Finding your academic writing workflow mojo Part 3: PDF annotators and readers

This posting follows Part 1 on writing tools and Part 2 on reference managers. Comparatively, PDF readers and annotators might seem less exciting, but they can be critical to your workflow and I'll share why. Researchers use PDFs in a particular way, and it is important to be able to annotate and recall our notes efficiently. While part of this organisation has to do with data management, there are ways to read and annotate PDFs in such a way as they can be better used by your data management tools, which I will explore in Part 4.

The basics of annotation are the ability to highlight text and add comments. Different applications implement this better than others, but basically it is all there. One thing to look for is that you can put your PDF annotator in highlight mode and highlight by highlighting with the mouse (commit on release) rather than by highlighting with the mouse and then clicking the highlighter button or highlighting colour to commit... that is ways too many clicks and disrupts the workflow. After reading hundreds or thousands of papers, these basics are not enough. The problem is recall: how to find the important stuff again. Adobe Acrobat Reader (Mac & Windows)

Okay, well, obviously, everyone knows Acrobat. Reader is free and reasonably effective, but it really only does the most basic annotation (maybe in the hopes that users upgrade to Acrobat Acrobat Pro, which I will not review since that is more of a PDF editor than annotator). I have been using the new Adobe Acrobat Reader DC lately, which Google Drive allows to open documents directly from Drive. This workflow works well with online reference managers that store to Google Drive like Paperpile. Preview (Mac only)

Every Mac comes bundled with Preview. Acrobat Reader and Preview always seem to be vying for the best offering to the user. Preview has some more PDF editing features than Reader does, but for the purposes of annotations, it works the same way. It has some nice settings like to open the file again where you left off instead of at the beginning, which I like.

Skim (Mac only) Skim is my PDF reader and annotator of choice for sole-authored work. Here is why it stands out: 1) Highlighted text and comments can automatically be exported as a text file on save. This is great for recall. It means that later, I can search only the text files so I limit my searches to only my notes and important text. 2) Comments can be inserted under several different categories, each with their own icon. So I can enter a comment as 'comment' , 'key', 'note', 'help', and a few editorial options like 'new paragraph' or 'insert'. like the others it is free, but it is also open source. It also opens to the last page viewed as an option. I like to use open-source software whenever possible, and Skim outcompetes its rivals in my opinion. The weakness here is that Skim annotations and Preview/Acrobat notes are not all that compatible. While Skim can read notes from those applications, they can't read Skim's. If you use multiple applications to take notes on a PDF, things can get messed up quickly.

MetaPDF MetaPDF is a new reader. Its advantages are that multiple users can comment on the same PDF at the same time. It can also read and be read by Adobe Acrobat Reader and Preview. It is web-based and you have to log on using your Google account. MetaPDF is from the Paperpile people, at which I looked in Part 2. You can export your annotations manually, where Skim does it automatically. As a web-based application, it is limited in terms of offline work, but they say that is coming on their website, as are some features I never use, like making shapes on the PDF. Meta PDF is in beta at the time I wrote this, but it is quite slick and easy to use. I can see myself moving to this, especially if I went with Paperpile on a collaborative project. UPDATE: The folks at PaperPile, who make MetaPDF, now have a built-in PDF reader in PaperPile. I think I love it... once you set PaperPile up to use its own PDF reader, you will find a reader that is great for parsing highlights and notes, and allowing you to highlight in different colours. Drawing functions are coming soon. I don't know what the plan is with MetaPDF and PaperPile PDF Reader, but it is the only PDF reader I use now when reading from PaperPile.

Utopia Docs (Mac & Windows)

I want to love Utopia Docs. It looks amazing and turns PDFs into active files that can be clicked through on references to continue searching for other papers within the PDF reader. This seems like it would be a great workflow, but it doesn't work with all PDFs. It seems that recent journal articles are the best bet, but in the social sciences a lot still don't work. It needs to be able to find the article in PubMed, or through a DOI reference or CorssRef or something like that. If it can find it, the result is quite cool. Utopia Docs links to all the documents to which the article refers, allowing the user to click through and keep reading. So it can be useful for doing the research in terms of article gathering, but it is not really an annotator.

Qualitative Data Analysis Software

I am grouping these together here because I look at them in Part 4. What I mean by QDA software are packages like Nvivo, Dedoose, Quirkos, MAXQDA and so on, often used by qualitative and mixed-method researchers. Conventionally, they are used for coding text from interviews or documents according to user-defined categories (nodes). Practically, they work by the user highlighting text (many of them can do this directly on a PDF) and then coding that text to a node. So, this could be done for literature highlighting also. The main advantage would be that the highlighted sections would not just be highlighted but coded. Later, when you code your interview data, you could run queries that would pull up both your literature and interviews at the same time... that could be very powerful although I have never done it that way, mostly because there is no way to connect a PDF annotated in QDA software to the reference manager, as far as I know. If there were, I would be keen to try this out. If you don't mind the double entry and disconnected files, this might be interesting, but has to be done from the beginning of your research project. Something else to keep in mind, which could also be said for any kind of literature annotation, is that often we don't know what the interesting bits are until we are well into our analysis... this might mean some re-coding of literature in the same way as we need to recode primary data. Once this is all done, it means that you could search for all your notes on a certain topic, for example, which would make finding things much easier than un-coded notes and keyword searches on which we otherwise have to rely. While many of the reference manager applications in Part 2 have the ability to annotate PDFs, I haven't found any that make this process as smooth as a dedicated PDF reader does. Most of them, including my favourite Sente and also EndNote, don't have a very smooth way of highlighting and require too many clicks to commit a highlight. Sente does allow the ability to search just notes, so that gets to some of where I get with Skim without any additional software. Sente also allows the attachment to be opened in a default PDF reader. It's an extra click, but it works. Note that because Skim is Mac-only, collaboration is not possible if you have non-Mac users on your collaboration. For collaboration, MetaPDF and PaperPile

Reader seem to be the way to go, and/or Acrobat Reader DC saved to a central location or with a paid Adobe subscription.

As I mentioned in Part 1, I don't know much about Windows software options, so there may be others that work in that environment.

This article was originally posted to the author's LinkedIn page.