Michel Dumontier

2020

Accelerating Discovery Science with an Internet of FAIR Data and Services

Dumontier, M., 2020, CIKM '20: PROCEEDINGS OF THE 29TH ACM INTERNATIONAL CONFERENCE ON INFORMATION & KNOWLEDGE MANAGEMENT. Association for Computing Machinery (ACM), p. 3-3 1 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference Abstract/Poster in proceeding › Academic

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

Vos, R. A., Katayama, T., Mishima, H., Kawano, S., Kawashima, S., Kim, J.-D., 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. & 57 others, 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.-H., 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.-L., 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.-H., Wilkinson, M., Yamada, I., Yamanaka, R., Yoshitake, K., Yoshizawa, A. C., Dumontier, M., Kosaki, K. & Takagi, T., 2020, In: F1000Research. 9, p. 136

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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

Zerka, F., Urovi, V., Vaidyanathan, A., Barakat, S., Leijenaar, R. T. H., Walsh, S., Gabrani-Juma, H., Miraglio, B., Woodruff, H. C., Dumontier, M. & Lambin, P., 2020, In: IEEE Access. 8, p. 183939-183951 13 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Considerations for the Conduction and Interpretation of FAIRness Evaluations

de Miranda Azevedo, R. & Dumontier, M., 1 Jan 2020, In: Data Intelligence. 2, 1-2, p. 285-292 8 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Distributed Analytics on Sensitive Medical Data: The Personal Health Train

Beyan, O., Choudhury, A., Van Soest, J., Kohlbacher, O., Zimmermann, L., Stenzhorn, H., Karim, M. R., Dumontier, M., Decker, S., Da Silva Santos, L. O. B. & Dekker, A., 1 Jan 2020, In: Data Intelligence. 2, 1-2, p. 96-107 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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. W., Imming, M., Jeffery, K. G. & Kaliyaperumal, R. & 24 others, 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.-A., 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. & Schultes, E., 31 Jan 2020, In: Data Intelligence. 2, 1-2, p. 10-29 20 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Introduction – FAIR data, systems and analysis

Groth, P. (Editor) & Dumontier, M., 12 Jun 2020, In: Data Science. 3, 1, p. 1-2

Research output: Contribution to journal › Editorial › Academic › peer-review

Open Access

Metadata standards for the FAIR sharing of vector embeddings in Biomedicine

Kafkas, S., Celebi, R., Ali, M., Jabeen, H., Dumontier, M. & Hoehndorf, R., 31 Oct 2020.

Research output: Contribution to conference › Paper › Academic

Preface

Dumontier, M. & Keet, C. M., 1 Jan 2020, Knowledge Engineering and Knowledge Management - 22nd International Conference, EKAW 2020, Proceedings. Keet, C. M. & Dumontier, M. (eds.). Springer Verlag, Vol. 12387 LNAI. p. v-vi 1 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 12387 LNAI).

Research output: Chapter in Book/Report/Conference proceeding › Foreword/postscript › Academic

Sleeping Beauties in Case Law

Hernandez Serrano, P. V., Moodley, K., Van Dijck, G. & Dumontier, M., 2020, LEGAL KNOWLEDGE AND INFORMATION SYSTEMS. Villata, S., Harasta, J. & Kremen, P. (eds.). IOS Press, Vol. 334. p. 231-234 4 p. (Frontiers in Artificial Intelligence and Applications, Vol. 334).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

Open Access

Ten simple rules for making training materials FAIR

Garcia, L., Batut, B., Burke, M. L., Kuzak, M., Psomopoulos, F., Arcila, R., Attwood, T. K., Beard, N., Carvalho-Silva, D., Dimopoulos, A. C., del Angel, V. D., Dumontier, M., Gurwitz, K. T., Krause, R., McQuilton, P., Le Pera, L., Morgan, S. L., Rauste, P., Via, A. & Kahlem, P. & 3 others, Rustici, G., van Gelder, C. W. G. & Palagi, P. M., May 2020, In: PLoS Computational Biology. 16, 5, 9 p., 1007854.

Research output: Contribution to journal › Editorial › Academic › peer-review

Open Access

The Case for a Linked Data Research Engine for Legal Scholars

Moodley, K., Hernández Serrano, P., Zaveri, A., Schaper, M., Dumontier, M. & van Dijck, G., Mar 2020, In: European Journal of Risk Regulation. 11, 1, p. 70-93 24 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Towards FAIR protocols and workflows: the OpenPREDICT use case

Celebi, R., Moreira, J. R., Hassan, A. A., Ayyar, S., Ridder, L., Kuhn, T. & Dumontier, M., 21 Sept 2020, In: PeerJ Computer Science. 29 p., 281.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

2019

Addendum: 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.-W., Santos, L. B. D. S., 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. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., Hoen, P. A. C. '., 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.-A., 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. & Mons, B., 19 Mar 2019, In: Scientific data. 6, 2 p., 6.

Research output: Contribution to journal › Erratum / corrigendum / retractions › Academic

Open Access

A linked data representation for summary statistics and grouping criteria

McCusker, J. P., Dumontier, M., Chari, S., Luciano, J. S. & McGuinness, D. L., 1 Jan 2019, Computer Vision Winter Workshop 2023. Vol. 2549. 159435. (CEUR Workshop Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

File

23 Downloads (Pure)

Annotation of existing databases using Semantic Web technologies: Making data more FAIR

van Soest, J., Choudhury, A., Gaikwad, N., Sloep, M., Dumontier, M. & Dekker, A., 1 Jan 2019, Semantic Web Applications and Tools for Health Care and Life Sciences. Vol. 2849. p. 94-101 8 p. (CEUR Workshop Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

File

13 Downloads (Pure)

A Novel Ensemble-Based Machine Learning Algorithm to Predict the Conversion From Mild Cognitive Impairment to Alzheimer's Disease Using Socio-Demographic Characteristics, Clinical Information, and Neuropsychological Measures

Alzheimer's Disease Neuroimaging Initiative, 16 Jul 2019, In: Frontiers in Neurology. 10, JUL, 15 p., 756.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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

Sun, C., Ippel, L., van Soest, J., Wouters, B., Malic, A., Adekunle, O., van den Berg, B., Mussmann, O., Koster, A., van der Kallen, C., van Oppen, C., Townend, D., Dekker, A. & Dumontier, M., 21 Aug 2019, In: Studies in Health Technology and Informatics. 264, p. 373-377 5 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework

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. & Schultes, E., 21 Oct 2019, In: Scientific data. 6, 1, 1 p., 230.

Research output: Contribution to journal › Erratum / corrigendum / retractions › Academic

Open Access

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combination DREAM Consortium, 17 Jun 2019, In: Nature Communications. 10, 1, 17 p., 2674.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Evaluating FAIR maturity through a scalable, automated, community-governed framework

Wilkinson, M. D., Dumontier, M., Sansone, S.-A., Santos, L. O. B. D. S., Prieto, M., Batista, D., McQuilton, P., Kuhn, T., Rocca-Serra, P., Crosas, M. & Schultes, E., 20 Sept 2019, In: Scientific data. 6, 1, 12 p., 174.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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

Celebi, R., Uyar, H., Yasar, E., Gumus, O., Dikenelli, O. & Dumontier, M., 18 Dec 2019, In: BMC Bioinformatics. 20, 1, 14 p., 726.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

FAIR Principles for Clinical Practice Guidelines in a Learning Health System

Leung, T. I. & Dumontier, M., 21 Aug 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All. Ohno-Machado, L. & Séroussi, B. (eds.). IOS Press, p. 1690-1691 2 p. (Studies in Health Technology and Informatics, Vol. 264).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

Clarke, D. J. B., Wang, L., Jones, A., Wojciechowicz, M. L., Torre, D., Jagodnik, K. M., Jenkins, S. L., McQuilton, P., Flamholz, Z., Silverstein, M. C., Schilder, B. M., Robasky, K., Castillo, C., Idaszak, R., Ahalt, S. C., Williams, J., Schurer, S., Cooper, D. J., Azevedo, R. D. M. & Klenk, J. A. & 14 others, Haendel, M. A., Nedzel, J., Avillach, P., Shimoyama, M. E., Harris, R. M., Gamble, M., Poten, R., Charbonneau, A. L., Larkin, J., Brown, C. T., Bonazzi, V. R., Dumontier, M. J., Sansone, S.-A. & Ma'ayan, A., 27 Nov 2019, In: Cell Systems. 9, 5, p. 417-421 5 p.

Research output: Contribution to journal › Editorial › Academic › peer-review

Open Access

File

100 Downloads (Pure)

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

Sang, S., Yang, Z., Liu, X., Wang, L., Lin, H., Wang, J. & Dumontier, M., 2019, In: IEEE Access. 7, p. 8404-8415 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data

Celebi, R., Walk, O. B. D., Movva, R., Alpsoy, S. & Dumontier, M., 20 Jun 2019, In: Scientific Reports. 9, 1, 10 p., 8949.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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

Havelange, N., Dumontier, M., Wouters, B., Linde, J., Townend, D., Riedl, A. & Urovi, V., 6 Aug 2019, Cornell University - arXiv, 14 p. (arXiv.org).

Research output: Working paper / Preprint › Preprint

Open Access

Putting FAIR Evidence into Practice

Leung, T. I. & Dumontier, M., Aug 2019, In: Journal of General Internal Medicine. 34, 8, p. 1369-1369 1 p.

Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

Open Access

File

52 Downloads (Pure)

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

Grigoriu, A., Zaveri, A., Weiss, G. & Dumontier, M., 2019.

Research output: Contribution to conference › Abstract › Academic

Similarity and relevance of court decisions: A computational study on CJEU cases

Moodley, K., Hernández Serrano, P., van Dijck, G. & Dumontier, M., Dec 2019, Legal knowledge and information systems. Araszkiewicz, M. & Rodríguez-Doncel, V. (eds.). Amsterdam/Berlin/Washington, DC: IOS Press, p. 63-72 10 p. (Frontiers in Artificial Intelligence and Applications, Vol. 322).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

File

236 Downloads (Pure)

The Biomedical Data Translator Program: Conception, Culture, and Community

The Biomedical Data Translator Consortium, Mar 2019, In: Clinical and Translational Science. 12, 2, p. 91-94 4 p.

Research output: Contribution to journal › Editorial › Academic › peer-review

Open Access

The current state of FAIR principles literature: a bibliometric review.

de M. Alencar, S., Moreira Da Rocha De Miranda Azevedo, R., Henning, P., Da Silva Santos, L. O. B. & Dumontier, M., 2019, In: Liinc em Revista.

Research output: Contribution to journal › Article › Academic

Toward A Universal Biomedical Data Translator

The Biomedical Data Translator Consortium, Mar 2019, In: Clinical and Translational Science. 12, 2, p. 86-90 5 p.

Research output: Contribution to journal › Editorial › Academic › peer-review

Open Access

Transformation and integration of heterogeneous health data in a privacy-preserving distributed learning infrastructure

Sun, C., Emonet, V., van Soest, J., Koster, A., Dekker, A. & Dumontier, M., 1 Jan 2019, Semantic Web Applications and Tools for Health Care and Life Sciences. Vol. 2849. p. 141-142 2 p. (CEUR Workshop Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

File

14 Downloads (Pure)

2018

A design framework and exemplar metrics for FAIRness

Wilkinson, M. D., Sansone, S.-A., Schultes, E., Doorn, P., Santos, L. O. B. D. S. & Dumontier, M., 26 Jun 2018, In: Scientific data. 5, 4 p., 180118.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Advancing discovery science with fair data stewardship: Findable, accessible, interoperable, reusable

Dumontier, M. & Wesley, K., 31 May 2018, In: Serials Librarian. 74, 1-4, p. 39-48 10 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

23 Downloads (Pure)

A model for capturing provenance of assertions about chemical substances

Moodley, K., Zaveri, A., Wu, C. & Dumontier, M., 2018, Semantic Web Applications and Tools for Health Care and Life Sciences. Baker, C. J. O., Waagmeester, A., Splendiani, A., Beyan, O. D. & Marshall, M. S. (eds.). Antwerp, Belgium: CEUR-WS.org, Vol. 2275.

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

Analyzing Partitioned FAIR Health Data Responsibly

Sun, C., Ippel, L., Wouters, B., Soest, J. V., Malic, A., Adekunle, O., Berg, B. V. D., Puts, M., Mussmann, O., Koster, A., Kallen, C. V. D., Townend, D., Dekker, A. & Dumontier, M., 2 Dec 2018, Cornell University - arXiv, p. 1-6, 6 p. (arXiv.org).

Research output: Working paper / Preprint › Preprint

Open Access

Assessing Schema.org's Coverage of Terms from Key Biomedical Datasets

Moodley, K., Hardi, J., Graybeal, J., Musen, M. A. & Dumontier, M., 6 Jul 2018.

Research output: Contribution to conference › Paper › Academic

A Web API Ecosystem through Feature Based Reuse

Verborgh, R. & Dumontier, M., 2018, In: Ieee Internet Computing. 22, 3, p. 29-37 9 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

77 Downloads (Pure)

Biotea: semantics for Pubmed Central

Garcia, A., Lopez, F., Garcia, L., Giraldo, O., Bucheli, V. & Dumontier, M., 2 Jan 2018, In: PEERJ. 6, 1, e4201.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records

Ta, C. N., Dumontier, M., Hripcsak, G., Tatonetti, N. P. & Weng, C., 27 Nov 2018, In: Scientific data. 5, 17 p., 180273.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

CrowdED: Guideline for Optimal Crowdsourcing Experimental Design

Zaveri, A., Serrano, P. H., Desai, M. & Dumontier, M., 2018, Companion Proceedings of the The Web Conference 2018. Republic and Canton of Geneva, Switzerland: International World Wide Web Conferences Steering Committee, p. 1109-1116 8 p. (WWW '18).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

File

115 Downloads (Pure)

Data2Services: enabling automated conversion of data to services

Emonet, V., Zaveri, A., Malic, A., Grigoriu, A. & Dumontier, M., Dec 2018, SWAT4LS.

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

File

79 Downloads (Pure)

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

Zhang, Y., Zheng, W., Lin, H., Wang, J., Yang, Z. & Dumontier, M., 1 Mar 2018, In: Bioinformatics. 34, 5, p. 828-835 8 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Evaluation of Knowledge Graph Embedding Approaches for Drug-Drug Interaction Prediction using Linked Open Data

Celebi, R., Yasar, E., Uyar, H., Gumus, O., Dikenelli, O. & Dumontier, M., 3 Dec 2018.

Research output: Contribution to conference › Paper › Academic

Fundamentals of clinical data science

Kubben, P. (Editor), Dumontier, M. (Editor) & Dekker, A. (Editor), 21 Dec 2018, Springer International Publishing. 219 p.

Research output: Book/Report › Book editing › Academic

Open Access

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

Kuhn, T., Meroño-Peñuela, A., Malic, A., Poelen, J. H., Hurlbert, A. H., Ortiz, E. C., Furlong, L. I., Queralt-Rosinach, N., Chichester, C., Banda, J. M., Willighagen, E., Ehrhart, F., Evelo, C., Malas, T. B. & Dumontier, M., 18 Sept 2018, 2018 IEEE 14th International Conference on e-Science (e-Science). IEEE, p. 83-92 10 p. (Proceeding IEEE International Conference on e-Science (e-Science)).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic

Open Access

Predicting the need for a reduced drug dose, at first prescription

Coulet, A., Shah, N. H., Wack, M., Chawki, M. B., Jay, N. & Dumontier, M., 22 Oct 2018, In: Scientific Reports. 8, 1, 11 p., 15558.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Quality Assessment of Biomedical Metadata Using Topic Modeling

Zaveri, A., Dumontier, M. & Nayak, S., 2018, Quality Assessment of Biomedical Metadata Using Topic Modeling. .

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

Open Access

Michel Dumontier

Research output

Search results