Systems and methods that control versioning of inferred data in isolated collections representing resources and relationships between those resources. Multiple versions of rulesets may be received or accessed. Execution of each ruleset generates inferred data, such as inferred relationships between resources represented in the isolated collection. A version identifier may be incorporated into each inferred relationship or other inferred data. The version identifier indicates the particular version of a ruleset that resulted in the creation of the corresponding inferred relationship. Upon receiving a query for data in the isolated collection, the query is parsed to determine a query version identifier. Based on the query version identifier, results to the query may be filtered to include inferred data resulting only from a particular version of a ruleset. The results may be displayed as a graph with nodes representing resources and edges representing relationships.