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Posted by Peter
Oct 7, 2009 at 08:01 AM


Mendeley apparently offers PDF annotation (attaching notes directly to a text passage rather than the entire document). Does anyone know if this feature available in any other application?


Posted by Peter
Oct 7, 2009 at 06:38 PM


A 24-hour update.

I’ve spent a few hours now reviewing Evernote, Mendeley and Zortero. (There is another review of these three programs here: http://nickprojects.com/category/management/.) Here are my quick reflections.

Evernote Pros & Cons
If the number of YouTube videos on how people use it in their everyday is an indication, Evernote seems to be gaining a kind of pop status, primarily among college students. Trendy or not, I found it’s online ocr capabilities unmatched in the other programs. Although I haven’ t tried it myself, there is a feature for sending images from a mobile phone and getting them automatically uploaded to your database for ocr processing (e.g business cards, menus, street signs) with very little effort. This has very interesting implications for any visual data gathering in the field. I also like the ease with which it handles note-taking and importing multiple file types (limited in the free version). It seems to offer a glimpse of how an internet of things might emerge (but now I’m getting off topic). On the downside, after only a brief amount of testing, my ‘Current Monthly Usage’ is about half empty which makes the ‘Premium’ option ($5/mo) a necessity. Also, it doesn’t handle pdf markup and you have to log on each time which makes offline work impossible.

Mendeley Pros and Cons
Mendely caters more to the professional academic which I like. However, like Zotero, it’s really a citation/reference manager (e.g. Endnote) on crack and not intended for writing text. This was not immediately obvious to me however but perhaps should have been. Still, it’s ability to annotate pdfs sets it apart from the others. It also has collaborative features which some people might find useful. Like the other two it can grab and import web selections as individual posts. The most frustrating aspect about Mendeley is the inability to create any kind of arbitrary note on the fly which definitely disqualifies it as a piece of writing software. It only manages imported material.

Zotero Pros and Cons
I don’t think I really have much anything new to say about Zotero since it seems like a fairly well known add-on for Mozilla. It’s an open source app that feels solid with a strong community of followers. Like Mendeley, it’s really a reference manager with some added features over a program like Endnote or Reference Manager. For one, it can search and find the reference information for a given website or pdf which helps reduce data entry. It also permits note-taking. It has a clean interface and I generally like it as well as Mendeley. On the downside, while it does annotate web captures, it cannot markup pdfs which was a disappointment. Also it’s tied to Mozilla which means if you’re on the net for research you’ll probably stuck with Firefox.

In the meantime I found this post that suggests Adobe Bridge can be used for pdf management which was an new twist:
http://peregrina.wordpress.com/2009/01/29/using-adobe-bridge-to-organize-documents/. I’m looking forward to try that out.

Zoot was a disappointment because is only imports the text and looses the pdf layout along with any comments. And similar to most of the other programs recommended in this thread the interface environment is just a little to harsh to be staring at it for more than a few minutes at a time. Maybe it’s time to get a Mac after all.

So, I’m still on the look out for the optimal PC Scrivener alternative and may just have to settle for the outline view in Word in the interim. :(

I hope somebody with find this useful!

Cheers, Peter



Posted by Lucas
Oct 7, 2009 at 06:50 PM


Peter wrote:
>Mendeley apparently offers PDF annotation (attaching notes directly to a text
>passage rather than the entire document). Does anyone know if this feature available
>in any other application? 

Hi Peter,

For PDF annotation I use PDF-XChange Viewer, which I’m very happy with. The website is:


The free version is adequate, but puts a watermark on your PDFs when you use certain advanced features. I eventually paid the very reasonable price ($34.50) for the Pro version, but many people use the free version and are satisfied with it (the free version includes annotation). One feature I particularly appreciate is that you can easily see a summary of all the notes you’ve taken on a particular document. (The notes show up in the particular passage where you placed them, but they also show up in the convenient summary.) I haven’t experimented with Mendeley, so I don’t know whether they offer this feature. In general, I find PDF-XChange Viewer to be a very solid and well-designed program.

I store all my PDFs in Zotero, and open them with PDF-XChange Viewer, so that the annotations are immediately saved and backed up. Also, if I open up Zotero on my Mac, the PDF annotations will be visible there too. (And if I want to annotate on the Mac, I just use Preview.)

I confess that Mendeley does sound promising as an integrated solution, but Zotero is currently working well for me, so I don’t particularly want to spend the time right now to switch over.



Posted by Wes Perdue
Oct 8, 2009 at 06:51 AM



About Evernote, you wrote:
>you have to log on each time which makes offline work impossible

I think you only need to log in if you are going to sync up to the cloud. I had the app save my credentials upon first install of the app on a system, so I am logged in automatically.  I create and update notes while offline on a regular basis; they always update via auto sync the next time I’m online. This is true for all three platforms I use regularly: PC, Mac, and iPhone. For iPhone, a note must be marked a favorite for it to be available offline.

Btw, I believe you can create local notebooks that are never sync’d.



Posted by Alexander Deliyannis
Oct 8, 2009 at 08:40 PM


Wes Perdue wrote:
>Btw, I believe you can create local
>notebooks that are never sync’d.

Yes you can. I have a ‘temporary’ notebook that I have selected not to sync. However, once you choose what type of notebook you want (local or synced) you can’t change your mind. This is not as bad as it sounds, because it’s very easy to create another notebook of the type you want, select and drag’n'drop all your notes there.

I very often work offline with no problem; all info, including attachments, is available locally. When I’m online again my changes will be synces. I have found no other that does this as seamlessly as Evernote though, as I’ve written elsewhere (in the post that Peter found me screaming :-), I expect many more information managers to become web-aware eventually.

However, there’s one very important reason that Evernote is, for me, completely unsuitable as a writing environment. You’ll have a hard time believing it, until you’ve tried it yourselves: there is no way to create a copy of a note within Evernote—other than create an empty note and copy/paste the content and title- which I find an unacceptable limitation (I have told the developers so, stressing that I am a Premium user, but so far nothing has changed).

So, to put it simply, if you want to use some collected material while preserving the original source, you have to start copying and pasting as if you were in Word.


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