A method, system and program product of managing multiple versions of enterprise meta-models within an enterprise model using semantic based indexing. The steps include: receiving a query; determining from the query a topic and at least two versions of a topic map meta-model of the enterprise meta-models to compare; applying the query to a merged topic map meta-model of the at least two versions of the topic map meta-model by searching a topic map based index of the merged topic map meta-model for the topic, producing a result; and using the result to translate the topic from the query in at least one of the at least two versions of the topic map meta-model to coexist and correspond to the other version of the topic map meta-model, allowing data between the at least two versions topic map meta-model of the enterprise meta-models within the enterprise model to be correlated.