIRsharing.org: CHEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: July 30, 2018, 6:43 p.m.; Last accessed: Aug 19 2018 4:10 p.m.
Record updated: July 30, 2018, 6:43 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.62qk8w' by 'The FAIRsharing Team' at 16:24, 12 Oct 2016 (approved): 'description' has been modified: Before: 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. ChEBI incorporates an ontological classification|whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI uses nomenclature|symbolism and terminology endorsed by the following international scientific bodies: International Union of Pure and Applied Chemistry (IUPAC) Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) Molecules directly encoded by the genome (e.g. nucleic acids|proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. 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. After: 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.
Edits to 'https://fairsharing.org/FAIRsharing.62qk8w' by 'The FAIRsharing Team' at 18:44, 30 Jul 2018 (not approved): 'description' has been modified: Before: 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. After: Chemical Entities of Biological Interest (ChEBI) is a free resource that describes 'small? chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, etc.. These molecular entities can interact with or affect the processes of living organisms.
Edits to 'https://fairsharing.org/FAIRsharing.62qk8w' by 'The FAIRsharing Team' at 09:01, 15 Jul 2018 (approved): 'deprecation_reason' has been modified: Before: None After: None
Edits to 'https://fairsharing.org/FAIRsharing.62qk8w' by 'The FAIRsharing Team' at 19:45, 15 Jul 2018 (approved): 'licences' has been modified: Before: After: Creative Commons Attribution 4.0 International (CC BY 4.0) | Data Added: Creative Commons Attribution 4.0 International (CC BY 4.0) | Data Removed:
No XSD schemas defined
Conditions of UseApplies to: Data use
SOAP Web Services
|ChEBI SOAP access||http://www.ebi.ac.uk/chebi/webServices.do|
ChEBI: an open bioinformatics and cheminformatics resource.
Degtyarenko K,Hastings J,de Matos P,Ennis M
Curr Protoc Bioinformatics 2009
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
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
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
No guidelines defined
Models and Formats
No identifier schema standards defined
GlycoNAVI is a gateway to free suite of carbohydrate research tools. It will let you access to variety of information and assist your research.
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
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 is a collection of metabolite structures. This resource provides information on the compound origins,the biological roles, locations and concentrations, as well as experimental data from metabolic experiments. The tools and capabilities of this database is firmly routed in collaborative working worldwie with the metabolomics community 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.
Integrated relational Enzyme database
IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.
Protein Data Bank in Europe
The Protein Data Bank in Europe is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.
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.
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
This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.
Kyoto Encyclopedia of Genes and Genomes
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
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.
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. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.
Microenvironment Perturbagen 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 (pharos.nih.gov). 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.
The Enzyme Portal integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.
A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
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Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
European Commision grants FELICS (Government body)
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)