Two 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.
Zotero
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.
Mendeley
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.”
Sente
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.
Papers
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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18 Responses to How Do You Organize and Annotate PDFs? (Reader Response Roundup)
owlattack - May 26, 2010 at 12:12 am
Thanks. This is a helpful post, but it appears that there is an error in your TextExpander snippet (assuming you’re using that) for “Windows” since “Widows” erroneously appears in its place.
relsimon - May 26, 2010 at 1:44 am
Thanks for both posts, they were very helpful. I have done a lot of research on this topic, as I am about to embark on writing my dissertation and want to use technology to my advantage as much as possible. Missing from your list is Microsoft OneNote, which has some very nice PDF related features – though, it is still far from perfect. Unfortunately, I have not been able to find the “perfect” program (for PC at least). In fact, there are three key functions which I have not found in any program: 1. Tag specific sections of a PDF. And then do a tag based search of all PDFs on the computer. Results will show the tagged sections of the PDFs.2. Take notes on a section of a PDF. Tag the note. Do a word search or tag search for all PDF notes on the computer. Results will show the note as well as the relevant portion of the PDF. 3. Do a word or tag based search through all PDFs and PDF-notes on the computer.If anyone has any suggestions, I would definitely appreciate it.
performance_expert2 - May 26, 2010 at 5:14 am
I’m stunned you used the L word. Respect.
m_dittman - May 26, 2010 at 9:56 am
I’m a little late to this party, but I’ve been using the Nitro beta http://www.nitroreader.com to prepare for a research trip to Philly next month and find it very intutitive and powerful.
libfac - May 26, 2010 at 10:33 am
A computer software program for content analysis such as NVivo is sometimes used for coding literature review sources. Some colleges have a site license for the software.
peril - May 26, 2010 at 11:03 am
Since the last post I’ve found a good tool, and working with another Prof Hacker (really all credit to him) and modified my initial script to add keywords to a file name.First off there’s a great PDF annotation tool for Mac it’s free called Skim: http://skim-app.sourceforge.net/Anyway, the real reason I’m replying: the script we worked out!First of all, the final version of this should be credited entirely to J. (feel free to claim it, I just don’t know how much name you’re comfortable with being used online ;)Using Memeo.com‘s document manager, this modified hazel rule set (hazel from noodlesoft.com is the one app I couldn’t live without- active userbase and responsive creator make it a great community. Rules and simple actions for files, what a concept!)(1) If all of the following are met: Kind is PDF(2) Run AppleScripttry tell application “PDFpen” activate hidden open theFile set theFile to document 1 ocr theFile repeat until performing ocr of theFile is false delay 1 end repeat save theFile close theFile end tellend try(3) Rename File: date created_comment_name extension(4) Run AppleScript (opening imports files)try tell application “Memeo Connect” activate open theFile end tellend try(5) Move file to folder “Processed”Hope someone else gets some use out of this also, it works really well.For PDF managers, if you can’t find an app, Hazel makes a great alternative until you do. It can automatically sort, run OCR applescript, name, and file (in my case it makes year and month sub folders depending on when I scanned the doc). Really slick software!
nmhouston - May 26, 2010 at 11:34 am
Since the Windows recommendations are somewhat minimal here, I’m just repeating my earlier suggestion that NitroPDF (http://www.nitropdf.com/index.asp) offers excellent full-featured PDF editing and annotation software as well as free online tools. I’ve been using it happily for years.
mposner - May 26, 2010 at 4:02 pm
I don’t know why Papers got such little support in your original post (which I unfortunately missed). I have been using it for two years and really like the app. I like the way you can organize pdfs into regular folders and smart folders, it is really easy to search for and download pdfs right from the app, and the full screen viewer is very nice. There are two features that it lacks: it does not produce reference lists and does not allow you to annotate pdfs (other than adding a note). But I simply export my Papers references to Endnote when I am writing something that needs a reference list, and you can open pdfs from Papers directly in another app like PDFPen to make annotations.One of my favorite features is the Authors view. This will list all authors in your collection, show the papers you have for each, and then do an automatic search for newer papers by that author in whatever database you choose. You can also save searches so that they are updated automatically each time you click on it. Finding new papers using Papers is really easy.Considering aesthetics, price and functionality I think your readers should give Papers a look. They also have an iPhone and iPad app that syncs with the desktop version, and a large and active user community.
billso - May 26, 2010 at 4:54 pm
Excellent summary, and the followup comments are great. As always, I’m happy to help!
jlowery - May 26, 2010 at 6:00 pm
Since the first post, I have been exploring and pleased with PDF-Xchange viewer [http://www.docu-track.com/product/pdf-xchange-viewer]. I will be recommending this free software to my students who want to make notes on my PDF handouts.
rickman - May 26, 2010 at 9:27 pm
I’d like to echo relsimon’s question (comment 2), which is equally relevant to Wi(n)dows and Mac. Sounds like the new holy grail of PDF management.For the moment, favored solutions on the Mac side tend to involve exporting reference information with tags and your own notes to something like DevonThink, alongside a link back to the reference item. Another hack is to split PDFs into multiple files (e.g. a file a page) and attach tags to each page that is useful to you. This won’t find the exact passage you’re looking for, and you have to be careful of sections that span two pages. Both of these approaches involve a fair bit of fiddly work, so being able to do the things relsimon mentions would be great.
cshea - May 27, 2010 at 12:01 pm
Let me put in a plug for my favorite Mac program for file storage, tagging, etc.: Eaglefiler. It always gets short shrift relative to DevonThink, but I think it’s superior. (I have not tried the “new” Devonthink.) Like some of the other options here, it uses the “iTunes” model, so files remain in their original format and place; no need worry about future inaccessibility.It does not include OCR, but the price of Eaglefiler plus PDFPen, which does OCR and a lot more (marking up PDFs, etc.) is about $90.No reference features, obviously. But for core file management, it can’t be beat.
ryancordell - May 27, 2010 at 2:40 pm
Ha! No, owlattack, that’s just a typo. Windows is a short word (and I type it so infrequently) that I don’t have a TextExpander snippet set up for it.[Which has been fixed by your friendly neighborhood editor.]
drgunn - May 28, 2010 at 1:29 am
Ryan – I’m glad my comments are useful to you. I’m happy to answer any Mendeley related questions anyone might have, and I just wanted to make it clear, since my profile isn’t linked in the original post, that I’m affiliated with Mendeley.I also wanted to make sure relsimon (#2) and others know that Mendeley is listening to them and to what they need. We’re almost there with his list of requests, too. For example, you can search across all or a selection of PDFs, you can tag PDFs, and you can add notes to specific sections. It shouldn’t take much work to link these features together to enable search across tagged notes.If anyone wants to submit an idea and get an email when the feature is completed, they can sign up at http://feedback.mendeley.com
nicolewyatt - May 28, 2010 at 5:05 pm
@drgunn Are there any plans for mobile versions if Mendeley? (I’m particularly interested in an ipad version myself.) Since I platform hop it is more attractive to me than the Mac or Windows only competitors, but I expect I will be doing more and more of my pdf reading on the ipad.
michaelnelson - June 2, 2010 at 10:03 pm
Annotation For the Mac:1. Preview (especially in Snow Leopard; integrated in Devonthink)2. Adobe Acrobat Professional (expensive)3. Skim (used this for a long time, until Snow Leopard improved Preview; it is still a fantastic app)Organization for the Mac:1. Devonthink Pro. (Can annotate using Preview)2. Bookends.Those are the ones I use.Others I have explored, and which are not listed in this post:Curio (some use it to annotate PDFs; closest thing a Mac has to Microsoft OneNote)YojimboSohoNotesEagle FilerAnd there are others that can do this kind of thing but it is a stretch: Notebook by Circus PoniesNoteTaker by AquamindsEverNoteJournlerAnd I could probably think of more I’ve tried if give a shove!
nicolewyatt - June 3, 2010 at 6:18 pm
I suspect that (a) no one is still reading these comments, and (b) that this won’t be news to anyone but me, but just in case: I discovered that with Mendeley I can set it to save the library to a folder in dropbox, and also get it to sync a bibtex file (or files) of my reference list there. Instant access to my reference library from many mobile devices. (Dropbox has iphone, ipad, and android clients, with a blackberry client in the works.) A Mendeley App would still be great, but this is a good solution in the meantime.I actually coughed up the money to try out Papers on the iPad and was as disappointed with it as I was with the Mac version. I can’t put my finger on what it is that doesn’t work for me, but it just isn’t quite right. I suspect it is subtle incompatibilities between my work habits and the interface.
jimme - June 8, 2010 at 6:09 pm
Hi Ryan,Thanks for this roundup and giving us the opportunity to promote some of the other PDF and research management tools out there.I have been coming at the research management problem from a different perspective. I decided to build Qiqqa (pronounced “Quicker”) at the same time as working towards my PhD.Although I did try using existing reference management applications to locate my papers, I found them all quite lacking in the ability to mark the interesting parts of my papers (text, formulae and diagrams) so that I can quickly review them every few months, and especially when it comes time to writing up my thesis! Searching the annotation comments also works (tagging them is coming soon as we have had several people ask for that one). GoogleScholar is still my method of choice for locating documents, so I made it easy to query Google Scholar while reading a PDF. Of course, using it all day, I have added in tons of little nifty features that save me loads of time (e.g. right-click text in PDF and lookup word in dictionary.com). Also, I found the text searching and exporting support from most of the other tools to be quite unreliable for scanned PDFs, so I built in OCR to tackle that.At the moment I don’t support bibliography management – although that is coming fast (I have only been working on Qiqqa since the beginning of this year and I don’t want to add yet-another-half-baked-references-manager to the world). But first I am testing out the synchronizing and backing up onto the Amazon S3 cloud so that I can work from the lab, my laptop and from home.I am hoping that others will find Qiqqa useful, and will enjoy using it as much as I have enjoyed writing it. I hope to get a lot of feedback from other students and researchers to learn how they are approaching their PhDs or research, and where they are hitting bottlenecks.It’s available at http://www.qiqqa.com.Thanks,Jimme (jimme@qiqqa.com)