Data structure, genomic annotation

The basic class definitions and other infrastructure are provided in the Biobase package. The base class is the eSet and it has places to store assay data, phenotypic information, and data about the features that were measured and about the experiment that was performed to collect these data. This basic class can then be extended in many different ways, specializing in some of the inputs, and in some cases adding new slots that are relevant to a specific type of experiment. The eSet class has been extended to support expression data, SNP data, and genomic annotation. For expression data the ExpressionSet class has been defined, and it too is quite general. The class can be used for any sort of expression (and is in no way restricted to microarray experiments for mRNA expression, although that is where it is used most). Similar data structures have been used for representing data from experiments in protein mass spectrometry and flow cytometry. 

The genome projects produce an enormous amount of sequence data that needs to be annotated in terms of molecular structure and biological function. 

The data are collected daily from a number of sources, including the National Center for Biotechnology Information (NCBI) and Gene Ontology (GO) Consortium. The warehouse includes sequences, structures, and complete genomes from Gen-Bank as well as annotation links such as NCBI taxon database terms, redundant sequences, sequence neighbors, conserved domains, Online Mendehan Inheritance in Man identifiers, GO terms, LocusLink identifiers, and PubMed links. 

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