Methodologies for extracting functional pharmacogenomic experiments from international repository.
Pharmacogenomic studies are studies designed to elucidate the relationships between drugs and genes on the genomic scale. Given the rapidly increasing amount of microarray data in international repositories, and the implicit drug information contained in PubMed, MeSH and UMLS, we propose automatic methods for identifying drug-related microarray experiments from NCBI GEO by the semantic connections between these data resources. In our study, we find that 51.5% of microarray experiments are associated with at least one PubMed identifier, 22.1% of these contain a MeSH term that relates to the UMLS Pharmacologic Substances semantic sub-tree. Our work shows an abundance of publicly available gene expression data available to enable the discovery of novel drug indications, drug classifications and other pharmacogenomic studies.
Lin
Yi-An
YA
Stanford University.
Chiang
Annie
A
Lin
Ray
R
Yao
Peggy
P
Chen
Rong
R
Butte
Atul Janardhan
AJ
D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling; D016247:Information Storage and Retrieval / Q000379:methods*; D046650:Medical Subject Headings; D020411:Oligonucleotide Array Sequence Analysis; D010597:Pharmacogenetics; D039781:PubMed; D012660:Semantics; D012985:Software Design; D017432:Unified Medical Language System