In order to assess the content overlap of the source databases and to reduce redundancy, we have applied a method to merge identical physical entities and identify similar interactions. The method is straightforward and efficient for the integration of networks from any single species. Simple physical entities of the same type (genes, proteins, transcripts, metabolites) are compared on the basis of common database identifiers like UniProt (21), Ensembl (22), Entrez (23), ChEBI (24), etc. Since different databases tend to annotate physical entities with different identifier types (e.g. some databases annotate proteins with UniProt identifiers, others with Ensembl identifiers), we first translated the annotations to a uniform identifier type, which is a UniProt entry name in case of proteins, Ensembl gene ID in case of genes and transcripts, and KEGG/ChEBI ID in case of metabolites. Protein complexes are compared according to their individual protein composition. Simple physical entities with the same identifier, and complexes with the same composition, are merged in ConsensusPathDB. Information provided by the according source databases for the merged entities is stored in a complementary manner.
