Research Output

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

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

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

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Distributed AUC algorithm: a privacy-preserving approach to measure the performance of Cox models

Masciocchi, C., Damiani, A., Capocchiano, N. D., Van Soest, J., Lenkowicz, J., Meldolesi, E., Chiloiro, G., Gambacorta, M. A., Dekker, A. & Valentini, V., 20 May 2019, In : Radiotherapy and Oncology. 133, Supplement 1, p. S1055-S1055 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

Open Access

Estimating Multilevel Models on Data Streams

Ippel, L., Kaptein, M. C. & Vermunt, J. K., Mar 2019, In : Psychometrika. 84, 1, p. 41-64 24 p.

Research output: Contribution to journalArticleAcademicpeer-review

External Validation of Radiation-Induced Dyspnea Models on Esophageal Cancer Radiotherapy Patients

Shi, Z., Foley, K. G., de Mey, J. P., Spezi, E., Whybra, P., Crosby, T., van Soest, J., Dekker, A. & Wee, L., 16 Dec 2019, In : Frontiers in Oncology. 9, 9 p., 1411.

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

Human exposure to trichloroethylene is associated with increased variability of blood DNA methylation that is enriched in genes and pathways related to autoimmune disease and cancer

Phillips, R. V., Rieswijk, L., Hubbard, A. E., Vermeulen, R., Zhang, J., Hu, W., Li, L., Bassig, B. A., Wong, J. Y. Y., Reiss, B., Huang, Y., Wen, C., Purdue, M., Tang, X., Zhang, L., Smith, M. T., Rothman, N. & Lan, Q., 2 Nov 2019, In : Epigenetics. 14, 11, p. 1112-1124 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Proposed Key Characteristics of Female Reproductive Toxicants as an Approach for Organizing and Evaluating Mechanistic Data in Hazard Assessment

Luderer, U., Eskenazi, B., Hauser, R., Korach, K. S., McHale, C. M., Moran, F., Rieswijk, L., Solomon, G., Udagawa, O., Zhang, L., Zlatnik, M., Zeise, L. & Smith, M. T., Jul 2019, In : Environmental Health Perspectives. 127, 7, 14 p., 075001.

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

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
4 Downloads (Pure)

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

The need and potential for use of big data for research and development of radiotherapy

Wee, L., Van Soest, J., Bermejo, I., Fijten, R. & Dekker, A., Apr 2019, In : Radiotherapy and Oncology. 133, p. S175-S175 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

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

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 linked open data representation of patents registered in the US from 2005-2017

Hassan, M. M., Zaveri, A. & Lehmann, J., 4 Dec 2018, In : Scientific data. 5, 9 p., 180279.

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

Analyzing Partitioned FAIR Health Data Responsibly

Adekunle, S., Dec 2018.

Research output: Working paperProfessional

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

Data Quality and Data Cleansing of Semantic Data

Zaveri, A. & Rula, A., 2018, Encyclopedia of Big Data Technologies. Sakr, S. & Zomaya, A. (eds.). Cham: Springer, p. 11-17 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Detecting Linked Data quality issues via crowdsourcing: A DBpedia study

Acosta, M., Zaveri, A., Simperl, E. P. B., Kontokostas, D., Flöck, F. & Lehmann, J., 2018, In : Semantic web. 9, p. 303-335 33 p.

Research output: Contribution to journalArticleAcademicpeer-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

Editorial: Special Issue on Quality Management of Semantic Web Assets (Data, Services and Systems)

Zaveri, A., Kontokostas, D., Hellmann, S. & Umbrich, J., 2018, In : Semantic web. 9, 1

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access

Emerging Topics in Semantic Technologies

Demidova, E., Zaveri, A. & Simperl, E., 2018, IOS Press/AKA. (Studies on the Semantic Web).

Research output: Book/ReportBookAcademic

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

Key Characteristics Approach to Carcinogenic Hazard Identification

Guyton, K. Z., Rieswijk, L., Wang, A., Chiu, W. A. & Smith, M. T., 17 Dec 2018, In : Chemical Research in Toxicology. 31, 12, p. 1290-1292 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

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

Discovering Hidden Course Requirements and Student Competences from Grade Data

Houbraken, M., Sun, C., Smirnov, E. & Driessens, K., 2017, Adjunct Publication of the 25th Conference on User Modeling, Adaptation and Personalization. New York, NY, USA: ACM, p. 147-152 6 p. (UMAP '17).

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

Open Access

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

Linked Data for Life Sciences

Zaveri, A. & Ertaylan, G., Dec 2017, In : Algorithms. 10, 4

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