Keyword tagging across scientific papers making it searchable One year into the research project I have now a nearly exhaustive list of keywords / themes characterising my topic. There are about 100 words, though some of them are so closely related that probably this can be a little bit reduced. However there are nuances, so for what it is worth I would like to keep it for now.

The plan is now to be able to go through all the literature again and tag the keywords when they or a close synonym is mentioned in the text. 

I have most of the literature in PDF, though some items are old school books. Now what I would like is eventually to have a search function where I can then search for a keyword and it finds all the text items where I tagged it. 

The keyword system of Citavi is close, but not quite. OneNote is great for searching, but pulling in 300 PDF research papers into OneNote is simply no option. What would be best is an annotation Program for PDF, that saves notes in a database format, e.g. saving 'Note Bla bla bla,Keywords abc, file X, page 7, line 20'

Whilst that is wishful thinking, thousands of people have come before me and tried to figure out this personal knowledgebase research thing, so I am a bit surprised there is no software for this, and all the discussions either peddle reference tools (Mendeley, Zotero) or Mindmapping (Xmind, …) which are really addressing different concerns. 

I also want to keep the original paper and my notes separate.

Any thoughts / suggestions ?
You could look into a noSLQ database. ElasticSearch or SOLR come to mind immediately. Most cloud services also offer their own flavors of this(DynamoDB on AWS for example). The solution could be designed to retain the original content, your notes (both searchable also), and your classification system. Most of these systems should have plugins to import various file formats directly.