Database schemas, interfaces and ontologies can enact actors in politically sensitive ways. This manifests clearly when such formal knowledge representations are used to establish intended identities of non-citizens. In this paper we present results from our semantic and computational analysis of ontologies of information systems used to identify and register migrants in Europe. By launching the “hotspot approach” in 2015, the European Commission has identified the use of information systems as an important element to de facto achieve a joint migration policy and to gain knowledge on non-EU citizens. However, differences (and similarities) exist among members states’ systems, as well as between member states’ and Europe-wide systems. At European level this is especially relevant as information systems are undergoing major changes following several proposals to make them semantically interoperable, and make their data more usable for EU policy-making. How then are migrants enacted by information systems designed for different purposes by different institutional actors? And what consequences are entailed by their ongoing integration? We present our method to analyse ontologies used in information systems aimed at identifying and registering people at border. This method is informed by discourse and network analysis, allowing us to make visible the politics of knowledge production and materialities of information. We introduce results from our comparative analysis of operational information systems used at EU hotspots. This method will contribute to scholarship in digital STS and the materialities of information with a new method based on the empirical analysis of ontologies.