Mark D. Wilkinson

According to our database, Mark D. Wilkinson authored at least 75 papers between 2002 and 2024.

Collaborative distances:

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

2024

FAIR Header Reference genome: a TRUSTworthy standard.

Adam Wright, Mark D. Wilkinson, Christopher J. Mungall, Scott Cain, Stephen Richards, Paul W. Sternberg, Ellen Provin, Jonathan L. Jacobs, Scott Geib, Daniela Raciti, Karen Yook, Lincoln Stein, David C. Molik

Briefings Bioinform., 2024

2023

FAIR Data Point: A FAIR-Oriented Approach for Metadata Publication.

Luiz Olavo Bonino da Silva Santos, Kees Burger, Rajaram Kaliyaperumal, Mark D. Wilkinson

Data Intell., 2023

The FAIR Data Point: Interfaces and Tooling.

Oussama Mohammed Benhamed, Kees Burger, Rajaram Kaliyaperumal, Luiz Olavo Bonino da Silva Santos, Marek Suchánek, Jan Slifka, Mark D. Wilkinson

Data Intell., 2023

Surveyed common data access policies preferences amongst European Reference Networks.

Alberto Cámara Ballesteros, Nirupama Benis, César Henrique Bernabé, Inés de Oliveira Coelho, Clémence M. A. Le Cornec, Aylin Demir, Bruna dos Santos Vieira, Jose Antonio Ramírez, K. Joeri van der Velde, Shuxin Zhang, Ronald Cornet, Annika Jacobsen, Marco Roos, Franz Schaefer, Morris A. Swertz, Mark D. Wilkinson

Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

2022

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data.

Rajaram Kaliyaperumal, Mark D. Wilkinson, Pablo Alarcón Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira, Michel Dumontier, César Henrique Bernabé, Annika Jacobsen, Clémence M. A. Le Cornec, Mario Prieto Godoy, Núria Queralt-Rosinach, Leo J. Schultze Kool, Morris A. Swertz, Philip van Damme, K. Joeri van der Velde, Nawel Lalout, Shuxin Zhang, Marco Roos

J. Biomed. Semant., 2022

Leveraging Biolink for Interoperability between Semantic Models.

Ian R. Braun, Pablo Alarcón Moreno, Emily Hartley, Daniel Olson, Nirupama Benis, Ronald Cornet, Mark D. Wilkinson, Ramona L. Walls

Proceedings of the AMIA 2022, 2022

2021

A Fresh Look at FAIR for Research Software.

Daniel S. Katz, Morane Gruenpeter, Tom Honeyman, Lorraine J. Hwang, Mark D. Wilkinson, Vanessa V. Sochat, Hartwig Anzt, Carole A. Goble

CoRR, 2021

Predicting microbiomes through a deep latent space.

Beatriz García Jiménez, Jorge Muñoz, Sara Cabello, Joaquín Medina, Mark D. Wilkinson

Bioinform., 2021

Reuse of Design Pattern Measurements for Health Data.

Núria Queralt-Rosinach, Mark D. Wilkinson, Rajaram Kaliyaperumal, César Henrique Bernabé, Qinqin Long, Michel Dumontier, Paul N. Schofield, Marco Roos

Proceedings of the Joint Ontology Workshops 2021 Episode VII: The Bolzano Summer of Knowledge co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021), 2021

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

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

The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data.

Peter Wittenburg, Hana Pergl Sustkova, Annalisa Montesanti, Margreet Bloemers, S. H. de Waard, Mark A. Musen, John Graybeal, Kristina M. Hettne, Annika Jacobsen, Robert Pergl, Rob W. W. Hooft, Christine Staiger, Celia W. G. van Gelder, Sebastiaan L. Knijnenburg, A. C. van Arkel, Bert Meerman, Mark D. Wilkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, Peter McQuilton, Alejandra N. González-Beltrán, G. J. C. Aben, Patrícia Henning, Maria Simone de Menezes Alencar, C. Ribeiro, C. R. L. Silva, Luís Fernando Sayão, Luana Sales, Viviane Veiga, Jefferson Lima, Simone Dib, Paula Xavier dos Santos, R. Murtinho, Jakob Tendel, B. F. Schaap, P. M. Brouwer, A. K. Gavai, Yamine Bouzembrak, Hans J. P. Marvin, Albert Mons, Tobias Kuhn, Alessa A. Gambardella, Ricardo de Miranda Azevedo, Vesa Muhonen, Mira van der Naald, N. W. Smit, M. J. Buys, Taco F. de Bruin, Fieke Schoots, H. J. E. Goodson, Henry S. Rzepa, Keith G. Jeffery, Hugh P. Shanahan, M. Axton, Veniamin Tkachenko, Anne Deslattes Mays, Natalie Meyers, Michael Conlon, Laurel L. Haak, Erik A. Schultes

CoRR, 2019

2018

Biological Metadata Management.

Zoé Lacroix, Cartik R. Kothari, Peter Mork, Mark D. Wilkinson, Sarah Cohen Boulakia

Proceedings of the Encyclopedia of Database Systems, Second Edition, 2018

Biological Resource Discovery.

Zoé Lacroix, Cartik R. Kothari, Peter Mork, Rami Rifaieh, Mark D. Wilkinson, Juliana Freire, Sarah Cohen Boulakia

Proceedings of the Encyclopedia of Database Systems, Second Edition, 2018

Web Services and the Semantic Web for Life Science Data.

Cartik R. Kothari, Mark D. Wilkinson

Proceedings of the Encyclopedia of Database Systems, Second Edition, 2018

MDPbiome: microbiome engineering through prescriptive perturbations.

Beatriz García Jiménez, Tomás de la Rosa, Mark D. Wilkinson

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

PeerJ Prepr., 2017

Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud.

Barend Mons, Cameron Neylon, Jan Velterop, Michel Dumontier, Luiz Olavo Bonino da Silva Santos, Mark D. Wilkinson

Inf. Serv. Use, 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

OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web.

Benjamin M. Good, Gavin Ha, Chi K. Ho, Mark D. Wilkinson

CoRR, 2015

Erratum to: Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases.

Alejandro Rodríguez González, Marcos Martínez Romero, Roberto Costumero, Mark D. Wilkinson, Ernestina Menasalvas Ruiz

Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015

Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases.

Alejandro Rodríguez González, Marcos Martínez Romero, Roberto Costumero, Mark D. Wilkinson, Ernestina Menasalvas Ruiz

Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015

2014

Health Web Science.

Joanne S. Luciano, Grant P. Cumming, Eva Kahana, Mark D. Wilkinson, Elizabeth H. Brooks, Holly Jarman, Deborah L. McGuinness, Minna S. Levine

Found. Trends Web Sci., 2014

L.U.St: a tool for approximated maximum likelihood supertree reconstruction.

Wasiu A. Akanni, Christopher J. Creevey, Mark D. Wilkinson, Davide Pisani

BMC Bioinform., 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

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

J. Biomed. Semant., 2014

Automatically exposing OpenLifeData via SADI semantic Web Services.

Alejandro Rodríguez González, Alison Callahan, José Cruz-Toledo, Adrian Garcia, Mikel Egaña Aranguren, Michel Dumontier, Mark D. Wilkinson

J. Biomed. Semant., 2014

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Michel Dumontier, Christopher J. O. Baker, Joachim Baran, Alison Callahan, Leonid L. Chepelev, Jose Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura Inés Furlong, Nichealla Keath, Dana Klassen, Jamie P. McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D. Wilkinson, Robert Hoehndorf

J. Biomed. Semant., 2014

Executing SADI services in Galaxy.

Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson

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

Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies.

Beatriz García Jiménez, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications, 2014

Nanopublishing Clinical Diagnoses: Tracking Diagnostic Knowledge Base Content and Utilization.

Alejandro Rodríguez González, Marcos Martínez Romero, Mikel Egaña Aranguren, Mark D. Wilkinson

Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical Systems, 2014

2013

SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

CoRR, 2013

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.

Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana, Chris Mungall, Alejandro Rodríguez González, Mark D. Wilkinson

J. Biomed. Semant., 2013

Plant Pathogen Interactions Ontology (PPIO).

Alejandro Rodriguez Iglesias, Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

2012

Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study.

Alejandro Rodríguez González, Javier Torres Niño, Miguel Angel Mayer, Giner Alor-Hernández, Mark D. Wilkinson

Comput. Math. Methods Medicine, 2012

SPARQL Assist language-neutral query composer.

E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson

BMC Bioinform., 2012

Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web.

Soroush Samadian, Bruce McManus, Mark D. Wilkinson

J. Biomed. Semant., 2012

OWL-DL Domain-Models as Abstract Workflows.

Ian Wood, Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies, 2012

Bioscientific Data Processing and Modeling.

Joost N. Kok, Anna-Lena Lamprecht, Fons J. Verbeek, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies, 2012

2011

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy

J. Biomed. Semant., 2011

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

J. Biomed. Semant., 2011

The SADI plug-in to IO informatics' sentient knowledge explorer.

Mark D. Wilkinson, E. Luke McCarthy

Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2011

SADI for GMOD: Semantic Web Services for Model Organism Databases.

Benjamin P. Vandervalk, Michel Dumontier, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the 3rd Canadian Semantic Web Symposium (CSWS2011), 2011

2010

SADI, SHARE, and the in silico scientific method.

Mark D. Wilkinson, E. Luke McCarthy, Benjamin P. Vandervalk, David Withers, Edward A. Kawas, Soroush Samadian

BMC Bioinform., 2010

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

J. Biomed. Semant., 2010

OWL2Perl: creating Perl modules from OWL class definitions.

Edward A. Kawas, Mark D. Wilkinson

Bioinform., 2010

SHARE & The Semantic Web - This Time it's Personal!

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins.

David Withers, Edward A. Kawas, E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification, and Validation, 2010

Tools in Scientific Workflow Composition.

Joost N. Kok, Anna-Lena Lamprecht, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification, and Validation, 2010

2009

Biological Metadata Management.

Zoé Lacroix, Cartik R. Kothari, Peter Mork, Mark D. Wilkinson, Sarah Cohen Boulakia

Proceedings of the Encyclopedia of Database Systems, 2009

Biological Resource Discovery.

Zoé Lacroix, Cartik R. Kothari, Peter Mork, Rami Rifaieh, Mark D. Wilkinson, Juliana Freire, Sarah Cohen Boulakia

Proceedings of the Encyclopedia of Database Systems, 2009

Web Services and the Semantic Web for Life Science Data.

Cartik R. Kothari, Mark D. Wilkinson

Proceedings of the Encyclopedia of Database Systems, 2009

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

Benjamin M. Good, Joseph T. Tennis, Mark D. Wilkinson

BMC Bioinform., 2009

Moby and Moby 2: Creatures of the Deep (Web).

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Briefings Bioinform., 2009

Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm.

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the 12th IEEE International Conference on Computational Science and Engineering, 2009

SHARE: A Semantic Web Query Engine for Bioinformatics.

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the Semantic Web, Fourth Asian Conference, 2009

SADI Semantic Web Services - 'cause you can't always GET what you want!.

Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy

Proceedings of the 4th IEEE Asia-Pacific Services Computing Conference, 2009

2008

Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework.

Michael DiBernardo, Rachel Pottinger, Mark D. Wilkinson

J. Biomed. Informatics, 2008

Structured Representation of Biomedical Experiments: A Bottom-Up Approach.

Cartik R. Kothari, Mark D. Wilkinson

Proceedings of the 2008 International Conference on Information & Knowledge Engineering, 2008

2007

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.

Young C. Song, Edward A. Kawas, Benjamin M. Good, Mark D. Wilkinson, Scott J. Tebbutt

Bioinform., 2007

Tag clouds for summarizing web search results.

Byron Yu-Lin Kuo, Thomas Hentrich, Benjamin M. Good, Mark D. Wilkinson

Proceedings of the 16th International Conference on World Wide Web, 2007

Ontology engineering using volunteer labor.

Benjamin M. Good, Mark D. Wilkinson

Proceedings of the 16th International Conference on World Wide Web, 2007

From chaos to order: A generic, distributed, ontology based annotation system.

Cartik R. Kothari, Mark D. Wilkinson

Proceedings of the 2007 International Conference on Information & Knowledge Engineering, 2007

Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services.

Paul M. K. Gordon, Edward A. Kawas, Mark D. Wilkinson, Christoph W. Sensen

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007

2006

Gbrowse Moby: a Web-based browser for BioMoby Services.

Mark D. Wilkinson

Source Code Biol. Medicine, 2006

BioMoby extensions to the Taverna workflow management and enactment software.

Edward A. Kawas, Martin Senger, Mark D. Wilkinson

BMC Bioinform., 2006

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.

Benjamin M. Good, Edward A. Kawas, Byron Yu-Lin Kuo, Mark D. Wilkinson

BMC Bioinform., 2006

The Life Sciences Semantic Web is Full of Creeps!

Benjamin M. Good, Mark D. Wilkinson

Briefings Bioinform., 2006

Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development.

Benjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, Mark D. Wilkinson

Proceedings of the Biocomputing 2006, 2006

2004

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt.

Phillip W. Lord, Sean Bechhofer, Mark D. Wilkinson, Gary S. Schiltz, Damian Gessler, Duncan Hull, Carole A. Goble, Lincoln Stein

Proceedings of the Semantic Web, 2004

2002

Genquire: genome annotation browser/editor.

Mark D. Wilkinson, David Block, William L. Crosby

Bioinform., 2002

BioMOBY: An Open Source Biological Web Services Proposal.

Mark D. Wilkinson, Matthew G. Links

Briefings Bioinform., 2002