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Knowledge organisation is pretty much what libraries have been doing for 2000 years: collecting information, arranging it, describing it and making it findable. When you systematically organize your literature, sources and notes in the course of a research project, you are basically building your personal library on a topic.
Being well organized means you keep track of your literature, notes, citations and summaries - and save time and nerves:
No lost notes and thoughts
Your knowledge remains findable and retrievable - even years later
Contents can be linked more easily
Consistent citations
No "PDF graveyards"
Protection against plagiarism
You can document your knowledge using various methods:
Linking information through a tag system
Enriching documents with metadata
Creating collections of quotations
Writing good summaries
The easiest way to combine several methods in one is to use