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Research Output

2020

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

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Finding the Evidence Base Using Citation Networks: Do 300 to 400 US Physicians Die by Suicide Annually?

Leung, T. I., Pendharkar, S., Chen, C-Y. A. & Dumontier, M., 27 May 2020, In : Journal of General Internal Medicine. 3 p.

Research output: Contribution to journalEditorialAcademicpeer-review

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 journalEditorialAcademicpeer-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 journalArticleAcademicpeer-review

Open Access
2019

3In-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, 10 p., 8949.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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 journalArticleAcademicpeer-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, p. 230 1 p., 230.

Research output: Contribution to journalErratum / corrigendumAcademic

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

AstraZeneca-Sanger Drug Combinatio, 17 Jun 2019, In : Nature Communications. 10, 17 p., 2674.

Research output: Contribution to journalArticleAcademicpeer-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 Sep 2019, In : Scientific data. 6, 12 p., 174.

Research output: Contribution to journalArticleAcademicpeer-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 journalArticleAcademicpeer-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 proceedingChapterAcademic

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 journalEditorialAcademicpeer-review

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 journalArticleAcademicpeer-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, In : arXiv . 14 p.

Research output: Contribution to journalArticleAcademic

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 journalComment/Letter to the editorAcademicpeer-review

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 proceedingConference article in proceedingAcademicpeer-review

Open Access
File
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The Biomedical Data Translator Program: Conception, Culture, and Community

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

Research output: Contribution to journalEditorialAcademicpeer-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 journalArticleAcademic

The FAIR Guiding Principles for scientific data management and stewardship (vol 15, 160018, 2016)

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. T., 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 journalErratum / corrigendumAcademic

Open Access

Toward A Universal Biomedical Data Translator

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

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access
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 journalArticleAcademicpeer-review

Open Access

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 proceedingConference article in proceedingAcademicpeer-review

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, In : arXiv . p. 1-6 6 p.

Research output: Contribution to journalArticleAcademic

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 conferencePaperAcademic

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 journalArticleAcademicpeer-review

Biotea: semantics for Pubmed Central

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

Research output: Contribution to journalArticleAcademicpeer-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 journalArticleAcademicpeer-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 proceedingConference article in proceedingAcademicpeer-review

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 proceedingConference article in proceedingAcademicpeer-review

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 journalArticleAcademicpeer-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 conferencePaperAcademic

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 Sep 2018, 2018 IEEE 14th International Conference on e-Science (e-Science). p. 83-92 10 p. (Proceedings of IEEE e-Science).

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademic

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, 11 p., 15558.

Research output: Contribution to journalArticleAcademicpeer-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 proceedingConference article in proceedingAcademicpeer-review

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

van Soest, J., Sun, C., Mussmann, O., Puts, M., van den Berg, B., Malic, A., van Oppen, C., Townend, D., Dekker, A. & Dumontier, M., 2018, p. 581-585. 5 p.

Research output: Contribution to conferencePaperAcademic

2017

Assessing the quality of manually curated drug indication and usage information via ontology term mappings

Moodley, K., Rieswijk, L., Oprea, T. I. & Dumontier, M., 21 Jul 2017.

Research output: Contribution to conferencePaperAcademic

BioSearch: a semantic search engine for Bio2RDF

Hu, W., Qiu, H., Huang, J. & Dumontier, M., 8 Aug 2017, In : Database-The Journal of Biological Databases and Curation. p. 1-13

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Hu, W., Zaveri, A., Qiu, H. & Dumontier, M., 18 Sep 2017, In : BMC Bioinformatics. 18

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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. & Wilkinson, M. D., 2017, In : Information Services and Use. 37, 1, p. 49-56 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop

Jagodnik, K. M., Koplev, S., Jenkins, S., Ohno-Machado, L., Paten, B., Schurer, S. C., Dumontier, M., Verborgh, R., Bui, A., Ping, P., McKenna, N. J., Madduri, R., Pillai, A. & Ma'ayan, A., Jul 2017, In : Journal of Biomedical Informatics. 71, p. 49-57 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Discovering associations between adverse drug events using pattern structures and ontologies

Personeni, G., Bresso, E., Devignes, M-D., Dumontier, M., Smail-Tabbone, M. & Coulet, A., 22 Aug 2017, In : Journal of biomedical semantics. 8

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Drug-drug interaction discovery and demystification using Semantic Web technologies

Noor, A., Assiri, A., Ayvaz, S., Clark, C. & Dumontier, M., 1 May 2017, In : Journal of the American Medical Informatics Association. 24, 3, p. 556-564 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Finding melanoma drugs through a probabilistic knowledge graph

McCusker, J. P., Dumontier, M., Yan, R., He, S., Dordick, J. S. & McGuinness, D. L., 13 Feb 2017, In : PeerJ Computer Science. 3, p. e106 20 p., 106.

Research output: Contribution to journalArticleAcademicpeer-review

Formalizing drug indications on the road to therapeutic intent

Nelson, S. J., Oprea, T. I., Ursu, O., Bologa, C. G., Zaveri, A., Holmes, J., Yang, J. J., Mathias, S. L., Mani, S., Tuttle, M. S. & Dumontier, M., 1 Nov 2017, In : Journal of the American Medical Informatics Association. 24, 6, p. 1169-1172 4 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

McMurry, J., Juty, N., Blomberg, N., Burdett, A., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D., Gonzalez-Beltran, A., Gormanns, P., Grethe, J., Hastings, J., Hermjakob, H., Heriche, J-K., Ison, J., Jimenez, R., Jupp, S., Kunze, J. & 24 others, Laibe, C., Novere, N. L., Malone, J. R., Martin, M-J., McEntyre, J., Morris, C., Muilu, J., Mueller, W., Rocca-Serra, P., Sansone, S-A., Sariyar, M., Snoep, J., Stanford, N. J., Soiland-Reyes, S., Swainston, N., Washington, N., Williams, A., Wimalaratne, S., Winfree, L., Wolstencroft, K., Goble, C., Mungall, C., Haendel, M. & Parkinson, H., 20 Mar 2017, bioRxiv, p. 1-27.

Research output: Working paperProfessional

Open Access

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D. K., Gonzalez-Beltran, A., Gormanns, P., Grethe, J. S., Hastings, J., Heriche, J-K., Hermjakob, H., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J. & 24 others, Laibe, C., Le Novere, N., Malone, J., Martin, M-J., McEntyre, J. R., Morris, C., Muilu, J., Mueller, W., Rocca-Serra, P., Sansone, S-A., Sariyar, M., Snoep, J. L., Soiland-Reyes, S., Stanford, N. J., Swainston, N., Washington, N. L., Williams, A. R., Wimalaratne, S. M., Winfree, L. M., Wolstencroft, K., Goble, C., Mungall, C. J., Haendel, M. A. & Parkinson, H., Jun 2017, In : Plos Biology. 15, 6, e2001414.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Interoperability and FAIRness through a novel combination of Web technologies

Wilkinson, M. D., Verborgh, R., Santos, L. O. B. D. S., Clark, T., Swertz, M. A., Kelpin, F. D. L., Gray, A. J. G., Schultes, E. A., van Mulligen, E. M., Ciccarese, P., Kuzniar, A., Gavai, A., Thompson, M., Kaliyaperumal, R., Bollema, J. T. & Dumontier, M., 24 Apr 2017, In : PeerJ Computer Science.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Boyce, R. D., Voss, E. A., Huser, V., Evans, L., Reich, C., Duke, J. D., Tatonetti, N. P., Lorberbaum, T., Dumontier, M., Hauben, M., Wallberg, M., Peng, L., Dempster, S., He, Y., Sena, A. G., Koutkias, V., Natsiavas, P. & Ryan, P. B., 7 Mar 2017, In : Journal of biomedical semantics. 8

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Machine Learning based Drug Indication Prediction using Linked Open Data

Celebi, R., Erten, O. & Dumontier, M., 2017, 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review