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2020 – today

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2023
[j12]
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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, 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, 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, Yuqi Wang:
Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinform. 39(1) (2023)
[c6]
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Jerven T. Bolleman, Alan J. Bridge, Nicole Redaschi, The UniProt Consortium:
Making expert curated knowledge graphs FAIR. SWAT4HCLS 2023: 116-117
[c5]
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Sebastien Gehant, Elisabeth Coudert, Anne Morgat, Jerven T. Bolleman, Nicole Redaschi, Alan J. Bridge, The UniProt Consortium:
UniProt, ChEBI and IDSM Sachem: exploring biologically relevant ligands. SWAT4HCLS 2023: 181-183
[e1]
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Atsuko Yamaguchi, Andrea Splendiani, M. Scott Marshall, Chris Baker, Jerven T. Bolleman, Albert Burger, Leyla Jael Castro, Ole Eigenbrod, Sabine Österle, Martin Romacker, Andra Waagmeester:
14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023. CEUR Workshop Proceedings 3415, CEUR-WS.org 2023 [contents]
2022
[j11]
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  - journals/biodb/MercierBCGBABBC22
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Philippe Le Mercier, Jerven T. Bolleman, Edouard De Castro, Elisabeth Gasteiger, Parit Bansal, Andrea H. Auchincloss, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Anne Estreicher, Marc Feuermann, Damien Lieberherr, Catherine Rivoire, Ivo Pedruzzi, Nicole Redaschi, Alan J. Bridge:
SwissBioPics - an interactive library of cell images for the visualization of subcellular location data. Database J. Biol. Databases Curation 2022(2022) (2022)
2021
[j10]
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  - journals/bioinformatics/MacDougallVSPZH21
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Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra E. Orchard, Andrea H. Auchincloss, Delphine Baratin, Jerven T. Bolleman, Elisabeth Coudert, Edouard De Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia N. 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:
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinform. 36(22-23): 5562 (2021)
[j9]
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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, 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, 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, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch, Douglas Teodoro:
UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49(Database-Issue): D480-D489 (2021)
2020
[j8]
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Anne Morgat, Thierry Lombardot, Elisabeth Coudert, Kristian B. Axelsen, Teresa Batista Neto, Sebastien Gehant, Parit Bansal, Jerven T. Bolleman, Elisabeth Gasteiger, Edouard De Castro, Delphine Baratin, Monica Pozzato, Ioannis Xenarios, Sylvain Poux, Nicole Redaschi, Alan J. Bridge, The UniProt Consortium:
Enzyme annotation in UniProtKB using Rhea. Bioinform. 36(6): 1896-1901 (2020)
[i5]
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  - journals/f1000research/VosKMKKKMTYYWAAAABBBBBCCD20
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Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi:
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9: 136 (2020)

2010 – 2019

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2019
[c4]
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Simon Heumos, Jerven T. Bolleman:
SemanticGenomeGraphs. SWAT4HCLS 2019: 167-168
[i4]
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Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019)
2017
[j7]
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  - journals/peerj-cs/WilkinsonVSCSKG17
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Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier:
Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Comput. Sci. 3: e110 (2017)
[i3]
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Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier:
Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Prepr. 5: e2522 (2017)
2016
[j6]
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Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul Jean Pierre Bonnal, Robert M. Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock:
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J. Biomed. Semant. 7: 39 (2016)
[i2]
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Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier:
Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Prepr. 4: e2522 (2016)
2015
[j5]
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Sarala M. Wimalaratne, Jerven T. Bolleman, Nick S. Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novère, Henning Hermjakob, Camille Laibe:
SPARQL-enabled identifier conversion with Identifiers.org. Bioinform. 31(11): 1875-1877 (2015)
2014
[j4]
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Simon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. García, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson:
The EBI RDF platform: linked open data for the life sciences. Bioinform. 30(9): 1338-1339 (2014)
[j3]
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Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-an Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin:
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J. Biomed. Semant. 5: 5 (2014)
[j2]
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  - journals/biomedsem/WuFYBY14
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Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven T. Bolleman, Atsuko Yamaguchi:
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. J. Biomed. Semant. 5: 32 (2014)
2013
[j1]
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  - journals/biomedsem/Aoki-KinoshitaBCKKLMORSSSSTYPN13
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Kiyoko F. Aoki-Kinoshita, Jerven T. Bolleman, Matthew P. Campbell, Shin Kawano, Jin-Dong Kim, Thomas Lütteke, Masaaki Matsubara, Shujiro Okuda, René Ranzinger, Hiromichi Sawaki, Toshihide Shikanai, Daisuke Shinmachi, Yoshinori Suzuki, Philip V. Toukach, Issaku Yamada, Nicolle H. Packer, Hisashi Narimatsu:
Introducing glycomics data into the Semantic Web. J. Biomed. Semant. 4: 39 (2013)
2012
[c3]
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Jerven T. Bolleman, Sebastien Gehant, Nicole Redaschi:
Catching Inconsistencies with the Semantic Web: A Biocuration Case Study. SWAT4LS 2012
2010
[c2]
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Jerven T. Bolleman, Alain Gateau, Sebastien Gehant, Nicole Redaschi:
Provenance and Evidence in UniProtKB. SWAT4LS 2010
[i1]
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  - journals/corr/abs-1012-1660
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Jerven T. Bolleman, Alain Gateau, Sebastien Gehant, Nicole Redaschi:
Provenance and evidence in UniProtKB. CoRR abs/1012.1660 (2010)

2000 – 2009

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2009
[c1]
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Jerven T. Bolleman, Thomas Kappler:
Weekend Triple Billionaire. SWAT4LS 2009

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