title: Relax with CouchDB--into the non-relational DBMS era of bioinformatics.
abstract: With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services.
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Ganiraju
authors.initials: G
authors.lastname: Manyam
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Payton
authors.forename: Jack A
authors.initials: JA
authors.lastname: Roth
authors.forename: Lynne V
authors.initials: LV
authors.lastname: Abruzzo
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Coombes
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D003628:Database Management Systems; D030541:Databases, Genetic; D060148:HapMap Project; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D006801:Humans; D020407:Internet