Mark Thompson

According to our database, Mark Thompson authored at least 28 papers between 2012 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research.

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

F1000Research, 2020

Making FAIR Easy with FAIR Tools: From Creolization to Convergence.

Mark Thompson, Kees Burger, Rajaram Kaliyaperumal, Marco Roos, Luiz Olavo Bonino da Silva Santos

Data Intell., 2020

The "A" of FAIR - As Open as Possible, as Closed as Necessary.

Annalisa Landi, Mark Thompson, Viviana Giannuzzi, Fedele Bonifazi, Ignasi Labastida, Luiz Olavo Bonino da Silva Santos, Marco Roos

Data Intell., 2020

A Generic Workflow for the Data FAIRification Process.

Annika Jacobsen, Rajaram Kaliyaperumal, Luiz Olavo Bonino da Silva Santos, Barend Mons, Erik Schultes, Marco Roos, Mark Thompson

Data Intell., 2020

FAIR Principles: Interpretations and Implementation Considerations.

Annika Jacobsen, Ricardo de Miranda Azevedo, Nick S. Juty, Dominique Batista, Simon J. Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. A. Evelo, Carole A. Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina M. Hettne, Jaap Heringa, Rob W. W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George O. Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes

Data Intell., 2020

2019

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.

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

F1000Research, 2019

2018

Wikidata as an intuitive resource towards semantic data modeling in data FAIRification.

Annika Jacobsen, Andra Waagmeester, Rajaram Kaliyaperumal, Gregory S. Stupp, Lynn M. Schriml, Mark Thompson, Andrew I. Su, Marco Roos

Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

2017

Interoperability and FAIRness through a novel combination of Web technologies.

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 K. Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier

PeerJ Prepr., 2017

Overview of a Suite of Tools and Training Material for Implementing FAIR Data Principles.

Mark Thompson, Luiz Olavo Bonino da Silva Santos, Kees Burger, Rajaram Kaliyaperumal, Erik A. Schultes, Annika Jacobsen, Claudio Carta, Richard Finkers, David van Enckevort, Mascha Jansen, Barend Mons, Marco Roos

Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

The FAIRification of Data and the Potential of FAIR Resources Demonstrated, in Practice, at the Rome Bring Your Own Data Workshop.

Claudio Carta, Marco Roos, Annika Jacobsen, Rajaram Kaliyaperumal, Mark Thompson, Mark D. Wilkinson, Ronald Cornet, Andra Waagmeester, David van Enckevort, Mascha Jansen, Luana Licata, Allegra Via, Domenica Taruscio

Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

2016

Interoperability and FAIRness through a novel combination of Web technologies.

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

PeerJ Prepr., 2016

Registries of Domain-Relevant Semantic Reference Models Help Bootstrap Interoperability in Domains with Fragmented Data Resources.

Marco Roos, Mark D. Wilkinson, Rajaram Kaliyaperumal, Mark Thompson, Claudio Carta, Ronald Cornet, Luiz Olavo Bonino da Silva Santos

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

2015

Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study.

Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, Eelke van der Horst, Zuotian Tatum, Kristina M. Hettne, Erik A. Schultes, Barend Mons, Marco Roos

J. Biomed. Semant., 2015

Finding Novel Associations Across Domains Using Linked Data: a Case Study on Genetic Variants Disrupting Transcription Start Sites.

Eelke van der Horst, Rajaram Kaliyaperumal, Zuotian Tatum, Mark Thompson, Erik A. Schultes, Eleni Mina, Ivo Fokkema, Johan T. den Dunnen, Marco Roos, Jeroen F. J. Laros, Barend Mons, Kristina M. Hettne, Peter A. C. 't Hoen

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Multidisciplinary Collaboration to Facilitate Hypotheses Generation in Huntington's Disease.

Eleni Mina, Mark Thompson, Kristina M. Hettne, Willeke M. C. van Roon-Mom, Rajaram Kaliyaperumal, Eelke van der Horst, Katherine Wolstencroft, Barend Mons, Marco Roos

Proceedings of the 11th IEEE International Conference on e-Science, 2015

2014

Applying linked data approaches to pharmacology: Architectural decisions and implementation.

Alasdair J. G. Gray, Paul Groth, Antonis Loizou, Sune Askjaer, Christian Y. A. Brenninkmeijer, Kees Burger, Christine Chichester, Chris T. A. Evelo, Carole A. Goble, Lee Harland, Steve Pettifer, Mark Thompson, Andra Waagmeester, Antony J. Williams

Semantic Web, 2014

A promoter-level mammalian expression atlas.

The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki

Nat., 2014

Explain your data by Concept Profile Analysis Web Services.

Kristina M. Hettne, Reinout van Schouwen, Eleni Mina, Eelke van der Horst, Mark Thompson, Rajaram Kaliyaperumal, Barend Mons, Erik M. van Mulligen, Jan A. Kors, Marco Roos

F1000Research, 2014

Preserving sequence annotations across reference sequences.

Zuotian Tatum, Marco Roos, Andrew P. Gibson, Peter E. M. Taschner, Mark Thompson, Erik A. Schultes, Jeroen F. J. Laros

J. Biomed. Semant., 2014

Structuring research methods and data with the research object model: genomics workflows as a case study.

Kristina M. Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julián Garrido, David De Roure, Óscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A. C. 't Hoen, Sean Bechhofer, Carole A. Goble, Marco Roos

J. Biomed. Semant., 2014

Bring Your Own Data Workshops: A Mechanism to Aid Data Owners to Comply with Linked Data Best Practices.

Marco Roos, Alasdair J. G. Gray, Andra Waagmeester, Mark Thompson, Rajaram Kaliyaperumal, Eelke van der Horst, Barend Mons, Mark D. Wilkinson

Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014

Genome Annotation using Nanopublications: An Approach to Interoperability of Genetic Data.

Rajaram Kaliyaperumal, Peter Bram 't Hoen, Mark Thompson, Eelke van der Horst, Marco Roos

Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014

A Nanopublishing Architecture for Biomedical Data.

Pedro Sernadela, Eelke van der Horst, Mark Thompson, Pedro Lopes, Marco Roos, José Luís Oliveira

Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014

2013

Nanopublications for Exposing Experimental Data in the Life-sciences: A Huntington's Disease Case Study.

Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, Kristina M. Hettne, Erik A. Schultes, Marco Roos

Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2013

2012

Data Publishing Using Nanopublications.

Mark Thompson, Erik A. Schultes, Marco Roos, Barend Mons

Adv. Math. Commun., 2012

Using Nanopublications to Incentivize the Semantic Exposure of Life Science Information.

Mark Thompson, Erik A. Schultes

Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Placing Landmarks in the Knowledge Space: A Web Tool for Crowd-sourcing Landmark Publications to Benchmark Text-mining Predictions.

Mark Thompson, Herman van Haagen, Erik A. Schultes

Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

The Pharmacology Workspace: A Platform for Drug Discovery.

Alasdair J. G. Gray, Sune Askjaer, Christian Y. A. Brenninkmeijer, Kees Burger, Christine Chichester, James M. Eales, Chris T. A. Evelo, Carole A. Goble, Paul Groth, Lee Harland, Antonis Loizou, Steve Pettifer, Rishi Ramgolam, Mark Thompson, Andra Waagmeester, Antony J. Williams

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012