The Swiss-Prot team excels in the art of generating machine-readable knowledge of biology from the ever growing body of scientific publications...
Focus on the group's mission
The Swiss-Prot team excels in the art of generating machine-readable knowledge of biology from the ever growing body of scientific publications. It is harnessing the power of deep learning to accelerate literature triage and information extraction, thus delivering the most accurate and informative evidence to users in a timely manner.
Biocuration and software development
Our team of biocurators and software developers annotate, maintain and develop a range of internationally renowned expert-curated knowledge resources:
The HAMAP and PROSITE databases of protein families and domains, the ENZYME database of enzyme nomenclature, the SwissLipids database of lipid structures and biological knowledge, the ViralZone portal, and SwissBioPics, a resource of interactive cellular images.
The group also participates in the development and maintenance of many of the protein analysis tools listed on Expasy, the Swiss Bioinformatics Resource Portal. Expasy's proteomics tool.
The team also supports the development of tools and resources for Swiss researchers and clinicians, such as the SVIP-O platform for the clinical interpretation of cancer variants.
Supporting AI with machine-readable biological knowledge
Knowledgebases like UniProtKB are an essential part of the AI ecosystem; the collective biological knowledge they contain, in the form of pathways, ontologies and networks, can be used to create generalizable and interpretable models that reveal actionable biological mechanisms.
Parit Bansal, Anne Morgat, Kristian B Axelsen, Venkatesh Muthukrishnan, Elisabeth Coudert, Lucila Aimo, Nevila Hyka-Nouspikel, Elisabeth Gasteiger, Arnaud Kerhornou, Teresa Batista Neto, Monica Pozzato, Marie-Claude Blatter, Alex Ignatchenko, Nicole Redaschi, Alan Bridge. Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res (2021) doi: 10.1093/nar/gkab1016
Marc Feuermann, Emmanuel Boutet, Anne Morgat, Kristian B Axelsen, Parit Bansal, Jerven Bolleman, Edouard de Castro, Elisabeth Coudert, Elisabeth Gasteiger, Sébastien Géhant, Damien Lieberherr, Thierry Lombardot, Teresa B Neto, Ivo Pedruzzi, Sylvain Poux, Monica Pozzato, Nicole Redaschi, Alan Bridge, On Behalf Of The UniProt Consortium. Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. Metabolites (2021) doi: 10.3390/metabo11010048
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar, Lowri Williams, Peer Bork, Alan Bridge, Julian Gough, Daniel H Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Marco Necci, Christine A Orengo, Arun P Pandurangan, Catherine Rivoire, Christian J A Sigrist, Ian Sillitoe, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Alex Bateman, Robert D Finn. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res (2021) doi: 10.1093/nar/gkaa977
Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res (2021) doi: 10.1093/nar/gkaa1113
Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra Orchard, Andrea H Auchincloss, Delphine Baratin, Jerven Bolleman, Elisabeth Coudert, Edouard de Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C R Vinayaka, Lai-Su Yeh, Darren A Natale, Kati Laiho, Maria-Jesus Martin, Alexandre Renaux, Klemens Pichler, UniProt Consortium. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinformatics (2020) doi: 10.1093/bioinformatics/btaa485
Anne Morgat, Thierry Lombardot, Elisabeth Coudert, Kristian Axelsen, Teresa Batista Neto, Sebastien Gehant, Parit Bansal, Jerven Bolleman, Elisabeth Gasteiger, Edouard de Castro, Delphine Baratin, Monica Pozzato, Ioannis Xenarios, Sylvain Poux, Nicole Redaschi, Alan Bridge, UniProt Consortium. Enzyme annotation in UniProtKB using Rhea. Bioinformatics (2020) doi: 10.1093/bioinformatics/btz817
Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A Cuche, Andrea H Auchincloss, Elisabeth Coudert, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios, Nicole Redaschi, Alan Bridge. HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. Gigascience (2020) doi: 10.1093/gigascience/giaa003
Leyla Garcia, Jerven Bolleman, Sebastien Gehant, Nicole Redaschi, Maria Martin, UniProt Consortium. FAIR adoption, assessment and challenges at UniProt. Sci Data (2019) doi: 10.1038/s41597-019-0180-9
M L Famiglietti, A Estreicher, L Breuza, S Poux, N Redaschi, I Xenarios, A Bridge, UniProt Consortium. An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. Database (Oxford) (2019) doi: 10.1093/database/baz040
Thierry Lombardot, Anne Morgat, Kristian B Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alex Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan Bridge. Updates in Rhea: SPARQLing biochemical reaction data. Nucleic acids research (2019) doi: 10.1093/nar/gky876
Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu. Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput Biol (2018) doi: 10.1371/journal.pcbi.1006390
We use cookies to ensure you get the best experience while browsing our website and to extract visits’ statistics. By using SIB’s website, we assume that you agree to their use. Read our privacy policy.
