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  2022 (5)
Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. Poza‐Viejo, L.; Payá‐Milans, M.; San Martín‐Uriz, P.; Castro‐Labrador, L.; Lara‐Astiaso, D.; Wilkinson, M., D.; Piñeiro, M.; Jarillo, J., A.; and Crevillén, P. Plant, Cell & Environment. 2 2022.
Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa [link]Website   doi   link   bibtex  
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. Kaliyaperumal, R.; Wilkinson, M., D.; Moreno, P., A.; Benis, N.; Cornet, R.; dos Santos Vieira, B.; Dumontier, M.; Bernabé, C., H.; Jacobsen, A.; Le Cornec, C., M., A.; Godoy, M., P.; Queralt-Rosinach, N.; Schultze Kool, L., J.; Swertz, M., A.; van Damme, P.; van der Velde, K., J.; Lalout, N.; Zhang, S.; and Roos, M. Journal of Biomedical Semantics, 13(1): 9. 12 2022.
doi   link   bibtex  
The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses. Ortiz-García, P.; Pérez-Alonso, M.; González Ortega-Villaizán, A.; Sánchez-Parra, B.; Ludwig-Müller, J.; Wilkinson, M., D.; and Pollmann, S. Frontiers in Plant Science, 13. 2022.
The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses [link]Website   doi   link   bibtex   abstract  
FAIR Data Point: A FAIR-oriented approach for metadata publication. da Silva Santos, L., O., B.; Burger, K.; Kaliyaperumal, R.; and Wilkinson, M., D. Data Intelligence,1-21. 8 2022.
FAIR Data Point: A FAIR-oriented approach for metadata publication [link]Website   doi   link   bibtex   abstract  
The FAIR Data Point: Interfaces and Tooling. Benhamed, O., M.; Burger, K.; Kaliyaperumal, R.; da Silva Santos, L., O., B.; Suchánek, M.; Slifka, J.; and Wilkinson, M., D. Data Intelligence,1-18. 9 2022.
doi   link   bibtex   abstract  
  2021 (6)
Predicting microbiomes through a deep latent space. García-Jiménez, B.; Muñoz, J.; Cabello, S.; Medina, J.; and Wilkinson, M., D. Bioinformatics, 37(10): 1444-1451. 6 2021.
Predicting microbiomes through a deep latent space [link]Website   doi   link   bibtex  
Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis. Pérez-Alonso, M.; Ortiz-García, P.; Moya-Cuevas, J.; Lehmann, T.; Sánchez-Parra, B.; Björk, R., G.; Karim, S.; Amirjani, M., R.; Aronsson, H.; Wilkinson, M., D.; and Pollmann, S. Journal of Experimental Botany, 72(2): 459-475. 2 2021.
Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis [link]Website   doi   link   bibtex   abstract  
Reuse of Design Pattern Measurements for Health Data. Queralt-Rosinach, N.; Wilkinson, M., D.; Kaliyaperumal, R.; Bernabé, C.; Long, Q.; Dumontier, M.; Schofield, P.; and Roos, M. In Sanfilippo, E., M.; Kutz, O.; Troquard, N.; Hahmann., T.; Masolo, C.; Hoehndorf, R.; and Vita, R., editor(s), 12th International Conference on Formal Ontology in Information Systems (FOIS 2021) Demonstrations, 2021.
Reuse of Design Pattern Measurements for Health Data [link]Website   link   bibtex  
FAIR Principles for Research Software (FAIR4RS Principles). Chue Hong, N., P.; Katz, D., S.; Barker, M.; Lamprecht, A.; Martinez, C.; Psomopoulos, F., E.; Harrow, J.; Castro, L., J.; Gruenpeter, M.; Martinez, P., A.; and Honeyman, T. . 2021.
FAIR Principles for Research Software (FAIR4RS Principles) [link]Website   doi   link   bibtex  
RO-Crate Metadata Specification 1.1.1. Sefton, P.; Carragáin, E., Ó.; Soiland-Reyes, S.; Corcho, O.; Garijo, D.; Palma, R.; Coppens, F.; Goble, C.; Fernández, J., M.; Chard, K.; Gomez-Perez, J., M.; Crusoe, M., R.; Eguinoa, I.; Juty, N.; Holmes, K.; Clark, J., A.; Capella-Gutierrez, S.; Gray, A., J., G.; Owen, S.; Williams, A., R.; Tartari, G.; Bacall, F.; Thelen, T.; Ménager, H.; Rodríguez-Navas, L.; Walk, P.; brandon whitehead; Wilkinson, M.; Groth, P.; Bremer, E.; Castro, L., J., G.; Sebby, K.; Kanitz, A.; Trisovic, A.; Kennedy, G.; Graves, M.; Koehorst, J.; Leo, S.; and Portier, M. 2 2021.
RO-Crate Metadata Specification 1.1.1 [link]Website   doi   link   bibtex  
A Fresh Look at FAIR for Research Software. Katz, D., S.; Gruenpeter, M.; Honeyman, T.; Hwang, L.; Wilkinson, M., D.; Sochat, V.; Anzt, H.; Goble, C.; and 1, f., F., S. 2021.
A Fresh Look at FAIR for Research Software [link]Website   doi   link   bibtex  
  2020 (5)
BioHackathon 2015: Semantics of data for life sciences and reproducible research. Vos, R., A.; Katayama, T.; Mishima, H.; Kawano, S.; Kawashima, S.; Kim, J.; Moriya, Y.; Tokimatsu, T.; Yamaguchi, A.; Yamamoto, Y.; Wu, H.; Amstutz, P.; Antezana, E.; Aoki, N., P.; Arakawa, K.; Bolleman, J., T.; Bolton, E.; Bonnal, R., J., P.; Bono, H.; Burger, K.; Chiba, H.; Cohen, K., B.; Deutsch, E., W.; Fernández-Breis, J., T.; Fu, G.; Fujisawa, T.; Fukushima, A.; García, A.; Goto, N.; Groza, T.; Hercus, C.; Hoehndorf, R.; Itaya, K.; Juty, N.; Kawashima, T.; Kim, J.; Kinjo, A., R.; Kotera, M.; Kozaki, K.; Kumagai, S.; Kushida, T.; Lütteke, T.; Matsubara, M.; Miyamoto, J.; Mohsen, A.; Mori, H.; Naito, Y.; Nakazato, T.; Nguyen-Xuan, J.; Nishida, K.; Nishida, N.; Nishide, H.; Ogishima, S.; Ohta, T.; Okuda, S.; Paten, B.; Perret, J.; Prathipati, P.; Prins, P.; Queralt-Rosinach, N.; Shinmachi, D.; Suzuki, S.; Tabata, T.; Takatsuki, T.; Taylor, K.; Thompson, M.; Uchiyama, I.; Vieira, B.; Wei, C.; Wilkinson, M.; Yamada, I.; Yamanaka, R.; Yoshitake, K.; Yoshizawa, A., C.; Dumontier, M.; Kosaki, K.; and Takagi, T. F1000Research, 9: 136. 2 2020.
BioHackathon 2015: Semantics of data for life sciences and reproducible research [link]Website   doi   link   bibtex   abstract  
Data-driven classification of the certainty of scholarly assertions. Prieto, M.; Deus, H.; de Waard, A.; Schultes, E.; García-Jiménez, B.; and Wilkinson, M., D. PeerJ, 8: e8871. 4 2020.
Data-driven classification of the certainty of scholarly assertions [link]Website   doi   link   bibtex   abstract  
FAIR Principles: Interpretations and Implementation Considerations. Jacobsen, A.; de Miranda Azevedo, R.; Juty, N.; Batista, D.; Coles, S.; Cornet, R.; Courtot, M.; Crosas, M.; Dumontier, M.; Evelo, C., T.; Goble, C.; Guizzardi, G.; Hansen, K., K.; Hasnain, A.; Hettne, K.; Heringa, J.; Hooft, R., W.; Imming, M.; Jeffery, K., G.; Kaliyaperumal, R.; Kersloot, M., G.; Kirkpatrick, C., R.; Kuhn, T.; Labastida, I.; Magagna, B.; McQuilton, P.; Meyers, N.; Montesanti, A.; van Reisen, M.; Rocca-Serra, P.; Pergl, R.; Sansone, S.; da Silva Santos, L., O., B.; Schneider, J.; Strawn, G.; Thompson, M.; Waagmeester, A.; Weigel, T.; Wilkinson, M., D.; Willighagen, E., L.; Wittenburg, P.; Roos, M.; Mons, B.; and Schultes, E. Data Intelligence, 2(1-2): 10-29. 1 2020.
FAIR Principles: Interpretations and Implementation Considerations [link]Website   doi   link   bibtex   abstract  
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering. García-Jiménez, B.; Carrasco, J.; Medina, J.; and Wilkinson, M., D. Research Square Preprints. 2020.
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering [link]Website   doi   link   bibtex  
Perturbations of the AMI1 IAM-amidohydrolase expression trigger plant stress responses in Arabidopsis thaliana. Pérez-Alonso, M., M.; Ortiz-Gárcia, P.; Moya-Cuevas, J.; Lehmann, T.; Sanchez-Parra, B.; Björk, R., G.; Karim, S.; Amirjani, M., R.; Aronsson, H.; Wilkinson, M., D.; and Pollmann, S. . 8 2020.
Perturbations of the AMI1 IAM-amidohydrolase expression trigger plant stress responses in Arabidopsis thaliana [link]Website   doi   link   bibtex  
  2019 (10)
Robust and automatic definition of microbiome states. García-Jiménez, B.; and Wilkinson, M., D. PeerJ, 7: e6657. 3 2019.
Robust and automatic definition of microbiome states [link]Website   doi   link   bibtex   abstract  
Data-driven classification of the certainty of scholarly assertions. Prieto, M.; Deus, H.; De Waard, A.; Schultes, E.; García-Jiménez, B.; and Wilkinson, M., D. PeerJ Preprints, 7: e27829v1. 6 2019.
Data-driven classification of the certainty of scholarly assertions [link]Website   doi   link   bibtex   abstract  
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data. Wittenburg, P.; Sustkova, H., P.; Montesanti, A.; Bloemers, S., M.; de Waard, S., H.; Musen, M., A.; Graybeal, J., B.; Hettne, K., M.; Jacobsen, A.; Pergl, R.; Hooft, R., W., W.; Staiger, C.; van Gelder, C., W., G.; Knijnenburg, S., L.; van Arkel, A., C.; Meerman, B.; Wilkinson, M., D.; Sansone, S.; Rocca-Serra, P.; McQuilton, P.; Gonzalez-Beltran, A., N.; Aben, G., J., C.; Henning, P.; Alencar, S.; Ribeiro, C.; Silva, C., R., L.; Sayao, L.; Sales, L.; Veiga, V.; Lima, J.; Dib, S.; Xavier, P.; Murtinho, R.; Tendel, J.; Schaap, B., F.; Brouwer, P., M.; Gavai, A., K.; Bouzembrak, Y.; Marvin, H., J., P.; Mons, A.; Kuhn, T.; Gambardella, A., A.; Azevedo, R., d., M.; Muhonen, V.; van der Naald, M.; Smit, N., W.; Buys, M., J.; de Bruin, T., F.; Schoots, F.; Goodson, H., J., E.; Rzepa, H., S.; Jeffery, K., G.; Shanahan, H., P.; Axton, M.; Tkachenko, V.; Maya, A., D.; Meyers, N., K.; Conlon, M.; Haak, L., L.; and Schultes, E., A. arXiv, arXiv:1902. 2 2019.
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data [link]Website   link   bibtex   abstract  
Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework. Wilkinson, M., D.; Dumontier, M.; Sansone, S.; da Silva Santos, L., O., B.; Prieto, M.; Batista, D.; McQuilton, P.; Kuhn, T.; Rocca-Serra, P.; Crosas, M.; and Schultes, E. bioRxiv. 2019.
Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework [link]Website   doi   link   bibtex   abstract  
Evaluating FAIR maturity through a scalable, automated, community-governed framework. Wilkinson, M., D.; Dumontier, M.; Sansone, S.; Bonino da Silva Santos, L., O.; Prieto, M.; Batista, D.; McQuilton, P.; Kuhn, T.; Rocca-Serra, P.; Crosas, M.; and Schultes, E. Scientific Data, 6(1): 174. 12 2019.
Evaluating FAIR maturity through a scalable, automated, community-governed framework [link]Website   doi   link   bibtex  
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. Katayama, T.; Kawashima, S.; Micklem, G.; Kawano, S.; Kim, J.; Kocbek, S.; Okamoto, S.; Wang, Y.; Wu, H.; Yamaguchi, A.; Yamamoto, Y.; Antezana, E.; Aoki-Kinoshita, K., F.; Arakawa, K.; Banno, M.; Baran, J.; Bolleman, J., T.; Bonnal, R., J.; Bono, H.; Fernández-Breis, J., T.; Buels, R.; Campbell, M., P.; Chiba, H.; Cock, P., J., A.; Cohen, K., B.; Dumontier, M.; Fujisawa, T.; Fujiwara, T.; Garcia, L.; Gaudet, P.; Hattori, E.; Hoehndorf, R.; Itaya, K.; Ito, M.; Jamieson, D.; Jupp, S.; Juty, N.; Kalderimis, A.; Kato, F.; Kawaji, H.; Kawashima, T.; Kinjo, A., R.; Komiyama, Y.; Kotera, M.; Kushida, T.; Malone, J.; Matsubara, M.; Mizuno, S.; Mizutani, S.; Mori, H.; Moriya, Y.; Murakami, K.; Nakazato, T.; Nishide, H.; Nishimura, Y.; Ogishima, S.; Ohta, T.; Okuda, S.; Ono, H.; Perez-Riverol, Y.; Shinmachi, D.; Splendiani, A.; Strozzi, F.; Suzuki, S.; Takehara, J.; Thompson, M.; Tokimatsu, T.; Uchiyama, I.; Verspoor, K.; Wilkinson, M., D.; Wimalaratne, S.; Yamada, I.; Yamamoto, N.; Yarimizu, M.; Kawamoto, S.; and Takagi, T. F1000Research, 8: 1677. 9 2019.
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services [link]Website   doi   link   bibtex   abstract  
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. Payá-Milans, M.; Poza-Viejo, L.; Martín-Uriz, P., S.; Lara-Astiaso, D.; Wilkinson, M., D.; and Crevillén, P. GigaScience, 8(12). 12 2019.
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa [link]Website   doi   link   bibtex   abstract  
Conserved Roles of the H3K27ME3 Epigenome on Plant Development. Crevillén, P.; Poza-Viejo, L.; Payá-Milans, M.; Del Olmo, I.; and Wilkinson​, M., D. IMPACT OF CHROMATIN DOMAINS ON PLANT PHENOTYPES,28. 2019.
Conserved Roles of the H3K27ME3 Epigenome on Plant Development [pdf]Website   link   bibtex   abstract  
Erratum: Addendum: The FAIR Guiding Principles for scientific data management and stewardship (Scientific data (2016) 3 (160018)). Wilkinson, M.; Dumontier, M.; Jan Aalbersberg, I.; Appleton, G.; Axton, M.; Baak, A.; Blomberg, N.; Boiten, J.; da Silva Santos, L.; Bourne, P.; Bouwman, J.; Brookes, A.; Clark, T.; Crosas, M.; Dillo, I.; Dumon, O.; Edmunds, S.; Evelo, C.; Finkers, R.; Gonzalez-Beltran, A.; Gray, A.; Groth, P.; Goble, C.; Grethe, J.; Heringa, J.; Hoen, P.; Hooft, R.; Kuhn, T.; Kok, R.; Kok, J.; Lusher, S.; Martone, M.; Mons, A.; Packer, A.; Persson, B.; Rocca-Serra, P.; Roos, M.; van Schaik, R.; Sansone, S.; Schultes, E.; Sengstag, T.; Slater, T.; Strawn, G.; Swertz, M.; Thompson, M.; van der Lei, J.; van Mulligen, E.; Jan Velterop; Waagmeester, A.; Wittenburg, P.; Wolstencroft, K.; Zhao, J.; and Mons, B. Scientific data, 6(1). 2019.
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Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework (Scientific Data, (2019), 6, 1, (174), 10.1038/s41597-019-0184-5). Wilkinson, M., D.; Dumontier, M.; Sansone, S., A.; Bonino da Silva Santos, L., O.; Prieto, M.; Batista, D.; McQuilton, P.; Kuhn, T.; Rocca-Serra, P.; Crosas, M.; and Schultes, E. Scientific Data, 6(1). 2019.
doi   link   bibtex   abstract  
  2018 (10)
Enrichment of rare disease patient registries by FAIRification. Jacobsen, A.; Thompson, M.; Schultes, E., A.; Cornet, R.; Wilkinson, M.; Thompson, R.; Mordenti, M.; Sangiorgi, L.; Carta, C.; Groenen, K.; Kersloot, M.; Schultze Kool, L.; van Enckevort, D.; and Roos, M. In ECRD 2018, pages POSTER, 2018.
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FAIRification of rare disease patient registries. Jacobsen, A.; Thompson, M.; Sernadela, P.; Ehrhart, F.; Carta, C.; Groenen, K.; Kersloot, M.; Kool, L., S.; Mordenti, M.; Locatelli, M.; Sangiorgi, L.; Schultes, E., A.; Cornet, R.; Wilkinson, M., D.; Taruscio, D.; Thompson, R.; van Enckevort, D.; Evelo, C.; and Roos, M. In Proceedings of the 2018 Annual Partner Meeting of RD Connect, 2018.
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A design framework and exemplar metrics for FAIRness. Wilkinson, M., D.; Sansone, S.; Schultes, E.; Doorn, P.; Bonino da Silva Santos, L., O.; and Dumontier, M. Scientific Data, 5: 180118. 6 2018.
A design framework and exemplar metrics for FAIRness [link]Website   doi   link   bibtex  
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. Townend, G., S.; Ehrhart, F.; van Kranen, H., J.; Wilkinson, M.; Jacobsen, A.; Roos, M.; Willighagen, E., L.; van Enckevort, D.; Evelo, C., T.; and Curfs, L., M., G. Human Mutation, 39(7): 914-924. 7 2018.
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases [link]Website   doi   link   bibtex  
Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus. Rodríguez-Romero, J.; Marconi, M.; Ortega-Campayo, V.; Demuez, M.; Wilkinson, M., D.; and Sesma, A. New Phytologist. 8 2018.
Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus [link]Website   doi   link   bibtex  
MDPbiome: microbiome engineering through prescriptive perturbations. García-Jiménez, B.; de la Rosa, T.; and Wilkinson, M., D. Bioinformatics, 34(17): i838-i847. 9 2018.
MDPbiome: microbiome engineering through prescriptive perturbations [link]Website   doi   link   bibtex  
Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework. Wilkinson, M., D.; Dumontier, M.; Sansone, S.; Bonino da Silva Santos, L., O.; Prieto, M.; Gautier, J.; McQuilton, P.; Murphy, D.; Crosas, M.; and Schultes, E. bioRxiv. 1 2018.
Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework [link]Website   link   bibtex   abstract  
Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae. Marconi, M.; Sesma, A.; Rodríguez-Romero, J., L.; González, M., L., R.; and Wilkinson, M., D. Scientific Data, 5: 180271. 11 2018.
Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae [link]Website   doi   link   bibtex  
Automatic definition of robust microbiome sub-states in longitudinal data. García-Jiménez, B.; and Wilkinson, M., D. PeerJ Preprints, 6: e26657v1. 3 2018.
Automatic definition of robust microbiome sub-states in longitudinal data [link]Website   doi   link   bibtex   abstract  
FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies. Sansone, S.; McQuilton, P.; Rocca-Serra, P.; Gonzalez-Beltran, A.; Izzo, M.; Lister, A.; Thurston, M.; Batista, D.; Granell, R.; Adekale, M.; Dauga, D.; Ganley, E.; Hodson, S.; Lawrence, R.; Khodiyar, V.; Tenenbaum, J.; Axton, J., M.; Ball, M.; Besson, S.; Bloom, T.; Bonazzi, V.; Jimenez, R.; Carr, D.; Chan, W., M.; Chung, C.; Clement-Stoneham, G.; Cousijn, H.; Dayalan, S.; Dumontier, M.; Dzale Yeumo, E.; Edmunds, S.; Everitt, N.; Fripp, D.; Goble, C.; Golebiewski, M.; Hall, N.; Hanisch, R.; Hucka, M.; Huerta, M.; Kenall, A.; Kiley, R.; Klenk, J.; Koureas, D.; Larkin, J.; Lemberger, T.; Lynch, N.; Schriml, L.; Ma\textquoterightayan, A.; MacCallum, C.; Mons, B.; Moore, J.; Muller, W.; Murray, H.; Nobusada, T.; Noesgaard, D.; Paxton-Boyd, J.; Orchard, S.; Rustici, G.; Schurer, S.; Sharples, K.; e Silva, M.; Stanford, N., J.; Subirats-Coll, I.; Swedlow, J.; Tong, W.; Wilkinson, M.; Wise, J.; and Yilmaz, P. bioRxiv. 2018.
FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies [link]Website   doi   link   bibtex   abstract  
  2017 (16)
Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae. Illana, A.; Marconi, M.; Rodríguez-Romero, J.; Xu, P.; Dalmay, T.; Wilkinson, M., D.; Ayllón, M., Á.; and Sesma, A. Archives of Virology, 162(3): 891-895. 3 2017.
Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae [link]Website   doi   link   bibtex  
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud. Mons, B.; Neylon, C.; Velterop, J.; Dumontier, M.; da Silva Santos, L., O., B.; and Wilkinson, M., D. Information Services & Use, 37(1): 49-56. 3 2017.
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud [link]Website   doi   link   bibtex  
Identifying Bioinformatics Subworkflows with SCOFF: Semantic Clustering Of Functional Fragments. García-Jiménez, B.; and Wilkinson​, M., D. SUBMITTED. 2017.
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Boosting health care and life science research on rare diseases by creating a robust infrastructure of independently Findable, Accessible, Interoperable, and Reusable (FAIR) biobanks, registries, and molecular data resources. Enckevort, D., v.; Thompson, R.; Carta, C.; Wilkinson, M.; and Roos, M. In IRDiRC 2017, 2017.
Boosting health care and life science research on rare diseases by creating a robust infrastructure of independently Findable, Accessible, Interoperable, and Reusable (FAIR) biobanks, registries, and molecular data resources [pdf]Website   link   bibtex  
Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies. Enckevort, D., v.; Carta, C.; Thompson, R.; Thompson, M.; Ehrhart, F.; Kaliyaperumal, R.; Sernadela, P.; Reihs, R.; Jacobsen, A.; da Silva Santos, L., O., B.; Wilkinson, M., D.; Muller, H.; Oliviera, J., L.; Evelo, C., T.; Taruscio, D.; ‘t Hoen, P., A.; and Roos, M. In ESHG 2017, 2017.
Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies [link]Website   link   bibtex  
Findable, Accessible, Interoperable and Reusable data resources to speed up research on rare diseases. Carta, C.; Roos, M.; Jansen, M.; Enckevort, D., v.; Wilkinson, M., D.; Kaliyaperumal, R.; Thompson, M.; Torreri, P.; da Silva Santos, L., O., B.; Cornet, R.; Kodra, Y.; and Taruscio, D. Technical Report 2017.
Findable, Accessible, Interoperable and Reusable data resources to speed up research on rare diseases. [link]Website   link   bibtex   abstract  
Preparing Data at the Source to Foster Interoperability across Rare Disease Resources. Roos, M.; López Martin, E.; and Wilkinson, M., D. Rare Diseases Epidemiology: Update and overview 2nd Edition, pages 165-179. Posada, M.; and Groft, S., editor(s). Springer International Publishing AG, 2017.
Rare Diseases Epidemiology: Update and overview 2nd Edition [link]Website   doi   link   bibtex  
Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies. Enckevort, D., v.; Claudio, C.; Thompson, R.; Thompson, M.; Ehrhart, F.; Kaliyaperumal, R.; Sernadela, P.; Da Silva Santos, L., O., B.; Jacobsen, A.; Wilkinson, M.; Müller, H.; Reihs, R.; Oliviera, J., L.; Evelo, C.; Taruscio, D.; 'T Hoen, P.; and Roos, M. In BioSB2017, 2017.
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Interoperability and FAIRness through a novel combination of Web technologies. Wilkinson, M., D.; van Mulligen, E., M.; Ciccarese, P.; Schultes, E., A.; Verborgh, R.; Kaliyaperumal, R.; Clark, T.; Bolleman, J., T.; Thompson, M.; Kelpin, F., D.; Swertz, M., A.; Dumontier, M.; Bonino da Silva Santos, L., O.; Gray, A., J.; Kuzniar, A.; and Gavai, A. PeerJ Computer Science, 3: e110. 4 2017.
Interoperability and FAIRness through a novel combination of Web technologies [link]Website   doi   link   bibtex   abstract  
Overview of a suite of tools and training material for implementing FAIR data principles. Thompson, M.; Wilkinson, M.; Kaliyaperumal, R.; Burger, K.; Leeuwen, S., v.; Jacobsen, A.; Carta, C.; Schultes, E.; Finkers, R.; Enckevort, D., v.; Jansen, M.; Roos, M.; Mons, B.; and Bonino, L. In ELIXIR Webinar, 2017.
Overview of a suite of tools and training material for implementing FAIR data principles [link]Website   link   bibtex  
Implementing ELSI 2.0 for international collaborative research: improving access to clinical and genetics data by connecting ELSI policies, FAIR data software solutions, and ELIXIR-AAI. Gainotti, S.; Petrini, C.; Mascalzoni, D.; Floridia, G.; Riva, L.; Wilkinson, M.; and Roos, M. In SWAT4HCLS 2017, pages POSTER, 2017.
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The FAIRification of data and the potentialities of FAIR resources showed, in practice, at the Rome “Bring Your Own Data” workshop. Carta, C.; Roos, M.; Jacobsen, A.; Kaliyaperumal, R.; Thompson, M.; Wilkinson, M.; Cornet, R.; Waagmeester, A.; van Enckevort, D.; Jansen, M.; Licata, L.; Via, A.; and Taruscio, D. In Proceedings of SWAT4HCLS 2017, 2017.
The FAIRification of data and the potentialities of FAIR resources showed, in practice, at the Rome “Bring Your Own Data” workshop [pdf]Website   link   bibtex  
FAIRMetrics/Metrics: Initial set of proposed FAIR Metrics for community discussion. Wilkinson, M.; Sansone, S.; Bonino, L., O.; Schultes, E.; Doorn, P.; and Dumontier, M. Technical Report 11 2017.
FAIRMetrics/Metrics: Initial set of proposed FAIR Metrics for community discussion [link]Website   doi   link   bibtex  
A design framework and exemplar metrics for FAIRness. Wilkinson, M., D.; Sansone, S.; Schultes, E.; Doorn, P.; da Silva Santos, L., O., B.; and Dumontier, M. bioRxiv. 2017.
doi   link   bibtex  
Overview of a suite of middle-ware services for implementing FAIR data principles. Thompson, M.; Bonino, L.; Wilkinson, M.; Kaliyaperumal, R.; Burger, K.; Van Leeuwen, S.; Jacobsen, A.; Carta, C.; Schultes, E.; Van Enckevort, D.; Finkers, R.; Jansen, M.; Mons, B.; and Roos, M. In CEUR Workshop Proceedings, volume 2042, 2017.
link   bibtex  
Bring Your Own Data workshop is an excellent tool to promote the establishment of Findable, Accessible, Interoperable, and Reusable rare disease registries. Carta, C.; Roos, M.; Jansen, M.; Wilkinson, M., D.; Bonino da Silva Santos, L.; van Enckevort, D.; and Taruscio, D. In Procedigs of the European Human Genetics Conference 2017, 2017.
Bring Your Own Data workshop is an excellent tool to promote the establishment of Findable, Accessible, Interoperable, and Reusable rare disease registries [link]Website   link   bibtex  
  2016 (8)
The FAIR Guiding Principles for scientific data management and stewardship. Wilkinson, M., D.; Dumontier, M.; Aalbersberg, I., J.; Appleton, G.; Axton, M.; Baak, A.; Blomberg, N.; Boiten, J.; da Silva Santos, L., B.; Bourne, P., E.; Bouwman, J.; Brookes, A., J.; Clark, T.; Crosas, M.; Dillo, I.; Dumon, O.; Edmunds, S.; Evelo, C., T.; Finkers, R.; Gonzalez-Beltran, A.; Gray, A., J.; Groth, P.; Goble, C.; Grethe, J., S.; Heringa, J.; ’t Hoen, P., A.; Hooft, R.; Kuhn, T.; Kok, R.; Kok, J.; Lusher, S., J.; Martone, M., E.; Mons, A.; Packer, A., L.; Persson, B.; Rocca-Serra, P.; Roos, M.; van Schaik, R.; Sansone, S.; Schultes, E.; Sengstag, T.; Slater, T.; Strawn, G.; Swertz, M., A.; Thompson, M.; van der Lei, J.; van Mulligen, E.; Velterop, J.; Waagmeester, A.; Wittenburg, P.; Wolstencroft, K.; Zhao, J.; and Mons, B. Scientific Data, 3: 160018. 3 2016.
The FAIR Guiding Principles for scientific data management and stewardship [link]Website   doi   link   bibtex  
Temporal microbiome road-maps guided by perturbations. García-Jiménez, B.; and Wilkinson, M. bioRxiv,049510. 4 2016.
Temporal microbiome road-maps guided by perturbations [link]Website   doi   link   bibtex   abstract  
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. Rodríguez-Iglesias, A.; Rodríguez-González, A.; Irvine, A., G.; Sesma, A.; Urban, M.; Hammond-Kosack, K., E.; and Wilkinson, M., D. Frontiers in Plant Science, 7. 5 2016.
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base [link]Website   doi   link   bibtex  
MDPbiome: Predicting temporal microbiome dynamics influenced by external perturbations. García-Jiménez, B.; and Wilkinson, M. In XIII Symposium on Bioinformatics, 2016.
MDPbiome: Predicting temporal microbiome dynamics influenced by external perturbations [pdf]Website   link   bibtex  
From hypothesis construction, through experimental execution, to result publication and citation. Wilkinson, M., D. In Francisco de Asis, A., H.; Gutiérrez-Cortines, M., E.; Fernández Hernández, J., A.; Baille, A., D.; and Calatrava Leyva, J., editor(s), Proceedings of the 4th Workshop on agri-food research, pages 14, 2016.
From hypothesis construction, through experimental execution, to result publication and citation [link]Website   link   bibtex  
Interoperability and FAIRness through a novel combination of Web technologies. Wilkinson​, M., D.; Verborgh, R.; da Silva Santos, L., O., B.; Clark, T.; Swertz, M., A.; Kelpin, F., D.; Gray, A., J., G.; Schultes, E., A.; Mulligen, E., M., v.; Ciccarese, P.; Thompson, M.; Kaliyaperumal, R.; Bolleman, J., T.; and Dumontier, M. PeerJ Preprints, 4(e2522v1). 2016.
doi   link   bibtex  
FAIR Data Points Supporting Big Data Interoperability. Bonino Da Silva Santos, L.; Wilkinson, M., D.; Kuzniar, A.; Kaliyaperumal, R.; Thompson, M.; Dumontier, M.; and Burger, K. Enterprise Interoperability in the Digitized and Networked Factory of the Future, pages 270-279. Zelm, M.; Doumeingts, G.; and Mendonça, J., P., editor(s). iSTE Press, 2016.
Enterprise Interoperability in the Digitized and Networked Factory of the Future [link]Website   link   bibtex  
Registries of domain-relevant semantic reference models help bootstrap interoperability in domains with fragmented data resources. Roos, M.; Wilkinson, M., D.; Kaliyaperumal, R.; Thompson, M.; Carta, C.; Cornet, R.; van Enckevort, D.; and Bonino, L. In Paschke, A.; Burger, A.; Splendiani, A.; Marshall, M., S.; and Romano, P., editor(s), Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016. CEUR Workshop Proceedings
Registries of domain-relevant semantic reference models help bootstrap interoperability in domains with fragmented data resources [pdf]Website   link   bibtex  
  2015 (6)
VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock. Nakada, T.; Boyd, J., H.; Russell, J., A.; Aguirre-Hern�ndez, R.; Wilkinson, M., D.; Thair, S., A.; Nakada, E.; McConechy, M., K.; Fjell, C., D.; and Walley, K., R. Journal of Innate Immunity, 7(5): 545-553. 4 2015.
<b><i>VPS13D</i></b> Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock [link]Website   doi   link   bibtex  
Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. Rodríguez-González, A.; Martínez-Romero, M.; Costumero, R.; Wilkinson, M., D.; and Menasalvas-Ruiz, E. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, pages 79-87. Overbeek, R.; Rocha, M., P.; Fdez-Riverola, F.; and Paz, J., F., D., editor(s). Springer International Publishing, 2015.
9th International Conference on Practical Applications of Computational Biology and Bioinformatics [link]Website   doi   link   bibtex   abstract  
DataFairPort: The Perl libraries version 0.231. Wilkinson, M.; Dumontier, M.; and Durbin, P. 11 2015.
DataFairPort: The Perl libraries version 0.231 [link]Website   doi   link   bibtex  
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. Aranguren, M., E.; and Wilkinson, M., D. GigaScience, 4(1): 59. 12 2015.
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker [link]Website   doi   link   bibtex  
Erratum to: Diagnostic knowledge extraction from MedlinePlus: An application for infectious diseases (9th International Conference on Practical Applications of Computational Biology and Bioinformatics, Advances in Intelligent Systems and Computing 375, 10. Rodríguez-González, A.; Martínez-Romero, M.; Costumero, R.; Wilkinson, M.; and Menasalvas-Ruiz, E. Volume 375 2015.
doi   link   bibtex  
  2014 (13)
Executing SADI services in Galaxy. Egaña Aranguren, M.; Rodríguez González, A.; and Wilkinson, M., D. Journal of Biomedical Semantics, 5(1): 42. 2014.
Executing SADI services in Galaxy [link]Website   doi   link   bibtex  
Nanopublishing clinical diagnoses: tracking diagnostic knowledge base content and utilization. Rodríguez-González, A.; Martinez-Romero, M.; Aranguren, M., E.; and Wilkinson, M., D. In CBMS '14 Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical Systems, pages 335-340, 2014.
doi   link   bibtex  
Bioinformatics Tools for Next-Generation RNA Sequencing Analysis. Marconi, M.; Rodriguez-Romero, J.; Sesma, A.; and Wilkinson, M., D. Fungal RNA biology, pages 371-391. Sesma, A.; and von der Haar, T., editor(s). Springer International Publishing, 2014.
Fungal RNA biology [link]Website   doi   link   bibtex   abstract  
The Crop Ontology, a resource for enabling access to breeders'data. Arnaud, E.; Matteis, L.; Laporte, M., A.; Espinosa, H.; Hyman, G.; Shrestha, R.; Portugal, A.; Chibon, P., Y.; Devare, M.; Akintunde, A.; White, J., W.; Wilkinson, M.; Caracciolo, C.; Celli, F.; and Mclaren, G. In In proceeding of: Plant and Animal Genome XXII, pages W352, 2014.
The Crop Ontology, a resource for enabling access to breeders'data [link]Website   link   bibtex   abstract  
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. Dumontier, M.; Baker, C., J.; Baran, J.; Callahan, A.; Chepelev, L.; Cruz-Toledo, J.; Del Rio, N., R.; Duck, G.; Furlong, L., I.; Keath, N.; Klassen, D.; McCusker, J., P.; Queralt-Rosinach, N.; Samwald, M.; Villanueva-Rosales, N.; Wilkinson, M., D.; and Hoehndorf, R. Journal of biomedical semantics, 5(1): 14. 3 2014.
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. [link]Website   doi   link   bibtex   abstract  
Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies. García-Jiménez, B.; and Wilkinson, M., D. In Margaria, T.; and Steffen, B., editor(s), Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications - 6th International Symposium, ISoLA 2014, Imperial, Corfu, Greece, October 8-11, 2014, Proceedings, Part II, volume 8803, of Lecture Notes in Computer Science, pages 464-478, 2014. Springer Berlin Heidelberg
Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies [link]Website   doi   link   bibtex  
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Katayama, T.; Wilkinson, M.; Aoki-Kinoshita, K.; Kawashima, S.; Yamamoto, Y.; Yamaguchi, A.; Okamoto, S.; Kawano, S.; Kim, J.; Wang, Y.; Wu, H.; Kano, Y.; Ono, H.; Bono, H.; Kocbek, S.; Aerts, J.; Akune, Y.; Antezana, E.; Arakawa, K.; Aranda, B.; Baran, J.; Bolleman, J.; Bonnal, R.; Buttigieg, P.; Campbell, M.; Chen, Y.; Chiba, H.; Cock, P.; Cohen, K.; and Constantin, A. Journal of Biomedical Semantics, 5(1): 5. 2014.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains [pdf]Paper   BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains [link]Website   doi   link   bibtex   abstract  
Automatic detection and resolution of measurement-unit conflicts in aggregated data. Samadian, S.; McManus, B.; and Wilkinson, M. BMC Medical Genomics, 7(Suppl 1): S12. 2014.
Automatic detection and resolution of measurement-unit conflicts in aggregated data [link]Website   doi   link   bibtex   abstract  
Automatically exposing OpenLifeData via SADI semantic Web Services. González, A., R.; Callahan, A.; Cruz-Toledo, J.; Garcia, A.; Egaña Aranguren, M.; Dumontier, M.; and Wilkinson, M., D. Journal of Biomedical Semantics, 5(1): 46. 2014.
Automatically exposing OpenLifeData via SADI semantic Web Services [link]Website   doi   link   bibtex   abstract  
The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus. Hily, J., M.; García, A.; Moreno, A.; Plaza, M.; Wilkinson, M., D.; Fereres, A.; Fraile, A.; and García-Arenal, F. PLoS pathogens, 10(11): e1004492. 11 2014.
The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus. [link]Website   doi   link   bibtex   abstract  
Health Web Science. Luciano, J., S.; Cumming, G., P.; Kahana, E.; Wilkinson, M., D.; Brooks, E., H.; Jarman, H.; McGuinness, D., L.; and Levine, M., S. Foundations and Trends® in Web Science, 4(4): 269-419. 2014.
Health Web Science [link]Website   doi   link   bibtex  
Bring Your Own Data workshops: a mechanism to aid data owners to comply with Linked Data best practices. Roos, M.; Gray, A., J., G.; Waagmeester, A.; Thompson, M.; Kaliyaperumal, R.; Horst, E., v., d.; Mons, B.; and Wilkinson, M., D. Proceedings of Semantic Web Applications and Tools for Life Sciences 2014. Paschke, A.; Burger, A.; Romano, P.; Marshall, M., S.; and Andrea, S., editor(s). CEUR Workshop Proceedings, Volume 132 edition, 2014.
Proceedings of Semantic Web Applications and Tools for Life Sciences 2014 [pdf]Website   link   bibtex  
Automatic annotation of bioinformatics workflows with biomedical ontologies. García-Jiménez, B.; and Wilkinson, M. Volume 8803 2014.
link   bibtex   abstract  
  2013 (8)
Plant Pathogen Interactions Ontology (PPIO). Iglesias, A., R.; Aranguren, M., E.; Gonzalez, A., R.; and Wilkinson, M., D. Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering,695-702. 2013.
link   bibtex  
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions. Vandervalk, B.; McCarthy, E., L.; Cruz-Toledo, J.; Klein, A.; Baker, C., J., O.; Dumontier, M.; and Wilkinson, M., D. JMIR Research Protocols, 2(1): e14. 4 2013.
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions [link]Website   doi   link   bibtex   abstract  
Plant Pathogen Interactions Ontology (PPIO). Iglesias, A., R.; Aranguren, M., E.; Gonzalez, A., R.; and Wilkinson, M., D. In Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering, pages 695-702, 2013.
link   bibtex  
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions. Vandervalk, B.; McCarthy, E., L.; Cruz-Toledo, J.; Klein, A.; Baker, C., J., O.; Dumontier, M.; and Wilkinson, M., D. JMIR Research Protocols, 2(1): e14. 4 2013.
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions [link]Website   doi   link   bibtex  
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Egaña Aranguren, M.; Fernández-Breis, J., T.; Antezana, E.; Mungall, C.; Rodríguez González, A.; and Wilkinson, M., D. Journal of biomedical semantics, 4(1): 2. 1 2013.
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. [link]Website   doi   link   bibtex   abstract  
The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Katayama, T.; Wilkinson, M., D.; Micklem, G.; Kawashima, S.; Yamaguchi, A.; Nakao, M.; Yamamoto, Y.; Okamoto, S.; Oouchida, K.; Chun, H.; Aerts, J.; Afzal, H.; Antezana, E.; Arakawa, K.; Aranda, B.; Belleau, F.; Bolleman, J.; Bonnal, R., J.; Chapman, B.; Cock, P.; Eriksson, T.; Gordon, P.; Goto, N.; Hayashi, K.; Horn, H.; Ishiwata, R.; Kaminuma, E.; Kasprzyk, A.; Kawaji, H.; Kido, N.; Kim, Y., J.; Kinjo, A., R.; Konishi, F.; Kwon, K.; Labarga, A.; Lamprecht, A.; Lin, Y.; Lindenbaum, P.; McCarthy, L.; Morita, H.; Murakami, K.; Nagao, K.; Nishida, K.; Nishimura, K.; Nishizawa, T.; Ogishima, S.; Ono, K.; Oshita, K.; Park, K.; Prins, P.; Saito, T., L.; Samwald, M.; Satagopam, V., P.; Shigemoto, Y.; Smith, R.; Splendiani, A.; Sugawara, H.; Taylor, J.; Vos, R.; Withers, D.; Yamasaki, C.; Zmasek, C., M.; Kawamoto, S.; Okubo, K.; Asai, K.; and Takagi, T. Journal of Biomedical Semantics, 4(1): 6. 2013.
The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies [link]Website   doi   link   bibtex  
Web Science Studies into Semantic Web Service-Based Research Environments (Awarded "Best Paper"). Wilkinson, M., D. The Fifth International Conferences on Advanced Service Computing, SERVICE COMPUTATION 2013, pages 71-74. Copyright (c) IARIA, 2013, 2013.
The Fifth International Conferences on Advanced Service Computing, SERVICE COMPUTATION 2013 [link]Website   link   bibtex   abstract  
The emergent discipline of health web science. Luciano, J., S.; Cumming, G., P.; Wilkinson, M., D.; and Kahana, E. Journal of medical Internet research, 15(8): e166. 1 2013.
The emergent discipline of health web science. [link]Website   doi   link   bibtex   abstract  
  2012 (11)
Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web. Samadian, S.; McManus, B.; and Wilkinson, M., D. Journal of biomedical semantics, 3(1): 6. 7 2012.
Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web. [link]Website   doi   link   bibtex   abstract  
SPARQL Assist language-neutral query composer. McCarthy, L.; Vandervalk, B.; and Wilkinson, M. BMC bioinformatics, 13 Suppl 1(Suppl 1): S2. 1 2012.
SPARQL Assist language-neutral query composer. [pdf]Paper   SPARQL Assist language-neutral query composer. [link]Website   doi   link   bibtex   abstract  
Genomics data resources: frameworks and standards. Wilkinson, M., D. Volume 856 . Methods in molecular biology (Clifton, N.J.), pages 489-511. 1 2012.
Methods in molecular biology (Clifton, N.J.) [link]Website   doi   link   bibtex   abstract  
OWL-DL Domain-Models as Abstract Workflows. Wood, I.; Vandervalk, B.; McCarthy, L.; and Wilkinson, M., D. Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies, pages 56-66. Margaria, T.; and Steffen, B., editor(s). Springer Berlin/Heidelberg, 2012.
doi   link   bibtex  
Bioscientific Data Processing and Modeling. Kok, J.; Lamprecht, A., L.; Verbeek, F.; and Wilkinson, M. Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies,7-11. 2012.
doi   link   bibtex  
Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study. Rodríguez-González, A.; Torres-Niño, J.; Mayer, M., A.; Alor-Hernandez, G.; and Wilkinson, M., D. Computational and Mathematical Methods in Medicine, 2012: 1-9. 2012.
Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study [link]Website   doi   link   bibtex  
A data-driven approach to automatic discovery of prescription drugs in cardiovascular risk management. Samadian, S.; Good, B., M.; McManus, B.; and Wilkinson, M., D. In Proceedings of The BioOntologies SIG, ISMB 2012, pages 14-17, 2012.
A data-driven approach to automatic discovery of prescription drugs in cardiovascular risk management [link]Website   link   bibtex   abstract  
Coherent 100G field trial over installed fiber links: Investigating key network scenarios and applications [Invited]. Zhou, Y.; Smith, K.; Wilkinson, M.; Payne, R.; Lord, A.; Bennett, T.; and Frankel, M. Journal of Optical Communications and Networking, 4(11). 2012.
doi   link   bibtex   abstract  
Coherent 100G field trial over installed fiber links: Investigating key network scenarios and applications. Zhou, Y.; Smith, K.; Wilkinson, M.; Payne, R.; Lord, A.; Bennett, T.; and Frankel, M. In National Fiber Optic Engineers Conference, NFOEC 2012, 2012.
link   bibtex   abstract  
Preface. Rodríguez-González, A.; Pathak, J.; Wilkinson, M.; Shah, N.; Stevens, R.; Boyce, R.; and García-Crespo, Á. In CEUR Workshop Proceedings, volume 930, 2012.
link   bibtex  
Coherent 100G field trial over installed fiber links: Investigating key network scenarios and applications. Zhou, Y.; Smith, K.; Wilkinson, M.; Payne, R.; Lord, A.; Bennett, T.; and Frankel, M. In National Fiber Optic Engineers Conference, NFOEC 2012, 2012.
link   bibtex   abstract  
  2011 (6)
The SADI plug-in to IO informatics' sentient knowledge explorer. Wilkinson, M., D.; and McCarthy, L. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, pages 116-118, 2011.
link   bibtex  
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation. Wilkinson, M., D.; Vandervalk, B.; and McCarthy, L. Journal of biomedical semantics, 2(1): 8. 10 2011.
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation. [link]Website   doi   link   bibtex   abstract  
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. Katayama, T.; Wilkinson, M.; Vos, R.; Kawashima, T.; Kawashima, S.; Nakao, M.; Yamamoto, Y.; Chun, H.; Yamaguchi, A.; Kawano, S.; Aerts, J.; Aoki-Kinoshita, K.; Arakawa, K.; Aranda, B.; Bonnal, R.; Fernandez, J.; Fujisawa, T.; Gordon, P.; Goto, N.; Haider, S.; Harris, T.; Hatakeyama, T.; Ho, I.; Itoh, M.; Kasprzyk, A.; Kido, N.; Kim, Y.; Kinjo, A.; Konishi, F.; Kovarskaya, Y.; von Kuster, G.; Labarga, A.; Limviphuvadh, V.; McCarthy, L.; Nakamura, Y.; Nam, Y.; Nishida, K.; Nishimura, K.; Nishizawa, T.; Ogishima, S.; Oinn, T.; Okamoto, S.; Okuda, S.; Ono, K.; Oshita, K.; Park, K.; Putnam, N.; Senger, M.; Severin, J.; Shigemoto, Y.; Sugawara, H.; Taylor, J.; Trelles, O.; Yamasaki, C.; Yamashita, R.; Satoh, N.; and Takagi, T. Journal of Biomedical Semantics, 2(1): 4. 2011.
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications [link]Website   doi   link   bibtex  
SADI for GMOD: Semantic Web Services for Model Organism Databases. Vandervalk, B.; Dumontier, M.; McCarthy, E., L.; and Wilkinson, M., D. In Proceedings of the Canadian Semantic Web Symposium 2011, 2011.
SADI for GMOD: Semantic Web Services for Model Organism Databases [pdf]Website   link   bibtex  
SADI for GMOD: Bringing Model Organism Data onto the Semantic Web. Vandervalk, B.; McCarthy, L.; and Wilkinson, M. In Proceedings of Bio Open Source Conference (BOSC) 2011, pages 36, 2011.
SADI for GMOD:  Bringing Model Organism Data onto the Semantic Web [pdf]Website   link   bibtex  
SADI for GMOD: Semantic web services for model organism databases. Vandervalk, B.; Dumontier, M.; McCarthy, E.; and Wilkinson, M. In CEUR Workshop Proceedings, volume 774, 2011.
link   bibtex   abstract  
  2010 (11)
SADI, SHARE, and the in silico scientific method. Wilkinson, M., D.; McCarthy, L.; Vandervalk, B.; Withers, D.; Kawas, E.; and Samadian, S. BMC Bioinformatics, 11(Suppl 12): S7. 2010.
SADI, SHARE, and the in silico scientific method [link]Website   doi   link   bibtex   abstract  
Tools in Scientific Workflow Composition. Kok, J.; Lamprecht, A.; and Wilkinson, M. In Leveraging Applications of Formal Methods, Verification, and Validation Lecture Notes in Computer Science, volume 6415, pages 258-260, 2010.
Tools in Scientific Workflow Composition [link]Website   link   bibtex  
SHARE & The Semantic Web - This Time it's Personal!. Vandervalk, B.; McCarthy, L.; and Wilkinson, M. In Proceedings of OWLED 2010, San Francisco, California, USA 21-22 June 2010, 2010.
SHARE & The Semantic Web - This Time it's Personal! [pdf]Website   link   bibtex  
Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins. Withers, D.; Kawas, E.; McCarthy, L.; Vandervalk, B.; and Wilkinson, M. In Leveraging Applications of Formal Methods, Verification, and Validation 4th International Symposium on Leveraging Applications, Lecture Notes in Computer Science, volume 6415, pages 301-312, 2010.
Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins [link]Website   link   bibtex  
SADI Semantic Web Services - 'cause you can't always GET what you want!. MD, W.; B, V.; and L, M. In Services Computing Conference, 2009. APSCC 2009. IEEE Asia-Pacific, pages 13-18, 1 2010.
SADI Semantic Web Services - 'cause you can't always GET what you want! [link]Website   doi   link   bibtex   abstract  
SPARQL Assist Language-Neutral Query Composer. McCarthy, L.; Vandervalk, B.; and Wilkinson, M. In Proceedings of Semantic Web Applications and Tools for Life Sciences 2010, 2010.
SPARQL Assist Language-Neutral Query Composer [link]Website   link   bibtex   abstract  
OWL2Perl: Creating Perl modules from OWL class definitions. Kawas, E.; and Wilkinson, M. Bioinformatics (Oxford, England). 7 2010.
OWL2Perl: Creating Perl modules from OWL class definitions. [link]Website   link   bibtex   abstract  
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. Katayama, T.; Arakawa, K.; Nakao, M.; Ono, K.; Aoki-Kinoshita, K., F.; Yamamoto, Y.; Yamaguchi, A.; Kawashima, S.; Chun, H.; Aerts, J.; Aranda, B.; Barboza, L., H.; Bonnal, R., J.; Bruskiewich, R.; Bryne, J., C.; Fernández, J., M.; Funahashi, A.; Gordon, P., M.; Goto, N.; Groscurth, A.; Gutteridge, A.; Holland, R.; Kano, Y.; Kawas, E., A.; Kerhornou, A.; Kibukawa, E.; Kinjo, A., R.; Kuhn, M.; Lapp, H.; Lehvaslaiho, H.; Nakamura, H.; Nakamura, Y.; Nishizawa, T.; Nobata, C.; Noguchi, T.; Oinn, T., M.; Okamoto, S.; Owen, S.; Pafilis, E.; Pocock, M.; Prins, P.; Ranzinger, R.; Reisinger, F.; Salwinski, L.; Schreiber, M.; Senger, M.; Shigemoto, Y.; Standley, D., M.; Sugawara, H.; Tashiro, T.; Trelles, O.; Vos, R., A.; Wilkinson, M., D.; York, W.; Zmasek, C., M.; Asai, K.; and Takagi, T. Journal of biomedical semantics, 1: 8. 2010.
doi   link   bibtex   abstract  
SHARE & the semantic web - This time it's personal!. Vandervalk, B.; McCarthy, L.; and Wilkinson, M. In CEUR Workshop Proceedings, volume 614, 2010.
link   bibtex   abstract  
Tools in scientific workflow composition. Kok, J.; Lamprecht, A.; and Wilkinson, M. Volume 6415 LNCS 2010.
doi   link   bibtex   abstract  
SPARQL assist language-neutral query composer. McCarthy, L.; Vandervalk, B.; and Wilkinson, M. In CEUR Workshop Proceedings, volume 698, 2010.
link   bibtex   abstract  
  2009 (6)
SHARE: A Semantic Web Query Engine for Bioinformatics. Vandervalk, B., P.; McCarthy, E., L.; and Wilkinson, M., D. Volume 5926 . The Semantic Web, Lecture Notes in Computer Science proceedings of the ASWC 2009, pages 367-369. 2009.
The Semantic Web, Lecture Notes in Computer Science proceedings of the ASWC 2009 [link]Website   doi   link   bibtex   abstract  
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. Good, B.; Tennis, J.; and Wilkinson, M. BMC Bioinformatics, 10(1): 313. 9 2009.
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics [link]Website   link   bibtex   abstract  
Moby and Moby 2: Creatures of the Deep (Web). Vandervalk, B.; McCarthy, E.; and Wilkinson, M. Briefings in Bioinformatics, 10(2): 114. 1 2009.
Moby and Moby 2: Creatures of the Deep (Web) [link]Website   link   bibtex   abstract  
Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm. Vandervalk, B.; McCarthy, L.; and Wilkinson, M. In IEEE International Conference on Computational Science and Engineering, volume 1, pages 330-337, 2009.
Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm [link]Website   link   bibtex  
Optimization of distributed SPARQL queries using edmonds' algorithm and prim's algorithm. Vandervalk, B.; McCarthy, E.; and Wilkinson, M. In Proceedings - 12th IEEE International Conference on Computational Science and Engineering, CSE 2009, volume 1, 2009.
doi   link   bibtex   abstract  
Effect of dynamic strain aging on fracture in aluminum alloy sheet materials AA5754. Kang, J.; Wilkinson, M.; Beaudoin, A.; Embury, J.; and Mishra, R. In 12th International Conference on Fracture 2009, ICF-12, volume 8, 2009.
link   bibtex   abstract  
  2008 (16)
Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Wilkinson, M., D.; Senger, M.; Kawas, E.; Bruskiewich, R.; Gouzy, J.; Noirot, C.; Bardou, P.; Ng, A.; Haase, D.; Saiz, E., d., A.; Wang, D.; Gibbons, F.; Gordon, P., M., K.; Sensen, C., W.; Carrasco, J., M., R.; Fernández, J., M.; Shen, L.; Links, M.; Ng, M.; Opushneva, N.; Neerincx, P., B., T.; Leunissen, J., A., M.; Ernst, R.; Twigger, S.; Usadel, B.; Good, B.; Wong, Y.; Stein, L.; Crosby, W.; Karlsson, J.; Royo, R.; Párraga, I.; Ramírez, S.; Gelpi, J., L.; Trelles, O.; Pisano, D., G.; Jimenez, N.; Kerhornou, A.; Rosset, R.; Zamacola, L.; Tarraga, J.; Huerta-Cepas, J.; Carazo, J., M.; Dopazo, J.; Guigo, R.; Navarro, A.; Orozco, M.; Valencia, A.; Claros, M., G.; Pérez, A., J.; Aldana, J.; Rojano, M., M.; Fernandez-Santa Cruz, R.; Navas, I.; Schiltz, G.; Farmer, A.; Gessler, D.; Schoof, H.; and Groscurth, A. Briefings in bioinformatics, 9(3): 220-31. 5 2008.
Interoperability with Moby 1.0--it's better than sharing your toothbrush! [link]Website   doi   link   bibtex   abstract  
Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. DiBernardo; M; Pottinger; R; and Wilkinson, M. Journal of Biomedical Informatics, 41(5): 837. 2008.
Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework [link]Website   link   bibtex   abstract  
The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science. R, B.; M, S.; G, D.; M, R.; M, R.; T, H.; M, T.; K, D.; K, S.; M, C.; R, S.; J, B.; A, A.; R, M.; S, W.; T, S.; M, A.; A, P.; Vj, U.; S, T.; K, B.; S, R.; A, D.; M, S.; E, R.; N, M.; G, P.; R, A.; R, A.; Lh, B.; J, D.; K, M.; Mj, M.; J, M.; B, P.; R, V.; Y, Z.; S, G.; J, H.; M, E.; Jm, Y.; A, F.; G, S.; J, L.; T, C.; P, J.; A, M.; M, W.; B, G.; J, W.; J, M.; D, M.; A, C.; S, K.; T, M.; G, M.; and Hintum, V. International Journal of Plant Genomics, 2008: 369601. 4 2008.
The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science [link]Website   link   bibtex   abstract  
DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data. Chan, F., C.; Kawas, E., A.; Wilkinson, M., D.; and Tebbutt, S., J. Journal of Proteomics & Bioinformatics, 1(4): 233-236. 7 2008.
DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data [link]Website   doi   link   bibtex   abstract  
Biological Metadata Management. Kothari, C.; and Wilkinson, M., D. Encyclopedia of Database Systems. Lacroix, Z.; Kothari, C.; Mork, P.; Wilkinson, M.; Freire, J.; and Cohen-Boulakia, S., editor(s). Springer, 2008.
Encyclopedia of Database Systems [link]Website   link   bibtex  
CardioSHARE: Web Services for the Semantic Web. Vandervalk, B.; McCarthy, L.; and Wilkinson, M. Technical Report 9 2008.
CardioSHARE: Web Services for the Semantic Web [pdf]Website   link   bibtex  
Structured Representation of Biomedical Experiments: A Bottom-Up Approach. Kothari, C.; and Wilkinson, M. In Proceedings of the 2008 International Conference on Information & Knowledge Engineering, IKE 2008. Las Vegas Nevada, USA, 2008.
Structured Representation of Biomedical Experiments: A Bottom-Up Approach [pdf]Website   link   bibtex   abstract  
The Semantic Health and Research Environment: SHARE-ing Deep Web Data on the Semantic Web. Vandervalk, B.; McCarthy, L.; and Wilkinson, M. In Proceedings of the 2008 Microsoft eScience Workshop, pages 127-128, 2008.
The Semantic Health and Research Environment: SHARE-ing Deep Web Data on the Semantic Web [link]Website   link   bibtex   abstract  
SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web. Vandervalk, B., P.; McCarthy, E., L.; and Wilkinson, M., D. In Third Asian Semantic Web Conference, ASWC2008, Workshops Proceedings (NEFORS2008), pages 69-78, 5 2008.
SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web [link]Website   link   bibtex   abstract  
Biological Resource Discovery. Kothari, C.; and Wilkinson, M., D. Encyclopedia of Database Systems. Lacroix, Z.; Kothari, C.; Mork, P.; Wilkinson, M.; and Cohen-Boulakia, S., editor(s). Springer, 2008.
Encyclopedia of Database Systems [link]Website   link   bibtex  
Web Services and the Semantic Web for Life Science Data. Kothari, C.; and Wilkinson, M. Encyclopedia of Database Systems. Lacroix, Z.; Kothari, C.; Mork, P.; Wilkinson, M.; and Cohen-Boulakia, S., editor(s). Springer, 2008.
Encyclopedia of Database Systems [link]Website   link   bibtex  
OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web. Good, B., M.; Ha, G.; Ho, C., K.; and Wilkinson, M., D. 2008.
OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web [link]Website   link   bibtex   abstract  
Structured representation of biomedical experiments: A bottom-up approach. Kothari, C.; and Wilkinson, M. In Proceedings of the 2008 International Conference on Information and Knowledge Engineering, IKE 2008, 2008.
link   bibtex   abstract  
Restoration of ethernet services over a dual-homed GPON system - Operator requirements and practical demonstration. Kang, J.; Wilkinson, M.; Smith, K.; and Nesset, D. In OFC/NFOEC 2008 - 2008 Conference on Optical Fiber Communication/National Fiber Optic Engineers Conference, 2008.
doi   link   bibtex   abstract  
Restoration of ethernet services over a dual-homed GPON system - Operator and practical demonstration. Kang, J.; Wilkinson, N.; Smith, K.; and Nesset, D. In Optics InfoBase Conference Papers, 2008.
link   bibtex   abstract  
The generation challenge programme platform: Semantic standards and workbench for crop science. Bruskiewich, R.; Senger, M.; Davenport, G.; Ruiz, M.; Rouard, M.; Hazekamp, T.; Takeya, M.; Doi, K.; Satoh, K.; Costa, M.; Simon, R.; Balaji, J.; Akintunde, A.; Mauleon, R.; Wanchana, S.; Shah, T.; Anacleto, M.; Portugal, A.; Ulat, V.; Thongjuea, S.; Braak, K.; Ritter, S.; Dereeper, A.; Skofic, M.; Rojas, E.; Martins, N.; Pappas, G.; Alamban, R.; Almodiel, R.; Barboza, L.; Detras, J.; Manansala, K.; Mendoza, M.; Morales, J.; Peralta, B.; Valerio, R.; Zhang, Y.; Gregorio, S.; Hermocilla, J.; Echavez, M.; Yap, J.; Farmer, A.; Schiltz, G.; Lee, J.; Casstevens, T.; Jaiswal, P.; Meintjes, A.; Wilkinson, M.; Good, B.; Wagner, J.; Morris, J.; Marshall, D.; Collins, A.; Kikuchi, S.; Metz, T.; McLaren, G.; and Van Hintum, T. International Journal of Plant Genomics, 2008. 2008.
doi   link   bibtex   abstract  
  2007 (11)
Tag clouds for summarizing web search results. Kuo, B., Y.; Hentrich, T.; Good, B., M., ..; and Wilkinson, M., D. In Proceedings of the 16th international conference on World Wide Web - WWW '07, pages 1203, 2007. ACM Press
Tag clouds for summarizing web search results [link]Website   doi   link   bibtex   abstract  
Using a novel data transformation technique to provide the EMBOSS software suite as Semantic Web Services. Gordon, P.; Kawas, E.; Wilkinson, M.; and Sensen, C. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 11 2007.
Using a novel data transformation technique to provide the EMBOSS software suite as Semantic Web Services [link]Website   link   bibtex  
DataBiNS: Data Mining Tool for Biological Pathways and Non-Synonymous SNPs. Song, Y.; Kawas, E.; Good, B.; Wilkinson, M.; and Tebbutt, S. Bioinformatics, 23(6): 780-782. 1 2007.
DataBiNS: Data Mining Tool for Biological Pathways and Non-Synonymous SNPs. [link]Website   link   bibtex   abstract  
Ontology Engineering Using Volunteer Labor. Good, B.; and Wilkinson, M. In Proceedings of the World Wide Web Conference (WWW2007), 2007.
Ontology Engineering Using Volunteer Labor [pdf]Website   link   bibtex   abstract  
From chaos to order: A generic, distributed, ontology based annotation system. Kothari, C.; and Wilkinson, M. In Proceedings of the 2007 International Conference on Information & Knowledge Engineering, IKE 2007, June 25-28, 2007. Las Vegas Nevada, USA, pages 141-145, 2007.
From chaos to order: A generic, distributed, ontology based annotation system [pdf]Website   link   bibtex   abstract  
Vcsa1 Gene Peptides for the Treatment of Inflammatory and Allergic Reactions. Morris, K.; Kuo, B.; Wilkinson, M.; Davison, J.; Befus, D.; and Mathison, R. Recent Patents on Inflammation & Allergy Drug Discovery, 1(2): 124-132. 2007.
Vcsa1 Gene Peptides for the Treatment of Inflammatory and Allergic Reactions [link]Website   link   bibtex  
Ontology engineering using volunteer labor. Good, B.; and Wilkinson, M. In 16th International World Wide Web Conference, WWW2007, 2007.
doi   link   bibtex   abstract  
DataBiNS: A BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. Song, Y.; Kawas, E.; Good, B.; Wilkinson, M.; and Tebbutt, S. Bioinformatics, 23(6). 2007.
doi   link   bibtex   abstract  
Designing a 21st and 22nd century fibre broadband access network. Davey, R.; Payne, D.; Barker, P.; Smith, K.; Wilkinson, M.; and Gunning, P. BT Technology Journal, 25(3-4). 2007.
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