In each research paper, there are a lot of things that I want to highlight for later use such as definitions, explanations and concepts... While most of them focus on the topic of the paper, there are some relating to a different or broader topics, e.g. a paper about investigating performance of a specific system may introduce different benchmarks and metrics for performance evaluation and explain why those approaches are applicable for this specific situation.
Normally, I just highlight all of them, put some notes directly into the paper or using Evernote. However, when I want to look for all highlights and notes about one specific topic, I find it difficult as they scatter in different papers and documents. So, are there any tools or techniques to affectively highlighting important points and group them by topic while reading research paper?