Michel Dumontier

According to our database, Michel Dumontier authored at least 210 papers between 2002 and 2024.

Collaborative distances:

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

2024

LSQ 2.0: A linked dataset of SPARQL query logs.

Claus Stadler, Muhammad Saleem, Qaiser Mehmood, Carlos Buil-Aranda, Michel Dumontier, Aidan Hogan, Axel-Cyrille Ngonga Ngomo

Semantic Web, 2024

Editorial of the special issue on semantic technologies for data and algorithmic governance.

Sabrina Kirrane, Oshani Seneviratne, Michel Dumontier

Semantic Web, 2024

CrowdED 1.0: Statistical Guideline for Designing Optimal Crowdsourcing Experiments.

Amrapali Zaveri, Pedro V. Hernandez Serrano, Michel Dumontier

Hum. Comput., 2024

Audio-Language Datasets of Scenes and Events: A Survey.

Gijs Wijngaard, Elia Formisano, Michele Esposito, Michel Dumontier

CoRR, 2024

Generative AI for Synthetic Data Across Multiple Medical Modalities: A Systematic Review of Recent Developments and Challenges.

Mahmoud Ibrahim, Yasmina Al Khalil, Sina Amirrajab, Chang Sun, Marcel Breeuwer, Josien P. W. Pluim, Bart Elen, Gokhan Ertaylan, Michel Dumontier

CoRR, 2024

Improving rule mining via embedding-based link prediction.

N'Dah Jean Kouagou, Arif Yilmaz, Michel Dumontier, Axel-Cyrille Ngonga Ngomo

CoRR, 2024

Towards Biomedical Neurosymbolic AI: From Knowledge Infrastructure to Explainable Predictions.

Michel Dumontier

Proceedings of the 7th Workshop on Semantic Web solutions for large-scale biomedical data analytics co-located with The ESWC 2024: Extended Semantic Web Conference (ESWC 2024), 2024

2023

ciTIzen-centric DAta pLatform (TIDAL): Sharing distributed personal data in a privacy-preserving manner for health research.

Chang Sun, Marc Gallofré Ocaña, Johan van Soest, Michel Dumontier

Semantic Web, 2023

Generating synthetic personal health data using conditional generative adversarial networks combining with differential privacy.

Chang Sun, Johan van Soest, Michel Dumontier

J. Biomed. Informatics, 2023

Models towards Risk Behavior Prediction and Analysis: A Netherlands Case study.

Onaopepo Adekunle, Arno Riedl, Michel Dumontier

CoRR, 2023

FAIR Begins at home: Implementing FAIR via the Community Data Driven Insights.

Carlos Utrilla Guerrero, Maria Vivas Romero, Marc Dolman, Michel Dumontier

CoRR, 2023

TAPS Responsibility Matrix: A tool for responsible data science by design.

Visara Urovi, Remzi Celebi, Chang Sun, Linda Rieswijk, Michael Erard, Arif Yilmaz, Kody Moodley, Parveen Kumar, Michel Dumontier

CoRR, 2023

Evidence From Data Science on the Relationship Between Individual Beliefs/Behaviors Survey During COVID-19 Pandemic and Risk Preference.

Onaopepo Adekunle, Arno Riedl, Michel Dumontier

Adv. Artif. Intell. Mach. Learn., 2023

Generating Knowledge Graph Based Explanations for Drug Repurposing Predictions.

Elif Ozkan, Remzi Celebi, Arif Yilmaz, Vincent Emonet, Michel Dumontier

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

Analyze Decentralized Personal Health Data Using Solid, Digital Consent, and Federated Learning.

Chang Sun, Johan van Soest, Michel Dumontier

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

Enhanced GAT: Expanding Receptive Field with Meta Path-Guided RDF Rules for Two-Hop Connectivity.

Julie Loesch, Michel Dumontier, Remzi Celebi

Proceedings of the Joint Proceedings of Scholarly QALD 2023 and SemREC 2023 co-located with 22nd International Semantic Web Conference ISWC 2023, 2023

Semantically-Informed Deep Neural Networks For Sound Recognition.

Michele Esposito, Giancarlo Valente, Yenisel Plasencia Calaña, Michel Dumontier, Bruno L. Giordano, Elia Formisano

Proceedings of the IEEE International Conference on Acoustics, 2023

ACES: Evaluating Automated Audio Captioning Models on the Semantics of Sounds.

Gijs Wijngaard, Elia Formisano, Bruno L. Giordano, Michel Dumontier

Proceedings of the 31st European Signal Processing Conference, 2023

On the Combination of Event Calculus and Empirical Semantic Drifts.

Franz Krause, Xi Yan, Baptiste Darnala, Michel Dumontier

Proceedings of the Joint Proceedings of the ESWC 2023 Workshops and Tutorials co-located with 20th European Semantic Web Conference (ESWC 2023), 2023

Graph-based Categorical Embedding.

Weiwei Wang, Stefano Bromuri, Michel Dumontier

Proceedings of the 31st European Symposium on Artificial Neural Networks, 2023

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 2022

Studying the association of diabetes and healthcare cost on distributed data from the Maastricht Study and Statistics Netherlands using a privacy-preserving federated learning infrastructure.

Chang Sun, Johan van Soest, Annemarie Koster, Simone J. P. M. Eussen, Miranda T. Schram, Coen D. A. Stehouwer, Pieter C. Dagnelie, Michel Dumontier

J. Biomed. Informatics, 2022

A formalization of one of the main claims of "The FAIR Guiding Principles for scientific data management and stewardship" by Wilkinson et al. 20161.

Michel Dumontier

Data Sci., 2022

Improving Correlation Capture in Generating Imbalanced Data using Differentially Private Conditional GANs.

Chang Sun, Johan van Soest, Michel Dumontier

CoRR, 2022

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science.

Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew H. Brush, Richard M. Bruskiewich, Paul A. Clemons, Vlado Dancík, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim E. Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall

CoRR, 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

CoRR, 2022

LUCE: A Blockchain-based data sharing platform for monitoring data license accountability and compliance.

Visara Urovi, Vikas Jaiman, Arno Angerer, Michel Dumontier

CoRR, 2022

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

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

J. Biomed. Semant., 2022

A Comprehensive Comparison of Automated FAIRness Evaluation Tools.

Chang Sun, Vincent Emonet, Michel Dumontier

Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

Automated Identification of Food Substitutions Using Knowledge Graph Embeddings.

Julie Loesch, Louis Meeckers, Ilse van Lier, Alie de Boer, Michel Dumontier, Remzi Celebi

Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

Nanotate: Semantically Annotating Experimental Protocols with Nanopublications.

Olga L. Giraldo, Miguel Ruano, Robin A. Richardson, Remzi Celebi, Michel Dumontier, Tobias Kuhn

Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

Semantic Correlation Graph Embedding.

Weiwei Wang, Yuchen Han, Stefano Bromuri, Michel Dumontier

Proceedings of the IEEE International Conference on Fuzzy Systems, 2022

2021

Comparison results of FAIR Evaluation tools.

Chang Sun, Vincent Emonet, Michel Dumontier

Dataset, September, 2021

Semantic micro-contributions with decentralized nanopublication services.

Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier

PeerJ Comput. Sci., 2021

Experience: Automated Prediction of Experimental Metadata from Scientific Publications.

Stuti Nayak, Amrapali Zaveri, Pedro Hernandez Serrano, Michel Dumontier

ACM J. Data Inf. Qual., 2021

Relation extraction from DailyMed structured product labels by optimally combining crowd, experts and machines.

Krist Shingjergji, Remzi Celebi, Jan C. Scholtes, Michel Dumontier

J. Biomed. Informatics, 2021

A systematic review on privacy-preserving distributed data mining.

Chang Sun, Lianne Ippel, Andre Dekker, Michel Dumontier, Johan van Soest

Data Sci., 2021

Privacy preserving distributed learning classifiers - Sequential learning with small sets of data.

Fadila Zerka, Visara Urovi, Fabio Bottari, Ralph T. H. Leijenaar, Sean Walsh, Hanif Gabrani-Juma, Martin Gueuning, Akshayaa Vaidyanathan, Wim Vos, Mariaelena Occhipinti, Henry C. Woodruff, Michel Dumontier, Philippe Lambin

Comput. Biol. Medicine, 2021

InContext: curation of medical context for drug indications.

Kody Moodley, Linda Rieswijk, Tudor I. Oprea, Michel Dumontier

J. Biomed. Semant., 2021

SIENA: Semi-automatic semantic enhancement of datasets using concept recognition.

Andreea Grigoriu, Amrapali Zaveri, Gerhard Weiss, Michel Dumontier

J. Biomed. Semant., 2021

Knowledge Graph Completeness: A Systematic Literature Review.

Subhi Issa, Onaopepo Adekunle, Fayçal Hamdi, Samira Si-Said Cherfi, Michel Dumontier, Amrapali Zaveri

IEEE Access, 2021

User-friendly Composition of FAIR Workflows in a Notebook Environment.

Robin A. Richardson, Remzi Celebi, Sven van der Burg, Djura Smits, Lars Ridder, Michel Dumontier, Tobias Kuhn

Proceedings of the K-CAP '21: Knowledge Capture Conference, 2021

Reuse of Design Pattern Measurements for Health Data.

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

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

2020

Ten simple rules for making training materials FAIR.

Leyla J. García, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis E. Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez Del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi

PLoS Comput. Biol., 2020

Towards FAIR protocols and workflows: the OpenPREDICT use case.

Remzi Celebi, Joao Rebelo Moreira, Ahmed A. Hassan, Sandeep Ayyar, Lars Ridder, Tobias Kuhn, Michel Dumontier

PeerJ Comput. Sci., 2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research.

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

F1000Research, 2020

FAIR Principles: Interpretations and Implementation Considerations.

Annika Jacobsen, Ricardo de Miranda Azevedo, Nick S. Juty, Dominique Batista, Simon J. Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. A. Evelo, Carole A. Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina M. Hettne, Jaap Heringa, Rob W. W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George O. Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes

Data Intell., 2020

Distributed Analytics on Sensitive Medical Data: The Personal Health Train.

Oya Beyan, Ananya Choudhury, Johan van Soest, Oliver Kohlbacher, Lukas Zimmermann, Holger Stenzhorn, Md. Rezaul Karim, Michel Dumontier, Stefan Decker, Luiz Olavo Bonino da Silva Santos, Andre Dekker

Data Intell., 2020

Considerations for the Conduction and Interpretation of FAIRness Evaluations.

Ricardo de Miranda Azevedo, Michel Dumontier

Data Intell., 2020

Introduction - FAIR data, systems and analysis.

Paul Groth, Michel Dumontier

Data Sci., 2020

Knowledge Graphs Evolution and Preservation - A Technical Report from ISWS 2019.

Nacira Abbas, Kholoud Alghamdi, Mortaza Alinam, Francesca Alloatti, Glenda C. M. Amaral, Claudia d'Amato, Luigi Asprino, Martin Beno, Felix Bensmann, Russa Biswas, Ling Cai, Riley Capshaw, Valentina Anita Carriero, Irene Celino, Amine Dadoun, Stefano De Giorgis, Harm Delva, John Domingue, Michel Dumontier, Vincent Emonet, Marieke van Erp, Paola Espinoza-Arias, Omaima Fallatah, Sebastián Ferrada, Marc Gallofré Ocaña, Michalis Georgiou, Genet Asefa Gesese, Frances Gillis-Webber, Francesca Giovannetti, María Granados Buey, Ismail Harrando, Ivan Heibi, Vitor A. C. Horta, Laurine Huber, Federico Igne, Mohamad Yaser Jaradeh, Neha Keshan, Aneta Koleva, Bilal Koteich, Kabul Kurniawan, Mengya Liu, Chuangtao Ma, Lientje Maas, Martin Mansfield, Fabio Mariani, Eleonora Marzi, Sepideh Mesbah, Maheshkumar Mistry, Alba Catalina Morales Tirado, Anna Nguyen, Viet Bach Nguyen, Allard Oelen, Valentina Pasqual, Heiko Paulheim, Axel Polleres, Margherita Porena, Jan Portisch, Valentina Presutti, Kader Pustu-Iren, Ariam Rivas Mendez, Soheil Roshankish, Sebastian Rudolph, Harald Sack, Ahmad Sakor, Jaime Salas, Thomas Schleider, Meilin Shi, Gianmarco Spinaci, Chang Sun, Tabea Tietz, Molka Tounsi Dhouib, Alessandro Umbrico, Wouter van den Berg, Weiqin Xu

CoRR, 2020

Blockchain for Privacy Preserving and Trustworthy Distributed Machine Learning in Multicentric Medical Imaging (C-DistriM).

Fadila Zerka, Visara Urovi, Akshayaa Vaidyanathan, Samir Barakat, Ralph T. H. Leijenaar, Sean Walsh, Hanif Gabrani-Juma, Benjamin Miraglio, Henry C. Woodruff, Michel Dumontier, Philippe Lambin

IEEE Access, 2020

Sleeping Beauties in Case Law.

Pedro V. Hernandez Serrano, Kody Moodley, Gijs van Dijck, Michel Dumontier

Proceedings of the Legal Knowledge and Information Systems, 2020

Accelerating Discovery Science with an Internet of FAIR Data and Services.

Michel Dumontier

Proceedings of the CIKM '20: The 29th ACM International Conference on Information and Knowledge Management, 2020

2019

MetaCrowd: Crowdsourcing Biomedical Metadata Quality Assessment.

Amrapali Zaveri, Wei Hu, Michel Dumontier

Hum. Comput., 2019

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi

F1000Research, 2019

Towards FAIR protocols and workflows: The OpenPREDICT case study.

Remzi Celebi, Joao Rebelo Moreira, Ahmed A. Hassan, Sandeep Ayyar, Lars Ridder, Tobias Kuhn, Michel Dumontier

CoRR, 2019

Privacy-Preserving Generalized Linear Models using Distributed Block Coordinate Descent.

Erik-Jan van Kesteren, Chang Sun, Daniel L. Oberski, Michel Dumontier, Lianne Ippel

CoRR, 2019

LUCE: A Blockchain Solution for monitoring data License accoUntability and CompliancE.

Nadine Havelange, Michel Dumontier, Birgit Wouters, Jona Linde, David Townend, Arno Riedl, Visara Urovi

CoRR, 2019

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings.

Remzi Celebi, Hüseyin Uyar, Erkan Yasar, Özgür Gümüs, Oguz Dikenelli, Michel Dumontier

BMC Bioinform., 2019

GrEDeL: A Knowledge Graph Embedding Based Method for Drug Discovery From Biomedical Literatures.

Shengtian Sang, Zhihao Yang, Xiaoxia Liu, Lei Wang, Hongfei Lin, Jian Wang, Michel Dumontier

IEEE Access, 2019

Transformation and Integration of Heterogeneous Health Data in a Privacy-preserving Distributed Learning Infrastructure.

Chang Sun, Vincent Emonet, Johan van Soest, Annemarie Koster, Andre Dekker, Michel Dumontier

Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

Annotation of Existing Databases using Semantic Web Technologies: Making Data more FAIR.

Johan van Soest, Ananya Choudhury, Nikhil Gaikwad, Matthijs Sloep, Michel Dumontier, Andre Dekker

Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

Reflections on: Finding Melanoma Drugs Through a Probabilistic Knowledge Graph.

Jamie P. McCusker, Michel Dumontier, Rui Yan, Sylvia He, Jonathan S. Dordick, Deborah L. McGuinness

Proceedings of the Journal Track co-located with the 18th International Semantic Web Conference (ISWC 2019), 2019

A Linked Data Representation for Summary Statistics and Grouping Criteria.

Jamie P. McCusker, Michel Dumontier, Shruthi Chari, Joanne S. Luciano, Deborah L. McGuinness

Proceedings of the Joint Proceedings of the International Workshops on Sensors and Actuators on the Web, 2019

A Privacy-Preserving Infrastructure for Analyzing Personal Health Data in a Vertically Partitioned Scenario.

Chang Sun, Lianne Ippel, Johan van Soest, Birgit Wouters, Alexander Malic, Onaopepo Adekunle, Bob van den Berg, Ole Mussmann, Annemarie Koster, Carla van der Kallen, Claudia van Oppen, David Townend, Andre Dekker, Michel Dumontier

Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019

FAIR Principles for Clinical Practice Guidelines in a Learning Health System.

Tiffany I. Leung, Michel Dumontier

Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019

Similarity and Relevance of Court Decisions: A Computational Study on CJEU Cases.

Kody Moodley, Pedro V. Hernandez Serrano, Gijs van Dijck, Michel Dumontier

Proceedings of the Legal Knowledge and Information Systems, 2019

Finding the evidence base using citation networks: Do 300 to 400 U.S. physicians die by suicide annually?

Tiffany I. Leung, Sima Pendharkar, Chwen-Yuen Angie Chen, Michel Dumontier

Proceedings of the AMIA 2019, 2019

2018

A Web API Ecosystem through Feature-Based Reuse.

Ruben Verborgh, Michel Dumontier

IEEE Internet Comput., 2018

Analyzing Partitioned FAIR Health Data Responsibly.

Chang Sun, Lianne Ippel, Birgit Wouters, Johan van Soest, Alexander Malic, Onaopepo Adekunle, Bob van den Berg, Marco Puts, Ole Mussmann, Annemarie Koster, Carla van der Kallen, David Townend, Andre Dekker, Michel Dumontier

CoRR, 2018

Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths.

Yijia Zhang, Wei Zheng, Hongfei Lin, Jian Wang, Zhihao Yang, Michel Dumontier

Bioinform., 2018

CrowdED: Guideline for Optimal Crowdsourcing Experimental Design.

Amrapali Zaveri, Pedro Hernandez Serrano, Manisha Desai, Michel Dumontier

Proceedings of the Companion of the The Web Conference 2018 on The Web Conference 2018, 2018

A model for capturing provenance of assertions about chemical substances.

Kody Moodley, Amrapali Zaveri, Chunlei Wu, Michel Dumontier

Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings.

Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf

Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Data2Services: enabling automated conversion of data to services.

Vincent Emonet, Amrapali Zaveri, Alexander Malic, Andreea Grigoriu, Michel Dumontier

Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction using Linked Open Data.

Remzi Çelebi, Erkan Yasar, Hüseyin Uyar, Özgür Gümüs, Oguz Dikenelli, Michel Dumontier

Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Using the Personal Health Train for Automated and Privacy-Preserving Analytics on Vertically Partitioned Data.

Johan van Soest, Chang Sun, Ole Mussmann, Marco Puts, Bob van den Berg, Alexander Malic, Claudia van Oppen, David Townend, Andre Dekker, Michel Dumontier

Proceedings of the Building Continents of Knowledge in Oceans of Data: The Future of Co-Created eHealth, 2018

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data.

Tobias Kuhn, Albert Meroño-Peñuela, Alexander Malic, Jorrit H. Poelen, Allen H. Hurlbert, Emilio Centeno Ortiz, Laura I. Furlong, Núria Queralt-Rosinach, Christine Chichester, Juan M. Banda, Egon L. Willighagen, Friederike Ehrhart, Chris T. A. Evelo, Tareq B. Malas, Michel Dumontier

Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017

Interoperability and FAIRness through a novel combination of Web technologies.

Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier

PeerJ Prepr., 2017

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

Maryam Panahiazar, Michel Dumontier, Olivier Gevaert

J. Biomed. Informatics, 2017

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri, Ajay Pillai, Avi Ma'ayan

J. Biomed. Informatics, 2017

Drug-drug interaction discovery and demystification using Semantic Web technologies.

Adeeb Noor, Abdullah Assiri, Serkan Ayvaz, Connor Clark, Michel Dumontier

J. Am. Medical Informatics Assoc., 2017

Formalizing drug indications on the road to therapeutic intent.

Stuart J. Nelson, Tudor I. Oprea, Oleg Ursu, Cristian Bologa, Amrapali Zaveri, Jayme Holmes, Jeremy J. Yang, Stephen L. Mathias, Subramani Mani, Mark S. Tuttle, Michel Dumontier

J. Am. Medical Informatics Assoc., 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

Genuine semantic publishing.

Tobias Kuhn, Michel Dumontier

Data Sci., 2017

Data Science - Methods, infrastructure, and applications.

Michel Dumontier, Tobias Kuhn

Data Sci., 2017

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata.

Wei Hu, Amrapali Zaveri, Honglei Qiu, Michel Dumontier

BMC Bioinform., 2017

Discovering associations between adverse drug events using pattern structures and ontologies.

Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet

J. Biomed. Semant., 2017

Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data.

Richard D. Boyce, Erica A. Voss, Vojtech Huser, Lee Evans, Christian G. Reich, Jon D. Duke, Nicholas P. Tatonetti, Tal Lorberbaum, Michel Dumontier, Manfred Hauben, Magnus Wallberg, Lili Peng, Sara Dempster, Yongqun He, Anthony G. Sena, Vassilis Koutkias, Pantelis Natsiavas, Patrick B. Ryan

J. Biomed. Semant., 2017

BioSearch: a semantic search engine for Bio2RDF.

Wei Hu, Honglei Qiu, Jiacheng Huang, Michel Dumontier

Database J. Biol. Databases Curation, 2017

Machine Learning Based Drug Indication Prediction Using Linked Open Data.

Remzi Çelebi, Özgün Erten, Michel Dumontier

Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

Bioschemas: schema.org for the Life Sciences.

Leyla J. García, Olga L. Giraldo, Alexander García Castro, Michel Dumontier, Bioschemas Community

Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

The SmartAPI Ecosystem for Making Web APIs FAIR.

Shima Dastgheib, Trish Whetzel, Amrapali Zaveri, Cyrus Afrasiabi, Pedro Assis, Paul Avillach, Kathleen M. Jagodnik, Gabor Korodi, Marcin Pilarczyk, Jeff de Pons, Stephan C. Schürer, Raymond Terryn, Ruben Verborgh, Chunlei Wu, Michel Dumontier

Proceedings of the ISWC 2017 Posters & Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 23rd - to, 2017

smartAPI: Towards a More Intelligent Network of Web APIs.

Amrapali Zaveri, Shima Dastgheib, Chunlei Wu, Trish Whetzel, Ruben Verborgh, Paul Avillach, Gabor Korodi, Raymond Terryn, Kathleen M. Jagodnik, Pedro Assis, Michel Dumontier

Proceedings of the Semantic Web - 14th International Conference, 2017

Is Crowdsourcing Patient-Reported Outcomes the Future of Evidence-Based Medicine? A Case Study of Back Pain.

Mor Peleg, Tiffany I. Leung, Manisha Desai, Michel Dumontier

Proceedings of the Artificial Intelligence in Medicine, 2017

2016

Publishing DisGeNET as nanopublications.

Núria Queralt-Rosinach, Tobias Kuhn, Christine Chichester, Michel Dumontier, Ferran Sanz, Laura I. Furlong

Semantic Web, 2016

Interoperability and FAIRness through a novel combination of Web technologies.

Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier

PeerJ Prepr., 2016

Finding melanoma drugs through a probabilistic knowledge graph.

Jamie P. McCusker, Michel Dumontier, Rui Yan, Sylvia He, Jonathan S. Dordick, Deborah L. McGuinness

PeerJ Prepr., 2016

Decentralized provenance-aware publishing with nanopublications.

Tobias Kuhn, Christine Chichester, Michael Krauthammer, Núria Queralt-Rosinach, Ruben Verborgh, George Giannakopoulos, Axel-Cyrille Ngonga Ngomo, Raffaele Viglianti, Michel Dumontier

PeerJ Prepr., 2016

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

Jonathan M. Mortensen, Natalie Telis, Jacob J. Hughey, Hua Fan-Minogue, Kimberly Van Auken, Michel Dumontier, Mark A. Musen

J. Biomed. Informatics, 2016

The structure and dynamics of the research fronts in HIV/AIDS research: part-whole and adaptive specialization.

David Fajardo-Ortiz, Malaquias Lopez-Cervantes, Luis Duran, Michel Dumontier, Miguel Lara, Hector Ochoa, Víctor M. Castaño

CoRR, 2016

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.

Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa N. Soldatova, Michel Dumontier, Nigam Shah

J. Biomed. Semant., 2016

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

Tiffany I. Leung, Michel Dumontier

J. Biomed. Semant., 2016

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul Jean Pierre Bonnal, Robert M. Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock

J. Biomed. Semant., 2016

Predicting structured metadata from unstructured metadata.

Lisa Posch, Maryam Panahiazar, Michel Dumontier, Olivier Gevaert

Database J. Biol. Databases Curation, 2016

The digital revolution in phenotyping.

Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier

Briefings Bioinform., 2016

Making Linked Data SPARQL with the InterMine Biological Data Warehouse.

Maxime Déraspe, Gail Binkley, Daniela Butano, Matthew Chadwick, J. Michael Cherry, Justin Clark-Casey, Sergio Contrino, Jacques Corbeil, Joshua Heimbach, Kalpana Karra, Rachel Lyne, Julie M. Sullivan, Yo Yehudi, Gos Micklem, Michel Dumontier

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

Ontology Mapping for Life Science Linked Data.

Amrapali Zaveri, Michel Dumontier

Proceedings of the First International Workshop on Biomedical Data Integration and Discovery (BMDID 2016) co-located with The 15th International Semantic Web Conference (ISWC 2016), 2016

Semantic Research Platform for Model Organisms.

Maxime Déraspe, Kalpana Karra, Gail Binkley, Julie M. Sullivan, Gos Micklem, Jacques Corbeil, J. Michael Cherry, Michel Dumontier

Proceedings of the First International Workshop on Biomedical Data Integration and Discovery (BMDID 2016) co-located with The 15th International Semantic Web Conference (ISWC 2016), 2016

Network Ranking Assisted Semantic Data Mining.

Jan Kralj, Anze Vavpetic, Michel Dumontier, Nada Lavrac

Proceedings of the Bioinformatics and Biomedical Engineering, 2016

Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy.

David J. Odgers, Natalie Telis, Heather Hall, Michel Dumontier

Proceedings of the Summit on Clinical Research Informatics, 2016

2015

Making Digital Artifacts on the Web Verifiable and Reliable.

Tobias Kuhn, Michel Dumontier

IEEE Trans. Knowl. Data Eng., 2015

Achieving human and machine accessibility of cited data in scholarly publications.

Joan Starr, Eleni Castro, Mercè Crosas, Michel Dumontier, Robert R. Downs, Ruth E. Duerr, Laurel L. Haak, Melissa A. Haendel, Iván Herman, Simon Hodson, Joe Hourclé, John Ernest Kratz, Jennifer Lin, Lars Holm Nielsen, Amy Nurnberger, Stefan Pröll, Andreas Rauber, Simone Sacchi, Arthur P. Smith, Michael Taylor, Tim Clark

PeerJ Prepr., 2015

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.

Matthias Samwald, José Antonio Miñarro-Giménez, Richard D. Boyce, Robert R. Freimuth, Klaus-Peter Adlassnig, Michel Dumontier

BMC Medical Informatics Decis. Mak., 2015

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

Gang Fu, Colin R. Batchelor, Michel Dumontier, Janna Hastings, Egon L. Willighagen, Evan Bolton

J. Cheminformatics, 2015

Toward a complete dataset of drug-drug interaction information from publicly available sources.

Serkan Ayvaz, John R. Horn, Oktie Hassanzadeh, Qian Zhu, Johann Stan, Nicholas P. Tatonetti, Santiago Vilar, Mathias Brochhausen, Matthias Samwald, Majid Rastegar-Mojarad, Michel Dumontier, Richard D. Boyce

J. Biomed. Informatics, 2015

The center for expanded data annotation and retrieval.

Mark A. Musen, Carol A. Bean, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Olivier Gevaert, Alejandra N. González-Beltrán, Purvesh Khatri, Steven H. Kleinstein, Martin J. O'Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jeffrey A. Wiser

J. Am. Medical Informatics Assoc., 2015

On Reasoning with RDF Statements about Statements using Singleton Property Triples.

Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan, Gang Fu, Evan Bolton, Núria Queralt Rosinach, Laura Inés Furlong, Michel Dumontier, Amit P. Sheth

CoRR, 2015

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans.

Alison Callahan, Juan Cifuentes, Michel Dumontier

BMC Bioinform., 2015

Special issue on bio-ontologies and phenotypes.

Larisa N. Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2015

SPARQL-enabled identifier conversion with Identifiers.org.

Sarala M. Wimalaratne, Jerven T. Bolleman, Nick S. Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novère, Henning Hermjakob, Camille Laibe

Bioinform., 2015

An Ebola virus-centered knowledge base.

Maulik R. Kamdar, Michel Dumontier

Database J. Biol. Databases Curation, 2015

Exposing Provenance Metadata Using Different RDF Models.

Gang Fu, Evan Bolton, Núria Queralt-Rosinach, Laura Inés Furlong, Vinh Nguyen, Amit P. Sheth, Olivier Bodenreider, Michel Dumontier

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data.

Tobias Kuhn, Christine Chichester, Michael Krauthammer, Michel Dumontier

Proceedings of the Semantic Web - ISWC 2015, 2015

Link Analysis of Life Science Linked Data.

Wei Hu, Honglei Qiu, Michel Dumontier

Proceedings of the Semantic Web - ISWC 2015, 2015

Provenance-Centered Dataset of Drug-Drug Interactions.

Juan M. Banda, Tobias Kuhn, Nigam H. Shah, Michel Dumontier

Proceedings of the Semantic Web - ISWC 2015, 2015

Comparing Drug-Disease Associations in Clinical Practice Guideline Recommendations and Drug Product Label Indications.

Tiffany I. Leung, Michel Dumontier

Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

A Preliminary Investigation into SPARQL Query Complexity and Federation in Bio2RDF.

Carlos Buil-Aranda, Martín Ugarte, Marcelo Arenas, Michel Dumontier

Proceedings of the 9th Alberto Mendelzon International Workshop on Foundations of Data Management, Lima, Peru, May 6, 2015

Drug-Disease Associations in Guidelines, Drug Labels, and Practice.

Tiffany I. Leung, Michel Dumontier

Proceedings of the AMIA 2015, 2015

2014

Special issue on Linked Data for Health Care and the Life Sciences.

Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Michel Dumontier

Semantic Web, 2014

Hash-URIs for Verifiable, Immutable, and Permanent Digital Artifacts.

Tobias Kuhn, Michel Dumontier

CoRR, 2014

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Philippe Rocca-Serra, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2014

Automatically exposing OpenLifeData via SADI semantic Web Services.

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

J. Biomed. Semant., 2014

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

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

J. Biomed. Semant., 2014

Mouse model phenotypes provide information about human drug targets.

Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier

Bioinform., 2014

Bio2RDF Release 3: A larger, more connected network of Linked Data for the Life Sciences.

Michel Dumontier, Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Vincent Emonet, François Belleau, Arnaud Droit

Proceedings of the ISWC 2014 Posters & Demonstrations Track a track within the 13th International Semantic Web Conference, 2014

A Nanopublication Framework for Biological Networks using Cytoscape.js.

Jamie P. McCusker, Rui Yan, Kusum Solanki, John S. Erickson, Cynthia Chang, Michel Dumontier, Jonathan S. Dordick, Deborah L. McGuinness

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Erratum: Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.

Tobias Kuhn, Michel Dumontier

Proceedings of the Semantic Web: Trends and Challenges - 11th International Conference, 2014

Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.

Tobias Kuhn, Michel Dumontier

Proceedings of the Semantic Web: Trends and Challenges - 11th International Conference, 2014

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines.

Tiffany I. Leung, Hawre Jalal, Donna M. Zulman, Douglas K. Owens, Mark A. Musen, Michel Dumontier, Mary K. Goldstein

Proceedings of the AMIA 2014, 2014

2013

1st Semantic Web Technologies for Libraries and Readers (STLR 2011).

Alison Callahan, Michel Dumontier, Jodi Schneider, Lars Svensson

Bull. IEEE Tech. Comm. Digit. Libr., 2013

State of the art and open challenges in community-driven knowledge curation.

Tudor Groza, Tania Tudorache, Michel Dumontier

J. Biomed. Informatics, 2013

Evaluation of the OQuaRE framework for ontology quality.

Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis, Miguela Iniesta-Moreno, Michel Dumontier, Mikel Egaña Aranguren, Stefan Schulz, Nathalie Aussenac-Gilles, Robert Stevens

Expert Syst. Appl., 2013

Ovopub: Modular data publication with minimal provenance

Alison Callahan, Michel Dumontier

CoRR, 2013

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Susanna-Assunta Sansone, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2013

Ontology-Based Querying with Bio2RDF's Linked Open Data.

Alison Callahan, Jose Cruz-Toledo, Michel Dumontier

J. Biomed. Semant., 2013

Evaluation of research in biomedical ontologies.

Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos

Briefings Bioinform., 2013

A Large-scale Gene-centric Semantic Web Knowledge Base for Molecular Biology.

Jose Cruz-Toledo, Alison Callahan, Michel Dumontier

Proceedings of the Informal Proceedings of the 2nd International Workshop on OWL Reasoner Evaluation (ORE-2013), 2013

An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics.

Matthias Samwald, Robert R. Freimuth, Joanne S. Luciano, Simon M. Lin, Robert L. Powers, M. Scott Marshall, Klaus-Peter Adlassnig, Michel Dumontier, Richard D. Boyce

Proceedings of the MEDINFO 2013, 2013

The Web as a Distributed Biochemical Reactor: Semantically Enabled Metabolic Fate Prediction.

Leonid L. Chepelev, Michel Dumontier

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

HyQue: A Semantic Web tool for evaluating scientific hypotheses.

Alison Callahan, Michel Dumontier

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data.

Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Michel Dumontier

Proceedings of the Semantic Web: Semantics and Big Data, 10th International Conference, 2013

Looking into Reactome through Biopax Lens.

Laleh Kazemzadeh, Helena F. Deus, Michel Dumontier, Frank Barry

Proceedings of the 4th Canadian Semantic Web Symposium part of the Semantic Trilogy 2013, 2013

2012

Linked Data in Drug Discovery.

Michel Dumontier, David J. Wild

IEEE Internet Comput., 2012

Towards quantitative measures in applied ontology

Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos

CoRR, 2012

Self-organizing ontology of biochemically relevant small molecules.

Leonid L. Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier

BMC Bioinform., 2012

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

Larisa N. Soldatova, Susanna-Assunta Sansone, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2012

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.

Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos

Bioinform., 2012

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments.

Jose Cruz-Toledo, Maureen McKeague, Xueru Zhang, Amanda Giamberardino, Erin McConnell, Tariq Francis, Maria C. DeRosa, Michel Dumontier

Database J. Biol. Databases Curation, 2012

Building an HIV data mashup using Bio2RDF.

Marc-Alexandre Nolin, Michel Dumontier, François Belleau, Jacques Corbeil

Briefings Bioinform., 2012

YummyData: Measuring the "Sparkliness" of Biomedical Sparql Endpoints.

Andrea Splendiani, Johan Nyström-Persson, Michel Dumontier, Yasunori Yamamoto

Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Improved Dataset Coverage and Interoperability with Bio2RDF Release 2.

Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Dana Klassen, Giovanni Tumarello, Michel Dumontier

Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Molecular Symmetry and Specialization of Atomic Connectivity by Class-based Reasoning of Chemical Structure.

Michel Dumontier

Proceedings of OWL: Experiences and Directions Workshop 2012, 2012

Role-based representation and inference of biochemical processes.

Christian Boelling, Michel Dumontier, Michael Weidlich, Hermann-Georg Holzhütter

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Evaluating Scientific Hypotheses Using the SPARQL Inferencing Notation.

Alison Callahan, Michel Dumontier

Proceedings of the Semantic Web: Research and Applications, 2012

2011

Taking flight with OWL2.

Michel Dumontier

Semantic Web, 2011

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration.

Leonid L. Chepelev, Michel Dumontier

J. Cheminformatics, 2011

Semantic Web integration of Cheminformatics resources with the SADI framework.

Leonid L. Chepelev, Michel Dumontier

J. Cheminformatics, 2011

MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets.

Alexander Gawronski, Michel Dumontier

Comput. Graph., 2011

Integrating systems biology models and biomedical ontologies.

Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos

BMC Syst. Biol., 2011

Prototype Semantic Infrastructure for Automated Small Molecule Classification and Annotation in Lipidomics.

Leonid L. Chepelev, Alexandre Riazanov, Alexandre Kouznetsov, Hong Sang Low, Michel Dumontier, Christopher J. O. Baker

BMC Bioinform., 2011

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.

Joanne S. Luciano, Bosse Andersson, Colin R. Batchelor, Olivier Bodenreider, Tim Clark, Christine K. Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter J. Kos, Julia Kozlovsky, Timothy Lebo, M. Scott Marshall, Jamie P. McCusker, Deborah L. McGuinness, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud'hommeaux, Matthias Samwald, Lynn M. Schriml, Peter J. Tonellato, Patricia L. Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier

J. Biomed. Semant., 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.

Adrien Coulet, Yael Garten, Michel Dumontier, Russ B. Altman, Mark A. Musen, Nigam H. Shah

J. Biomed. Semant., 2011

HyQue: evaluating hypotheses using Semantic Web technologies.

Alison Callahan, Michel Dumontier, Nigam H. Shah

J. Biomed. Semant., 2011

A common layer of interoperability for biomedical ontologies based on OWL EL.

Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos

Bioinform., 2011

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.

Robert Hoehndorf, Colin R. Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel, Neocles Leontis

Appl. Ontology, 2011

Chemical Hazard Estimation and Method Comparison with OWL-Encoded Toxicity Decision Trees.

Leonid L. Chepelev, Dana Klassen, Michel Dumontier

Proceedings of the 8th International Workshop on OWL: Experiences and Directions (OWLED 2011), 2011

Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine.

Matthias Samwald, Holger Stenzhorn, Michel Dumontier, M. Scott Marshall, Joanne Luciano, Klaus-Peter Adlassnig

Proceedings of the User Centered Networked Health Care - Proceedings of MIE 2011, 2011

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

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

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

2010

Modeling and querying graphical representations of statistical data.

Michel Dumontier, Leo Ferres, Natalia Villanueva-Rosales

J. Web Semant., 2010

Building an effective Semantic Web for health care and the life sciences.

Michel Dumontier

Semantic Web, 2010

Relations as patterns: bridging the gap between OBO and OWL.

Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre

BMC Bioinform., 2010

RKB: a Semantic Web knowledge base for RNA.

Jose Cruz-Toledo, Michel Dumontier, Marc Parisien, François Major

J. Biomed. Semant., 2010

Relational Patterns in OWL and Their Application to OBO.

Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Heinrich Herre, Dietrich Rebholz-Schuhmann

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

Representing Chemicals Using OWL, Description Graphs and Rules.

Janna Hastings, Michel Dumontier, Duncan Hull, Matthew Horridge, Christoph Steinbeck, Robert Stevens, Ulrike Sattler, Tertia Hörne, Katarina Britz

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

Realism for scientific ontologies.

Michel Dumontier, Robert Hoehndorf

Proceedings of the Formal Ontology in Information Systems, 2010

2009

Towards pharmacogenomics knowledge discovery with the semantic web.

Michel Dumontier, Natalia Villanueva-Rosales

Briefings Bioinform., 2009

Conjunctive Query Answering in Distributed Ontology Systems for Ontologies with Large OWL ABoxes.

Xueying Chen, Michel Dumontier

Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

A Platform for Reasoning with OWL-EL Knowledge Bases in a Peer-to-Peer Environment.

Alexander De Leon Battista, Michel Dumontier

Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

PDB2RDF - Exposing Molecular and Experimental Knowledge on the Semantic Web.

Jose Cruz-Toledo, Alexander De Leon Battista, Michel Dumontier

Proceedings of the 5th International Conference on Semantic Systems, 2009

Modeling tryptic digestion on the Cell BE processor.

James R. Green, Hanan Mahmoud, Michel Dumontier

Proceedings of the 22nd Canadian Conference on Electrical and Computer Engineering, 2009

2008

yOWL: An ontology-driven knowledge base for yeast biologists.

Natalia Villanueva-Rosales, Michel Dumontier

J. Biomed. Informatics, 2008

GridCell: a stochastic particle-based biological system simulator.

Laurier Boulianne, Sevin Al Assaad, Michel Dumontier, Warren J. Gross

BMC Syst. Biol., 2008

Report on semantic web for health care and life sciences workshop.

Huajun Chen, Kei-Hoi Cheung, Michel Dumontier, Eric Prud'hommeaux, Alan Ruttenberg, Susie Stephens, Yimin Wang

Proceedings of the 17th International Conference on World Wide Web, 2008

Modeling Life Science Knowledge with OWL 1.1.

Michel Dumontier, Natalia Villanueva-Rosales

Proceedings of the Fourth OWLED Workshop on OWL: Experiences and Directions, 2008

Situational Modeling: Defining Molecular Roles in Biochemical Pathways and Reactions.

Michel Dumontier

Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008

Publishing OWL Ontologies with Presto.

Alex DeLeon, Michel Dumontier

Proceedings of the Fourth OWLED Workshop on OWL: Experiences and Directions, 2008

Semantic Annotation and Question Answering of Statistical Graphs.

Michel Dumontier, Leo Ferres, Natalia Villanueva-Rosales

Proceedings of the MICAI 2008: Advances in Artificial Intelligence, 2008

Chemical Knowledge for the Semantic Web.

Mykola Konyk, Alexander De Leon Battista, Michel Dumontier

Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

2007

SMART: A Web-Based, Ontology-Driven, Semantic Web Query Answering Application.

Alexander De Leon Battista, Natalia Villanueva-Rosales, Myroslav Palenychka, Michel Dumontier

Proceedings of the Semantic Web Challenge 2007 co-located with ISWC 2007 + ASWC 2007, 2007

A stochastic particle-based biological system simulator.

Laurier Boulianne, Michel Dumontier, Warren J. Gross

Proceedings of the 2007 Summer Computer Simulation Conference, 2007

Describing Chemical Functional Groups in OWL-DL for the Classification of Chemical Compounds.

Natalia Villanueva-Rosales, Michel Dumontier

Proceedings of the OWLED 2007 Workshop on OWL: Experiences and Directions, 2007

Three-Layer OWL Ontology Design.

Michel Dumontier, Natalia Villanueva-Rosales

Proceedings of the 2nd International Workshop on Modular Ontologies, WoMO 2007, 2007

Semantic Query Answering with Time-Series Graphs.

Leo Ferres, Michel Dumontier, Natalia Villanueva-Rosales

Proceedings of the Workshops Proceedings of the 11th International IEEE Enterprise Distributed Object Computing Conference, 2007

2006

Domain-based small molecule binding site annotation.

Kevin A. Snyder, Howard J. Feldman, Michel Dumontier, John J. Salama, Christopher W. V. Hogue

BMC Bioinform., 2006

2005

The Biomolecular Interaction Network Database and related tools 2005 update.

C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, Martha Bajec, K. Bantoft, Doron Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, Ian M. Donaldson, D. Dorairajoo, Michel Justin Dumontier, M. R. Dumontier, V. Earles, R. Farrall, Howard J. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, Robin Haw, A. Hrvojic, L. Hurrell, Ruth Isserlin, F. Jack, F. Juma, A. Khan, T. Kon, S. Konopinsky, V. Le, E. Lee, S. Ling, M. Magidin, J. Moniakis, J. Montojo, S. Moore, B. Muskat, I. Ng, J. P. Paraiso, Benjamin D. Parker, Greg Pintilie, R. Pirone, John J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, Kevin A. Snyder, R. Stasiuk, D. Strumpf, Brigitte Tuekam, S. Tao, Z. Wang, M. White, R. Willis, Cheryl Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, Shudong Zhang, K. Zheng, Tony Pawson, B. F. Francis Ouellette, Christopher W. V. Hogue

Nucleic Acids Res., 2005

2002

SeqHound: biological sequence and structure database as a platform for bioinformatics research.

Katerina Michalickova, Gary D. Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin, Christopher W. V. Hogue

BMC Bioinform., 2002

Species-specific protein sequence and fold optimizations.

Michel Dumontier, Katerina Michalickova, Christopher W. V. Hogue

BMC Bioinform., 2002

NBLAST: a cluster variant of BLAST for NxN comparisons.

Michel Dumontier, Christopher W. V. Hogue

BMC Bioinform., 2002