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Research Output

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

A large-scale gene-centric semantic web knowledge base for molecular biology

Cruz-Toledo, J., Callahan, A. & Dumontier, M., 2013, In : CEUR Workshop Proceedings. 1015, p. 101-106 6 p.

Research output: Contribution to journalConference article in journalAcademicpeer-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

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

A nanopublication framework for biological networks using Cytoscape.js

McCusker, J. P., Yan, R., Solanki, K., Erickson, J., Chang, C., Dumontier, M., Dordick, J. S. & McGuinness, D. L., 2014, In : CEUR Workshop Proceedings. 1327, p. 90-92 3 p.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

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 platform for distributing and reasoning with owl-el knowledge bases in a peer-to-peer environment

Leon, AS. & Dumontier, M., 2009, In : CEUR Workshop Proceedings. 529, 8 p., 24.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

A preliminary investigation into SPARQL query complexity and federation in Bio2RDF

Buil-Aranda, C., Ugarte, M., Arenas, M. & Dumontier, M., 2015, In : CEUR Workshop Proceedings. 1378, p. 196-204 9 p.

Research output: Contribution to journalConference article in journalAcademicpeer-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

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

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

A stochastic particle-based biological system simulator

Boulianne, L., Dumontier, M. & Gross, W. J., 2007, SCSC '07: Proceedings of the 2007 Summer Computer Simulation Conference. Society for Computer Simulation, p. 794-801 8 p.

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

Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework

Wilkinson, M. D., Dumontier, M., Sansone, S-A., Bonino da Silva Santos, L. O., Prieto, M., Batista, D., McQuilton, P., Kuhn, T., Rocca-Serra, P., Crosas, M. & Schultes, E., 21 Oct 2019, In : Scientific data. 6, 1, p. 230 1 p., 230.

Research output: Contribution to journalErratum / corrigendumAcademic

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

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines

Leung, T. I., Jalal, H., Zulman, D. M., Dumontier, M., Owens, D. K., Musen, M. A. & Goldstein, M. K., 2015, In : AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2015, p. 456-60 5 p.

Research output: Contribution to journalConference article in journalAcademicpeer-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
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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)

Bio2RDF release 2: Improved coverage, interoperability and provenance of life science linked data

Callahan, A., Cruz-Toledo, J., Ansell, P. & Dumontier, M., 2013, The Semantic Web: Semantics and Big Data: 10th International Conference, ESWC 2013, Montpellier, France, May 26-30, 2013. Proceedings. Springer, p. 200-212 13 p. (Lecture Notes in Computer Science, Vol. 7882).

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

Open Access

Bio2RDF release 3: A larger connected network of linked data for the life sciences

Dumontier, M., Callahan, A., Cruz-Toledo, J., Ansell, P., Emonet, V., Belleau, F. & Droit, A., 2014, In : CEUR Workshop Proceedings. 1272, p. 401-404 4 p., 121.

Research output: Contribution to journalConference article in journalAcademicpeer-review

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

Chemical knowledge for the semantic web

Konyk, M., Leon, AS. & Dumontier, M., 2008, Data Integration in the Life Sciences: 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008. Proceedings. Springer, p. 169-176 8 p. (Lecture Notes in Computer Science, Vol. 5109).

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

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

Computational Methods For Predicting Protein-Protein Interactions

Pitre, S., Alamgir, M., Green, J. R., Dumontier, M., Dehne, F. & Golshani, A., 2008, PROTEIN - PROTEIN INTERACTION. Vol. 110. p. 247-267 (Advances in Biochemical Engineering-Biotechnology).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Conjunctive query answering in distributed ontology systems for ontologies with large OWL ABoxes

Chen, X. & Dumontier, M., 2009, In : CEUR Workshop Proceedings. 529, 4 p., 30.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

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

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