Year for Productivity: Session 13: Annotation Software

If you are like meyear_productivity_graphic_13, you probably spent a good many years in school reading articles, textbooks and class notes.  You, like I, were probably also busy highlighting and writing notes in the margins of those same items.  I have spent so many years in study that I can hardly read a non-fiction book any longer without a highlighter and pad/pen by my side.  While I was in school, I would then go back through all my notes and highlights to try to piece together my report or paper.  Do any of you remember having a pile of numbered slips of paper with quotes which would be mixed and matched for content?

These days, I try to rely more and more on totally electronic methods of organizing my resources from start to finish.  I haven’t found the perfect method for me, but I continue to try new things and adjust my workflow.  Have I totally broken the habit of taking notes with a pen and paper notebook?  No, I’m not there yet, but now if I take notes by hand (often when reading a library book), I scan my notes so I can file them electronically.  I also tend to file them either in OneNote or Evernote.  Both will OCR the documents so that I can search within them later.  Yay!

This year, Mary and I have been using Evernote to complete and track all the research we are doing in order to bring this series to all of you.  I have found it to be a nice application for our purposes.  We created a note for each topic planned throughout the year, and then have been adding links, quotes, pdfs, etc that we find on each of the topics as we go through our daily curation activities. Some of our notes have become very long, which is not my preference, but it has been quite adequate for our purposes.  And isn’t that the key? Not necessarily looking for the most elaborate tool, but the tool that fits the need of the task at hand.

Today, as you have guessed by now, we are going to focus on one of the key tasks in the academic research workflow: annotating our research.  Let’s begin by thinking about the characteristics of note-taking. What kinds of tasks do we ideally want an annotation tool to solve for us?

  • Highlighting in multiple colors
  • Ability to add in-line notes of any length.
  • Ability to sort on keywords in the in-line notes.
  • Ability to export pdfs with notes/highlights intact.
  • Ability to ALSO export without notes/highlights (professors like this in particular so a clean copy of an article can be distributed to their class)
  • Ability to print highlighting/notes with the article.
  • Can handle citation creation or a tool that “talks to” other citation software.
  • Ability to share pdfs with others and to “discover” like research in a community of users.

Annotation software is one area of PKM that I feel still has a long way to go.  I have yet to find a product that I am totally happy with, and some of the most promising products are written for those in a MAC environment (Devonthink or Sente , for example) or have recently been purchased by major academic vendors (Springer’s purchase of Papers, Elsevier’s purchase of both Quosa and Mendeley to name only a few).  I’ve listed some key articles on several of the more popular annotation tools in the Selected Readings section, and the Wikipedia article “Web Annotation”  has a nice table comparing a list of web annotation systems on various criteria.  While there are several alternatives for MAC and mobile tools, major PC annotation program options took a big hit when Mendeley was purchased by Elsevier.  While it is still a good tool, and may even have exciting improvements for Elsevier clients, it’s long-term future for non-Elsevier clients is less clear.  Endnote, a key player in the citation software arena, has added annotation features to its product, however, it still has a long way to go.

I’ll close our discussion today with one newer tool called Qiqqa (rhymes with “quicker”). Created by a Cambridge University graduate, Qiqqa’s beta version launched in 2010.  By 2011, it was winning several award competitions.  It features reference management and annotation capabilities, a mindmapping feature and manages to plays nice with Microsoft Word and LaTeX.  It offers a free version for desktop use with a small(200 MB) online storage option.  Best of all, it works on Windows and Android operating platforms.  The Professional version (8000 MB) is $3.99 a month. I plan to play with this tool a little more myself, and will hopefully be able to post a more detailed review in the future.

For Further Exploration and Insight:

  1.  Take five minutes and think about your research process.  Do you annotate as you read?  How do you use those annotations?  How do you store both the PDFs and the annotations? Outline your process, noting any weaknesses or disconnects in your process.  Put a star next to any parts of the process that are working well.
  2. Explore one of the products listed either in the selected readings below, or from the Wikipedia article on Annotation Software.  Does the tool you explore solve any of your weaknesses in question 1?  Does it create other problems instead?


Selected Readings:

Especially for Mobile Devices:

Springer Gets Reference Manager Papers (2012.)
This newsbreak from Infotoday discusses many of the various tools that compete with Papers, outlining their capabilities.

Sente vs. Papers: What is the best PDF management system? (Parts 1 &2)
Part 1:

Part 2:

The ultimate guide on how to annotate PDF files on the iPad:

DevonThink (MAC):

Steven Berliner Johnson provides two illustrative posts on how he uses DevonThink:
First Post:  Followup post:

Chad Black, an Associate Professor at University of Tennessee-Knoxville, did several posts back in 2008 on how he used DevonThink:


The Qiqqa User Manual:

Qiqqa YouTube Channel:

Good Review which highlights the strengths and weaknesses of this product (March 2012):


This review suggests that what ReadCube does is good, but may still miss key research elements:

PCWorld Review (11/2012):


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