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The European Plate Observing System (EPOS, www.epos-eu.org) is a multidisciplinary pan-European research infrastructure for solid Earth science. It integrates a series of domain-specific service hubs (Thematic Core Service, TCS) such as the Geological Information and Modelling, which provides access to data, data products and services on European boreholes, geological maps, mineral occurrences, mines and 3D models. TCS GIM services are hosted by a group of European Geological Surveys and a couple of national research organizations. This paper presents novel data discovery and integration, facilitated using borehole logging information with on-demand web services to produce 3D geological structures. This domain interoperability across EPOS was created for the purpose of research, but it is also highly relevant for the response to societal grand challenges such as natural hazards and climate change. European and international interoperability implementation frameworks are well described and used (e.g., INSPIRE, ISO, OGC, and IUGS/CGI). It can be difficult for data providers to deploy web services that support the full semantic data definition (e.g., OGC Complex Feature) to expose several millions of geological entities through web-enabled data portals as required by pan-European projects. The TCS GIM group implemented and innovatively extended two standardized descriptions, i.e. GeoSciML-Lite and EarthResourceML-Lite, with an important reuse of content from Linked Data Registries. This approach was applied to design and implement the European Borehole Index and associated web services (View-WMS and Discovery-WFS), extended to 3D models, geological maps as well as mineral occurrences and mines. Results presented here apply the Linked Data approach ensuring optimal semantic description and enriching the data graphs, with complex descriptions and contents. In this way, it is now possible to traverse from one Borehole Index instance to linked richer information such as the borehole geological log, groundwater levels, rock sample description, analyses, etc. All this detailed information is served following international interoperability standards (Observations & Measurements, GroundWaterML 2.0, GeoSciML4, amongst others).