Friday, October 07, 2011

Mendeley, Sente, or Papers? No, Zotero and iAnnotate will do.

This is a nerdy blog post, relevant only for researchers.

Every researcher needs to read academic papers. I often do this while commuting or being away from office. It often happens that I don't have a hard copy of the paper that I want to read while being away from office. I never know which paper I want to read in advance.

With the advent of iPad, this problem can be solved by storing all the academic papers in iPad. But that's not the end of the solution. Two more things need to be solved: annotation and bibliography management.

I often highlight some sentences in an academic paper. I also often add a note to the paper. I even sometimes draw a simple graph on the paper. This needs to be done on the iPad screen.

Plus, I need to manage bibliography. Currently, I'm using Zotero for bibliography management, but this Firefox plugin doesn't allow me to read a PDF file with the annotation function. Ideally, every time I download a PDF copy of an academic paper onto iPad, a new entry should automatically be created in this bibliography. Then it's going to be easy to create the section of references in my own paper, in my lecture syllabus, or in an email message that I write to refer my colleagues to the papers they might be interested in.

It seems there is no perfect solution for all these. Partial solutions are provided by Sente, Papers, Mendeley, and iAnnotate.

If I don't need to use an iPad (which is totally out of question but...), Mendeley is the best solution because you can automatically sync with Zotero, which is still the best solution to easily create bibliography while downloading a PDF file of the paper. After visiting the webpage of an academic paper in Firefox, click the reference icon that shows up on the address bar of the Firefox, and then bibliography information will be stored to Zotero and thus to Mendeley. Then download a PDF file from the same webpage to a folder on my desktop computer and drag the icon to Mendeley window. This allows me to read the PDF file on Mendeley, which allows me to annotate.

The problem with Mendeley is that its iPad application does not allow you to annotate. How stupid it is.

Annotation on iPad is not a problem with Sente or Papers. But both are rather poorly designed in terms of the automatic bibliography entry creation while downloading a PDF file of the academic paper. Plus, Sente's annotation function is stupid in the sense that you cannot associate your note to a particular sentence that's highlighted. Notes are only associated with a page.

In terms of annotation on iPad, iAnnotate seems to be the best application. However, it doesn't come with the bibliographic management function. An ideal solution is to combine iAnnotate with Mendeley, but Mendeley does not allow you to read the PDF file annotated with iAnnotate.

What makes things worse is that any of these iPad applications (Sente, Papers, and iAnnotate) is not free. There's even no trial version. Each costs less than 10 US dollars, but should I buy all of these to test which is the best among available?

It seems that's the way to go in the world of Apps. Buy several alternative applications for your iPad (or iPhone) and choose the best....

It seems the quick solution is to use Zotero for bibliography management and iAnnotate for annotation on iPad (with Dropbox used for transferring PDF files from the desktop computer to iPad).

Zotero is very powerful. When you log on to a webpage of an journal article, the address bar shows an icon which can be clicked to create a new entry in the bibliography AND to associate this entry with the link to a PDF file on the web. Clicking this PDF link allows me to save a PDF copy. Since I don't use Firefox for any other purposes (Google Chrome is much better to surf the net), I can set a Dropbox folder for PDF copies of academic papers as the default download folder.

Then on iPad, launch iAnnotate, click the download button on the top-left corner (which shows the list of folders in my Dropbox), then click the PDF copy folder. This updates the list of PDF files in iPad. You need a WiFi for syncing PDF files between the desktop computer and the iPad, but in my office there is an eduroam wireless network. So there's no problem.

So, after reaching a webpage of an journal article, I only need to click four times (twice on the desktop and twice on iPad). Then I'm able to read a PDF copy on iPad. This is very efficient.


massi182 said...

Had the exactly same problem with Mendely and Iannotate, after nearly one year this issue is still up... I'll try what you suggest

Anonymous said...

Awesome post. I'm was a biomedical grad student with the same problem. I also like searching for literature on my iPad. How do you get papers found, saved, and annotated initially on the iPad onto your desktop?

Anonymous said...

I always use Google Scholar. If you're connected to the Internet via your academic institution, there should be a link in each search result to your institution's library webpage from which you can access to journal articles as long as the library subscribes to the journal.

JB said...

I am one of the founders of Docear, which is a new software for organizing, creating, and discovering academic literature. Today, we released version 1.0 of Docear after a ~2 year beta phase. If you are interested in reference management, you might want to have a look at Docear. The three most distinct features of Docear are:

1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, ... and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).

2. A 'literature suite concept' that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.

3. A research paper recommender system that allows you to discover new academic literature.

And Docear is free and open source and available for Windows, Mac, and Linux. More information can be found in our Blog, including a detailed explanation of what makes Docear superior to Mendeley, Zotero, etc. (at least in our opinion :-) ).

If you don't like reading, there is also a 6 minute introduction video on our homepage ;-)

In case you are using a BibTeX based reference manager such as JabRef (and you don't want to use Docear), you might still be interested in Docear4Word Docear4Word allows you to insert references and bibliographies from BibTeX files to MS-Word documents. Hence, it makes writing papers much easier, since e.g. JabRef has no own MS Word add-on.

Finally, I would like to point you to a recent Blog post I wrote about what makes an evil reference manager. Maybe the post helps you deciding which reference manager to use (even if it's not Docear).