How to create ontologies to develop sharable understandings on a vast subject/domain?

I have least understanding on ontology but trying to explain what I want to achieve using graph DB.

I would like to have a tool which can help me do below mentioned things:

  • Create a knowledge graph to manage exerpts/concepts from different sources (usually PDF files) for varied subjects in a domain.
  • Most of these topics are inter-dependent or derived out of another concept. So, linking of the concepts in a hierarchical manner will help me trace back the source/origin of the idea.
  • This hierarchies can help me find the missing pieces or loosely coupled entities in the development of those areas. Which I can exploit efficiently to contribute in the future advancements.

I am sure, there should be something already available which does this tedious task. Can someone please help me on this?