Relax with CouchDB - Into the non-relational DBMS era of bioinformatics

Ganiraju Manyam, Michelle A. Payton, Jack A. Roth, Lynne V. Abruzzo, Kevin R. Coombes

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1-7
Number of pages7
JournalGenomics
Volume100
Issue number1
DOIs
StatePublished - Jul 2012
Externally publishedYes

Keywords

  • Copy number variation
  • Data integration
  • Drug-target interaction
  • NoSQL database

ASJC Scopus subject areas

  • Genetics

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