Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, the study and use of protein-protein interactions is one area where there is an important need for data integration. Without good integration strategies, it is difficult to assess how much interaction data is available and its properties.

Results: We present a data integration approach for protein-protein interactions. This integrative approach has been implemented into PIANA, a protein-protein interaction software framework under the GNU Public License (http://sbi.imim.es/piana). We find that the integrated network of interactions shows properties very similar to those observed in previously reported protein interaction networks. We also find that interaction prediction methods find interactions for many proteins for which experimental methods have not produced any information.

Conclusions: PIANA´s approach to protein interaction data integration solves many of the nomenclature issues common to systems dealing with biological data. The concept presented here can be extended to other types of biological data. The integration of all available protein interaction data is fundamental to obtaining a comprehensive picture of the interactions taking place in the cell.