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Research Output

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

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

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

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 journalConference article in journalAcademicpeer-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

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 proceedingConference article in proceedingAcademicpeer-review

Open Access
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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 journalConference article in journalAcademicpeer-review

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

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

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

HyQue: A Semantic Web tool for evaluating scientific hypotheses

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

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

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 journalConference article in journalAcademicpeer-review

Open Access

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

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

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 proceedingChapterAcademic

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

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 journalConference article in journalAcademicpeer-review

Open Access
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

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 proceedingConference article in proceedingAcademicpeer-review

Open Access

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

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 journalConference article in journalAcademicpeer-review

Open Access

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

Molecular symmetry and specialization of atomic connectivity by class-based reasoning of chemical structure

Dumontier, M., 2012, In : CEUR Workshop Proceedings. 849, 5 p., 33.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Role-based representation and inference of biochemical processes

Bölling, C., Dumontier, M., Weidlich, M. & Holzhütter, H-G., 2012, In : CEUR Workshop Proceedings. 897, 3 p.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

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

The YummyData Initiative: How SPARQL-y is your biomedical endpoint?

Splendiani, I. A., Nystrom-Persson, J., Dumontier, M. & Yamamoty, Y., 2012, In : CEUR Workshop Proceedings. 952, 2 p., 44.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access
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

Hazard estimation and method comparison with OWL-encoded toxicity decision trees

Chepelev, L., Klassen, D. & Dumontier, M., 2011, In : CEUR Workshop Proceedings. 796, 10 p., 1.

Research output: Contribution to journalConference article in journalAcademicpeer-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

SADI for GMOD: Semantic web services for model organism databases

Vandervalk, B., Dumontier, M., McCarthy, E. L. & Wilkinson, M. D., 2011, In : CEUR Workshop Proceedings. 774, p. 70-75 6 p.

Research output: Contribution to journalConference article in journalAcademicpeer-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