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Research Output

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Article
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

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

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

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

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

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

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

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

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

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
2017

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. 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

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

Panahiazar, M., Dumontier, M. & Gevaert, O., Aug 2017, In : Journal of Biomedical Informatics. 72, p. 132-139

Research output: Contribution to journalArticleAcademicpeer-review

Semantics-Powered Healthcare Engineering and Data Analytics

He, Z., Tao, C., Bian, J., Dumontier, M. & Hogan, W. R., 2017, In : Journal of Healthcare Engineering.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The emergence and evolution of the research fronts in HIV/AIDS research

Fajardo-Ortiz, D., Lopez-Cervantes, M., Duran, L., Dumontier, M., Lara, M., Ochoa, H. & Castano, V. M., 25 May 2017, In : PLOS ONE. 12, 5, p. e0178293 13 p., 0178293.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2016

A Web API ecosystem through feature-based reuse

Verborgh, R. & Dumontier, M., 22 Sep 2016, In : arXiv . 1609.07108

Research output: Contribution to journalArticleAcademic

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Comment: The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, IJ. 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., 't 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., 15 Mar 2016, In : Scientific data. 3, 9 p., 160018.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Sieberts, S. K., Zhu, F., García-García, J., Stahl, E. A., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J., Eksi, R., Fornés, O., Guney, E., Li, H., Marín, M. A., Panwar, B., Planas-Iglesias, J., Poglayen, D., Cui, J., Falcao, A. O. & 86 others, Suver, C., Hoff, B., Balagurusamy, V. S. K., Dillenberger, D., Neto, E. C., Norman, T., Aittokallio, T., Ammad-Ud-Din, M., Azencott, C-A., Bellón, V., Boeva, V., Bunte, K., Chheda, H., Cheng, L., Corander, J., Dumontier, M., Goldenberg, A., Gopalacharyulu, P., Hajiloo, M., Hidru, D., Jaiswal, A., Kaski, S., Khalfaoui, B., Khan, S. A., Kramer, E. R., Marttinen, P., Mezlini, A. M., Molparia, B., Pirinen, M., Saarela, J., Samwald, M., Stoven, V., Tang, H., Tang, J., Torkamani, A., Vert, J-P., Wang, B., Wang, T., Wennerberg, K., Wineinger, N. E., Xiao, G., Xie, Y., Yeung, R., Zhan, X., Zhao, C., Greenberg, J., Kremer, J., Michaud, K., Barton, A., Coenen, M., Mariette, X., Miceli, C., Shadick, N., Weinblatt, M., de Vries, N., Tak, P. P., Gerlag, D., Huizinga, T. W. J., Kurreeman, F., Allaart, C. F., Louis Bridges, S., Criswell, L., Moreland, L., Klareskog, L., Saevarsdottir, S., Padyukov, L., Gregersen, P. K., Friend, S., Plenge, R., Stolovitzky, G., Oliva, B., Guan, Y., Mangravite, L. M., Bridges, S. L., Criswell, L., Moreland, L., Klareskog, L., Saevarsdottir, S., Padyukov, L., Gregersen, P. K., Friend, S., Plenge, R., Stolovitzky, G., Oliva, B., Guan, Y. & Mangravite, L. M., 23 Aug 2016, In : Nature Communications. 7, p. 12460 9 p., 12460.

Research output: Contribution to journalArticleAcademicpeer-review

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

Bolleman, J. T., Mungall, C. J., Strozzi, F., Baran, J., Dumontier, M., Bonnal, R. J. P., Buels, R., Hoehndorf, R., Fujisawa, T., Katayama, T. & Cock, P. J. A., 13 Jun 2016, In : Journal of biomedical semantics. 7, 39.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Feasibility of Prioritizing Drug-Drug-Event Associations Found in Electronic Health Records

Banda, J. M., Callahan, A., Winnenburg, R., Strasberg, H. R., Cami, A., Reis, B. Y., Vilar, S., Hripcsak, G., Dumontier, M. & Shah, N. H., Jan 2016, In : Drug Safety. 39, 1, p. 45-57

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Mortensen, J. M., Telis, N., Hughey, J. J., Fan-Minogue, H., Van Auken, K., Dumontier, M. & Musen, M. A., Apr 2016, In : Journal of Biomedical Informatics. 60, p. 199-209

Research output: Contribution to journalArticleAcademicpeer-review

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

Leung, T. I. & Dumontier, M., 8 Jun 2016, In : Journal of biomedical semantics. 7, 37.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Predicting structured metadata from unstructured metadata

Posch, L., Panahiazar, M., Dumontier, M. & Gevaert, O., 13 Jun 2016, In : Database-The Journal of Biological Databases and Curation. baw097.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Publishing DisGeNET as nanopublications

Queralt-Rosinach, N., Kuhn, T., Chichester, C., Dumontier, M., Sanz, F. & Furlong, L. I., 2016, In : Semantic web. 7, 5, p. 519-528

Research output: Contribution to journalArticleAcademicpeer-review

The digital revolution in phenotyping

Oellrich, A., Collier, N., Groza, T., Rebholz-Schuhmann, D., Shah, N., Bodenreider, O., Boland, M. R., Georgiev, I., Liu, H., Livingston, K., Luna, A., Mallon, A-M., Manda, P., Robinson, P. N., Rustici, G., Simon, M., Wang, L., Winnenburg, R. & Dumontier, M., Sep 2016, In : Briefings in Bioinformatics. 17, 5, p. 819-830

Research output: Contribution to journalArticleAcademicpeer-review

The health care and life sciences community profile for dataset descriptions

Dumontier, M., Gray, A. J. G., Marshall, M. S., Alexiev, V., Ansell, P., Bader, G., Baran, J., Bolleman, J. T., Callahan, A., Cruz-Toledo, J., Gaudet, P., Gombocz, E. A., Gonzalez-Beltran, A. N., Groth, P., Haendel, M., Ito, M., Jupp, S., Juty, N., Katayama, T., Kobayashi, N. & 10 others, Krishnaswami, K., Laibe, C., Le Novere, N., Lin, S., Malone, J., Miller, M., Mungall, C. J., Rietveld, L., Wimalaratne, S. M. & Yamaguchi, A., 16 Aug 2016, In : PEERJ. 4, 2331.

Research output: Contribution to journalArticleAcademicpeer-review

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

Verspoor, K., Oellrich, A., Collier, N., Groza, T., Rocca-Serra, P., Soldatova, L., Dumontier, M. & Shah, N., 12 Dec 2016, In : Journal of biomedical semantics. 7, 66.

Research output: Contribution to journalArticleAcademicpeer-review

The Ontology for Biomedical Investigations

Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., Clancy, K., Courtot, M., Derom, D., Dumontier, M., Fan, L., Fostel, J., Fragoso, G., Gibson, F., Gonzalez-Beltran, A., Haendel, M. A., He, Y., Heiskanen, M., Hernandez-Boussard, T., Jensen, M. & 24 others, Lin, Y., Lister, A. L., Lord, P., Malone, J., Manduchi, E., McGee, M., Morrison, N., Overton, J. A., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S-A., Scheuermann, R. H., Schober, D., Smith, B., Soldatova, L. N., Stoeckert, C. J. . J., Taylor, C. F., Torniai, C., Turner, J. A., Vita, R., Whetzel, P. L. & Zheng, J., 29 Apr 2016, In : PLOS ONE. 11, 4

Research output: Contribution to journalArticleAcademicpeer-review

Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy

Odgers, D. J., Tellis, N., Hall, H. & Dumontier, M., 2016, In : AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2016, p. 176-83 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

2015

Achieving human and machine accessibility of cited data in scholarly publications

Starr, J., Castro, E., Crosas, M., Dumontier, M., Downs, R. R., Duerr, R., Haak, L. L., Haendel, M. A., Herman, I., Hodson, S., Hourclé, J., Kratz, J. E., Lin, J., Nielsen, L. H., Nurnberger, A., Proell, S., Rauber, A., Sacchi, S., Smith, A., Taylor, M. & 1 others, Clark, T., 15 Jul 2015, In : PeerJ. Computer science. 1, e1.

Research output: Contribution to journalArticleAcademicpeer-review

Analysis of In Vitro Aptamer Selection Parameters

McKeague, M., McConnell, E. M., Cruz-Toledo, J., Bernard, E. D., Pach, A., Mastronardi, E., Zhang, X., Beking, M., Francis, T., Giamberardino, A., Cabecinha, A., Ruscito, A., Aranda-Rodriguez, R., Dumontier, M. & DeRosa, M. C., Dec 2015, In : Journal of Molecular Evolution. 81, 5-6, p. 150-161

Research output: Contribution to journalArticleAcademicpeer-review

An Ebola virus-centered knowledge base

Kamdar, M. R. & Dumontier, M., 8 Jun 2015, In : Database-The Journal of Biological Databases and Curation. bav049.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Callahan, A., Cifuentes, J. J. & Dumontier, M., 7 Feb 2015, In : BMC Bioinformatics. 16

Research output: Contribution to journalArticleAcademicpeer-review

Open Access