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A Search for a Collaborative Notetaking and pdf Annotation Tool

I am looking for a few different things in a collaborative notetaking/annotation tool or set of tools. I’ll list these later, but provide a bit of background first. I want to be able to have one place to go for all of my study notes and research. This might include concept maps, website links, screenshots and PDFs of journal articles. Right now I use a combination of OneDrive and OneNote. I keep links and articles I want to save in OneNote. I also have frequently used bookmarks in Firefox. As far as PDFs, I use Mendeley to store citations and the PDFs. In Mendeley I can also annotate.

This is my current set of apps, but previously I’ve tried others. For citation management, I’ve used both EndNote and Zotero pretty extensively. I like Mendeley, but have been having trouble getting the actual PDFs to sync on various devices – it’s a new system for me, adopted in the last month. I like being able to annotate directly in the citation manager though. Mendeley also has an option to open with another annotation app if needed. Other annotation solutions I’ve tried are Acrobat, OneDrive, and MarginNote. These are great, but don’t really have powerful searching and tagging like a citation manager does.
Last, I mentioned a notetaking solution. I do like OneNote, but it isn’t perfect. I have used Evernote, but I like the office integration (since I’m already paying for it…). It doesn’t really work well with PDFs though. I can import them but not annotate them.
So for this post I have spent the week looking at different solutions that have any combination of these affordances. In that process, I found Diigo, a social bookmarking tool that has been around for some time. While I had previously used Delicious – years ago – what caught my attention with Diigo was the ability to annotate websites and PDFs. This led me to a new family of apps, as there are several that allow for web/pdf annotation and discussion. Collaborative discussion of documents and websites (similar to Now Comment) is something I might like to explore as well.

While it would be ideal to have one app that could do all of the things mentioned above, and serve as my auxiliary brain, I feel it might not be in existence yet. However, part of what I am looking for is a better organizational workflow, perhaps using a combination of apps. With all of that said, I will likely be focusing on Diigo or Hypothes.is for my first review. This family of discussion apps will be interesting for me to explore through the semester. However, I may choose to create a workflow using these apps in conjunction with others to really make it relevant to my research for this program.