Enzyme annotation in UniProtKB using Rhea Article Swipe
Anne Morgat
,
Thierry Lombardot
,
Elisabeth Coudert
,
Kristian B. Axelsen
,
Teresa Batista Neto
,
Sébastien Géhant
,
Parit Bansal
,
Jerven Bolleman
,
Elisabeth Gasteiger
,
Edouard de Castro
,
Delphine Baratin
,
Monica Pozzato
,
Ioannis Xénarios
,
Sylvain Poux
,
Nicole Redaschi
,
Alan Bridge
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/709899
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/709899
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 ontology ChEBI (Chemical Entities of Biological Interest). 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/sparql ; Rhea at https://www.rhea-db.org/ . Contact [email protected]
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/709899
- https://www.biorxiv.org/content/biorxiv/early/2019/07/22/709899.full.pdf
- OA Status
- green
- Cited By
- 9
- References
- 37
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2963795778
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2963795778Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/709899Digital Object Identifier
- Title
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Enzyme annotation in UniProtKB using RheaWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2019Year of publication
- Publication date
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2019-07-22Full publication date if available
- Authors
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Anne Morgat, Thierry Lombardot, Elisabeth Coudert, Kristian B. Axelsen, Teresa Batista Neto, Sébastien Géhant, Parit Bansal, Jerven Bolleman, Elisabeth Gasteiger, Edouard de Castro, Delphine Baratin, Monica Pozzato, Ioannis Xénarios, Sylvain Poux, Nicole Redaschi, Alan BridgeList of authors in order
- Landing page
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https://doi.org/10.1101/709899Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2019/07/22/709899.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2019/07/22/709899.full.pdfDirect OA link when available
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UniProt, SPARQL, Annotation, Computer science, Ontology, Leverage (statistics), Information retrieval, Oomycete, World Wide Web, Semantic Web, RDF, Biology, Artificial intelligence, Genetics, Epistemology, Gene, PhilosophyTop concepts (fields/topics) attached by OpenAlex
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9Total citation count in OpenAlex
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2023: 1, 2022: 1, 2021: 3, 2020: 3, 2019: 1Per-year citation counts (last 5 years)
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37Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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