Name Type/scope Reference Notes
Oncomine Gene expression, limited scope [17] Cancer-specific; relevant datasets from public repositories have been picked, array design and sample descriptions were reannotated, and a range of statistical processing techniques were performed to make data from different datasets comparable.
Genevestigator Gene expression, limited scope [14] Similar to Oncomine, but for Arabidopsis.
ArrayExpress warehouse Gene expression, wide scope [6] Along with the ArrayExpress repository forms the ArrayExpress resource, one of two large public gene expression databases. Provides gene-oriented query capabilities; access to individual profiles of gene expression; uniform, cleaned up annotation; and statistics-based ranking of query results.In 2009 superseded by Gene Expression Atlas.
METLIN Metabonomics [19] Provides flexible search facilities.
Uniprot Proteins  [9] Protein sequence and functional information.
Biozon Genes, proteins, pathways [13] A unified biological resource of DNA sequences, proteins and pathways.
FlyMine Organism-specific, Drosophila [16] Sequence, functional, interaction and gene expression data. Covers a wide range of Drosophila related information and provides sophisticated query capabilities. Interesting work from the software engineering perspective, where popular queries are optimized by dynamically constructing the necessary structures in the database.
GeneCards Organism-specific, Homo sapiens [18] Proteomic, transcriptomic, genomic, genetic and functional information.     
BioMart Software for in-house installation [8] Query-oriented data management system that provides capabilities to transform any database into a query-oriented warehouse, a generated website and programmatic access methods. Works well for one dimensional information (e.g., lists of genes) and sequence information.
BioWarehouse Software for in-house installation [15] Software environment for integrating biological databases into a single data warehouse suitable for data management, mining and exploration. 
Table 1: Representative examples of different types of data warehousing efforts.