Mark D. Wilkinson

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. Biomedical Semantics 4: 2 (2013)

Soroush Samadian, Bruce McManus, Mark D. Wilkinson: Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web. J. Biomedical Semantics 3: 6 (2012)

E. Luke McCarthy, Benjamin P. Vandervalk, Mark Wilkinson: SPARQL Assist language-neutral query composer. BMC Bioinformatics 13(S-1): S2 (2012)

Alejandro Rodríguez González, Javier Torres Niño, Miguel A. Mayer, Giner Alor-Hernández, Mark D. Wilkinson: Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study. Comp. Math. Methods in Medicine 2012 (2012)

Joost N. Kok, Anna-Lena Lamprecht, Fons J. Verbeek, Mark D. Wilkinson: Bioscientific Data Processing and Modeling. ISoLA (2) 2012: 7-11

Ian Wood, Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson: OWL-DL Domain-Models as Abstract Workflows. ISoLA (2) 2012: 56-66

Alejandro Rodríguez González, Jyotishman Pathak, Mark Wilkinson, Nigam Shah, Robert Stevens, Richard Boyce, Ángel García-Crespo (Eds.): 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

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 J. P. Bonnal, José M. Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd 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 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. Biomedical Semantics 2: 4 (2011)

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. Biomedical Semantics 2: 8 (2011)

Mark D. Wilkinson, E. Luke McCarthy: The SADI plug-in to IO informatics' sentient knowledge explorer. SWAT4LS 2011: 116-118

Edward A. Kawas, Mark D. Wilkinson: OWL2Perl: creating Perl modules from OWL class definitions. Bioinformatics 26(18): 2357-2358 (2010)

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 J. P. Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José M. 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 York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi: The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomedical Semantics 1: 8 (2010)

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 Bioinformatics 11(S-12): S7 (2010)

Joost N. Kok, Anna-Lena Lamprecht, Mark D. Wilkinson: Tools in Scientific Workflow Composition. ISoLA (1) 2010: 258-260

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

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson: SHARE & The Semantic Web - This Time it's Personal! OWLED 2010

E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson: SPARQL Assist Language-Neutral Query Composer. SWAT4LS 2010

E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson: SPARQL Assist Language-Neutral Query Composer. CoRR abs/1012.1666 (2010)

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson: Moby and Moby 2: Creatures of the Deep (Web). Briefings in Bioinformatics 10(2): 114-128 (2009)

Benjamin M. Good, Joseph T. Tennis, Mark D. Wilkinson: Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. BMC Bioinformatics 10: 313 (2009)

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

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson: SHARE: A Semantic Web Query Engine for Bioinformatics. ASWC 2009: 367-369

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

Zoé Lacroix, Cartik R. Kothari, Peter Mork, Mark Wilkinson, Sarah Cohen Boulakia: Biological Metadata Management. Encyclopedia of Database Systems 2009: 215-219

Zoé Lacroix, Cartik R. Kothari, Peter Mork, Rami Rifaieh, Mark Wilkinson, Juliana Freire, Sarah Cohen Boulakia: Biological Resource Discovery. Encyclopedia of Database Systems 2009: 220-223

Cartik R. Kothari, Mark D. Wilkinson: Web Services and the Semantic Web for Life Science Data. Encyclopedia of Database Systems 2009: 3513-3520

Michael DiBernardo, Rachel Pottinger, Mark Wilkinson: Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. Journal of Biomedical Informatics 41(5): 837-847 (2008)

Cartik R. Kothari, Mark Wilkinson: Structured Representation of Biomedical Experiments: A Bottom-Up Approach. IKE 2008: 199-204

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. Bioinformatics 23(6): 780-782 (2007)

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

Cartik R. Kothari, Mark Wilkinson: From chaos to order: A generic, distributed, ontology based annotation system. IKE 2007: 141-145

Byron Yu-Lin Kuo, Thomas Hentrich, Benjamin M. Good, Mark D. Wilkinson: Tag clouds for summarizing web search results. WWW 2007: 1203-1204

Benjamin M. Good, Mark D. Wilkinson: Ontology engineering using volunteer labor. WWW 2007: 1243-1244

Benjamin M. Good, Mark D. Wilkinson: The Life Sciences Semantic Web is Full of Creeps! Briefings in Bioinformatics 7(3): 275-286 (2006)

Edward A. Kawas, Martin Senger, Mark D. Wilkinson: BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 7: 523 (2006)

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 Bioinformatics 7: 534 (2006)

Mark Wilkinson: Gbrowse Moby: a Web-based browser for BioMoby Services. Source Code for Biology and Medicine 1 (2006)

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

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

Mark D. Wilkinson, Matthew Links: BioMOBY: An Open Source Biological Web Services Proposal. Briefings in Bioinformatics 3(4): 331-341 (2002)

Mark D. Wilkinson, David Block, William L. Crosby: Genquire: genome annotation browser/editor. Bioinformatics 18(10): 1398-1399 (2002)