How Do You Organize and Annotate PDFs? (Reader Response Roundup)

stacked_file_cabinetsTwo weeks ago I asked ProfHacker readers, “How Do You Organize and Annotate PDFs?”, and you rose to the challenge. I can’t recount the entire discussion here (though it’s well worth reading through in full), but I can round-up some of the most popular suggestions.

Commenter rickman (#38-39) helpfully distinguished between applications designed primarily to store documents and applications designed primarily to manage references. In my initial post I concentrated entirely on PDF storage applications such as Evernote and DEVONthink. Honestly, I wasn’t thinking of reference managers at all.


Luckily, you were. Tee_bee (#3), guesti (#12), brianborchers (#16), shannonmattern (#17) and eileenqueen (#18) all recommended Zotero from the Center for History and New Media. To quote from Zotero’s front page, “Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, cite, and share your research sources. It lives right where you do your work—in the web browser itself.” Over the past several years Zotero has become the standard reference manager for many scholars—and a favorite of the Profs. Hacker (see Amy Cavender’s posts,“Getting Started with Zotero” and “Getting Started with Zotero, part 2″). Zotero allows users to store files (including PDFs) in their libraries alongside archived webpages and citations, to share their libraries with other users, and to access their libraries from just about any computer. Zotero allows users to associate detailed metadata with items, but in order to directly annotate PDFs users must open them in another program and then save them back to Zotero.

Exciting Zotero news: My own Zotero use has slowed significantly since I switched to Chrome as my primary browser. The folks at CHNM know that many users are moving away from Firefox (or, more generally, that folks prefer to not be locked into one browser in a constantly-shifting browser market). To that end, they’ve recently announced that they’re working on a standalone version of the software that will work with multiple browsers. There’s not yet an ETA for this upgrade, but the news is welcome nonetheless.

Zotero is free, though users with very large libraries might need to purchase extra storage space.


Next, drgunn (#11), veirs (#30), and timewaster123 (#33) recommended that ProfHacker readers check out the cross-platform reference manager Mendeley. Mendeley Desktop can be downloaded for Windows, OS X, or Linux, and allows users to collect and organize PDFs and citations. The desktop client automatically backs up the information users collect to Mendeley Web, and users can access their library online from any computer. Drgunn (#11) notes that Mendeley will automatically “extract the citation information” from PDFs and “organize them in a familiar interface,” and rickman (#38) loves the way extracts reference information from PDFs by “scanning the first page of a PDF for strings that look like titles, authors, journal names, and so on,” which “works better than programs that favor online lookup.” Timewaster123 (#33) does caution that “mendeley is not great for annotating.”

Mendeley is free, though the company notes in its FAQ that “at a later point in time” they plan to introduce new features to the software that “will be available for a (very reasonable) fee.”


Peripatetic322 (#19) praised the Mac-only reference manager Sente by Third Street Software: “Version 6 is approaching perfection.” According to peripatetic322, “Sente handles organization, annotation, bibliographic needs, and the searching for an annotating of new pdfs from any site to which my university has access.” Moreover, the folders Sente creates “are accessible from the Finder,” so users are locked into Sente for viewing their documents, and “[t]he annotations I make [in Sente] are viewable in Preview.” Rickman (#38) calls Sente “the slickest…of all the reference manager type programs” with “excellent notetaking capabilities.”

Third Street Software trumpets Sente’s “real Mac interface…designed by Mac people for Mac people.” If that’s important to you, then Sente might be the best solution. Sente does come with a stereotypically Mac price, though: an academic single-user license costs $89.95.

Sente may also be the best solution for fans of the iPad. Third Street Software announced in January that they’re working on an iPad version of Sente that will synchronize with the desktop client.


In my initial post I asked readers their opinions of Mekentosj’s Papers, and the response was mostly tepid. Mitchkeller (#4) noted that he “checked out Papers last summer and liked it,” but he was frustrated by the way it exported BibTeX files. Peril (#9) described Papers as “so-so”: “It seems to try really hard to have a complete feature set, but falls short on usability.” Rickman (#38) calls Papers “a strange beast.” Rickman likes the fact that Papers already offers an iPhone/iPod touch/iPad companion app, but wonders why Papers cannot make bibliographies in APA or MLA formats. Overall, I’m not encouraged to pursue Papers any further.

Annotation Apps

ProfHacker readers also recommended several apps for annotating PDFs directly. Nmhouston (#26) distinguishes between adding tags or notes to a PDF file, which most of the reference managers listed above can do, and actually writing “on the PDF itself directly, using highlights or comment boxes,” which “requires a program that actually edits PDFs.” Mendeley and Sente allow users to annotate in both of the ways Nmhouston mentions.

For Windows users looking for a specialized tool for direct annotation, however, guesti (#12) and rungun (#29) recommend Grahl Software Design’s PDF Annotator, and Nsmith1017 (#31) recommends Microsoft’s Onenote.

Shannonmattern (#17) recommends Adobe’s cross-platform Acrobat Pro. Lincolnmullen (#1) assures ProfHacker readers that “An academic license isn’t too expensive” for Acrobat Pro.

Finally, peril (#8) and billso (#23) both recommend that Mac users check out SmileOnMyMac’s PDFpen, which will “annotate, OCR, break apart, and put together PDF files in just about anyway you’d expect.” ProfHacker readers know I’m a big fan of SmileOnMyMac’s Textexpander, and I’ll definitely be checking out PDFpen.

Further Conversation

As I noted above, I wasn’t able to compile all of your suggestions here. I’ve tried to highlight those programs that were recommended by multiple commenters. I plan to try out Mendeley and Sente myself (and to revisit Zotero as a PDF manager). I welcome your notes and annotations in the comments.

[Creative Commons licensed photo by Flickr user redjar.]

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