The IdMappingRetrieval package in Bioconductor: Collecting and caching identifier mappings from online sources

Research which integrates data from multiple data platforms must of course merge on samples processed in parallel on the platforms. However, exploiting the full biological significance of the data depends on merging on the respective features as well. The features have platform-specific biological identifiers, so identifier mapping is critical to this merging. The IdMappingRetrieval package allows initial acquisition of biological identifier mappings (ID maps) from online bioinformatics services, with caching in localdata repositories for subsequent fast retrieval. An ID map is a one-to-many map from one ID type (called the primary key) to another (called the secondary key). The services currently supported are NetAffx and Ensembl. The package employs a unified interface for accessing these services, so that the local repositories will be easy to create, update, and use. Aside from identifier maps themselves, the the service’s complete annotation data sets are also accessible through the same mechanism. . Therefore, although ID mapping is the primary goal, secondarily the package performs as a generic annotation data collection tool if desired. The objects produced by this package are specifically suited for use by the package IdMappingAnalysis, currently in preparation for Bioconductor. The purpose of IdMappingAnalysis is to characterize and compare two or more ID maps. Retrieval is typically subsetted by Affymetrix array.