title: Methodologies for extracting functional pharmacogenomic experiments from international repository.
abstract: 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.
authors.affiliation: Stanford University.
authors.forename: Yi-An
authors.initials: YA
authors.lastname: Lin
authors.forename: Annie
authors.initials: A
authors.lastname: Chiang
authors.forename: Ray
authors.initials: R
authors.lastname: Lin
authors.forename: Peggy
authors.initials: P
authors.lastname: Yao
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Atul Janardhan
authors.initials: AJ
authors.lastname: Butte
mesh_terms: 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