Categories are named as Tags in the Cytoscape app codebase and database.
In Cytoscape/apps/models.py we have the tag model.
According to Django application , A model is a class that represents table or collection in our DB, and where every attribute of the class is a field of the table or collection.
So, We can safely say that Categories (Tag) table separately exists in our database. Also App model has attribute called tags which is associated with Tag model.

But there is no flow regarding how each app is classified into certain categories. When I studied Manifest file of the app from live app store , there are no tags ( categories) passed by the user. Also Its not supplied by the developers while creating app objects while storing. So in order to investigate deeply regarding categories tagged to a particular app, we might need some data sample or schema for the app.

Schema of the appstore is received and there is a separate table with app id and tag id from which we get all the tags associated with the app. This table is generated after normalization process.

From the flow of code, I have seen that the app is not submitted with any tags ( categories) associated with it. Its not mentioned in the MANIFEST format given by the Cytoscape app store. So, categories must be a predefined set which is present in Tag table. There are few references of Tag.objects.all() to get all the tags in the Tag table.