The pdfs can be inserted and Docear also extracts their annotations. I actually export my Zotero collection (subset) for use in Docear and can arrange the references on the mind map to get an idea of the outline. Of course Scrivener is great for this also. I have also used Docear, but mainly for creating an outline in the mind map. I have also been frustrated with Spotlight not finding my files and have been using the trial version of Foxtrot which works brilliantly. Zotero has a great add-on to extract annotations from pdfs and it is now also integrated with Scrivener via a plugin for Zotero: This way I will be able to more easily organise the few dozen references I need rather than having an extra hundred or so I don’t. One thing I realized after starting to use Scrivener and dragging a couple of hundred pdfs into it is that I really should probably be doing it one at a time as I cite them and according to whether I have notes and annotations that can be added to Scrivener. I use Zotero’s collection to organize my references and their attached pdfs according to writing projects. If you want to you can make a “collection” in Zotero for each folder you have your pdfs in and drag them into there. One thing you might also like is the ability to drag and drop any number of pdfs from Finder into the central pane of Zotero and then right click on them to have the meta-data extracted and make a parent reference item. Here is a youtube demo of how to cite in Word with Zotero: ! If you use Zotero standalone or Zotero for Firefox you will be able to download the Mac plugin for Word from this page: It integrates very nicely with Word and LibreOffice (even with LaTex). Zotero works best as a Firefox plugin but also works well as a standalone app which is also compatible with Chrome and Safari. It also accepts DOIs and ISBNs for the creation of entries (you can copy and paste these from pdfs that have text layers). Its best feature is probably the robust ability to gather metadata from various sites: Google Scholar, Amazon, Worldcat etc. I settled on Zotero because it is open source, free and compares favourably in many ways with most of the others. I looked at many citation managers after deciding to ditch Endnote because of their proprietary format, high cost and charging for new releases. I would be interested to hear about your experiences using it. I am also using Scrivener, although I only just started. I am afraid I only just came across your post on Docear’s forum. I know about the stress and frustrations of writing a PhD.
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