I'm looking for software for macs geared towards organizing and referencing the text in notes. I'm currently studying pathology and would like to be able to "tag" a topic/heading within my notes (not the entire note itself) with a keyword that is searchable. For example, if I have Rheumatoid Arthritis, I'd like to be able to highlight it, and tag it with multiple keywords or hashtags such as "hypersensitivity reaction type IV" or "#hypersensitivityrxntypeIV" and be able to search those keywords and have any of those topics I've tagged show up in the results. Anyone have any suggestions?
You may be interested in using MaxQDA, they are just now preparing to release a mac version. Although it is a software geared towards textual analysis and qualitative researchers, it can tag pieces of text pretty much like you say you want to do.
For regular note taking, I use Evernote and Google Drive. Both tools are very useful for writing when you are 'in the wild' (e.g. at meetings or observing cultural behaviour). If tagging the specific file is sufficient, Evernote is brilliant for just this purpose.
However, for analysis purpose I have recently grown very fond of MaxQDA. Among a bunch of great features, this tool allows for 'coding' (tagging) paragraphs within notes and transcribing recordings. You can try it for free for 30 days.
I believe in using the right tool for specific purposes and will therefore recommend Evernote or Google Drive for note-taking and MaxQDA for the actual analysis.