Although I continue to advocate storing pretty much everything in Evernote — alongside efficient tagging and organization — I still really wanted to find a way to integrate annotating PDFs directly into my favored citation manager, Zotero. I’m hoping that I’ve hit on a solution.
1) I use the Zotero extension Zotfile to organize and rename attachments to Zotero entries into a folder on my desktop. The attachments are therefore links to local files, not files stored in the Zotero servers.
2) That folder is synced to the cloud — and my office PC — using SugarSync.
3) I open and annotate the PDF using GoodReader, which will then automatically sync the annotations with the files linked to the Zotero entry.
I had been using ZotFile’s “send to tablet” function, alongside iAnnotatePDF’s Aji Reader Service to push files back and forth from my tablet to my PC and then to both Zotero and the cloud. This new method avoids a number of problems that method entailed. First, everything is done without having to download individual files via the web or selecting individual files to sync and instead is done automatically. This ensures that I always have access to the files without worrying about finding the most recent version. It also means that I don’t have to be on my home network to update my files. Second, the files remain on my desktop in addition to the cloud and are automatically organized. Third, I avoid quickly exceeding Zotero’s limited free storage space.
I still also e-mail the annotated files to Evernote, since I also want to have all my notes in one place. But until Zotero includes a more robust note taking system, an integrated PDF viewer and/or an iPad app, this method seems to be the best way I’ve found to link annotated articles directly to their metadata.