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- 2019
- Published
- PublishedCelebi, R., Walk, O. B. D., Movva, R., Alpsoy, S., & Dumontier, M. (2019). 3In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. Scientific Reports, 9, [8949]. https://doi.org/10.1038/s41598-019-45236-6
- PublishedAstraZeneca-Sanger Drug Combinatio (2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications, 10, [2674]. https://doi.org/10.1038/s41467-019-09799-2
- PublishedWilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., ... Mons, B. (2019). The FAIR Guiding Principles for scientific data management and stewardship (vol 15, 160018, 2016). Scientific data, 6, [6]. https://doi.org/10.1038/s41597-019-0009-6
- PublishedBiomed Data Translator Consortium (2019). The Biomedical Data Translator Program: Conception, Culture, and Community. Clinical and Translational Science, 12(2), 91-94. https://doi.org/10.1111/cts.12592
- PublishedBiomed Data Translator Consortium (2019). Toward A Universal Biomedical Data Translator. Clinical and Translational Science, 12(2), 86-90. https://doi.org/10.1111/cts.12591
- PublishedSang, S., Yang, Z., Liu, X., Wang, L., Lin, H., Wang, J., & Dumontier, M. (2019). GrEDeL: A Knowledge Graph Embedding Based Method for Drug Discovery From Biomedical Literatures. IEEE Access, 7, 8404-8415. https://doi.org/10.1109/ACCESS.2018.2886311
- 2018
- PublishedCelebi, R., Yasar, E., Uyar, H., Gumus, O., Dikenelli, O., & Dumontier, M. (2018). Evaluation of Knowledge Graph Embedding Approaches for Drug-Drug Interaction Prediction using Linked Open Data.
- Published
- PublishedEmonet, V., Zaveri, A., Malic, A., Grigoriu, A., & Dumontier, M. (2018). Data2Services: enabling automated conversion of data to services. In SWAT4LS
- PublishedTa, C. N., Dumontier, M., Hripcsak, G., Tatonetti, N. P., & Weng, C. (2018). Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records. Scientific data, 5, [180273]. https://doi.org/10.1038/sdata.2018.273
- PublishedCoulet, A., Shah, N. H., Wack, M., Chawki, M. B., Jay, N., & Dumontier, M. (2018). Predicting the need for a reduced drug dose, at first prescription. Scientific Reports, 8, [15558]. https://doi.org/10.1038/s41598-018-33980-0
- PublishedKuhn, T., Meroño-Peñuela, A., Malic, A., Poelen, J. H., Hurlbert, A. H., Ortiz, E. C., ... Dumontier, M. (2018). Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. In 2018 IEEE 14th International Conference on e-Science (e-Science) (pp. 83-92). (Proceedings of IEEE e-Science).
- PublishedMoodley, K., Hardi, J., Graybeal, J., Musen, M. A., & Dumontier, M. (2018). Assessing Schema.org's Coverage of Terms from Key Biomedical Datasets. Paper presented at Bio-Ontologies, Prague, Czech Republic.
- PublishedWilkinson, M. D., Sansone, S-A., Schultes, E., Doorn, P., Santos, L. O. B. D. S., & Dumontier, M. (2018). A design framework and exemplar metrics for FAIRness: A design framework and exemplar metrics for FAIRness. Scientific data, 5, [180118]. https://doi.org/10.1038/sdata.2018.118
- PublishedZhang, Y., Zheng, W., Lin, H., Wang, J., Yang, Z., & Dumontier, M. (2018). Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths. Bioinformatics, 34(5), 828-835. https://doi.org/10.1093/bioinformatics/btx659
- PublishedGarcia, A., Lopez, F., Garcia, L., Giraldo, O., Bucheli, V., & Dumontier, M. (2018). Biotea: semantics for Pubmed Central. PEERJ, 6, [e4201]. https://doi.org/10.7717/peerj.4201
- PublishedMoodley, K., Zaveri, A., Wu, C., & Dumontier, M. (2018). A model for capturing provenance of assertions about chemical substances. In C. J. O. Baker, A. Waagmeester, A. Splendiani, O. D. Beyan, & M. S. Marshall (Eds.), Semantic Web Applications and Tools for Health Care and Life Sciences (Vol. 2275). Antwerp, Belgium: CEUR-WS.org.
- PublishedVerborgh, R., & Dumontier, M. (2018). A Web API Ecosystem through Feature Based Reuse. Ieee Internet Computing, 22(3), 29-37. https://doi.org/10.1109/MIC.2018.032501515
- PublishedZaveri, A., Serrano, P. H., Desai, M., & Dumontier, M. (2018). CrowdED: Guideline for Optimal Crowdsourcing Experimental Design. In Companion Proceedings of the The Web Conference 2018 (pp. 1109-1116). (WWW '18). Republic and Canton of Geneva, Switzerland: International World Wide Web Conferences Steering Committee. https://doi.org/10.1145/3184558.3191543
- PublishedZaveri, A., Dumontier, M., & Nayak, S. (2018). Quality Assessment of Biomedical Metadata Using Topic Modeling. In Quality Assessment of Biomedical Metadata Using Topic Modeling.
- Publishedvan Soest, J., Sun, C., Mussmann, O., Puts, M., van den Berg, B., Malic, A., ... Dumontier, M. (2018). Using the Personal Health Train for Automated and Privacy-Preserving Analytics on Vertically Partitioned Data. 581-585.
- 2017
- PublishedNelson, S. J., Oprea, T. I., Ursu, O., Bologa, C. G., Zaveri, A., Holmes, J., ... Dumontier, M. (2017). Formalizing drug indications on the road to therapeutic intent. Journal of the American Medical Informatics Association, 24(6), 1169-1172. https://doi.org/10.1093/jamia/ocx064
- Published
- PublishedPersoneni, G., Bresso, E., Devignes, M-D., Dumontier, M., Smail-Tabbone, M., & Coulet, A. (2017). Discovering associations between adverse drug events using pattern structures and ontologies. Journal of biomedical semantics, 8. https://doi.org/10.1186/s13326-017-0137-x
- PublishedHu, W., Qiu, H., Huang, J., & Dumontier, M. (2017). BioSearch: a semantic search engine for Bio2RDF. Database-The Journal of Biological Databases and Curation, 1-13. https://doi.org/10.1093/database/bax059
- PublishedPanahiazar, M., Dumontier, M., & Gevaert, O. (2017). Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO). Journal of Biomedical Informatics, 72, 132-139. https://doi.org/10.1016/j.jbi.2017.06.017
- PublishedMoodley, K., Rieswijk, L., Oprea, T. I., & Dumontier, M. (2017). Assessing the quality of manually curated drug indication and usage information via ontology term mappings. Paper presented at Bio-Ontologies, Prague, Czech Republic.
- PublishedJagodnik, K. M., Koplev, S., Jenkins, S., Ohno-Machado, L., Paten, B., Schurer, S. C., ... Ma'ayan, A. (2017). Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Informatics, 71, 49-57. https://doi.org/10.1016/j.jbi.2017.05.006
- PublishedMcMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., ... Parkinson, H. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biology , 15(6), [ e2001414]. https://doi.org/10.1371/journal.pbio.2001414
- PublishedFajardo-Ortiz, D., Lopez-Cervantes, M., Duran, L., Dumontier, M., Lara, M., Ochoa, H., & Castano, V. M. (2017). The emergence and evolution of the research fronts in HIV/AIDS research. PLOS ONE, 12(5), e0178293. [0178293]. https://doi.org/10.1371/journal.pone.0178293
- Noor, A., Assiri, A., Ayvaz, S., Clark, C., & Dumontier, M. (2017). Drug-drug interaction discovery and demystification using Semantic Web technologies. Journal of the American Medical Informatics Association, 24(3), 556-564. https://doi.org/10.1093/jamia/ocw128
- PublishedZaveri, A., Dastgheib, S., Whetzel, T., Verborgh, R., Avillach, P., Korodi, G., ... Dumontier, M. (2017). smartAPI: Towards a more intelligent network of Web APIs. In E. Blomqvist, D. Maynard, A. Gangemi, R. Hoekstra, P. Hitzler, & O. Hartig (Eds.), Proceedings of the 14th ESWC (Vol. 10250, pp. 154-169). (Lecture Notes in Computer Science). Springer. https://doi.org/10.1007/978-3-319-58451-5_11
- PublishedWilkinson, M. D., Verborgh, R., Santos, L. O. B. D. S., Clark, T., Swertz, M. A., Kelpin, F. D. L., ... Dumontier, M. (2017). Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Computer Science. https://doi.org/10.7717/peerj-cs.110
- Boyce, R. D., Voss, E. A., Huser, V., Evans, L., Reich, C., Duke, J. D., ... Ryan, P. B. (2017). Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. Journal of biomedical semantics, 8. https://doi.org/10.1186/s13326-017-0115-3
- McCusker, J. P., Dumontier, M., Yan, R., He, S., Dordick, J. S., & McGuinness, D. L. (2017). Finding melanoma drugs through a probabilistic knowledge graph. PeerJ Computer Science, 3, e106. [106]. https://doi.org/10.7717/peerj-cs.106
- PublishedMons, B., Neylon, C., Velterop, J., Dumontier, M., Da Silva Santos, L. O. B., & Wilkinson, M. D. (2017). Cloudy, increasingly FAIR; Revisiting the FAIR Data guiding principles for the European Open Science Cloud. Information Services and Use, 37(1), 49-56. https://doi.org/10.3233/ISU-170824
- McMurry, J., Juty, N., Blomberg, N., Burdett, A., Conlin, T., Conte, N., ... Parkinson, H. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. bioRxiv. https://doi.org/10.1101/117812
- PublishedCelebi, R., Erten, O., & Dumontier, M. (2017). Machine Learning based Drug Indication Prediction using Linked Open Data. In 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences
- PublishedZaveri, A., & Dumontier, M. (2017). MetaCrowd: Crowdsourcing Biomedical Metadata Quality Assessment.. Paper presented at Bio-Ontologies, Prague, Czech Republic.
- PublishedHe, Z., Tao, C., Bian, J., Dumontier, M., & Hogan, W. R. (2017). Semantics-Powered Healthcare Engineering and Data Analytics. Journal of Healthcare Engineering. https://doi.org/10.1155/2017/7983473
- PublishedDastgheib, S., Whetzel, T., Zaveri, A., Afrasiabe, C., Assis, P., Availlach, P., ... Dumontier, M. (2017). The smartAPI ecosystem for making Web APIs FAIR. In The smartAPI ecosystem for making web APIs FAIR (Vol. 1931, pp. 1-4)
- 2016
- Verspoor, K., Oellrich, A., Collier, N., Groza, T., Rocca-Serra, P., Soldatova, L., ... Shah, N. (2016). Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. Journal of biomedical semantics, 7, [66]. https://doi.org/10.1186/s13326-016-0108-7
- Sieberts, S. K., Zhu, F., García-García, J., Stahl, E. A., Pratap, A., Pandey, G., ... Members of the Rheumatoid Arthritis Challenge Consortium (2016). Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7, 13205. [13205]. https://doi.org/10.1038/ncomms13205
- PublishedVerborgh, R., & Dumontier, M. (2016). A Web API ecosystem through feature-based reuse. arXiv , (1609.07108).
- Oellrich, A., Collier, N., Groza, T., Rebholz-Schuhmann, D., Shah, N., Bodenreider, O., ... Dumontier, M. (2016). The digital revolution in phenotyping. Briefings in Bioinformatics, 17(5), 819-830. https://doi.org/10.1093/bib/bbv083
- Sieberts, S. K., Zhu, F., García-García, J., Stahl, E. A., Pratap, A., Pandey, G., ... Mangravite, L. M. (2016). Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7, 12460. [12460]. https://doi.org/10.1038/ncomms12460
- PublishedDumontier, M., Gray, A. J. G., Marshall, M. S., Alexiev, V., Ansell, P., Bader, G., ... Yamaguchi, A. (2016). The health care and life sciences community profile for dataset descriptions. PEERJ, 4, [2331]. https://doi.org/10.7717/peerj.2331
- Bolleman, J. T., Mungall, C. J., Strozzi, F., Baran, J., Dumontier, M., Bonnal, R. J. P., ... Cock, P. J. A. (2016). FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. Journal of biomedical semantics, 7, [39]. https://doi.org/10.1186/s13326-016-0067-z
- Posch, L., Panahiazar, M., Dumontier, M., & Gevaert, O. (2016). Predicting structured metadata from unstructured metadata. Database-The Journal of Biological Databases and Curation, [baw097]. https://doi.org/10.1093/database/baw097