HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes

Autor: Edouard de Castro, Chantal Hulo, Delphine Baratin, Béatrice A. Cuche, Sebastien Gehant, Elisabeth Coudert, Catherine Rivoire, Ivo Pedruzzi, Nicole Redaschi, Alan Bridge, Patrick Masson, Ioannis Xenarios, Jerven Bolleman, Andrea H. Auchincloss

Publikováno v: GigaScience

BackgroundGenome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to enco

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::062c6c5b522d83eaa721e99f0199938b
https://doi.org/10.1093/gigascience/giaa003

Enzyme annotation in UniProtKB using Rhea

Autor: Sylvain Poux, Delphine Baratin, Ioannis Xenarios, Teresa Batista Neto, Elisabeth Gasteiger, Sebastien Gehant, Nicole Redaschi, Anne Morgat, Thierry Lombardot, Jerven Bolleman, Edouard de Castro, Parit Bansal, Monica Pozzato, Elisabeth Coudert, Kristian B. Axelsen, Alan Bridge

Publikováno v: Bioinformatics

MotivationTo 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 Enti

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::094df19a76493513f1d0258b3b046420
https://doi.org/10.1093/bioinformatics/btz817

UniProt: a hub for protein information

Autor: Ursula Hinz, Prudence Mutowo, Laure Verbregue, Weizhong Li, Nadine Gruaz-Gumowski, Chantal Hulo, Hermann Zellner, Shyamala Sundaram, P Lemercier, Guoying Qi, Parit Bansal, Tony Sawford, Sebastien Gehant, Delphine Baratin, Francesco Fazzini, Monica Pozzato, Séverine Duvaud, Lai-Su L. Yeh, Nicole Redaschi, Emma Hatton-Ellis, Darren A. Natale, Damien Lieberherr, Luis Figueira, Bernd Roechert, Borisas Bursteinas, Gayatri Chavali, Brigitte Boeckmann, Cristina Casal-Casas, Baris E. Suzek, Cathy H. Wu, Paul Gane, Ghislaine Argoud-Puy, Klemens Pichler, Rachael P. Huntley, Sangya Pundir, Alan Bridge, Edouard de Castro, Benoit Bely, Kristian B. Axelsen, Emmanuel Boutet, Andre Stutz, Penelope Garmiri, Christian J. A. Sigrist, John S. Garavelli, Rolf Apweiler, Peter B. McGarvey, Patrick Masson, Maria Jesus Martin, K Sonesson, Xavier Watkins, Ioannis Xenarios, Vladimir Volynkin, Hamish McWilliam, Mark Bingley, Guillaume Keller, Hongzhan Huang, Rabie Saidi, Sylvain Poux, Tunca Doğan, Yuqi Wang, Diego Poggioli, Rodrigo Lopez, Alistair MacDougall, Kati Laiho, Qinghua Wang, W Liu, Carlos Bonilla, Duncan Legge, C. R. Vinayaka, Anne Morgat, Thierry Lombardot, Jerven Bolleman, Nevila Nouspikel, Aleksandra Shypitsyna, Emanuele Alpi, Yongxing Chen, Anne Lise Veuthey, Andrew Nightingale, Béatrice A. Cuche, Alex Bateman, Ramona Britto, Alan Wilter Sousa da Silva, Jie Luo, Lionel Breuza, Marie Claude Blatter, Elena Cibrian-Uhalte, Michel Schneider, Chuming Chen, Michele Magrane, L Famiglietti, Meher Shruti Yerramalla, Lydie Bougueleret, Vivienne Baillie Gerritsen, Anne Estreicher, Dolnide Dornevil, Catherine Rivoire, Jian Zhang, S Staehli, Andrew Peter Cowley, Tony Wardell, Ivo Pedruzzi, Andrea H. Auchincloss, Salvo Paesano, Elisabeth Gasteiger, Luis Pureza, Marc Feuermann, Leslie Arminski, Xavier D. Martin, Teresa Batista Neto, Steven Rosanoff, Florence Jungo, Sandra Orchard, Claire O'Donovan, Elisabeth Coudert, Ricardo Antunes, Sandrine Pilbout, Vicente Lara, Arnaud Gos, Reija Hieta, Manuela Pruess, Joanna Arganiska, Edward Turner, Maurizio De Giorgi, M Doche, Cecilia N. Arighi, Michael Tognolli, Leyla Jael Garcia Castro, Lucila Aimo

Publikováno v: Nucleic Acids Research

UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::429cad485e24854c12fb7ce51fdc3b2a
https://pubmed.ncbi.nlm.nih.gov/25348405

Ongoing and future developments at the Universal Protein Resource

Autor: Vicente Lara, Arnaud Gos, Nikolas Pontikos, L. Bollondi, L Famiglietti, Barker Wc, Chuming Chen, Michael Tognolli, Patrick Masson, Salvo Paesano, Tony Sawford, Sandrine Pilbout, Jerven Bolleman, Jian Zhang, S Staehli, Elisabeth Gasteiger, David Binns, Ursula Hinz, Nadine Gruaz-Gumowski, Chantal Hulo, Maria Jesus Martin, M. Corbett, Veuthey Al, Paul Browne, Guillaume Keller, S. Jimenez, Roberts Nv, Brigitte Boeckmann, Natale Da, Suzek Be, Edward Turner, T. Kappler, Steven Rosanoff, Leslie Arminski, Florence Jungo, M Donnelly, P. Dubey, Ruth Y. Eberhardt, Lydie Bougueleret, Vivienne Baillie Gerritsen, Maria Victoria Schneider, Lionel Breuza, Isabelle Cusin, Delphine Baratin, E. Dimmer, Rachael P. Huntley, Julius O.B. Jacobsen, Arighi Cn, Quintaje Sb, Alan Bridge, Nicole Redaschi, Shyamala Sundaram, Peter B. McGarvey, Rebecca E. Foulger, Duncan Legge, Andre Stutz, Monica Pozzato, Raja Mazumder, Anne Morgat, M Doche, K Sonesson, Anne Estreicher, Blatter Mc, Manuela Pruess, Serenella Ferro, Séverine Duvaud, F. Fazzini, Rolf Apweiler, Natarajan Tg, E. Stanley, M Feuermann, Claire O'Donovan, J. James, Ivo Pedruzzi, Castro Lg, Wu Ch, M Bingley, W Liu, He Huang, Bernd Roechert, Laure Verbregue, Elisabeth Coudert, Ioannis Xenarios, M. Moinat, Sandra Orchard, P Lemercier, Damien Lieberherr, Ricardo Antunes, Ghislaine Argoud-Puy, Sebastien Gehant, Qiang Wang, Klemens Pichler, S. Patient, Nicolas Hulo, Diego Poggioli, J. Nchoutmboube, Emmanuel Boutet, H. Sehra, Chan Wm, Yasmin Alam-Faruque, M. Kleen, Van Rensburg P, Kati Laiho, Kristian B. Axelsen, John S. Garavelli, Christian J. A. Sigrist, Amos Marc Bairoch, Yongxing Chen, A. Fedotov, Yeh Ls, Sylvain Poux, Lynette Bower, Quan Lin, Daniel Barrell, Benoit Bely, U. Ugochukwu, Xavier D. Martin, Catherine Rivoire, E. Decastro, Jie Luo, Alain Gateau, Michele Magrane, Dolnide Dornevil, Vinayaka Cr, Andrea H. Auchincloss, Yuqi Wang

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, 2011, 39 (Database issue), pp.D214-9. ⟨10.1093/nar/gkq1020⟩
Nucleic Acids Research, Oxford University Press, 2011, 39 (Database issue), pp.D214-9. ⟨10.1093/nar/gkq1020⟩
Nucleic Acids Research; Vol 39
Nucleic Acids Research, vol. 39, no. Database issue, pp. D214-D219

International audience; The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with exten

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2bb13db339c56730c1ada1950020ba13
https://inria.hal.science/hal-00746843

Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB

Autor: 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

Publikováno v: Metabolites, Vol 11, Iss 1, p 48 (2021)

The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers genomes and proteomes from tens of thousands of taxa, including a broad range of plants an

Externí odkaz: https://doaj.org/article/d83825c386eb4381973c7daef4eabd30