Interacting with data bases, XML, and other programs

Motivation and relevance

• Better to exploit existing resources with tools designed for the job (e.g., SQL, XML, …) than to make a copy of the data in R's native format.

• Better to exploit existing tools for what they're good at (e.g., formulating queries on relational data) than mimicing behavior with R 'equivalent' functions (e.g,. merge()).

• Use in Bioconductor:

  • SQL: annotation packages
  • XML: biomaRt and other queries to web resources; GEOquery, interoperability with other software (e.g., RCytoscape) and file formats (e.g., mzID, GSEABase).