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# 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][]).
    
[biomaRt]: http://bioconductor.org/packages/devel/bioc/html/biomaRt.html
[GEOquery]: http://bioconductor.org/packages/devel/bioc/html/GEOquery.html
[RCytoscape]: http://bioconductor.org/packages/devel/bioc/html/RCytoscape.html
[mzID]: http://bioconductor.org/packages/devel/bioc/html/mzID.html
[GSEABase]: http://bioconductor.org/packages/devel/bioc/html/GSEABase.html
