Interaction data in ConsensusPathDB currently originates from 12 interaction databases and comprises physical interactions, biochemical reactions and gene regulations. The data are gathered in different formats: database dumps, standard interaction file formats like BioPAX (25) or PSI-MI (26), database-specific flat or XML files, or is retrieved through web services. All interaction data are translated to the schema of our relational database and are integrated using the method described above. The database has a graph-like architecture: its three main classes are ‘Interaction’, ‘Physical entity’ and ‘Edge’. The first two classes store information about different interaction types and physical entities, respectively, and edges connect both, indicating that a specific entity participates in a specific interaction. Edges are carriers of information on the particular role, stoichiometry, state and compartment of the physical entity in the particular interaction, if such information is available from the source databases. Several other classes in our database contain information about the source databases, external identifiers of entities or interactions, literature references, cellular compartments, biological pathways, etc. Importantly, the source of physical entities and interactions is always recorded, which allows linking to the original data in the source database.
