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October 17, 2013

In Pursuit of a Digital Academic Workflow: Putting Digital Reading, Annotating, and Citation Management to Work for Your Studies

October 17, 2013 | By | 4 Comments

I’ve always been one of those students who had trouble taking notes from readings.  I’ve tried a variety of strategies with varying degrees of success and most of these revolved around ways to write notes on paper, Word documents, or annotate hard copy texts themselves. Yet, I encountered problems with keeping track of notes and citations over time and even the basic step of making enough time to read AND take good notes.  I also experienced some bibliophilic trauma when I moved a few years ago and had to give away much of my personal library of heavily annotated books.  These experiences motivated me to explore ways to develop a digital workflow, so that I could keep as much of my library, as well as notes and annotations, on my computer or online for greater durability of access through life’s changes.  What follows is what I have found to be a useful digital academic workflow to minimally supplement the study habits of today’s students and scholars.

I developed the workflow below with the following goals in mind. I wanted:

-The ability to read, annotate, write notes, and organize these across digital platforms, with secure storage on my computer, but also available online and easily accessible;

-The ability to do all that with a more natural feel for the reading experience, i.e. something that felt like reading a hard copy but was actually digital;

-To keep clean copy of my digitized documents as well as an annotated copy, stored in the same place;

-To automatically extract digitized annotations as notes to be held separate from but near the PDF document, with an easy option for online viewing of the notes.

I have attempted to achieve these goals with minimum possible costs, given one’s access to a computer and tablet or smart phone, and maximum durability of the products of reading and notetaking labor.  I should note that I have a Mac computer and an Android tablet and smart phone, and this somewhat tense combination of devices is the basis for my workflow.  I also want to add that I don’t condone the use of any of the strategies reviewed below for any illegal purpose.

CREATE A CITATION RECORD:

There are many different citation manager programs out there for managing bibliographies, such as EndNote, Mendeley, and Zotero.  Personally, I have found Zotero most useful for my digital workflow and will refer to this program in the discussion below.

The first thing to do to ensure quality organization of your work is to create a citation record in Zotero of the book, article, or other resource you want to digitally read and annotate. This can be done in a few different ways.  One way to quickly and easily add a book citation is by looking it up on the Google Books or WorldCat database and use the Zotero plugin for you internet browser (Firefox, Chrome, or Safari) to automatically import citation information into a Zotero record. If you want to add a larger volume of books or sources at once, I recommend signing up for a free WorldCat account, saving a list of the multiple sources you want on their website, and using the Zotero plugin to import them all at once.  This ‘touch of a button’ method also works with many other websites, like JSTOR, where the plugin can also import a PDF article along with the citation, if you have access to it.

With this and all methods, it is important to double check your imported citation record in your library to ensure the information was imported correctly and with all the necessary information.  You may notice, for instance, Google Books is notorious for omitting the location of the publisher, but handy for importing descriptions of a book.  WorldCat frequently imports book titles in sentence-case rather than in title-case and often omits descriptions, but usually gathers complete citation data.

There is also a handy smart phone citation importation tool called Scanner for Zotero, which can be downloaded from the Android market.  This tool allows you to scan the barcode of a hard copy book with your smart phone and the program automatically uploads the citation record into your Zotero library.

Alternatively, you can work from a pdf itself by selecting a pdf that has been added to Zotero and choosing “create bibliography from item” to extract metadata and create the record. This works especially well on most contemporary digital articles. If the program doesn’t automatically recognize any metadata, try choosing the “retrieve metadata from pdf” option, but be sure the PDF has searchable text (a key feature for notetaking as well!). If all else fails, just manually input in the citation information. I know it can be tedious, but the above options work enough of the time, that manual inputs shouldn’t be too burdensome.

Now you have your citation record!  This will be the home for all your information about the source and can hold multiple PDF files, note files, image, audio and video files, as well as any useful web addresses you may want to include.  In addition to storing full-text PDFs, I have found the citation record particularly useful to store recorded lectures of authors, as well as book review documents.  Be sure you clarify the different file names of attachments under the same citation record!

GET A DIGITAL DOCUMENT:

The next step is to obtain a digital copy of your source, and make sure it is digitally searchable.  Many academic articles are already digitized and available online, and there are also many e-books available (for example, see this link).  However, if you only have access to a hard copy, you can easily digitize the article or book or book sections, by using a scanner.  I have found it most convenient to use my smart phone for this purpose.  I use an Android program called CamScanner to take pictures of a text and easily align and clean up the pages and convert them into a single PDF document, all on the phone.

You can then take this document and open it in Adobe Acrobat Pro or a similar program to reduce its file size and run an Optical Character Recognition (OCR) tool that converts the single images of the text pages into ‘readable’ or machine-encoded text.  This step is vital for quality notetaking as it allows you to highlight, underline, and perform other annotations to the digital document.  Then, just attach the document to the citation record in Zotero by a simple ‘drag and drop.’

Short of adding the PDF document to your Zotero library, it is also possible to use other resources like Ebrary.com, which lets you view many books online (with a university or personal account) or use Adobe Digital Editions to view a book you check out.  This resource also allows you to copy up to 30 pages of a text in PDF form.

READ AND ANNOTATE DIGITAL DOCUMENTS:

Your document is now ready to be read and annotated!  Of course, you have the option to read and annotate your source on the computer, right from Zotero. The note section of Zotero can open as a separate pop-up screen, resembling an actual document file.  However, if you, like me, crave a more natural reading experience that mimics reading and annotating a hard copy, I suggest reading on a tablet.  The tablet is where the whole digital workflow experience becomes very enjoyable and efficient, but the following steps also apply to reading on your smart phone.

The first step here is to download and install the ZotFile Reader, which is an invaluable plugin for Zotero.  This plugin will allow you to perform a number of features, two of which I find very important.  First, it allows you send your PDF document from Zotero to a cloud account (like Dropbox), where it can be retrieved by your tablet.  After some minor setup, you simply click “send to tablet” from your PDF in Zotero and then open the document on your tablet, using your preferred PDF annotation program.  I use iAnnotate, a free Android/iOS program with a lovely interface for reading and annotating PDF documents.  The only drawback of this program is that it can be difficult to erase annotations once you finish making them, making your annotations resemble ink.  Otherwise, it works wonderfully.

Once you have finished reading and annotating the text on your tablet, enjoying the natural experience, enhanced mobility, and ability to read in the dark, simply close the program and the changes should be automatically saved to your cloud account.  You then open Zotero on your computer, and on the record of the PDF you just processed, select the “get from tablet” option.  This pulls the most recent edited version of the PDF from the cloud and automatically stores it back in Zotero.  There is also a feature in Zotero to keep a “clean” PDF version and your “annotated” version automatically, both within the same record!

Now, we finally get to the second and best feature of the Zotfile Reader plugin.  In Zotero, select the PDF and choose “extract annotations.”  This feature automatically extracts all of the text you highlighted and underlined, as well as the notes you made in the margins, and saves them to your citation record as a separate note file.  Not only that, but it also automatically records the page number that the note is pulled from!  This is an amazingly useful feature that really impacts the ease and convenience of reading and annotating digital documents, especially from multiple devices.

With Zotero, you have a citation manager program on your computer that syncs to an online Zotero account.  This means that even if you don’t have your PDFs backed up online (which can come with a cost), you can access your notes online with ease and for free.  I have found that having this online backup of citation records and reading notes is very useful for working on the go and from any device.  You can also add notes to your online Zotero library from anywhere, and this will sync up to your computer easily.

I also think it’s useful to use programs like Evernote to take notes and sync them through multiple devices, but I always add the notes to Zotero afterward so that all notes have a central location tied to citation data.

WORKFLOW SUMMARIZED:

So, here is the very simple workflow I’ve worked out, again.

1. Add a citation record to Zotero from any of the convenient methods discussed above and attach the searchable PDF document to it. Make sure the full text document carries the name of citation as opposed to a book review or audio file that may also be attached.

2. Click “send to tablet” on the PDF in Zotero. This sends the document to your cloud account under a specially designated ‘tablet readings’ folder.

3. Open the document from the cloud in a PDF annotation program like iAnnotate from your tablet or phone.

4. Joyfully read and annotate with highlighting, underlining, striking out, in text notes, etc.

5. When you finish reading, close the tablet and open Zotero on the computer and click the citation and choose “retrieve from tablet.” This saves the annotated doc, as well as a back up clean version in Zotero.

6. Finally, click “extract annotations” and Zotero extracts all the annotations with related page numbers and saves them as a separate note file which can also be viewed online at the Zotero website even without saving any PDFs to the site.

Be sure to download the Zotero internet browser plugin, the ZotFile Reader plugin for Zotero, and any of the useful Zotero mobile applications which can be found at http://www.zotero.org/support/mobile to get the full features discussed above.

That’s all for this consideration for an academic digital workflow. Please contribute any ideas or recommendations for an academic workflow you have figured out in the comments section below.  Happy studying!

By Shanti Zaid

Comments

  1. do you know docear? it’s a new software for literature management (which i am developing). it is particularly useful if you want to annotate PDFs. you may also use it together with zotero and, more or less, with mendeley. if you are interested in having a try, look at http://www.docear.org/2013/10/17/docear-1-0-stable-a-new-video-new-manual-new-homepage-new-details-page/ (we just released docear 1.0 after a ~2 year beta phase).

  2. Chris

    Thanks, Shanti. It works for me – I have the same setup but I use Copy instead of Dropbox. However I notice that iAnnotate pdf for Android had a Dropbox option so that might work better.

  3. Alex Charnley

    Thank you so much for this. Fantastically set out!

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