Michel Dumontier

Summary

Affiliation: Carleton University
Country: Canada

Publications

  1. pmc Ontology-Based Querying with Bio2RDF's Linked Open Data
    Alison Callahan
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada
    J Biomed Semantics 4:S1. 2013
  2. pmc Semantic Web integration of Cheminformatics resources with the SADI framework
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    J Cheminform 3:16. 2011
  3. pmc Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    J Cheminform 3:20. 2011
  4. pmc Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data
    Matthias Samwald
    Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland
    Chin Med 5:43. 2010
  5. pmc Integrating systems biology models and biomedical ontologies
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
    BMC Syst Biol 5:124. 2011
  6. pmc GridCell: a stochastic particle-based biological system simulator
    Laurier Boulianne
    Department of Electrical and Computer Engineering, McGill University, Montreal, QC, H3A 2A7, Canada
    BMC Syst Biol 2:66. 2008
  7. pmc Domain-based small molecule binding site annotation
    Kevin A Snyder
    The Blueprint Initiative, Toronto ON, M5T 1K4, Canada
    BMC Bioinformatics 7:152. 2006
  8. pmc Relations as patterns: bridging the gap between OBO and OWL
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 11:441. 2010
  9. doi request reprint Towards pharmacogenomics knowledge discovery with the semantic web
    Michel Dumontier
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
    Brief Bioinform 10:153-63. 2009
  10. doi request reprint Building an HIV data mashup using Bio2RDF
    Marc Alexandre Nolin
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
    Brief Bioinform 13:98-106. 2012

Collaborators

Detail Information

Publications19

  1. pmc Ontology-Based Querying with Bio2RDF's Linked Open Data
    Alison Callahan
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada
    J Biomed Semantics 4:S1. 2013
    ..However, querying Bio2RDF remains difficult due to the lack of uniformity in the representation of Bio2RDF datasets...
  2. pmc Semantic Web integration of Cheminformatics resources with the SADI framework
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    J Cheminform 3:16. 2011
    ..abstract:..
  3. pmc Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    J Cheminform 3:20. 2011
    ..abstract:..
  4. pmc Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data
    Matthias Samwald
    Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland
    Chin Med 5:43. 2010
    ..The approach is based on our initial experiences with implementing an integrated web of data for a selected use-case, i.e., the identification of plant species used in Chinese medicine that indicate potential antidepressant activities...
  5. pmc Integrating systems biology models and biomedical ontologies
    Robert Hoehndorf
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
    BMC Syst Biol 5:124. 2011
    ..Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology...
  6. pmc GridCell: a stochastic particle-based biological system simulator
    Laurier Boulianne
    Department of Electrical and Computer Engineering, McGill University, Montreal, QC, H3A 2A7, Canada
    BMC Syst Biol 2:66. 2008
    ..Increasingly accurate simulators may provide insights into the regulation of biological processes due to stochastic or spatial effects...
  7. pmc Domain-based small molecule binding site annotation
    Kevin A Snyder
    The Blueprint Initiative, Toronto ON, M5T 1K4, Canada
    BMC Bioinformatics 7:152. 2006
    ....
  8. pmc Relations as patterns: bridging the gap between OBO and OWL
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 11:441. 2010
    ..Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately...
  9. doi request reprint Towards pharmacogenomics knowledge discovery with the semantic web
    Michel Dumontier
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
    Brief Bioinform 10:153-63. 2009
    ....
  10. doi request reprint Building an HIV data mashup using Bio2RDF
    Marc Alexandre Nolin
    Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
    Brief Bioinform 13:98-106. 2012
    ....
  11. pmc HyQue: evaluating hypotheses using Semantic Web technologies
    Alison Callahan
    Department of Biology, Carleton University, Ottawa, Ontario, Canada
    J Biomed Semantics 2:S3. 2011
    ..Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks...
  12. doi request reprint yOWL: an ontology-driven knowledge base for yeast biologists
    Natalia Villanueva-Rosales
    School of Computer Science, Carleton University, Ottawa, Ont, Canada K1S5B6
    J Biomed Inform 41:779-89. 2008
    ..Based on yeast data obtained from the Saccharomyces Genome Database and UniProt, we discuss the challenges encountered during the building of the knowledge base and how they were overcome...
  13. pmc Self-organizing ontology of biochemically relevant small molecules
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    BMC Bioinformatics 13:3. 2012
    ..Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest...
  14. pmc Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments
    Jose Cruz-Toledo
    Department of Biology, Carleton University, Ottawa, ON, Canada
    Database (Oxford) 2012:bas006. 2012
    ..DATABASE URL: http://aptamer.freebase.com...
  15. pmc Mouse model phenotypes provide information about human drug targets
    Robert Hoehndorf
    Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth SY23 2AX, Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    Bioinformatics 30:719-25. 2014
    ..One set of resources that has been relatively neglected for drug repurposing is animal model phenotype...
  16. pmc RKB: a Semantic Web knowledge base for RNA
    Jose Cruz-Toledo
    Department of Biology, Carleton University 1125 Colonel By Drive, K1S5B6, Ottawa, Canada
    J Biomed Semantics 1:S2. 2010
    ..We show queries to the RKB using description logic reasoning, thus opening the door to question answering over independently-published RNA knowledge using Semantic Web technologies...
  17. ncbi request reprint CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules
    Howard J Feldman
    The Blueprint Initiative of the Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON, Canada
    FEBS Lett 579:4685-91. 2005
    ..This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities...
  18. pmc Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics
    Leonid L Chepelev
    Department of Biology, Carleton University, Ottawa, Canada
    BMC Bioinformatics 12:303. 2011
    ..Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality...
  19. doi request reprint Disruption of fungal cell wall by antifungal Echinacea extracts
    Nadereh Mir-Rashed
    Biology Department, Carleton University, Ottawa, Ontario, Canada
    Med Mycol 48:949-58. 2010
    ....