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1. Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Author

Elisabeth Coudert, Sebastien Gehant, Edouard De Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J. A. Sigrist, Nicole Redaschi, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny 0002, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra 0004, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang 0003, and Yuqi Wang

Published
2023
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2. UniProt: the universal protein knowledgebase in 2021.

Author

Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny 0002, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra 0004, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang 0003, Yuqi Wang, Lai-Su Yeh, Jian Zhang 0051, Patrick Ruch, and Douglas Teodoro

Published
2021
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5. PIRSF: family classification system at the Protein Information Resource.

Author

Cathy H. Wu, Anastasia N. Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, Cholanayakanahalli R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang 0051, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, and Winona C. Barker

Published
2004
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6. The Protein Information Resource.

Author

Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Cholanayakanahalli R. Vinayaka, Jian Zhang 0051, and Winona C. Barker

Published
2003
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8. UniProt: the universal protein knowledgebase in 2021

Author

Fábio Madeira, Emmanuel Boutet, Ursula Hinz, Teresa Batista Neto, Parit Bansal, Manuela Pruess, Kristian B. Axelsen, Arnaud Kerhornou, Cecilia N. Arighi, Lai-Su L. Yeh, Shadab Ahmad, John S. Garavelli, Cathy H. Wu, Florence Jungo, Alan Bridge, Leonardo Gonzales, Sandra Orchard, Patrick Masson, Douglas Teodoro, Maria Jesus Martin, Anne Estreicher, Kamal Chikh Echioukh, Hongzhan Huang, Patrick Ruch, Christian J. A. Sigrist, C. R. Vinayaka, Yvonne Lussi, Anne Morgat, Yongxing Chen, Austra Cukura, Emanuele Alpi, Ramona Britto, Alexandr Ignatchenko, Sylvain Poux, Rizwan Ishtiaq, Lionel Breuza, Jun Fan, Edouard de Castro, Petteri Jokinen, Nicole Redaschi, Darren A. Natale, Daniel Rice, Giuseppe Insana, George Georghiou, Nevila Hyka-Nouspikel, Karen E. Ross, Katie Moulang, Vicente Lara, Arnaud Gos, Michael Tognolli, Alok Mishra, Ivo Pedruzzi, Nidhi Tyagi, Leyla Jael Garcia Castro, Edward Turner, Cristina Casals-Casas, Tunca Doğan, Nadine Gruaz-Gumowski, Chantal Hulo, Maria Livia Famiglietti, Andrew Nightingale, Paul Denny, Lucila Aimo, Rossana Zaru, Vishal Joshi, Alistair MacDougall, Andre Stutz, Penelope Garmiri, Carla Susana Oliveira, Hermann Zellner, Marie-Claude Blatter, Emily H Bowler-Barnett, Philippe Le Mercier, Abdulrahman Hussein, Catherine Rivoire, Tony Sawford, Milagros Rodriguez Lopez, Salvo Paesano, Vladimir Volynkin, Manuela Menchi, Hema Bye-A-Jee, Monica Pozzato, Kati Laiho, Delphine Baratin, Qinghua Wang, Leslie Arminski, Preethi Vasudev, Sangya Pundir, Jian Zhang, Emma Hatton-Ellis, Kate Warner, Lucille Pourcel, Elisabeth Gasteiger, Marc Feuermann, Thierry Lombardot, Jerven Bolleman, Mahdi Mahmoudy, Shyamala Sundaram, Alex Bateman, Xavier Watkins, Rahat Agivetova, Guoying Qi, Peter B. McGarvey, Xavier D. Martin, Chuming Chen, Jie Luo, Ray Coetzee, K Sonesson, Alan Wilter Sousa da Silva, ThankGod Ebenezer, Elena Speretta, Rodrigo Lopez, Elisabeth Coudert, Aurelien Luciani, Vivienne Baillie Gerritsen, Yuqi Wang, M Doche, Michele Magrane, Antonia Lock, Dolnide Dornevil, Sandrine Pilbout, Borisas Bursteinas, Andrea H. Auchincloss, Béatrice A. Cuche, Dushyanth Jyothi, Rabie Saidi, Joseph Sampson, Laure Verbregue, Sebastien Gehant, Guillaume Keller, Shriya Raj, Damien Lieberherr, Ghislaine Argoud-Puy, and Teodoro, Douglas

Subjects
Proteomics, COVID-19 / virology, Computational Biology / methods, Molecular Sequence Annotation / methods, Proteome, AcademicSubjects/SCI00010, Knowledge Bases, Computational biology, Proteomics / methods, Biology, ddc:616.0757, SARS-CoV-2 / physiology, COVID-19 / epidemiology, User-Computer Interface, Viral Proteins, 03 medical and health sciences, 0302 clinical medicine, SARS-CoV-2 / genetics, Data Curation / methods, Genetics, Redundancy (engineering), Viral Proteins / genetics, Humans, Database Issue, SARS-CoV-2 / metabolism, Databases, Protein, Pandemics, Data Curation, Proteome / metabolism, 030304 developmental biology, Proteome / genetics, Internet, 0303 health sciences, SARS-CoV-2, COVID-19 / prevention & control, COVID-19, Computational Biology, Molecular Sequence Annotation, Viral Proteins / metabolism, UniProt Knowledgebase, UniProt, 030217 neurology & neurosurgery
Abstract

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

Published
2020

9. Activities at the Universal Protein Resource (UniProt)

Author

Borisas Bursteinas, L-S Yeh, Klemens Pichler, Guillaume Keller, C Casal-Casas, Gerritsen, A Da Silva, Prudence Mutowo, Xavier D. Martin, Peter B. McGarvey, Volynkin, J Lew, K Sonesson, M. C. Blatter, L Pureza, Rodrigo Lopez, Anne Estreicher, Alex Bateman, Ramona Britto, A-L Veuthey, Penelope Garmiri, Patrick Masson, Baris E. Suzek, Cathy H. Wu, Paul Gane, Maria Jesus Martin, Shyamala Sundaram, Yasmin Alam-Faruque, Ioannis Xenarios, Alan Bridge, WM Chan, Guoying Qi, L Famiglietti, Christian J. A. Sigrist, Nadine Gruaz-Gumowski, Chantal Hulo, Hermann Zellner, Matthew Corbett, Monica Pozzato, Thierry Lombardot, S Staehli, Jerven Bolleman, Sylvain Poux, Séverine Duvaud, Tony Sawford, Chuming Chen, Xavier Watkins, Yuqi Wang, Elisabeth Gasteiger, Kati Laiho, Qinghua Wang, M Bingley, Lydie Bougueleret, Kristian B. Axelsen, Yongxing Chen, Salvo Paesano, Andrew Nightingale, Nicole Redaschi, Emma Hatton-Ellis, John S. Garavelli, Delphine Baratin, Darren A. Natale, Gayatri Chavali, E de Castro, Leslie Arminski, Damien Lieberherr, Elena Cibrian-Uhalte, Catherine Rivoire, Bernd Roechert, Yerramalla, Hongzhan Huang, Alistair MacDougall, Edd Turner, Maria Victoria Schneider, Aleksandra Shypitsyna, Jie Zhang, Michele Magrane, Dolnide Dornevil, Lara, M Donnelly, F. Fazzini, Andrea H. Auchincloss, Emanuele Alpi, Benoit Bely, Brigitte Boeckmann, Rolf Apweiler, Rachael P. Huntley, Lionel Breuza, Sangya Pundir, Lorenzo Cerutti, Tunca Doğan, EB Casanova, P van Rensburg, Rabie Saidi, Jie Luo, Mickael Goujon, Laure Verbregue, Tony Wardell, W Liu, Andre Stutz, P Lemercier, Hamish McWilliam, Ivo Pedruzzi, P-A Binz, Sebastien Gehant, Béatrice A. Cuche, Carlos Bonilla, Duncan Legge, C. R. Vinayaka, Anne Morgat, Diego Poggioli, J Arganiska, Teresa Batista Neto, Emmanuel Boutet, Florence Jungo, Ursula Hinz, Parit Bansal, Sandra Orchard, Ricardo Antunes, Manuela Pruess, M Feuermann, S. Rosanoff, Claire O'Donovan, Cecilia N. Arighi, J. James, M Doche, Elisabeth Coudert, M De Giorgi, Reija Hieta, Sandrine Pilbout, Arnaud Gos, Michael Tognolli, Leyla Jael Garcia Castro, and Lucila Aimo

Subjects
Proteomics, 0303 health sciences, Internet, Representation (systemics), Genome database, Proteins, Molecular Sequence Annotation, Computational biology, Genomics, Biology, Ontology (information science), Universal Protein Resource, II. Protein sequence and structure, motifs and domains, 03 medical and health sciences, Annotation, 0302 clinical medicine, Gene Ontology, Sequence Analysis, Protein, 030220 oncology & carcinogenesis, Genetics, UniProt, Databases, Protein, 030304 developmental biology
Abstract

The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

Published
2013

10. UniProt: a hub for protein information

Author

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, and Lucila Aimo

Subjects
Proteome, Computer science, Molecular Sequence Annotation, Computational biology, Accession number (bioinformatics), DNA sequencing, World Wide Web, Identifier, Annotation, Sequence Analysis, Protein, Genetics, Database Issue, natural sciences, UniProt, Databases, Protein
Abstract

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 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.

Published
2014

11. Ongoing and future developments at the Universal Protein Resource

Author

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, An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institut de Microélectronique, Electromagnétisme et Photonique - Laboratoire d'Hyperfréquences et Caractérisation (IMEP-LAHC), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie et de physique des milieux condensés (IMPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria), Université de Lausanne (UNIL), Université Pierre et Marie Curie - Paris 6 (UPMC)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), UniProt Consortium, Apweiler, R., Martin, MJ., O'Donovan, C., Magrane, M., Alam-Faruque, Y., Antunes, R., Barrell, D., Bely, B., Bingley, M., Binns, D., Bower, L., Browne, P., Chan, WM., Dimmer, E., Eberhardt, R., Fazzini, F., Fedotov, A., Foulger, R., Garavelli, J., Castro, LG., Huntley, R., Jacobsen, J., Kleen, M., Laiho, K., Legge, D., Lin, Q., Liu, W., Luo, J., Orchard, S., Patient, S., Pichler, K., Poggioli, D., Pontikos, N., Pruess, M., Rosanoff, S., Sawford, T., Sehra, H., Turner, E., Corbett, M., Donnelly, M., van Rensburg, P., Xenarios, I., Bougueleret, L., Auchincloss, A., Argoud-Puy, G., Axelsen, K., Bairoch, A., Baratin, D., Blatter, MC., Boeckmann, B., Bolleman, J., Bollondi, L., Boutet, E., Quintaje, SB., Breuza, L., Bridge, A., deCastro, E., Coudert, E., Cusin, I., Doche, M., Dornevil, D., Duvaud, S., Estreicher, A., Famiglietti, L., Feuermann, M., Gehant, S., Ferro, S., Gasteiger, E., Gateau, A., Gerritsen, V., Gos, A., Gruaz-Gumowski, N., Hinz, U., Hulo, C., Hulo, N., James, J., Jimenez, S., Jungo, F., Kappler, T., Keller, G., Lara, V., Lemercier, P., Lieberherr, D., Martin, X., Masson, P., Moinat, M., Morgat, A., Paesano, S., Pedruzzi, I., Pilbout, S., Poux, S., Pozzato, M., Redaschi, N., Rivoire, C., Roechert, B., Schneider, M., Sigrist, C., Sonesson, K., Staehli, S., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Verbregue, L., Veuthey, AL., Wu, CH., Arighi, CN., Arminski, L., Barker, WC., Chen, C., Chen, Y., Dubey, P., Huang, H., Mazumder, R., McGarvey, P., Natale, DA., Natarajan, TG., Nchoutmboube, J., Roberts, NV., Suzek, BE., Ugochukwu, U., Vinayaka, CR., Wang, Q., Wang, Y., Yeh, LS., and Zhang, J.

Subjects
Proteomics, 0303 health sciences, Sequence database, 030302 biochemistry & molecular biology, Proteins, Articles, Computational biology, Biology, Bioinformatics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Systems Integration, Universal Protein Resource, 03 medical and health sciences, Information resource, Protein sequencing, Sequence Analysis, Protein, Metagenomics, UniProt Knowledgebase, Genetics, Databases, Protein/trends, Proteins/chemistry, Proteins/genetics, UniProt, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Databases, Protein, 030304 developmental biology
Abstract

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 extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.

Published
2011
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12. PIRSF: family classification system at the Protein Information Resource

Author

Anastasia N. Nikolskaya, Robert S. Ledley, Yongxing Chen, Jorge Castro-Alvear, Winona C. Barker, Sandeep Kumar, Leslie Arminski, Lai-Su L. Yeh, Sehee Chung, Zhang-Zhi Hu, Raja Mazumder, Darren A. Natale, Jian Zhang, Georgi Dinkov, Jorge Louie Cardenas, Hongzhan Huang, Panagiotis Kourtesis, Baris E. Suzek, Cathy H. Wu, and C. R. Vinayaka

Subjects
Internet, Subfamily, Phylogenetic tree, Architecture domain, Protein family, Amino Acid Motifs, Computational Biology, Information Storage and Retrieval, Proteins, Sequence alignment, Computational biology, Articles, Biology, Bioinformatics, Protein Structure, Tertiary, Evolution, Molecular, Annotation, ComputingMethodologies_PATTERNRECOGNITION, Similarity (network science), Protein Annotation, Genetics, Animals, Humans, Databases, Protein
Abstract

The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.

Published
2004

13. Theory for vesicle—vesicle and vesicle-plasmalemma interactions

Author

Sheldon Weinbaum, Shu Chien, and Leslie Arminski

Subjects
Chemistry, Diffusion, Vesicle, Equations of motion, Electron, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Biomaterials, symbols.namesake, Crystallography, Colloid and Surface Chemistry, Viscous resistance, Membrane, Chemical physics, symbols, van der Waals force, Cytoplasmic region
Abstract

A theory for predicting the approach velocity of a vesicle diffusing toward another vesicle or plasmalemma membrane is presented. This theory takes account of the shift between retarded and nonretarded van der Waals forces of attraction, the electrostatic forces of repulsion, and a spatially varying diffusion coefficient that considers the changing viscous resistance as the intervening fluid gap narrows. Velocities are calculated as a function of gap distance by substituting the above-mentioned forces, which are found by differentiation of existing expressions for free energy of interaction, in a quasi-steady equation of motion. Calculations are presented which show that it is necessary to have a correct hydrodynamic description of the process in order to obtain accurate velocities. It is shown that a critical spacing dependent on cation concentration exists, where the velocity of approach becomes zero due to the presence of a secondary minimum. For a Ca2+ concentration of 5 × 10−2 M, a Na+ concentration of 0.1 M, and a pH of 7.4, this distance is found to be less than 20 A for a 700-A phosphatidylserine vesicle approaching a plasmalemma and 25–30 A for a vesicle approaching an identical vesicle. These results are used to explain why fused or aggregated vesicles are seen less frequently than isolated vesicles in the central cytoplasmic region of mammalian endothelial cells in electron micrographic studies.

Published
1982
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14. Introduction to the operational aspects of digital fluoroscopy

Author

Thomas J. Golab, Louis S. Rotolo, Robert S. Ledley, Leslie Arminski, and James B. Wilson

Subjects
Block cipher mode of operation, medicine.medical_specialty, medicine.diagnostic_test, Computers, business.industry, Angiography, Image processing, Equipment Design, Edge enhancement, Radiographic Image Enhancement, Software, Mode (computer interface), Progressive scan, Fluoroscopy, Picture processing, Humans, Medicine, Radiology, Nuclear Medicine and imaging, Radiology, business, Technology, Radiologic
Abstract

A tutorial is presented on the operational aspects of digital fluoroscopy using the Georgetown University Digital Fluoroscopy Unit (GUDFU) to illustrate the principles. Both the spot-film high milliamp mode and the fluoroscopic, low milliamp mode of operation are described. The hardware and software of the system are discussed and the operation of the system is followed. The picture processing unit, TEXAC, used in the GUDFU is described together with the picture processing language called PPL. Finally, the results are given of experiments that were designed to illustrate the image manipulation capability that could be included in a digital fluoroscopy unit.

Published
1983
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15. The Protein Information Resource

Author

C. R. Vinayaka, Leslie Arminski, Yongxing Chen, Lai-Su L. Yeh, Jorge Castro-Alvear, Jian Zhang, Panagiotis Kourtesis, Zhang-Zhi Hu, Robert S. Ledley, Winona C. Barker, Hongzhan Huang, Baris E. Suzek, and Cathy H. Wu

Subjects
Internet, Information retrieval, Architecture domain, Sequence database, Protein family, Proteins, Articles, Biology, Bioinformatics, Databases, Bibliographic, Identification (information), Annotation, Knowledge extraction, Informatics, Genetics, RefSeq, Animals, Amino Acid Sequence, Databases, Protein
Abstract

The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.

16. Effect of waveform and duration of impulse on the solution to the Basset−Langevin equation

Author

Sheldon Weinbaum and Leslie Arminski

Subjects
Physics, media_common.quotation_subject, General Engineering, Reynolds number, Mechanics, Impulse (physics), Inertia, Physics::Fluid Dynamics, Langevin equation, Boundary layer, symbols.namesake, Classical mechanics, Drag, symbols, Waveform, Transient response, media_common
Abstract

New analytic solutions to the continuum hydrodynamic equations for the transient response of a spherical particle at low Reynolds number to several simple excitation forces f(t) of varying duration and different waveforms are presented. The new solutions permit the exploration of the effect of the waveform and the duration of impulse on the relative magnitude of the inertia, quasi‐steady Stokes’ drag and unsteady boundary layer (Basset) force components throughout the time history of the motion. It is shown that for an impulse of constant magnitude the net displacement of the particle is independent of both the duration and waveform of the excitation force. This simple result is used to explain why one obtains the correct Stokes−Einstein expression for the infinite time diffusion coefficient from a traditional Langevin analysis in which, historically, an incorrect quasi‐steady linear Stokes resistance law has been used.

Published
1979
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