Custom Ontology is a module for Omeka S that allows to create specific classes and properties to describe resources when no standard ontologies are available. It is useful to manage internal properties, or for researchers who are creating new data. The properties and classes are available via the standard api of Omeka S too, like any other ontology.
In fact, this module is a replacement of an existing feature on Omeka Classic, where it was allowed to edit and create item types, equivalent of resource classes and resource templates, and to create new elements, equivalent of properties. In Omeka S, in order to share data and to follow the standards of the semantic web, this feature was not ported.
Note that it is always recommended to search and use existing ontologies first, because it will be simpler to share data and to link them semantically. If the properties are known only by you and are not described anywhere, it will be hard to match them and to make relations with other.
This module avoids to create a specific rdf vocabulary, turtle or n3 file too, so anybody can use Omeka S like wished, with any documents or resources.
Furthermore, it makes old Omeka Classic sites fully upgradable automatically into Omeka S via the plugin Upgrade To Omeka S.