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2015

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

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

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 journalArticleAcademicpeer-review

Open Access

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, e933.

Research output: Contribution to journalArticleAcademicpeer-review

Making Digital Artifacts on the Web Verifiable and Reliable

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

Research output: Contribution to journalArticleAcademicpeer-review

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 journalArticleAcademicpeer-review

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 Sep 2015, In : arXiv .

Research output: Contribution to journalArticleAcademic

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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, 12.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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, p. 34

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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 journalArticleAcademicpeer-review

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 journalArticleAcademicpeer-review

Open Access

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, 40.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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 journalArticleAcademicpeer-review

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 journalArticleAcademicpeer-review

Open Access
2014

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

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

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

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 journalArticleAcademicpeer-review

Open Access

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 journalArticleAcademicpeer-review

Open Access

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 journalArticleAcademicpeer-review

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, 14.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2013

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

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

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, p. S1

Research output: Contribution to journalArticleAcademicpeer-review

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, p. I1

Research output: Contribution to journalArticleAcademicpeer-review

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 journalArticleAcademicpeer-review

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 journalArticleAcademicpeer-review

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 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

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 journalArticleAcademicpeer-review

Linked Data in Drug Discovery

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

Research output: Contribution to journalArticleAcademicpeer-review

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Soldatova, L. N., Sansone, S-A., Dumontier, M. & Shah, N. H., 24 Apr 2012, In : Journal of biomedical semantics. 3 Suppl 1, p. I1

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Self-organizing ontology of biochemically relevant small molecules

Chepelev, L. L., Hastings, J., Ennis, M., Steinbeck, C. & Dumontier, M., 6 Jan 2012, In : BMC Bioinformatics. 13, 3.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Semantically enabling pharmacogenomic data for the realization of personalized medicine

Samwald, M., Coulet, A., Huerga, I., Powers, R. L., Luciano, J. S., Freimuth, R. R., Whipple, F., Pichler, E., Prud'hommeaux, E., Dumontier, M. & Marshall, M. S., Jan 2012, In : Pharmacogenomics. 13, 2, p. 201-212

Research output: Contribution to journalArticleAcademicpeer-review

2011

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

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

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

HyQue: evaluating hypotheses using Semantic Web technologies

Callahan, A., Dumontier, M. & Shah, N. H., 17 May 2011, In : Journal of biomedical semantics. 2 Suppl 2, p. S3

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Integrating systems biology models and biomedical ontologies

Hoehndorf, R., Dumontier, M., Gennari, J. H., Wimalaratne, S., de Bono, B., Cook, D. L. & Gkoutos, G. V., 11 Aug 2011, In : BMC Systems Biology. 5, 124.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Integration and publication of heterogeneous text-mined relationships on the Semantic Web

Coulet, A., Garten, Y., Dumontier, M., Altman, R. B., Musen, M. A. & Shah, N. H., 17 May 2011, In : Journal of biomedical semantics. 2 Suppl 2, p. S10

Research output: Contribution to journalArticleAcademicpeer-review

Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning

Hoehndorf, R., Dumontier, M., Oellrich, A., Rebholz-Schuhmann, D., Schofield, P. N. & Gkoutos, G. V., 18 Jul 2011, In : PLOS ONE. 6, 7, e22006.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets

Gawronski, A. & Dumontier, M., Aug 2011, In : Computers & Graphics. 35, 4, p. 823-830

Research output: Contribution to journalArticleAcademicpeer-review

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

Chepelev, L. L., Riazanov, A., Kouznetsov, A., Low, H. S., Dumontier, M. & Baker, C. J. O., 26 Jul 2011, In : BMC Bioinformatics. 12, 303.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Semantic Web integration of Cheminformatics resources with the SADI framework

Chepelev, L. L. & Dumontier, M., 16 May 2011, In : Journal of Cheminformatics. 3, 16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Taking flight with OWL2

Dumontier, M., 2011, In : Semantic web. 2, 2, p. 67-70

Research output: Contribution to journalArticleAcademicpeer-review

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Hastings, J., Chepelev, L., Willighagen, E., Adams, N., Steinbeck, C. & Dumontier, M., 3 Oct 2011, In : PLOS ONE. 6, 10, e25513.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Hoehndorf, R., Batchelor, C., Bittner, T., Dumontier, M., Eilbeck, K., Knight, R., Mungall, C. J., Richardson, J. S., Stombaugh, J., Westhof, E., Zirbel, C. L. & Leontis, N. B., 2011, In : Applied Ontology. 6, 1, p. 53-89

Research output: Contribution to journalArticleAcademicpeer-review

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

Luciano, J. S., Andersson, B., Batchelor, C., Bodenreider, O., Clark, T., Denney, C. K., Domarew, C., Gambet, T., Harland, L., Jentzsch, A., Kashyap, V., Kos, P., Kozlovsky, J., Lebo, T., Marshall, M. S., McCusker, J. P., McGuinness, D. L., Ogbuji, C., Pichler, E., Powers, R. L. & 8 others, Prud'hommeaux, E., Samwald, M., Schriml, L., Tonellato, P. J., Whetzel, P. L., Zhao, J., Stephens, S. & Dumontier, M., 17 May 2011, In : Journal of biomedical semantics. 2 Suppl 2, p. S1

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Towards an interoperable information infrastructure providing decision support for genomic medicine

Samwald, M., Stenzhorn, H., Dumontier, M., Marshall, M. S., Luciano, J. S. & Adlassnig, K-P., 2011, In : Studies in Health Technology and Informatics. 169, p. 165-9 5 p.

Research output: Contribution to journalArticleAcademicpeer-review