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Research Output

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Conference article in journal
2016

Making linked data SPARQL with the InterMine biological data warehouse

Déraspe, M., Binkley, G., Butano, D., Chadwick, M., Cherry, J. M., Clark-Casey, J., Contrino, S., Corbeil, J., Heimbach, J., Karra, K., Lyne, R., Sullivan, J., Yehudi, Y., Micklem, G. & Dumontier, M., 2016, In : CEUR Workshop Proceedings. 1795

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access
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Network ranking assisted semantic data mining

Kralj, J., Vavpetič, A., Dumontier, M. & Lavrač, N., 2016, In : Lecture Notes in Computer Science. 9656, p. 752-764 13 p.

Research output: Contribution to journalConference article in journalAcademicpeer-review

2015

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

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

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 journalConference article in journalAcademicpeer-review

Open Access

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 journalConference article in journalAcademicpeer-review

Open Access
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 journalConference article in journalAcademicpeer-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

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

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

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

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

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

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

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

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

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
2010

Relational patterns in OWL and their application to OBO

Hoehndorf, R., Oellrich, A., Dumontier, M., Kelso, J., Herre, H. & Rebholz Schuhmann, D., 2010, In : CEUR Workshop Proceedings. 614, 10 p., 1.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Representing chemicals using OWL, description graphs and rules

Hastings, J., Dumontier, M., Hull, D., Horridge, M., Steinbeck, C., Sattler, U., Stevens, R., Hörne, T. & Britz, K., 2010, In : CEUR Workshop Proceedings. 614, 10 p., 2.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access
2009

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

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

Modeling life science knowledge with OWL 1.1

Dumontier, M. & Villanueva-Rosales, N., 2009, In : CEUR Workshop Proceedings. 496, 10 p., 14.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Publishing owl ontologies with Presto

DeLeon, A. & Dumontier, M., 2009, In : CEUR Workshop Proceedings. 496, 9 p., 13.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Situational modeling: Defining molecular roles in biochemical pathways and reactions

Dumontier, M., 2009, In : CEUR Workshop Proceedings. 432, 12 p., 13.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access
2007

Describing chemical functional groups in OWL-DL for the classification of chemical compounds

Villanueva-Rosales, N. & Dumontier, M., 2007, In : CEUR Workshop Proceedings. 258, 10 p., 22.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

SMART: A web-based, ontology-driven, semantic web query answering application

De Leon Battista, A., Villanueva-Rosales, N., Palenychka, M. & Dumontier, M., 2007, In : CEUR Workshop Proceedings. 295, 8 p., 17.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Three-layer OWL ontology design

Dumontier, M. & Villanueva-Rosales, N., 2007, In : CEUR Workshop Proceedings. 315, 6 p., 3.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access