During operation, a system for processing queries of a graph database executes a set of processes for processing queries of a graph database storing a graph, wherein the graph comprises a set of nodes, a set of edges between pairs of nodes in the set of nodes, and a set of predicates. When a query of the graph database is received, the system obtains, from the query, a compound comprising a compound type and a set of identity-giving nodes. Next, the system uses the compound to access a tuple for storage in a log-based representation of the graph database, wherein the tuple includes the compound type and the identity-giving nodes. The system then uses the tuple to generate a result of the query and provides the result in a response to the query.