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ORCIDMark D. Wilkinson
Person information
- affiliation: Technical University of Madrid, Center for Plant Biotechnology and Genomics (CBGP), Spain
- affiliation: James Hogg iCAPTURE Center, Vancouver, BC, Canada
- affiliation (PhD): University of British Columbia, Department of Medical Genetics, BC, Canada
- affiliation: Max Planck Institute for Plant Breeding Research, Cologne, Germany
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2020 – today
- 2020
[j29]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:
FAIR Principles: Interpretations and Implementation Considerations. Data Intell. 2(1-2): 10-29 (2020)
2010 – 2019
- 2019
- [i7]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, A. 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:
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data. CoRR abs/1902.11162 (2019) - 2018
- [j28]Beatriz García Jiménez, Tomás de la Rosa, Mark D. Wilkinson:
MDPbiome: microbiome engineering through prescriptive perturbations. Bioinform. 34(17): i838-i847 (2018) - [r6]Cartik R. Kothari, Mark D. Wilkinson:
Web Services and the Semantic Web for Life Science Data. Encyclopedia of Database Systems (2nd ed.) 2018 - [r5]Zoé Lacroix, Cartik R. Kothari, Peter Mork, Rami Rifaieh, Mark D. Wilkinson, Juliana Freire, Sarah Cohen Boulakia:
Biological Resource Discovery. Encyclopedia of Database Systems (2nd ed.) 2018 - [r4]Zoé Lacroix, Cartik R. Kothari, Peter Mork, Mark D. Wilkinson, Sarah Cohen Boulakia:
Biological Metadata Management. Encyclopedia of Database Systems (2nd ed.) 2018 - 2017
- [j27]Barend Mons, Cameron Neylon, Jan Velterop, Michel Dumontier, Luiz Olavo Bonino da Silva Santos, Mark D. Wilkinson:
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud. Inf. Serv. Use 37(1): 49-56 (2017) - [j26]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) - [c26]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:
The FAIRification of Data and the Potential of FAIR Resources Demonstrated, in Practice, at the Rome Bring Your Own Data Workshop. SWAT4LS 2017 - [i6]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
- [c25]Marco Roos, Mark D. Wilkinson, Rajaram Kaliyaperumal, Mark Thompson, Claudio Carta, Ronald Cornet, Luiz Olavo Bonino da Silva Santos:
Registries of Domain-Relevant Semantic Reference Models Help Bootstrap Interoperability in Domains with Fragmented Data Resources. SWAT4LS 2016 - [i5]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
- [c24]Alejandro Rodríguez González, Marcos Martínez Romero, Roberto Costumero, Mark D. Wilkinson, Ernestina Menasalvas Ruiz:
Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. PACBB 2015: 79-87 - [c23]Alejandro Rodríguez González, Marcos Martínez Romero, Roberto Costumero, Mark D. Wilkinson, Ernestina Menasalvas Ruiz:
Erratum to: Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. PACBB 2015: E1 - [i4]Benjamin M. Good, Gavin Ha, Chi K. Ho, Mark D. Wilkinson:
OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web. CoRR abs/1502.06025 (2015) - 2014
- [j25]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) - [j24]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, James P. McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D. Wilkinson, Robert Hoehndorf:
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J. Biomed. Semant. 5: 14 (2014) - [j23]Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson:
Executing SADI services in Galaxy. J. Biomed. Semant. 5: 42 (2014) - [j22]Alejandro Rodríguez González, Alison Callahan, José Cruz-Toledo, Adrian Garcia, Mikel Egaña Aranguren, Michel Dumontier, Mark D. Wilkinson:
Automatically exposing OpenLifeData via SADI semantic Web Services. J. Biomed. Semant. 5: 46 (2014) - [j21]Wasiu A. Akanni, Christopher J. Creevey, Mark D. Wilkinson, Davide Pisani:
L.U.St: a tool for approximated maximum likelihood supertree reconstruction. BMC Bioinform. 15: 183 (2014) - [j20]Joanne S. Luciano, Grant P. Cumming, Eva Kahana, Mark D. Wilkinson, Elizabeth H. Brooks, Holly Jarman, Deborah L. McGuinness, Minna S. Levine:
Health Web Science. Found. Trends Web Sci. 4(4): 269-419 (2014) - [c22]Alejandro Rodríguez González, Marcos Martínez Romero, Mikel Egaña Aranguren, Mark D. Wilkinson:
Nanopublishing Clinical Diagnoses: Tracking Diagnostic Knowledge Base Content and Utilization. CBMS 2014: 335-340 - [c21]Beatriz García Jiménez, Mark D. Wilkinson:
Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies. ISoLA (2) 2014: 464-478 - [c20]Marco Roos, Alasdair J. G. Gray, Andra Waagmeester, Mark Thompson, Rajaram Kaliyaperumal, Eelke van der Horst, Barend Mons, Mark D. Wilkinson:
Bring Your Own Data Workshops: A Mechanism to Aid Data Owners to Comply with Linked Data Best Practices. SWAT4LS 2014 - [i3]Beatriz García Jiménez, Mark D. Wilkinson:
Automatic annotation of bioinformatics workflows with biomedical ontologies. CoRR abs/1407.0165 (2014) - 2013
- [j19]Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana, Chris Mungall, Alejandro Rodríguez González, Mark D. Wilkinson:
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. J. Biomed. Semant. 4: 2 (2013) - [c19]Alejandro Rodriguez Iglesias, Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson:
Plant Pathogen Interactions Ontology (PPIO). IWBBIO 2013: 695-702 - [i2]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web. CoRR abs/1305.4455 (2013) - 2012
- [j18]Soroush Samadian, Bruce McManus, Mark D. Wilkinson:
Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web. J. Biomed. Semant. 3: 6 (2012) - [j17]E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist language-neutral query composer. BMC Bioinform. 13(S-1): S2 (2012) - [j16]Alejandro Rodríguez González, Javier Torres Niño, Miguel Angel Mayer, Giner Alor-Hernández, Mark D. Wilkinson:
Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study. Comput. Math. Methods Medicine 2012: 367345:1-367345:9 (2012) - [c18]Joost N. Kok, Anna-Lena Lamprecht, Fons J. Verbeek, Mark D. Wilkinson:
Bioscientific Data Processing and Modeling. ISoLA (2) 2012: 7-11 - [c17]Ian Wood, Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
OWL-DL Domain-Models as Abstract Workflows. ISoLA (2) 2012: 56-66 - [e1]Alejandro Rodríguez González, Jyotishman Pathak, Mark D. Wilkinson, Nigam Shah, Robert Stevens, Richard D. Boyce, Ángel García-Crespo:
Proceedings of the Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine, Boston, USA, November 12, 2012. CEUR Workshop Proceedings 930, CEUR-WS.org 2012 [contents] - 2011
- [j15]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:
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semant. 2: 4 (2011) - [j14]Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy:
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation. J. Biomed. Semant. 2: 8 (2011) - [c16]Benjamin P. Vandervalk, Michel Dumontier, E. Luke McCarthy, Mark D. Wilkinson:
SADI for GMOD: Semantic Web Services for Model Organism Databases. CSWS 2011: 70-75 - [c15]Mark D. Wilkinson, E. Luke McCarthy:
The SADI plug-in to IO informatics' sentient knowledge explorer. SWAT4LS 2011: 116-118 - 2010
- [j13]Edward A. Kawas, Mark D. Wilkinson:
OWL2Perl: creating Perl modules from OWL class definitions. Bioinform. 26(18): 2357-2358 (2010) - [j12]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:
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1: 8 (2010) - [j11]Mark D. Wilkinson, E. Luke McCarthy, Benjamin P. Vandervalk, David Withers, Edward A. Kawas, Soroush Samadian:
SADI, SHARE, and the in silico scientific method. BMC Bioinform. 11(S-12): S7 (2010) - [c14]Joost N. Kok, Anna-Lena Lamprecht, Mark D. Wilkinson:
Tools in Scientific Workflow Composition. ISoLA (1) 2010: 258-260 - [c13]David Withers, Edward A. Kawas, E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins. ISoLA (1) 2010: 301-312 - [c12]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
SHARE & The Semantic Web - This Time it's Personal! OWLED 2010 - [c11]E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist Language-Neutral Query Composer. SWAT4LS 2010 - [i1]E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist Language-Neutral Query Composer. CoRR abs/1012.1666 (2010)
2000 – 2009
- 2009
- [j10]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
Moby and Moby 2: Creatures of the Deep (Web). Briefings Bioinform. 10(2): 114-128 (2009) - [j9]Benjamin M. Good, Joseph T. Tennis, Mark D. Wilkinson:
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. BMC Bioinform. 10: 313 (2009) - [c10]Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy:
SADI Semantic Web Services -- 'cause you can't always GET what you want!. APSCC 2009: 13-18 - [c9]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
SHARE: A Semantic Web Query Engine for Bioinformatics. ASWC 2009: 367-369 - [c8]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm. CSE (1) 2009: 330-337 - [r3]Zoé Lacroix, Cartik R. Kothari, Peter Mork, Mark D. Wilkinson, Sarah Cohen Boulakia:
Biological Metadata Management. Encyclopedia of Database Systems 2009: 215-219 - [r2]Zoé Lacroix, Cartik R. Kothari, Peter Mork, Rami Rifaieh, Mark D. Wilkinson, Juliana Freire, Sarah Cohen Boulakia:
Biological Resource Discovery. Encyclopedia of Database Systems 2009: 220-223 - [r1]Cartik R. Kothari, Mark D. Wilkinson:
Web Services and the Semantic Web for Life Science Data. Encyclopedia of Database Systems 2009: 3513-3520 - 2008
- [j8]Michael DiBernardo, Rachel Pottinger, Mark D. Wilkinson:
Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. J. Biomed. Informatics 41(5): 837-847 (2008) - [c7]Cartik R. Kothari, Mark D. Wilkinson:
Structured Representation of Biomedical Experiments: A Bottom-Up Approach. IKE 2008: 199-204 - 2007
- [j7]Young C. Song, Edward A. Kawas, Benjamin M. Good, Mark D. Wilkinson, Scott J. Tebbutt:
DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. Bioinform. 23(6): 780-782 (2007) - [c6]Paul M. K. Gordon, Edward A. Kawas, Mark D. Wilkinson, Christoph W. Sensen:
Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services. BIBM 2007: 117-124 - [c5]Cartik R. Kothari, Mark D. Wilkinson:
From chaos to order: A generic, distributed, ontology based annotation system. IKE 2007: 141-145 - [c4]Byron Yu-Lin Kuo, Thomas Hentrich, Benjamin M. Good, Mark D. Wilkinson:
Tag clouds for summarizing web search results. WWW 2007: 1203-1204 - [c3]Benjamin M. Good, Mark D. Wilkinson:
Ontology engineering using volunteer labor. WWW 2007: 1243-1244 - 2006
- [j6]Benjamin M. Good, Mark D. Wilkinson:
The Life Sciences Semantic Web is Full of Creeps! Briefings Bioinform. 7(3): 275-286 (2006) - [j5]Edward A. Kawas, Martin Senger, Mark D. Wilkinson:
BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinform. 7: 523 (2006) - [j4]Benjamin M. Good, Edward A. Kawas, Byron Yu-Lin Kuo, Mark D. Wilkinson:
iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website. BMC Bioinform. 7: 534 (2006) - [j3]Mark D. Wilkinson:
Gbrowse Moby: a Web-based browser for BioMoby Services. Source Code Biol. Medicine 1 (2006) - [c2]Benjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, Mark D. Wilkinson:
Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development. Pacific Symposium on Biocomputing 2006: 128-139 - 2004
- [c1]Phillip W. Lord, Sean Bechhofer, Mark D. Wilkinson, Gary S. Schiltz, Damian Gessler, Duncan Hull, Carole A. Goble, Lincoln Stein:
Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt. International Semantic Web Conference 2004: 350-364 - 2002
- [j2]Mark D. Wilkinson, Matthew Links:
BioMOBY: An Open Source Biological Web Services Proposal. Briefings Bioinform. 3(4): 331-341 (2002) - [j1]Mark D. Wilkinson, David Block, William L. Crosby:
Genquire: genome annotation browser/editor. Bioinform. 18(10): 1398-1399 (2002)
Coauthor Index
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