Review: Docear

We’ve talked about Docear the Visual Citation Manager on the blog before, before my time, but it’s been a while we’ll revisit it. Though, the most recent major update to the software was in 2015, and based on the forums it seems that Docear has struggled with finding funding. However, the researchers behind this project are still active. That being said, in the worst case scenario, Docear is an open source project and if things went south, you could still get your information out. If you are considering relying on this software for organizing very long term research projects you need to use an external cloud backup service as their My Docear service is no longer available and supported if it ever existed at all.

Docear

Screenshot of Docear demo mindmap

Docear paper demo mindmap showing linked annotated PDF

Docear is an open source mind mapping, reference, and citation management software for those who want a visual way to keep their research organized. It is available for Windows, Mac, and Linux computers. Docear provides plenty of support and useful instructions through their official user manual. The examples on the app itself for trying out the mind map and PDF capability incorporate some of the research behind the product itself and makes for an informative, if somewhat meta, experience. Docear staff like to compare the software to Zotero and Mendeley, but it’s a very different type of beast. Specifically, a combination of Jabref (without the OpenOffice support) and Freeplane for mind maps, and, depending on what type of PDF viewer you use, a document annotation software. To enjoy the full capability of this software you also have to download PDF X-change viewer, though you can still do some annotating with other less supported PDF editors. Docear also uses Mr. DLib or Machine-readable digital library cataloging. While Mr. DLib has not really caught on elsewhere, it is featured as part of JabRef and specifically powers the article recommendation function. If they ever get their funding together, Docear could become a space where you can research, organize, and write an article. And unlike some of the software options discussed on this blog and in our LibGuides, you can download Docear from a zip file and run it to full capacity on Scholarly Commons computers.

Although Docear is not quite the all-encompassing research suite the creators envisioned, there are still lots of funky little features not found in other services. For example, in the Tools and Settings tab you can add map locations with OpenMaps (unfortunately there is no search function — you have to zoom and select your location) to add a geographic component to your otherwise mental map,which you can see by clicking on “View Open Maps Location” later.

Screenshot of Docear Open Maps features

You can also add time alerts for time management in Tools and Settings. But before we get ahead of ourselves, it’s easy to add a node with keyboard shortcuts and the node panel in the toolbar. You can add links to websites and other nodes right in your mind map by right clicking on a node. Apparently, you can add formulas to your mind map using LaTex but I didn’t try it, as I am not one of the people who cares about that sort of thing.

And while you do have the option of writing in Docear itself, there is a plugin for MS Word, but only on Windows. On the one hand, the plugin is old and hasn’t been updated in a few years, and it doesn’t work on the computers at Scholarly Commons. But on the other hand, since it’s based in BibTeX, if it actually does work the way they say it does, you should be able to use it with any BibTeX bibliography, and not just Docear. This means, it could give you that MS Word integration that you might be lacking with another reference manager.

Overall, if you wanted a reference manager and document annotator that is easy to get started on this is NOT the one for you, but for those patient enough to deal with the learning curve, Docear can be a good addition to your research strategy. I really hope this project gets the funding it needs to fully live up to its potential, but for now it’s still a solid option for researchers looking for a unique way to organize their work.

Getting Started With Paperpile

Did the Paperpile Review leave you interested in learning more?

To use Paperpile you need an Internet connection, Google Chrome, and a Google account. Since student/personal use accounts do not require a dot edu email, I recommend using your Google Apps @ Illinois account  for this because you can fully use and enjoy unlimited free storage from Google to store your PDFs. Paperpile offers one month free; afterwards, it’s $36 for the year. You can download the extension for Chrome here. If you already use Mendeley or Zotero you can import all of your files and information from these programs to Paperpile. In order to use Paperpile, you will need the app on each version of Chrome you use. It should sync as part of your Chrome extensions, and you can install it on Chrome on University Library computers as well.

You can import PDFs and metadata by clicking on the Paperpile logo on Chrome.

Paperpile import tool located just right of the search bar in Chrome

On your main page you can create folders, tag items, and more! You can also search for new articles in the app itself.

Paperpile Main Menu

If you didn’t import enough information about a source or it didn’t import the correct information you can easily add more details by clicking the check mark next to the document in the menu and clicking edit on the top menu next to the search box for your papers.

Paperpile

Plus, from the main page, when you click “View PDF” you can also use the beta annotations feature by clicking the pen icon. This feature lets you highlight and comment on your PDF and it saves the highlighted text and comments in order by page in notes. It can then be exported as plain text or as very pretty printouts. It is rectangle-based highlighting and can be a little bit annoying, especially when highlighting doesn’t always covered the text that was copied. Like a highlighter in real life you cannot continue to highlight onto the next page.

Highlighted and copied sentence split by page boundary

When you leave the app, the highlighting is saved on the PDF in your Google Drive and you can your highlights on the PDF wherever you use Google Drive. The copied text and comments can be exported into a very pretty printout or a variety of plaintext file formats.

Print screen of exported annotated notes on Paperpile

Not the prettiest example but you get the idea.

Once you get to actually writing your paper you can add citations to your paper in Google docs by clicking the Paperpile tab on your Google doc. You can search your library or the web for a specific article. Click format citations and follow the instructions for how to download the add-on for Google docs.

Paperpile cite while you write in Google Docs

I didn’t try it but there’s a Google Docs sidebar so that anyone can add references, regardless of whether or not they are a Paperpile user, to a Google Doc. I imagine this is great for those group projects where the “group” is not just the person who cares the most.


Troubleshooting

Paperpile includes a support chat box, which is located on your main page, and is very useful for troubleshooting. For example, one problem I ran into with Paperpile is that you cannot change the page number to match what it actually is in the article and page number is based on the PDF file in the notes feature. I messaged and  I got a response with a professional tone within twenty-four hours. Turns out, they are working on this problem and eventually PDFs will be numbered by actual page number, but they can’t say when they will have it fixed.

For other problems, there is an official help page  with a lot of instructions about using the software and answers to frequently asked questions. There is also a blog and a  forum which is particularly nice because you can see if other people are experiencing the same problem and what the company plans to do about it.

Scholarly Commons runs a variety of Savvy Researcher workshops throughout the year including personal information management and citation managers. And let us know in the comments about your favorite citation/reference management software and your way of keeping your research organized!

And for the curious, the examples in this post are based from the undergraduate research collection in IDEALS. Specifically:

Kountz, Erik. 2013. “Cascades of Cacophony.” Equinox Literary and Arts Magazine. http://hdl.handle.net/2142/89474.

Liao, Ethel. 2013. “Nutella, Dear Nutella.” Equinox Literary and Arts Magazine. http://hdl.handle.net/2142/89476.

Montesinos, Gary. 2015. “The Invisible (S)elf: Identity in House Elves and Harry Potter.” Re:Search: The Undergraduate Literary Criticism Journal 2 (1). http://hdl.handle.net/2142/78004.

Review: Paperpile Citation Manager

Are you addicted to Google Docs and are looking for a citation manager, PDF reader, or research workflow system? Do you wish you could just cite while you write in Google docs like you do with Zotero or Mendeley in Word? Do you have an extra $36 a year to spare?

Then you might want to try Paperpile!

Paperpile App Main Menu

Paperpile is a simplified reference management system and research workflow program for Google Chrome created by three computational biologists based in Vienna.

Pros:

  • Easy to use
  • Can organize your sources when you’re trying to write a paper or doing readings
  • A lot of explanatory text in the app
  • Allows you to import metadata and PDFs from your browser (similar to Zotero’s one click import) and asks you if you want to add the item (PDF and details) to Paperpile
  • The annotations feature makes readings and notes for classes a lot of fun with very pretty colors
  • When the PDF is not encrypted, if you highlight the text it will copy the highlighted text into notes with your annotations that you can then copy and paste when writing a paper
  • Wide range of document types and citation styles
  • You can cite while you write in Google Docs
  • Provides look up to find similar journal articles to what you are researching, which allows you to do research through the app, especially if you’re doing research from science databases
  • Keyboard shortcuts
  • 15 GB of free space through Google
  • Good customer service
  • Thorough explanatory material
Highlighted text with annotations in the Paperpile app

Excerpt from Montesinos, Gary. 2015. “The Invisible (S)elf: Identity in House Elves and Harry Potter.” Re:Search: The Undergraduate Literary Criticism Journal 2 (1). https://www.ideals.illinois.edu/handle/2142/78004.
And check out Re:Search: The Undergraduate Literary Criticism Journal and more great undergraduate research in IDEALS!

Cons:

  • High cost ($36), especially compared to solid free options like Mendeley and Zotero
  • Requires Internet access
  • Although the company is in the process of developing a plugin for MS Word, currently, Paperpile is heavily reliant on Google and Google Drive
  • Paperpile is a proprietary software and a startup so there are risks that they will go out of business or be bought by a larger company
    • Though, should the worst happen Paperpile uses open standards that will allow you to get your PDFs, citations out — even if they are in an ugly format — as well as the highlighted text saved in your PDFs, which can be downloaded through Google Drive
  • Paperpile is a very new product and there are still a lot of features to be worked out
    • I will say however that it is a lot less buggy than a lot of comparable reference management / PDF annotation software that have been around longer and aren’t classified as in beta, like Readcube and Highlights

Paperpile is comparable to: Mendeley, iLibrarian, colwiz, Highlights.

Learn more about personal information management through our PIM Libguide, various Savvy Researcher workshops and more! Let us know about your strategies for keeping everything organized in the comments!