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Research Output 1998 2019

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

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

17 Jun 2019, In : Nature Communications. 10, 17 p., 2674.

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

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

1 Downloads (Pure)

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

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

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

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access
Open Access

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 journalArticleAcademicpeer-review

Open Access

Toward A Universal Biomedical Data Translator

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: 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. 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

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., 2017, In : bioRxiv.

Research output: Contribution to journalArticleAcademic

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

MetaCrowd: Crowdsourcing Biomedical Metadata Quality Assessment.

Zaveri, A. & Dumontier, M., 2017.

Research output: Contribution to conferencePaperAcademic

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

smartAPI: Towards a more intelligent network of Web APIs

Zaveri, A., Dastgheib, S., Whetzel, T., Verborgh, R., Avillach, P., Korodi, G., Terryn, R., Jagodnik, K. M., Assis, P., Wu, C. & Dumontier, M., 1 May 2017, Proceedings of the 14th ESWC. Blomqvist, E., Maynard, D., Gangemi, A., Hoekstra, R., Hitzler, P. & Hartig, O. (eds.). Springer, Vol. 10250. p. 154-169 16 p. (Lecture Notes in Computer Science).

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

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

The smartAPI ecosystem for making Web APIs FAIR

Dastgheib, S., Whetzel, T., Zaveri, A., Afrasiabe, C., Assis, P., Availlach, P., Jagodnik, K., Korodi, G., Pilarczyk, M., De Pons, J., Schürer, S., Terryn, R., Verborgh, R., Wu, C. & Dumontier, M., 2017, The smartAPI ecosystem for making web APIs FAIR. Vol. 1931. p. 1-4 4 p.

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

2016
197 Downloads (Pure)

A Web API ecosystem through feature-based reuse

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

Research output: Contribution to journalArticleAcademic

File
64 Citations (Scopus)

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

Erratum: 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. & 30 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., 10 Oct 2016, In : Nature Communications. 7, p. 13205 1 p., 13205.

Research output: Contribution to journalErratum / corrigendumAcademic

Open Access
3 Citations (Scopus)

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
5 Citations (Scopus)

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