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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 can be configured for specific domains, such as inscriptions, letters, or social media posts.