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Enzyme annotation in UniProtKB using Rhea
MOTIVATION: To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology. RESULTS: We replac...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162351/ https://www.ncbi.nlm.nih.gov/pubmed/31688925 http://dx.doi.org/10.1093/bioinformatics/btz817 |
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author | Morgat, Anne Lombardot, Thierry Coudert, Elisabeth Axelsen, Kristian Neto, Teresa Batista Gehant, Sebastien Bansal, Parit Bolleman, Jerven Gasteiger, Elisabeth de Castro, Edouard Baratin, Delphine Pozzato, Monica Xenarios, Ioannis Poux, Sylvain Redaschi, Nicole Bridge, Alan |
author_facet | Morgat, Anne Lombardot, Thierry Coudert, Elisabeth Axelsen, Kristian Neto, Teresa Batista Gehant, Sebastien Bansal, Parit Bolleman, Jerven Gasteiger, Elisabeth de Castro, Edouard Baratin, Delphine Pozzato, Monica Xenarios, Ioannis Poux, Sylvain Redaschi, Nicole Bridge, Alan |
author_sort | Morgat, Anne |
collection | PubMed |
description | MOTIVATION: To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology. RESULTS: We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that Rhea and ChEBI provide. AVAILABILITY AND IMPLEMENTATION: UniProtKB at https://www.uniprot.org; UniProt REST API at https://www.uniprot.org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot.org/; Rhea at https://www.rhea-db.org. |
format | Online Article Text |
id | pubmed-7162351 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71623512020-04-22 Enzyme annotation in UniProtKB using Rhea Morgat, Anne Lombardot, Thierry Coudert, Elisabeth Axelsen, Kristian Neto, Teresa Batista Gehant, Sebastien Bansal, Parit Bolleman, Jerven Gasteiger, Elisabeth de Castro, Edouard Baratin, Delphine Pozzato, Monica Xenarios, Ioannis Poux, Sylvain Redaschi, Nicole Bridge, Alan Bioinformatics Original Papers MOTIVATION: To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology. RESULTS: We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that Rhea and ChEBI provide. AVAILABILITY AND IMPLEMENTATION: UniProtKB at https://www.uniprot.org; UniProt REST API at https://www.uniprot.org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot.org/; Rhea at https://www.rhea-db.org. Oxford University Press 2020-03-15 2019-11-05 /pmc/articles/PMC7162351/ /pubmed/31688925 http://dx.doi.org/10.1093/bioinformatics/btz817 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Morgat, Anne Lombardot, Thierry Coudert, Elisabeth Axelsen, Kristian Neto, Teresa Batista Gehant, Sebastien Bansal, Parit Bolleman, Jerven Gasteiger, Elisabeth de Castro, Edouard Baratin, Delphine Pozzato, Monica Xenarios, Ioannis Poux, Sylvain Redaschi, Nicole Bridge, Alan Enzyme annotation in UniProtKB using Rhea |
title | Enzyme annotation in UniProtKB using Rhea |
title_full | Enzyme annotation in UniProtKB using Rhea |
title_fullStr | Enzyme annotation in UniProtKB using Rhea |
title_full_unstemmed | Enzyme annotation in UniProtKB using Rhea |
title_short | Enzyme annotation in UniProtKB using Rhea |
title_sort | enzyme annotation in uniprotkb using rhea |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162351/ https://www.ncbi.nlm.nih.gov/pubmed/31688925 http://dx.doi.org/10.1093/bioinformatics/btz817 |
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