As I begin my doctoral studies, I’ve struggled to find the best tool for recording research, taking research notes, taking reading notes, writing responses, and maintaining a collection of annotated PDFs. The digital age offers so many tools for conducting research and recording notes, but I’ve not found the single tool that will do everything seamlessly.

Here’s what I’m seeking:

A research tool, like a journal, that will collect all of the many random and esoteric searches—and the more focused and results-oriented paper research—that I’ve already started doing. Zotero is working well for this segment of my needs.

A research note-taking tool that will allow me to take, collect, tag, and organize notes by source and page number (as applicable) that is seamlessly integrated into the research tool. Zotero and Easybib offer this functionality, but both feel a bit clunky. I’d like these notes to also be available to, if not integrated with, my writing tool.

A PDF annotating tool that enables me to record notes on PDF documents. Yes, I could print and annotate them by hand, but then I’ve lost the ability to tag and organize the notes digitally. I’d like this tool to be available to, if not integrated with, my writing tool. At the moment, built-in Preview (I’m a Mac user) is working well for this, and I’ve been able to import annotated PDFs into Evernote and Scrivener. But neither Evernote nor Scrivener appears able to access the annotation text for searching and organizing.

A general note-taking tool that enables me to collect, tag, and annotate class notes and general summary/response and DAR (descriptive, analytic, responsive) reading notes. These notes are extremely helpful for remembering what I’ve read for class discussions, online discussions, and those dreaded comps that I know are coming. I’ve tried Google Drive Docs, Evernote, and Scrivener for this purpose, and I’ve concluded that I prefer Evernote’s cloud-based storage but Scrivener’s annotation and integration as a writing tool.

A writing tool that enables everything that a good writing tool should provide, including import/export abilities, outlining, word processing, and clear-screen focused writing opportunities. I’ve settled, for the moment, on Scrivener for this process with my files saved to Dropbox for cloud-based syncing.

And I want all of that to be integrated seamlessly.

I haven’t found the “just-right” tool yet. I’ve copied and pasted content back and forth between Evernote and Scrivener to see which works better for me, and I have to admit that I really like both of them. I’m settling on Scrivener for this semester, at least—and I’m going to fork over the payment in a week or so after I have a chance to test it out really thoroughly—but I’m going to keep my eyes open for new tools that hit the market.

So I’m using Zotero to track my research, Scrivener for taking class notes and general reading notes and for writing responses and assignments, importing annotated PDFs from Preview into Scrivener for tagging and searching (I hope), and using either Zotero or, more likely, Scrivener, for taking research notes for assignment and writing purposes.

I’d also like Scrivener to publish directly to blogs and Blackboard, but I think I’m asking for too much there.