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I'm currently a postdoctoral researcher working with Larry Hunter in the Department of Pharmacology of the University of Colorado at Denver and Health Sciences Center (the Denver-area branch of the University of Colorado).
I received my Ph.D. from Stanford University in 2003, working with Russ Altman on the ontological representation of biochemical and biophysical data and its application, particularly toward macromolecular modeling and natural-language query interface construction. Afterward, I completed a one-and-a-half-year postdoc with Robert Stevens in the Department of Computer Science of the University of Manchester in Manchester, England, where I mined for associations between GO terms and applied description-logic-based technology to build a tool to intelligently guide users in annotating genes and gene products using these associations.
Here at UCDHSC, I'm currently researching the semiautomatic enrichment of OBOs (Open Biomedical Ontologies), i.e., the addition of semantic links between existing terms of OBOs so as to explicitly represent their interrelationships. I've created an integrated frame-based version of the Gene Ontology, the Chemical Entities of Biological Interest (ChEBI) ontology, and the Cell Ontology. I've also mined the term names to extensively enrich this integrated set of ontologies to link previously unlinked terms, resulting in over 9,000 additional edges among the ontological terms. I'm also responsible for the knowledge-management issues toward our lab's biomedical natural-language-processing projects. In particular, I colead our manual annotation projects, in which human annotators mark up short biomedical texts with semantic and linguistic terms from ontologies to create gold standards for our lab's computational annotation work.
A list of my publications can be seen here.
