Faculty Publications

Congratulations to CTS faculty Liz Chen and Neil Sarkar on their recent publication:


Journal of Biomedical Informatics, In Press, Corrected Proof, Available online 20 October 2009
http://dx.doi.org/10.1016/j.jbi.2009.10.003

MeSHing molecular sequences and clinical trials: A feasibility study

Elizabeth S. Chen^a, b, d and Indra Neil Sarkar^{a, c, d, ,} 

^aCenter for Clinical and Translational Science, University of Vermont, Burlington, VT, USA

^bDivision of General Internal Medicine, Department of Medicine, University of Vermont, Burlington, VT, USA

^cDepartment of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA

^dDepartment of Computer Science, University of Vermont, Burlington, VT, USA

Received 3 September 2009.  

Available online 20 October 2009. 

Abstract

The centralized and public availability of molecular sequence and clinical trial data presents an opportunity to identify potentially valuable linkages across the bench-to-bedside “T1” translational barrier. In this study, we sought to leverage keyword metadata (Medical Subject Heading [MeSH] descriptors) to infer relationships between molecular sequences and clinical trials, as indexed by GenBank and ClinicalTrials.gov. The results of this feasibility study found that approximately 30% of sequences in GenBank could be linked to trials and over 90% of trials in ClinicalTrials.gov could be linked to sequences through MeSH descriptors. In a cursory evaluation, we were able to consistently identify meaningful linkages between molecular sequences and clinical trials. Based on our findings, there may be promise in subsequent studies aiming to identify linkages across the T1 translational barrier using existing large repositories.