Search

Your search keyword '"Shyamala Sundaram"' showing total 11 results
Start Over Author "Shyamala Sundaram"
11 results on '"Shyamala Sundaram"'

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
Full Text
View/download PDF

2. The Gene Ontology resource: enriching a GOld mine.

Author

Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny 0002, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, and Justin Elser

Published
2021
Full Text
View/download PDF

3. 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
Full Text
View/download PDF

4. The UniProt-GO Annotation database in 2011.

Author

Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Y. Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan J. Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek Roggli, Ioannis Xenarios, and Rolf Apweiler

Published
2012
Full Text
View/download PDF

5. A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer’s Disease Through Expert Curation of Key Protein Targets

Author

Michele Magrane, Sandra Orchard, George Georghiou, Ruth C. Lovering, Livia Perfetto, Lionel Breuza, Sylvain Poux, Ghislaine Argoud-Puy, Cristina Casals-Casas, Nadine Gruaz-Gumowski, Shyamala Sundaram, Maria Livia Famiglietti, Elizabeth Wu, Ursula Hinz, Arnaud Gos, Barbara Kramarz, Yvonne Lussi, Christian J. Stoeckert, Cecilia N. Arighi, Anne Estreicher, Milagros Rodríguez-López, Li-San Wang, Nevila Hyka-Nouspikel, and Patrick Masson

Subjects
0301 basic medicine, Cytoscape network analysis, Computer science, Expert Systems, Bioinformatics, Public domain, Set (abstract data type), 03 medical and health sciences, Annotation, 0302 clinical medicine, Alzheimer Disease, Humans, Protein Interaction Maps, Databases, Protein, Alzheimer’s disease, data curation, database, neurobiology, protein, Biological data, Public Sector, Data curation, General Neuroscience, Computational Biology, General Medicine, Identifier, Psychiatry and Mental health, Clinical Psychology, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Data quality, Geriatrics and Gerontology, UniProt, 030217 neurology & neurosurgery, Research Article
Abstract

Background: The analysis and interpretation of data generated from patient-derived clinical samples relies on access to high-quality bioinformatics resources. These are maintained and updated by expert curators extracting knowledge from unstructured biological data described in free-text journal articles and converting this into more structured, computationally-accessible forms. This enables analyses such as functional enrichment of sets of genes/proteins using the Gene Ontology, and makes the searching of data more productive by managing issues such as gene/protein name synonyms, identifier mapping, and data quality. Objective: To undertake a coordinated annotation update of key public-domain resources to better support Alzheimer’s disease research. Methods: We have systematically identified target proteins critical to disease process, in part by accessing informed input from the clinical research community. Results: Data from 954 papers have been added to the UniProtKB, Gene Ontology, and the International Molecular Exchange Consortium (IMEx) databases, with 299 human proteins and 279 orthologs updated in UniProtKB. 745 binary interactions were added to the IMEx human molecular interaction dataset. Conclusion: This represents a significant enhancement in the expert curated data pertinent to Alzheimer’s disease available in a number of biomedical databases. Relevant protein entries have been updated in UniProtKB and concomitantly in the Gene Ontology. Molecular interaction networks have been significantly extended in the IMEx Consortium dataset and a set of reference protein complexes created. All the resources described are open-source and freely available to the research community and we provide examples of how these data could be exploited by researchers.

Published
2020

6. 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

7. The UniProt-GO Annotation database in 2011

Author

Rachael P. Huntley, Florence Jungo, Tony Sawford, Harminder Sehra, Shyamala Sundaram, Phillippe Lemercier, Bernd Roechert, Silvia Braconi-Quintaje, Guillaume Keller, Madelaine Moinat, Sylvain Poux, Paul Browne, Rolf Apweiler, Kristian B. Axelsen, Kati Laiho, Andre Stutz, Janet James, Catherine Rivoire, Diego Poggioli, Wei Mun Chan, Ivo Pedruzzi, Anne Estreicher, Silvia Jimenez, Paula Duek Roggli, Michael Gardner, Serenella Ferro-Rojas, Claire O'Donovan, Patrick Masson, Maria Jesus Martin, Michele Magrane, Elizabeth Coudert, Benoit Bely, Michael Tognolli, Emmanuel Boutet, Isabelle Cusin, Andrea H. Auchincloss, Yasmin Alam-Faruque, Klemens Pichler, Nadine Gruaz-Gumowski, Chantal Hulo, Ursula Hinz, Ruth Y. Eberhardt, Duncan Legge, L Famiglietti, E. Dimmer, Michael Schneider, Marc Feuermann, Lionel Breuza, Arnaud Gos, Damien Lieberherr, Ghislaine Argoud-Puy, Marie-Claude Blatter, Lydie Bougueleret, Ioannis Xenarios, and Alan Bridge

Subjects
0303 health sciences, business.industry, Databases, Protein, Molecular Sequence Annotation/standards, Vocabulary, Controlled, Molecular Sequence Annotation, Articles, Biology, File format, Bioinformatics, World Wide Web, 03 medical and health sciences, Consistency (database systems), Annotation, 0302 clinical medicine, 030220 oncology & carcinogenesis, Controlled vocabulary, Genetics, Data set (IBM mainframe), The Internet, UniProt, business, 030304 developmental biology
Abstract

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.

Published
2017

8. 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

9. The Gene Ontology: enhancements for 2011

Author

P D'Eustachio, Benjamin C. Hitz, Julie Park, Paul Browne, Douglas G. Howe, Cynthia J. Krieger, Kalpana Karra, Stan Laulederkind, Karen R. Christie, Susan Tweedie, Eurie L. Hong, Lydie Bougueleret, Michele Magrane, Cathy R. Gresham, Rolf Apweiler, Lisa Matthews, Dong Li, Philippa J. Talmud, Ioannis Xenarios, J. M. Cherry, Tanya Z. Berardini, Deborah A. Siegele, Rama Balakrishnan, D. Sitnikov, A. Auchinchloss, Selina S. Dwight, Tony Sawford, Paul J. Kersey, Ruth C. Lovering, Ruth Y. Eberhardt, Ursula Hinz, Lakshmi Pillai, Sylvain Poux, Edith D. Wong, Klemens Pichler, Kati Laiho, Malcolm J. Gardner, Stephen G. Oliver, Lionel Breuza, Kara Dolinski, P Lemercier, Kristian B. Axelsen, Midori A. Harris, Adrienne E. Zweifel, H. Drabkin, Guillaume Keller, Marek S. Skrzypek, Daniel M. Staines, Fiona M. McCarthy, Nicholas H. Brown, Mark D. McDowall, Antonia Lock, Mary Shimoyama, Maria C. Costanzo, Teresia Buza, S. Jimenez, Rex L. Chisholm, Paul W. Sternberg, Hui Wang, Nadine Gruaz-Gumowski, Chantal Hulo, Rebecca E. Foulger, Melinda R. Dwinell, Judith A. Blake, Marcus C. Chibucos, B. K. McIntosh, C. D. Amundsen, Jane Lomax, L Famiglietti, Tom Hayman, Michael Tognolli, Eva Huala, James C. Hu, Patrick Masson, Maria Jesus Martin, Benoit Bely, Shuai Weng, Heather C. Wick, E. Dimmer, L. Ni, Catherine Rivoire, Christopher J. Mungall, H. Sehra, P. Duek-Roggli, Maria Victoria Schneider, Dianna G. Fisk, Michael S. Livstone, Ivo Pedruzzi, Shyamala Sundaram, Donna K. Slonim, Isabelle Cusin, Stuart R. Miyasato, Timothy F. Lowry, Varsha K. Khodiyar, Seth Carbon, Elisabeth Coudert, Jürg Bähler, Juancarlos Chan, Evelyn Camon, Daniel P. Renfro, Anne Estreicher, M. C. Blatter, Robert S. Nash, P Gaudet, Sven Heinicke, K. Van Auken, Stacia R. Engel, Alan Bridge, Ralf Stephan, Mary E. Dolan, Shane C. Burgess, Petra Fey, Shur-Jen Wang, Damien Lieberherr, Duncan Legge, P. Porras Millán, Andre Stutz, Yasmin Alam-Faruque, Gail Binkley, Bernd Roechert, S. Branconi-Quintaje, Ghislaine Argoud-Puy, S. Basu, Kim Rutherford, M. Moinat, Monte Westerfield, Arnaud Gos, Eleanor J Stanley, Valerie Wood, Ranjana Kishore, Diego Poggioli, S. Ferro-Rojas, Victoria Petri, Florence Jungo, Suzanna E. Lewis, Emmanuel Boutet, Warren A. Kibbe, M Feuermann, Claire O'Donovan, W. M. Chan, J. James, David P. Hill, Rachael P. Huntley, M. Gwinn Giglio, Paul Thomas, Jodi E. Hirschman, Paola Roncaglia, Gene Ontology Consortium, Blake, JA., Dolan, M., Drabkin, H., Hill, DP., Ni, L., Sitnikov, D., Burgess, S., Buza, T., Gresham, C., McCarthy, F., Pillai, L., Wang, H., Carbon, S., Lewis, SE., Mungall, CJ., Gaudet, P., Chisholm, RL., Fey, P., Kibbe, WA., Basu, S., Siegele, DA., McIntosh, BK., Renfro, DP., Zweifel, AE., Hu, JC., Brown, NH., Tweedie, S., Alam-Faruque, Y., Apweiler, R., Auchinchloss, A., Axelsen, K., Argoud-Puy, G., Bely, B., Blatter, M-., Bougueleret, L., Boutet, E., Branconi, S., Breuza, L., Bridge, A., Browne, P., Chan, WM., Coudert, E., Cusin, I., Dimmer, E., Duek-Roggli, P., Eberhardt, R., Estreicher, A., Famiglietti, L., Ferro-Rojas, S., Feuermann, M., Gardner, M., Gos, A., Gruaz-Gumowski, N., Hinz, U., Hulo, C., Huntley, R., James, J., Jimenez, S., Jungo, F., Keller, G., Laiho, K., Legge, D., Lemercier, P., Lieberherr, D., Magrane, M., Martin, MJ., Masson, P., Moinat, M., O'Donovan, C., Pedruzzi, I., Pichler, K., Poggioli, D., Porras Millán, P., Poux, S., Rivoire, C., Roechert, B., Sawford, T., Schneider, M., Sehra, H., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Xenarios, I., Foulger, R., Lomax, J., Roncaglia, P., Camon, E., Khodiyar, VK., Lovering, RC., Talmud, PJ., Chibucos, M., Gwinn Giglio, M., Dolinski, K., Heinicke, S., Livstone, MS., Stephan, R., Harris, MA., Oliver, SG., Rutherford, K., Wood, V., Bahler, J., Lock, A., Kersey, PJ., McDowall, MD., Staines, DM., Dwinell, M., Shimoyama, M., Laulederkind, S., Hayman, T., Wang, S-., Petri, V., Lowry, T., D'Eustachio, P., Matthews, L., Amundsen, CD., Balakrishnan, R., Binkley, G., Cherry, JM., Christie, KR., Costanzo, MC., Dwight, SS., Engel, SR., Fisk, DG., Hirschman, JE., Hitz, BC., Hong, EL., Karra, K., Krieger, CJ., Miyasato, SR., Nash, RS., Park, J., Skrzypek, MS., Weng, S., Wong, ED., Berardini, TZ., Li, D., Huala, E., Slonim, D., Wick, H., Thomas, P., Chan, J., Kishore, R., Sternberg, P., Van Auken, K., Howe, D., and Westerfield, M.

Subjects
Quality Control, 0303 health sciences, media_common.quotation_subject, Databases, Genetic, Molecular Sequence Annotation/standards, Vocabulary, Controlled, Inference, Molecular Sequence Annotation, Articles, Biology, Ontology (information science), World Wide Web, Open Biomedical Ontologies, 03 medical and health sciences, Annotation, 0302 clinical medicine, Resource (project management), Controlled vocabulary, Genetics, Social media, Function (engineering), 030217 neurology & neurosurgery, 030304 developmental biology, media_common
Abstract

The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.

Published
2011

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

Catalog

Books, media, physical & digital resources
See catalog results