The increasing amount of information available for biomedical research has led to issues related to knowledge discovery in large collections of data. Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains—e.g. clinical and genetic data. One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases. In this work, we describe an approach to overcome heterogeneities in identifiers inside queries. We present an ontology classifying the most common identifier semantic heterogeneities, and a service that makes use of it to cope with the problem using the described approach. Finally, we illustrate the solution by analysing a set of real queries.