Michel Dumontier

Research output

Research output per year 1998 2011 2012 2013 2015 2016 2017 2018 2019 2020 2021 2022 2024

• 151 Article
• 42 Conference article in proceeding
• 29 Conference article in journal
• 8 Editorial
• 34 More
  • 6 Chapter
  • 6 Preprint
  • 5 Paper
  • 4 Book editing
  • 4 Erratum / corrigendum / retractions
  • 2 Foreword/postscript
  • 2 Abstract
  • 2 Comment/Letter to the editor
  • 1 Conference Abstract/Poster in proceeding
  • 1 Conference Abstract/Poster in journal
  • 1 Discussion paper

Research output per year

Research output per year

Search results

• 2015

  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 journal › Conference article in journal › Academic › peer-review

  • Multiple Chronic Conditions 100%
  • Clinical Practice Guidelines 100%
  • Disease 100%
  • guidelines 100%
  • Comorbidity 100%

• 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 journal › Article › Academic › peer-review

  • Guideline Recommendations 100%
  • Clinical Practice Guidelines 100%
  • Drug-disease Association 100%
  • Structured Product Labels 100%
  • Drug Substance 100%

• Exposing provenance metadata using different RDF models

  Fu, G., Bolton, E., Queralt-Rosinach, N., Furlong, L. I., Nguyen, V., Sheth, A., Bodenreider, O. & Dumontier, M., 2015, In: CEUR Workshop Proceedings. 1546, p. 167-176 10 p.

  Research output: Contribution to journal › Conference article in journal › Academic › peer-review

  Open Access

  • resources 100%
  • data 42%
  • performance 28%
  • Query Performance 28%
  • diseases 14%

• Finding Our Way through Phenotypes

  Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, J. G., Chanet, B., Cooper, L. D., Courtot, M., Csoesz, S., Cui, H., Dahdul, W., Das, S., Dececchi, T. A., Dettai, A., Diogo, R. & Druzinsky, R. E. & 54 others, Dumontier, M., Franz, N. M., Friedrich, F., Gkouto, G. V., Haendel, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Koehler, S., Lecointre, G., Lapp, H., Lawrence, C. J., Le Novere, N., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Miko, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramirez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., Squires, R. B., Thacker, R. W., Thessen, A., Fernandez-Triana, J., Vihinen, M., Vize, P. D., Vogt, L., Wall, C. E., Walls, R. L., Westerfeld, M., Wharton, R. A., Wirkner, C. S., Woolley, J. B., Yoder, M. J., Zorn, A. M. & Mabee, P. M., Jan 2015, In: Plos Biology. 13, 1, e1002033.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Community-based 100%
  • Funding Agencies 100%
  • Systems Biology 100%
  • Environmental Context 100%
  • Phenotypic Data 100%

• GFVO: the Genomic Feature and Variation Ontology

  Baran, J., Durgahee, B. S. B., Eilbeck, K., Antezana, E., Hoehndorf, R. & Dumontier, M., 5 May 2015, In: PEERJ. 3, 5, e933.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Genomic Variation 100%
  • Genomic Features 100%
  • Variation Ontology 100%
  • data 100%
  • variations 100%

• Link analysis of life science linked data: The Semantic Web - ISWC 2015

  Hu, W., Qiu, H. & Dumontier, M., 2015, In: Lecture Notes in Computer Science. 9367, p. 446-462 17 p.

  Research output: Contribution to journal › Conference article in journal › Academic › peer-review

  • Semantic Web 100%
  • Life Sciences 100%
  • Linkage Analysis 100%
  • Linked Data 100%
  • Link Analysis 100%

• Making Digital Artifacts on the Web Verifiable and Reliable

  Kuhn, T. & Dumontier, M., Sept 2015, In: Ieee Transactions on Knowledge and Data Engineering. 27, 9, p. 2390-2400

  Research output: Contribution to journal › Article › Academic › peer-review

  • data 100%
  • values 100%
  • resources 100%
  • design 100%
  • evaluation 100%

• Mining Electronic Health Records using Linked Data

  Odgers, D. J. & Dumontier, M., 2015, In: AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2015, p. 217-21 5 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  • Electronic Health Records 100%
  • Clinical Data Warehouse 100%
  • Linked Data 100%
  • Clinical Data 100%
  • data 100%

• On Reasoning with RDF Statements about Statements using Singleton Property Triples

  Nguyen, V. X., Bodenreider, O., Thirunarayan, K., Fu, G., Bolton, E., Rosinach, N. Q., Furlong, L. I., Dumontier, M. & Sheth, A., 15 Sept 2015, Cornell University - arXiv, (arXiv.org).

  Research output: Working paper / Preprint › Preprint

  Open Access

  • data 100%
  • datasets 100%
  • rdf 100%
  • Singleton 100%
  • Singletons 100%
  99 Downloads (Pure)

• Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies

  Samwald, M., Gimenez, J. A. M., Boyce, R. D., Freimuth, R. R., Adlassnig, K.-P. & Dumontier, M., 22 Feb 2015, In: BMC Medical Informatics and Decision Making. 15, 1, 12.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Knowledge Representation & Reasoning 100%
  • OWL Ontology 100%
  • Clinical Decision Support 100%
  • Pharmacogenomics 100%
  • data 100%

• Provenance-centered dataset of drug-drug interactions

  Banda, J. M., Kuhn, T., Shah, N. H. & Dumontier, M., 2015, The Semantic Web - ISWC 2015: 14th International Semantic Web Conference, Bethlehem, PA, USA, October 11-15, 2015, Proceedings, Part II. Springer, Cham, Vol. 2. p. 293-300 8 p. (Lecture Notes in Computer Science, Vol. 9367). (Information Systems and Applications, incl. Internet/Web, and HCI, Vol. 9367).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

  • Prediction Method 100%
  • Drug Interactions 100%
  • drugs 100%
  • datasets 100%
  • interactions 100%

• PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

  Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Willighagen, E. & Bolton, E., 1 Jan 2015, In: Journal of Cheminformatics. 7, 1, p. 34

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Ontology 100%
  • Resource Description Framework 100%
  • Semantic Annotation 100%
  • Web Service 100%
  • Chemical Structure 100%

• Publishing without publishers: A decentralized approach to dissemination, retrieval, and archiving of data

  Kuhn, T., Chichester, C., Krauthammer, M. & Dumontier, M., 2015, The Semantic Web - ISWC 2015: 14th International Semantic Web Conference, Bethlehem, PA, USA, October 11-15, 2015, Proceedings, Part I. Springer, Cham, Vol. 2. p. 656-672 17 p. (Lecture Notes in Computer Science, Vol. 9366). (Information Systems and Applications, incl. Internet/Web, and HCI, Vol. 9366).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

  Open Access

  • Nanopublication 100%
  • Decentralized Approach 100%
  • Publishing Company 100%
  • Scientific Data 100%
  • data 100%

• Ranking Adverse Drug Reactions With Crowdsourcing

  Gottlieb, A., Hoehndorf, R., Dumontier, M. & Altman, R. B., Mar 2015, In: Journal of Medical Internet Research. 17, 3, e80.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Decision-Making 100%
  • Intention 100%
  • Epidermal Growth Factor Receptor 100%
  • Glioblastoma Multiforme 100%
  • Celecoxib 100%

• SPARQL-enabled identifier conversion with Identifiers.org

  Wimalaratne, S. M., Bolleman, J., Juty, N., Katayama, T., Dumontier, M., Redaschi, N., Le Novere, N., Hermjakob, H. & Laibe, C., 1 Jun 2015, In: Bioinformatics. 31, 11, p. 1875-1877

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Resource Identifier 100%
  • Linked Data 100%
  • Semantic Web 100%
  • Multiple Resource 100%
  • Resource Record 100%

• Special issue on bio-ontologies and phenotypes

  Soldatova, L. N., Collier, N., Oellrich, A., Groza, T., Verspoor, K., Rocca-Serra, P., Dumontier, M. & Shah, N. H., 17 Dec 2015, In: Journal of biomedical semantics. 6, 1, 40.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Bio-ontologies 100%
  • phenotype 100%
  • Quality Assessment 33%
  • Fully-automatic 33%
  • Phenotypic Variation 33%

• The center for expanded data annotation and retrieval

  Musen, M. A., Bean, C. A., Cheung, K.-H., Dumontier, M., Durante, K. A., Gevaert, O., Gonzalez-Beltran, A., Khatri, P., Kleinstein, S. H., O'Connor, M. J., Pouliot, Y., Rocca-Serra, P., Sansone, S.-A. & Wiser, J. A., Nov 2015, In: Journal of the American Medical Informatics Association. 22, 6, p. 1148-1152

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Biomedical Data 100%
  • Data Annotation 100%
  • Data Retrieval 100%
  • Annotation 100%
  • data 100%

• The semantic Web - ISWC 2015: 14th International Semantic Web Conference, Bethlehem, PA, USA, October 11-15, 2015 proceedings, Part II

  Arenas, M. (Editor), Corcho, O. (Editor), Simperl, E. (Editor), Strohmaier, M. (Editor), D'Aquin, M. (Editor), Srinivas, K. (Editor), Groth, P. (Editor), Dumontier, M. (Editor), Heflin, J. (Editor), Thirunarayan, K. (Editor) & Staab, S. (Editor), 2015, Springer, Cham. (Lecture Notes in Computer Science, Vol. 9367). (Information Systems and Applications, incl. Internet/Web, and HCI, Vol. 9367).

  Research output: Book/Report › Book editing › Academic

• Toward a complete dataset of drug-drug interaction information from publicly available sources

  Ayvaz, S., Horn, J., Hassanzadeh, O., Zhu, Q., Stan, J., Tatonetti, N. P., Vilar, S., Brochhausen, M., Samwald, M., Rastegar-Mojarad, M., Dumontier, M. & Boyce, R. D., Jun 2015, In: Journal of Biomedical Informatics. 55, p. 206-217

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Publicly Available 100%
  • Potential Drug-drug Interactions 100%
  • Drug Interactions 100%
  • Interaction Information 100%
  • information 100%
• 2014

  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 journal › Conference article in journal › Academic › peer-review

  Open Access

  • drugs 100%
  • Web Service Framework 100%
  • data 50%
  • control 50%
  • Entity Interaction 33%

• 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, 1, 46.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Data Access 100%
  • SPARQL Endpoint 100%
  • Semantic Web Services 100%
  • Linked Data 100%
  • Web Service 100%

• 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 journal › Conference article in journal › Academic › peer-review

  • Linked Data 100%
  • Connected Network 100%
  • data 100%
  • datasets 60%
  • Open Source Project 33%

• 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.-A., 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, 1, 5.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Semantic Technologies 100%
  • Ontology 100%
  • Life Sciences 100%
  • Scientific Domain 100%
  • BioHackathon 100%

• 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 journal › Article › Academic › peer-review

  Open Access

  • Health Outcomes 100%
  • Knowledge Base 100%
  • Knowledge Integration 100%
  • Drug Treatment Outcomes 100%
  • Information Island 100%

• Drug-drug interaction data source survey and linking

  Ayvaz, S., Zhu, Q., Hochheiser, H., Brochhausen, M., Horn, J., Dumontier, M., Samwald, M. & Boyce, R. D., 2014, In: AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2014, p. 16

  Research output: Contribution to journal › Conference article in journal › Academic › peer-review

  • data 100%
  • drugs 100%
  • surveys 100%
  • interactions 100%
  • Publicly Available 100%

• Mouse model phenotypes provide information about human drug targets

  Hoehndorf, R., Hiebert, T., Hardy, N. W., Schofield, P. N., Gkoutos, G. V. & Dumontier, M., 1 Mar 2014, In: Bioinformatics. 30, 5, p. 719-725

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • humans 100%
  • information 100%
  • drugs 100%
  • phenotype 100%
  • mice 100%

• Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

  Soldatova, L. N., Rocca-Serra, P., Dumontier, M. & Shah, N. H., 3 Jun 2014, In: Journal of biomedical semantics. 5, S1, L1.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Group Meetings 100%
  • Special Interest Groups 100%
  • Bio-ontologies 100%
  • data 100%
  • interest groups 100%

• Special issue on Linked Data for Health Care and the Life Sciences

  Aranguren, M. E., Fernandez-Breis, J. T. & Dumontier, M., 2014, In: Semantic web. 5, 2, p. 99-100

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

• The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

  Dumontier, M., Baker, C. J. O., Baran, J., Callahan, A., Chepelev, L., Cruz-Toledo, J., Del Rio, N. R., Duck, G., Furlong, L. I., Keath, N., Klassen, D., McCusker, J. P., Queralt-Rosinach, N., Samwald, M., Villanueva-Rosales, N., Wilkinson, M. D. & Hoehndorf, R., 6 Mar 2014, In: Journal of biomedical semantics. 5, 1, 14.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • data 100%
  • levels 100%
  • information 100%
  • design 100%
  • foundations 100%

• Trusty URIs: Verifiable, immutable, and permanent digital artifacts for linked data

  Kuhn, T. & Dumontier, M., 16 Jan 2014, The Semantic Web: Trends and Challenges: 11th International Conference, ESWC 2014, Anissaras, Crete, Greece, May 25-29, 2014. Proceedings. Springer, Cham, p. 395-410 16 p. (Lecture Notes in Computer Science, Vol. 8465).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

  Open Access

  File

  • Digital Artifacts 100%
  • data 100%
  • resources 100%
  • Linked Data 100%
  • Digital Artifact 100%
  77 Downloads (Pure)
• 2013

  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 journal › Conference article in journal › Academic › peer-review

  Open Access

  • data 100%
  • genes 100%
  • knowledge base 100%
  • molecular biology 100%
  • Hierarchical Taxonomy 100%

• 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, 1-2, p. 539-542 4 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Knowledge Base 100%
  • Decision Support 100%
  • Resource Description Framework 100%
  • Query Answering 100%
  • Clinical Genetics 100%

• 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 proceeding › Conference article in proceeding › Academic › peer-review

  Open Access

  • Life Sciences 100%
  • Bio2RDF 100%
  • Interoperability 100%
  • Linked Data 100%
  • data 100%

• 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 journal › Article › Academic › peer-review

  Open Access

  • Biomedical Ontologies 100%
  • Ontology 100%
  • Research Evaluation 100%
  • applications 100%
  • evaluation 100%

• 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 journal › Article › Academic › peer-review

  • Ontology 100%
  • Ontology Evaluation 100%
  • OQuaRE 100%
  • evaluation 100%
  • Weakness 100%

• HyQue: A Semantic Web tool for evaluating scientific hypotheses

  Callahan, A. & Dumontier, M., 2013, In: CEUR Workshop Proceedings. 1060

  Research output: Contribution to journal › Conference Abstract/Poster in journal › Academic

  Open Access

• Looking into Reactome through Biopax lens

  Kazemzadeh, L., Deus, H. F., Dumontier, M. & Barry, F., 2013, In: CEUR Workshop Proceedings. 1054, p. 37-40 4 p., 9.

  Research output: Contribution to journal › Conference article in journal › Academic › peer-review

  Open Access

  • proteins 100%
  • lenses 100%
  • Biological Pathway 100%
  • Protein-Protein Interaction 100%
  • Protein Characterization 100%

• Ontology-Based Querying with Bio2RDF's Linked Open Data

  Callahan, A., Cruz-Toledo, J. & Dumontier, M., 15 Apr 2013, In: Journal of biomedical semantics. 4 Suppl 1, 1, p. S1

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Bio2RDF 100%
  • Ontological Basis 100%
  • Linked Open Data 100%
  • Ontology 100%
  • Open Data 100%

• Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

  Soldatova, L. N., Sansone, S.-A., Dumontier, M. & Shah, N. H., 15 Apr 2013, In: Journal of biomedical semantics. 4 Suppl 1, 1, p. I1

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Group Meetings 100%
  • Special Interest Groups 100%
  • Bio-ontologies 100%
  • data 100%
  • applications 100%

• 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 Sept 2013.

  Research output: Contribution to conference › Abstract › Academic

• Semantic systems biology: Formal knowledge representation in systems biology for model construction, retrieval, validation and discovery

  Dumontier, M., Chepelev, L. & Hoehndorf, R., 2013, Systems Biology: Integrative Biology and Simulation Tools. Prokop, A. & Csukás, B. (eds.). Springer, Vol. 2. p. 355-373 19 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

  • Systems Biology 100%
  • Model Building 100%
  • Formal Knowledge Representation 100%
  • Model Retrieval 100%
  • Semantic Systems Biology 100%

• State of the art and open challenges in community-driven knowledge curation

  Groza, T., Tudorache, T. & Dumontier, M., Feb 2013, In: Journal of Biomedical Informatics. 46, 1, p. 1-4

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

• The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions

  Vandervalk, B., McCarthy, E. L., Cruz-Toledo, J., Klein, A., Baker, C. J. O., Dumontier, M. & Wilkinson, M. D., 5 Apr 2013, In: JMIR Research Protocols. 2, 1, p. e14

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Automated Discovery 100%
  • Personal Health 100%
  • Drug Interactions 100%
  • Web Browser 100%
  • Automated Integration 100%

• The web as a distributed biochemical reactor: Semantically enabled metabolic fate prediction

  Chepelev, L. & Dumontier, M., 2013, In: CEUR Workshop Proceedings. 1060, p. 113-116 4 p.

  Research output: Contribution to journal › Conference article in journal › Academic › peer-review

  Open Access

  • prediction 100%
  • reactors 100%
  • Semantic Web Service 100%
  • Biochemical Reactor 100%
  • Metabolic Pathway 100%
• 2012

  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 journal › Article › Academic › peer-review

  Open Access

  • information 100%
  • knowledge base 100%
  • Aptamer 100%
  • SELEX 100%
  • Collaborative Knowledge Base 100%

• 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 journal › Article › Academic › peer-review

  Open Access

  • Bio2RDF 100%
  • Data Mashup 100%
  • HIV Data 100%
  • data 100%
  • humans 100%

• Evaluating scientific hypotheses using the SPARQL inferencing notation

  Callahan, A. & Dumontier, M., 2012, The Semantic Web: Research and Applications: 9th Extended Semantic Web Conference, ESWC 2012, Heraklion, Crete, Greece, May 27-31, 2012. Proceedings. Springer, p. 647-658 12 p. (Lecture Notes in Computer Science, Vol. 7295).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

  Open Access

  • SPARQL 100%
  • Scientific Hypothesis 100%
  • Linked Data 100%
  • Semantic Web Technology 100%
  • Background Knowledge 100%

• Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics

  Hoehndorf, R., Dumontier, M. & Gkoutos, G. V., 15 Aug 2012, In: Bioinformatics. 28, 16, p. 2169-2175

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Disease Pathways 100%
  • Knowledge Analysis 100%
  • Pharmacogenomics 100%
  • diseases 100%
  • Disease 100%

• Improved dataset coverage and interoperability with Bio2RDF Release 2

  Callahan, A., Cruz-Toledo, J., Ansell, P., Klassen, D., Tum-Marello, G. & Dumontier, M., 2012, In: CEUR Workshop Proceedings. 952, 15 p., 18.

  Research output: Contribution to journal › Conference article in journal › Academic › peer-review

  Open Access

  • Interoperability 100%
  • Open Source Project 100%
  • Linked Data 100%
  • Semantic Web 100%
  • Search Engine 100%

• Linked Data in Drug Discovery

  Dumontier, M. & Wild, D. J., 2012, In: Ieee Internet Computing. 16, 6, p. 68-71

  Research output: Contribution to journal › Article › Academic › peer-review

  • data 100%
  • drugs 100%
  • Drug Discovery 100%
  • chemistry 33%
  • biology 33%