HowTo: Querying online Data

This article demonstrates how you can make use of the tools that have been provided for on-line querying of data resources. These tools rely on others (such as the NLM and NCBI) providing and documenting appropriate web interfaces. The tools described here allow you to either retrieve the data (usually in XML) or have it rendered in a browser on the local machine. To do this you will need the Biobase, XML, and annotate packages. The functionality in this article was first described in (Gentleman and Gentry, 2002), although some enhancements have been made since the writing of that article. Assembling and using meta-data annotation is a non-trivial task. In the Bioconductor Project we have developed tools to support two different methods of accessing meta-data. One is based on obtaining data from a variety of sources, of curating it and packaging it in a form that is suitable for analysing microarray data. The second method is to make use of on-line resources such as those provided by NLM and NCBI. The functions described in this vignette provide infrastructure for that second type of meta-data usage. We first describe the functions that allow users to specify queries and open the appropriate web page on their local machine. Then, we investigate the much richer set of tools that are provided by NLM for accessing and working with PubMed data.