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Epigraf stores data using a relational database management system (MariaDB) and in the file system. There is one application database epigraf for user management, pipelines, help pages, and other application-wide content. This goes along with a file system area for application-wide images and other files.

For the research data, Epigraf manages multiple project databases, each prefixed with epi_. Project databases have their own subfolders for images and other files. Each project database is structured according to the Relational Article Model (RAM) and can be configured for specific domains, such as inscriptions, letters, or social media posts.