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Dumontier, Michel Professor

Dr. Michel Dumontier is an Associate Professor of Medicine (Biomedical Informatics) at Stanford University. His research focuses on the development of computational methods to increase our understanding of how living systems respond to chemical agents. At the core of the research program is the development and use of Semantic Web technologies to formally represent and reason about data and services so as (1) to facilitate the publishing, sharing and discovery of scientific knowledge, (2) to enable the formulation and evaluation scientific hypotheses and (3) to create and make available computational methods to investigate the structure, function and behaviour of living systems. Dr. Dumontier serves as a co-chair for the World Wide Web Consortium Semantic Web for Health Care and Life Sciences Interest Group (W3C HCLSIG) and is the Scientific Director for Bio2RDF, a widely recognized open-source project to create and provide linked data for life sciences.

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selected publications

academic article
- Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 7:543-543. 2014
- Evaluation of research in biomedical ontologies. Briefings in bioinformatics. 14:696-712. 2013
- State of the art and open challenges in community-driven knowledge curation. Journal of biomedical informatics. 46:1-4. 2013
- Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database. 2012:bas006-bas006. 2012
- Building an HIV data mashup using Bio2RDF. Briefings in bioinformatics. 13:98-106. 2012
- Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinformatics (Oxford, England). 28:2169-2175. 2012
- Linked Data in Drug Discovery. IEEE internet computing. 16:68-71. 2012
- Self-organizing ontology of biochemically relevant small molecules. BMC Bioinformatics. 13:3. 2012
- A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (Oxford, England). 27:1001-1008. 2011
- Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. Journal of Cheminformatics. 3:20. 2011
- Integrating systems biology models and biomedical ontologies. BMC Systems Biology. 5:124. 2011
- MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets. Computers & graphics. 35:823-830. 2011
- Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. BMC Bioinformatics. 12:303. 2011
- Semantic Web integration of Cheminformatics resources with the SADI framework. Journal of Cheminformatics. 3:16. 2011
- Computational approaches toward the design of pools for the in vitro selection of complex aptamers. RNA (New York, N.Y.). 16:2252-2262. 2010
- Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data. Chinese Medicine. 5:43. 2010
- Modeling and querying graphical representations of statistical data. Web semantics (Online). 8:241-254. 2010
- Towards pharmacogenomics knowledge discovery with the semantic web. Briefings in bioinformatics. 10:153-163. 2009
- Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic acids research. 36:4286-4294. 2008
- Armadillo: Domain Boundary Prediction by Amino Acid Composition. Journal of molecular biology. 350:1061-1073. 2005
- CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. FEBS letters. 579:4685-4691. 2005
- The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Research. 33:D418-D424. 2004
- Taking flight with OWL2. Semantic web. 2:67-70.
- The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Applied ontology. 6:53-89.
- Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine. Studies in health technology and informatics. 169:165-169.
chapter
- Evaluating Scientific Hypotheses Using the SPARQL Inferencing Notation. Lecture Notes in Computer Science. 647-658. 2012
- Development of Small-Molecule Ligands and Inhibitors. Protein Targeting with Small Molecules. 115-147.
- Target Profiling of Small Molecules. Protein Targeting with Small Molecules. 11-38.
conference paper