With QGIS I can manipulate data stored on a PostGIS Geodatabase.
In order to query to the geodatabase, is it better to do it from QGIS or directly in PostGIS?
What are the benefits of querying in PostGIS?
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You would use PGAdmin instead - which is the GUI to PostgreSQL - which gives access to all the functions in PostGIS through the SQL window.
We use PostGIS every day - but rarely write SQL queries in DBManager (QGIS Plugin). Although access to the spatial functions is a bit more intuitive in DBManager, PGAdmin is really the tool to interact with our data - QGIS is the tool to visualize it.
PGAdmin is also better for viewing your database components, saving and running saved .SQL files, etc.