The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Rhea, the reaction knowledgebase in 2022
Open accessAbstract
Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities of Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number of key developments in Rhea since our last report in the database issue of Nucleic Acids Research in 2019. These include improved reaction coverage in Rhea, the adoption of Rhea as the reference vocabulary for enzyme annotation in the UniProt knowledgebase UniProtKB (https://www.uniprot.org), the development of a new Rhea website, and the designation of Rhea as an ELIXIR Core Data Resource. We hope that these and other developments will enhance the utility of Rhea as a reference resource to study and engineer enzymes and the metabolic systems in which they function.
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Cites
Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2016239118 · Cited by 3,286
Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2019) · doi:10.1101/622803 · Cited by 3,280
Modeling the language of life – Deep Learning Protein Sequences
Heinzinger, M., Elnaggar, A., Wang, Y., Dallago, C., Nechaev, D., Matthes, F., & Rost, B. (2019) · doi:10.1101/614313 · Cited by 606
Learning the protein language: Evolution, structure, and function
Bepler, T., & Berger, B. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.017 · Cited by 483
LitSuggest: a web-based system for literature recommendation and curation using machine learning
Allot, A., Lee, K., Chen, Q., Luo, L., & Lu, Z. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab326 · Cited by 61 · cited 1×
“Rhea reaction data is curated from the literature by expert biochemists, supported by nat-ural language processing (NLP) tools such as LitSuggest, a web-based system for literature recommendation and curation (25).”
Cited by
UniProt: the Universal Protein Knowledgebase in 2023
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1052 · Cited by 7,210
Self-citationUniProt: the Universal Protein Knowledgebase in 2025
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Adesina, A., Ahmad, S., Bowler-Barnett, E. H., Bye-A-Jee, H., Carpentier, D., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1010 · Cited by 2,537
Self-citationAnnotation of biologically relevant ligands in UniProtKB using ChEBI
Coudert, E., Gehant, S., de Castro, E., Pozzato, M., Baratin, D., Neto, T., Sigrist, C. J. A., Redaschi, N., Bridge, A., The UniProt Consortium, et al. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btac793 · Cited by 350
Self-citationA general model to predict small molecule substrates of enzymes based on machine and deep learning
Kroll, A., Ranjan, S., Engqvist, M. K. M., & Lercher, M. J. (2023) · Nature Communications · doi:10.1038/s41467-023-38347-2 · Cited by 193
Fujita, S., & Terada, T. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.11.028 · Cited by 13
BioTransformer 4.0 a comprehensive computational tool for small molecule metabolism prediction
Tian, S., Feunang, Y. D., Oler, E., Wang, F., Greiner, R., Palm, E. H., Schymanski, E. L., Manach, C., & Wishart, D. S. (2025) · doi:10.1101/2025.07.28.667289 · Cited by 5
Vaparanta, K., Merilahti, J. A. M., Ojala, V. K., & Elenius, K. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100780 · Cited by 3
Metadata
- Authors
- Bansal, P., Morgat, A., Axelsen, K. B., Muthukrishnan, V., Coudert, E., Aimo, L., Hyka-Nouspikel, N., Gasteiger, E., Kerhornou, A., Neto, T. B., Pozzato, M., Blatter, M.-C., Ignatchenko, A., Redaschi, N., & Bridge, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-11-10
- Volume
- 50
- Issue
- D1
- Pages
- D693-D700
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3211718555
- Cited by
- 253
- References
- 5
- FWCI
- 8.92
- Type
- journal article
- Language
- en
- Open access
- gold
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