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Research Output

Abstract

Semantic annotation of PubChem databases

Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Kuecuek, H., Schurer, S. C., Vempati, U., Willighagen, E. & Bolton, E., 8 Sep 2013.

Research output: Contribution to conferenceAbstractAcademic

Article

3D topography of noncompact zone Golgi tubules in rat spermatids: A computer-assisted serial section reconstruction study

Thorne-Tjomsland, G., Dumontier, M. & Jamieson, JC., Apr 1998, In : ANATOMICAL RECORD. 250, 4, p. 381-396

Research output: Contribution to journalArticleAcademicpeer-review

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

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

A common layer of interoperability for biomedical ontologies based on OWL EL

Hoehndorf, R., Dumontier, M., Oellrich, A., Wimalaratne, S., Rebholz-Schuhmann, D., Schofield, P. & Gkoutos, G. V., 1 Apr 2011, In : Bioinformatics. 27, 7, p. 1001-1008

Research output: Contribution to journalArticleAcademicpeer-review

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

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

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

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
Open Access

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics

Samwald, M., Freimuth, R. R., Luciano, J. S., Lin, S. M., Powers, R. L., Marshall, M. S., Adlassnig, K-P., Dumontier, M. & Boyce, R. D., 2013, In : Studies in Health Technology and Informatics. 192, p. 539-542 4 p.

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

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments

Cruz-Toledo, J., McKeague, M., Zhang, X., Giamberardino, A., McConnell, E., Francis, T., DeRosa, M. C. & Dumontier, M., 20 Mar 2012, In : Database-The Journal of Biological Databases and Curation. bas006.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Armadillo: Domain boundary prediction by amino acid composition

Dumontier, M., Yao, R., Feldman, HJ. & Hogue, CWV., 29 Jul 2005, In : Journal of Molecular Biology. 350, 5, p. 1061-1073

Research output: Contribution to journalArticleAcademicpeer-review

Automatically exposing OpenLifeData via SADI semantic Web Services

Rodriguez Gonzalez, A., Callahan, A., Cruz-Toledo, J., Garcia, A., Egana Aranguren, M., Dumontier, M. & Wilkinson, M. D., 19 Nov 2014, In : Journal of biomedical semantics. 5, 46.

Research output: Contribution to journalArticleAcademicpeer-review

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

Open Access
File
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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
237 Downloads (Pure)

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J-D., Wang, Y., Wu, H., Kano, Y., Ono, H., Bono, H., Kocbek, S., Aerts, J., Akune, Y., Antezana, E., Arakawa, K., Aranda, B. & 65 others, Baran, J., Bolleman, J., Bonnal, R. J. P., Buttigieg, P. L., Campbell, M. P., Chen, Y., Chiba, H., Cock, P. J. A., Cohen, K. B., Constantin, A., Duck, G., Dumontier, M., Fujisawa, T., Fujiwara, T., Goto, N., Hoehndorf, R., Igarashi, Y., Itaya, H., Ito, M., Iwasaki, W., Kalas, M., Katoda, T., Kim, T., Kokubu, A., Komiyama, Y., Kotera, M., Laibe, C., Lapp, H., Luetteke, T., Marshall, M. S., Mori, T., Mori, H., Morita, M., Murakami, K., Nakao, M., Narimatsu, H., Nishide, H., Nishimura, Y., Nystrom-Persson, J., Ogishima, S., Okamura, Y., Okuda, S., Oshita, K., Packer, N. H., Prins, P., Ranzinger, R., Rocca-Serra, P., Sansone, S., Sawaki, H., Shin, S-H., Splendiani, A., Strozzi, F., Tadaka, S., Toukach, P., Uchiyama, I., Umezaki, M., Vos, R., Whetzel, P. L., Yamada, I., Yamasaki, C., Yamashita, R., York, W. S., Zmasek, C. M., Kawamoto, S. & Takagi, T., 5 Feb 2014, In : Journal of biomedical semantics. 5, 5.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

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

Bridging Islands of Information to Establish an Integrated Knowledge Base of Drugs and Health Outcomes of Interest

Boyce, R. D., Ryan, P. B., Noren, G. N., Schuemie, M. J., Reich, C., Duke, J., Tatonetti, N. P., Trifiro, G., Harpaz, R., Overhage, J. M., Hartzema, A. G., Khayter, M., Voss, E. A., Lambert, C. G., Huser, V. & Dumontier, M., Aug 2014, In : Drug Safety. 37, 8, p. 557-567

Research output: Contribution to journalArticleAcademicpeer-review

Building an effective Semantic Web for health care and the life sciences

Dumontier, M., 2010, In : Semantic web. 1, 1-2, p. 131-135 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Building an HIV data mashup using Bio2RDF

Nolin, M-A., Dumontier, M., Belleau, F. & Corbeil, J., Jan 2012, In : Briefings in Bioinformatics. 13, 1, p. 98-106

Research output: Contribution to journalArticleAcademicpeer-review

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration

Chepelev, L. L. & Dumontier, M., 19 May 2011, In : Journal of Cheminformatics. 3, 20.

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

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules

Feldman, HJ., Dumontier, M., Sue-Ling, H. M., Haider, N. & Hogue, CWV., 29 Aug 2005, In : Febs Letters. 579, 21, p. 4685-4691

Research output: Contribution to journalArticleAcademicpeer-review

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

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

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

Comparing Drug-Disease Associations in Clinical Practice Guideline Recommendations and Drug Product Label Indications

Leung, T. I. & Dumontier, M., 2015, In : Studies in Health Technology and Informatics. 216, p. 1039

Research output: Contribution to journalArticleAcademicpeer-review

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

Luo, X., McKeague, M., Pitre, S., Dumontier, M., Green, J., Golshani, A., Derosa, M. C. & Dehne, F., Nov 2010, In : Rna-A Publication of the Rna Society. 16, 11, p. 2252-2262

Research output: Contribution to journalArticleAcademicpeer-review

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

Controlled vocabularies and semantics in systems biology

Courtot, M., Juty, N., Knuepfer, C., Waltemath, D., Zhukova, A., Draeger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., Hoops, S., Keating, S., Kell, D. B., Kerrien, S., Lawson, J., Lister, A., Lu, J., Machne, R., Mendes, P., Pocock, M. & 7 others, Rodriguez, N., Villeger, A., Wilkinson, D. J., Wimalaratne, S., Laibe, C., Hucka, M. & Le Novere, N., Oct 2011, In : Molecular Systems Biology. 7

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

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

Disruption of fungal cell wall by antifungal Echinacea extracts

Mir-Rashed, N., Cruz, I., Jessulat, M., Dumontier, M., Chesnais, C., Ng, J., Amiguet, V. T., Golshani, A., Arnason, J. T. & Smith, M. L., Nov 2010, In : Medical Mycology. 48, 7, p. 949-958

Research output: Contribution to journalArticleAcademicpeer-review

Domain-based small molecule binding site annotation

Snyder, K. A., Feldman, H. J., Dumontier, M., Salama, J. J. & Hogue, C. W. V., 17 Mar 2006, In : BMC Bioinformatics. 7, p. 152

Research output: Contribution to journalArticleAcademicpeer-review

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

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

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

Evaluation of research in biomedical ontologies

Hoehndorf, R., Dumontier, M. & Gkoutos, G. V., Nov 2013, In : Briefings in Bioinformatics. 14, 6, p. 696-712

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Evaluation of the OQuaRE framework for ontology quality

Duque-Ramos, A., Tomas Fernandez-Breis, J., Iniesta, M., Dumontier, M., Egana Aranguren, M., Schulz, S., Aussenac-Gilles, N. & Stevens, R., 1 Jun 2013, In : Expert Systems with Applications. 40, 7, p. 2696-2703

Research output: Contribution to journalArticleAcademicpeer-review

FAIR Principles: Interpretations and Implementation Considerations

Jacobsen, A., De Miranda Azevedo, R., Juty, N., Batista, D., Coles, S., Cornet, R., Courtot, M., Crosas, M., Dumontier, M., Evelo, C. T., Goble, C., Guizzardi, G., Hansen, K. K., Hasnain, A., Hettne, K., Heringa, J., Hooft, R. W. W., Imming, M., Jeffery, K. G., Kaliyaperumal, R. & 24 others, Kersloot, M. G., Kirkpatrick, C. R., Kuhn, T., Labastida, I., Magagna, B., Mcquilton, P., Meyers, N., Montesanti, A., Van Reisen, M., Rocca-serra, P., Pergl, R., Sansone, S., Da Silva Santos, L. O. B., Schneider, J., Strawn, G., Thompson, M., Waagmeester, A., Weigel, T., Wilkinson, M. D., Willighagen, E. L., Wittenburg, P., Roos, M., Mons, B. & Schultes, E., 31 Jan 2020, In : Data Intelligence. p. 10-29

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

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