If you're looking for ontologies:
But there's maybe 5k ontologies, how do you hope to overview them and learn about them? You should start from a specific (narrow) problem domain.
Are these required and recommended properties only a thing which is understandable for the Google search algorithms to work well?
Yes. Follow additional guidelines in the documentation for your specific type. E.g., for Movie: required properties are name and image.
See also https://github.com/schemaorg/schemaorg/issues/1715.
https://www.w3.org/annotation/ is what you need (http://www.w3.org/TR/annotation-model/, http://www.w3.org/TR/annotation-vocab/).
This can be used for bookmarking or any other pointer or a comment on a web resource. You may need to invent a new motivation value.
http://www.w3.org/TR/selectors-states/ may also be relevant as it allows to:
say "this web ...
Well yeah CSO is not an ontology but a thesaurus.
Here's an idea: compare it to Microsoft Academic Graph's "Fields of Science".
Also, you need to include some actual papers in your study, indexed with the two, and assess the accuracy/adequacy of indexing with the two topic thesauri.
For a straight theme, use <doc> dc:subject "foo"
To add confidence, you can use RDF*:
<< <doc> dc:subject "foo" >> my:confidence 0.962
But maybe RDF* is an overkill.
You can use the NIF (NLP Interchange Format) ontology. Use its:taIdentRef to point to the theme (has to be a URL), and I think its:taIdentConf is ...