Abstract This paper surveys the area of biological data integration and data warehousing, which has become a major focus of the data integration research field in the last few decades. The challenges in biological data integration are caused by several factors such as the variety and amount of available data, the heterogeneity of the data in different sources, and the autonomy and different capabilities of the sources. This paper gives insight into a small selection of important biological databases and the problems in biological data integration. We would like to focus on data warehouses that have become a popular approach in bioinformatics and life sciences. We will also introduce major existing integration systems that have been developed such as SRS, DiscoveryLink, BioWarehouse and ONDEX. Finally, this paper presents an in-house data warehouse approach for biological data.