BioMOBY: An Open Source Biological Web Services Proposal. - Mark D. Wilkinson; Matthew G. Links (Briefings Bioinform., 2002)

Genquire: genome annotation browser/editor. - Mark D. Wilkinson; David Block; William L. Crosby (Bioinform., 2002)

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 (ISWC, 2004)

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 (Pacific Symposium on Biocomputing, 2006)

The Life Sciences Semantic Web is Full of Creeps! - Benjamin M. Good; Mark D. Wilkinson (Briefings 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)

BioMoby extensions to the Taverna workflow management and enactment software. - Edward A. Kawas; Martin Senger; Mark D. Wilkinson (BMC Bioinform., 2006)

Gbrowse Moby: a Web-based browser for BioMoby Services. - Mark D. Wilkinson (Source Code Biol. Medicine, 2006)

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 (BIBM, 2007)

From chaos to order: A generic, distributed, ontology based annotation system. - Cartik R. Kothari; Mark D. Wilkinson (IKE, 2007)

Ontology engineering using volunteer labor. - Benjamin M. Good; Mark D. Wilkinson (WWW, 2007)

Tag clouds for summarizing web search results. - Byron Yu-Lin Kuo; Thomas Hentrich; Benjamin M. Good; Mark D. Wilkinson (WWW, 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)

Structured Representation of Biomedical Experiments: A Bottom-Up Approach. - Cartik R. Kothari; Mark D. Wilkinson (IKE, 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)

SADI Semantic Web Services - 'cause you can't always GET what you want!. - Mark D. Wilkinson; Benjamin P. Vandervalk; E. Luke McCarthy (APSCC, 2009)

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

Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm. - Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (CSE (1), 2009)

Moby and Moby 2: Creatures of the Deep (Web). - Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (Briefings Bioinform., 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)

Web Services and the Semantic Web for Life Science Data. - Cartik R. Kothari; Mark D. Wilkinson (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 (Encyclopedia of Database Systems, 2009)

Biological Metadata Management. - Zoé Lacroix; Cartik R. Kothari; Peter Mork; Mark D. Wilkinson; Sarah Cohen Boulakia (Encyclopedia of Database Systems, 2009)

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

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

OWL2Perl: creating Perl modules from OWL class definitions. - Edward A. Kawas; Mark D. Wilkinson (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; et al. (J. Biomed. Semant., 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)

SADI for GMOD: Semantic Web Services for Model Organism Databases. - Benjamin P. Vandervalk; Michel Dumontier; E. Luke McCarthy; Mark D. Wilkinson (CSWS, 2011)

The SADI plug-in to IO informatics' sentient knowledge explorer. - Mark D. Wilkinson; E. Luke McCarthy (SWAT4LS, 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; et al. (J. Biomed. Semant., 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)

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

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

SPARQL Assist language-neutral query composer. - E. Luke McCarthy; Benjamin P. Vandervalk; Mark D. Wilkinson (BMC Bioinform., 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)

Plant Pathogen Interactions Ontology (PPIO). - Alejandro Rodriguez Iglesias; Mikel Egaña Aranguren; Alejandro Rodríguez González; Mark D. Wilkinson (IWBBIO, 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)

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)

Nanopublishing Clinical Diagnoses: Tracking Diagnostic Knowledge Base Content and Utilization. - Alejandro Rodríguez González; Marcos Martínez Romero; Mikel Egaña Aranguren; Mark D. Wilkinson (CBMS, 2014)

Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies. - Beatriz García Jiménez; Mark D. Wilkinson (ISoLA (2), 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 002; Rajaram Kaliyaperumal; Eelke van der Horst; Barend Mons; Mark D. Wilkinson (SWAT4LS, 2014)

Executing SADI services in Galaxy. - Mikel Egaña Aranguren; Alejandro Rodríguez González; 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; et al. (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)

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 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 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)

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)

Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. - Alejandro Rodríguez González; Marcos Martínez Romero; Roberto Costumero; Mark D. Wilkinson; Ernestina Menasalvas Ruiz (PACBB, 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 (PACBB, 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)

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 002; Claudio Carta; Ronald Cornet; Luiz Olavo Bonino da Silva Santos (SWAT4LS, 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 002; Rajaram Kaliyaperumal; et al. (PeerJ Prepr., 2016)

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 002; Mark D. Wilkinson; Ronald Cornet; Andra Waagmeester; David van Enckevort; Mascha Jansen; Luana Licata; Allegra Via; et al. (SWAT4LS, 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)

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; et al. (PeerJ Prepr., 2017)

MDPbiome: microbiome engineering through prescriptive perturbations. - Beatriz García Jiménez; Tomás de la Rosa; Mark D. Wilkinson (Bioinform., 2018)

Web Services and the Semantic Web for Life Science Data. - Cartik R. Kothari; Mark D. Wilkinson (Encyclopedia of Database Systems (2nd ed.), 2018)

Biological Resource Discovery. - Zoé Lacroix; Cartik R. Kothari; Peter Mork; Rami Rifaieh; Mark D. Wilkinson; Juliana Freire; Sarah Cohen Boulakia (Encyclopedia of Database Systems (2nd ed.), 2018)

Biological Metadata Management. - Zoé Lacroix; Cartik R. Kothari; Peter Mork; Mark D. Wilkinson; Sarah Cohen Boulakia (Encyclopedia of Database Systems (2nd ed.), 2018)

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 B. Graybeal; Kristina M. Hettne; Annika Jacobsen; Robert Pergl; Rob W. W. Hooft; Christine Staiger; et al. (CoRR, 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 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

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; et al. (Data Intell., 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; et al. (F1000Research, 2020)

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 (JOWO, 2021)

Predicting microbiomes through a deep latent space. - Beatriz García Jiménez; Jorge Muñoz; Sara Cabello; Joaquín Medina; Mark D. Wilkinson (Bioinform., 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)

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 (AMIA, 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; et al. (J. Biomed. Semant., 2022)

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; et al. (SWAT4HCLS, 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)

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)

Privacy-Preserving Linkage of Distributed Pseudonymised Datasets in a Virtual European Rare Disease Platform. - Dieter Hayn; Emanuel Sandner; Abishaa Vengadeswaran; Mark D. Wilkinson; Marc Hanauer; Karl Kreiner; Günter Schreier 001 (MIE, 2024)

Take CARE of your patient data. Clinical And Registry Entries (CARE) Semantic Model. - Pablo Alarcón Moreno; Mark Denis Wilkinson (SWAT4HCLS, 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; et al. (Briefings Bioinform., 2024)

Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution. - César Henrique Bernabé; Lieze Thielemans; Rajaram Kaliyaperumal; Claudio Carta; Shuxin Zhang; Celia W. G. van Gelder; Nirupama Benis; Luiz Olavo Bonino da Silva Santos; Ronald Cornet; Bruna dos Santos Vieira; Nawel Lalout; Inês Henriques; et al. (Data Intell., 2024)