ChEBI in 2016: Improved services and an expanding collection of metabolites
Open accessAbstract
ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46,000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a 'live' website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.
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The ChEBI database has approximately 1,000 annotations for glucose.
“For example, the ChEBI database [34] has approximately 1,000 annotations for glucose.”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [34]
The Introduction (page not provided) identifies ChEBI as a database whose entries have multiple metadata annotations. It does not report approximately 1,000 annotations for glucose; searches for glucose and that annotation count found no supporting passage. (LLM, conf=0.85)
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UniProt: a hub for protein information
The UniProt Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku989 · Cited by 5,106 · see citing works
MassBank: a public repository for sharing mass spectral data for life sciences
Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., et al. (2010) · Journal of Mass Spectrometry · doi:10.1002/jms.1777 · Cited by 2,529 · see citing works
HMDB: a knowledgebase for the human metabolome
Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., Hau, D., Psychogios, N., Dong, E., Bouatra, S., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn810 · Cited by 1,874 · see citing works
GMD@CSB.DB: the Golm Metabolome Database
Kopka, J., Schauer, N., Krueger, S., Birkemeyer, C., Usadel, B., Bergmuller, E., Dörmann, P., Weckwerth, W., Gibon, Y., Stitt, M., et al. (2004) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti236 · Cited by 1,374 · see citing works
ChEBI: a database and ontology for chemical entities of biological interest
Degtyarenko, K. N., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M., & Ashburner, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm791 · Cited by 1,130 · see citing works
Self-citationA community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019 · see citing works
Self-citationAfendi, F. M., Okada, T., Yamazaki, M., Morita, A. H., Nakamura, Y. K., Nakamura, K., Ikeda, S., Takahashi, H., Altaf‐Ul‐Amin, M., Darusman, L. K., et al. (2011) · Plant and Cell Physiology · doi:10.1093/pcp/pcr165 · Cited by 742 · see citing works
Haug, K., Salek, R. M., Conesa, P., Hastings, J., de Matos, P., Rijnbeek, M. L., Mahendraker, T., Williams, M., Neumann, S., Rocca‐Serra, P., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1004 · Cited by 647 · see citing works
Self-citationThe 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. I., Turner, S., Williams, M., et al. (2012) · Nucleic Acids Res. · doi:10.1093/nar/gks1146 · Cited by 613 · see citing works
Self-citationHerrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588 · see citing works
Self-citationChemical Entities of Biological Interest: an update
de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., & Steinbeck, C. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp886 · Cited by 319 · see citing works
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PubChemRDF: towards the semantic annotation of PubChem compound and substance databases
Fu, G., Batchelor, C. R., Dumontier, M., Hastings, J., Willighagen, E., & Bolton, E. (2015) · Journal of Cheminformatics · doi:10.1186/s13321-015-0084-4 · Cited by 139 · see citing works
Self-citationThe University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
Ellis, L. B. M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg048 · Cited by 72 · see citing works
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
Hill, D. P., Adams, N., Bada, M., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-513 · Cited by 55 · see citing works
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Karulin, B., & Kozhevnikov, M. (2011) · Journal of Cheminformatics · doi:10.1186/1758-2946-3-s1-p3 · Cited by 44 · see citing works
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Moreno, P. A., Beisken, S., Harsha, B., Muthukrishnan, V., Tudose, I., Dekker, A., Dornfeldt, S., Taruttis, F., Große, I., Hastings, J., et al. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0486-3 · Cited by 40 · see citing works
Self-citationOWL 2 Web Ontology Language Manchester Syntax (Second Edition)
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Lamúrias, A., Ferreira, J. D., & Couto, F. M. (2015) · Journal of Cheminformatics · doi:10.1186/1758-2946-7-s1-s13 · Cited by 29 · see citing works
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Tudose, I., Hastings, J., Muthukrishnan, V., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt514 · Cited by 11 · see citing works
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Research works printed but not linked: 1
- [12]Rauter A.P. Nomenclature of flavonoids September 2015, date last accessed http://www.iupac.org/home/publications/provisional-recommendations/under-review-by-the-authors/under-review-by-the-authors-container/nomenclature-of-flavonoids.html
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Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac956 · Cited by 3,443 · see citing works
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Fernández-Torras, A., Duran-Frigola, M., Bertoni, M., Locatelli, M., & Aloy, P. (2022) · Nature Communications · doi:10.1038/s41467-022-33026-0 · Cited by 59 · see citing works
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- Authors
- Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., Turner, S., Swainston, N., Mendes, P., & Steinbeck, C.
- Affiliations
- European Bioinformatics Institute (GB)
- University of Manchester (GB)
- Corresponding author
- Hastings, Janna
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-13
- Volume
- 44
- Issue
- D1
- Pages
- D1214-D1219
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4702775
- OpenAlex
- W1935434993
- Cited by
- 1,083
- References
- 21
- Citations by year
- 2026: 98 · 2025: 132 · 2024: 136 · 2023: 154 · 2022: 128 · 2021: 119 · 2020: 124 · 2019: 86 · 2018: 52 · 2017: 28 · 2016: 21 · 2015: 2
- FWCI
- 16.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (submittedVersion, cc-by)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/M017702/1, BB/K019783/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- ChEBI, chemical entity, metabolites, ontology (information science), endogenous metabolites, chemical databases, Binche, web frontend, JavaScript, programmatic access
- MeSH terms
- Animals, Humans, Metabolism, Software, Mice, Metabolomics, Databases, Chemical
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