In my work at Duke University on simulation, games-based learning, and learning technology, I frequently read and write scientific information. I’ve developed a series of workflows to help me efficiently deal with information when writing papers and grants. In a previous entry I talked about how I try to batch operations, doing similar things at the same time. This entry will be about my workflow for reading scientific manuscripts.

I use Skim for scientific reading, typically using the bottom pane of the “Split PDF” feature to look at the title of references as I come across them in the body of the manuscript. On average, I’m interested in downloading about 10% of these references to my personal library.

Although I love Skim, one feature I have not been able to figure out is how to highlight items in the bottom split screen. Thus, I’ve created a workaround. Before I start reading an article in Skim, I create a note called “Get Manuscripts” As I’m reading, I merely record the references number of articles I want to fetch in my “Get References” note. Because I create this note first it’s always located at the top of my Skim Notes. When I’m done reading the current article and processing my annotations, I retrieve the supporting articles I identified while reading. 

To do this, I use a phenomenal program called KeyBoard Maestro. Keyboard Maestro lets me type a single keyboard command to trigger an entire workflow. One by one, I work through my “Get References” numbers, highlighting the title of each corresponding article. After highlighting each title, Keyboard Maestro does the rest (invoked by Command-Option-R).

Keyboard Maestro automatically  (1) copies my highlighted text, (2) surfs to the Duke Library literature search page, (3) pastes the text string into the appropriate field, and (4) submits the search. Thus, with a single key combination, I am able to download the full text of supporting literature. Once I find the full text I’m interested in (usually a PDF), I save it to my Download Folder, where Hazel takes over and imports the paper into my Papers Library.

If I’m not ready to retrieve the articles, I create an Omnifocus Action for each to be collected at a later time.

My macro is not limited to Skim, it works with any text I’ve highlighted, be it on the web, in a manuscript, or somewhere else. Here is a picture of the programming, but obviously, you’ll have to modify it for your own favorite full-text repository. Enjoy!

Maestro Automate Full Text Retrieval


Addendum (January 14, 2014): If you’re searching at Duke, you’ve probably noticed the library changed its search interface. I’ve updated the Keyboard Maestro Script accordingly. It’s only configured to search for peer-reviewed articles. Download the script and import it into Keyboard Maestro (will only work for Duke Libraries).

Tagged with →  

5 Responses to Writing and Reading Workflow: Batching and Automating Full-Text Retrieval

  1. John Burrows says:

    Have you given up reading in Papers? I don’t know why it didn’t dawn on me that, rather than paste my highlights into notes when reading with Papers (which Skim deciphered correctly more often than highlights), just read it in Skim to begin with. Thanks!

  2. Jeff Pooley says:

    Very, very impressive. And didn’t even know about the split pdf view in Skim–terrific. Many thanks.

  3. Martin W says:

    Great workflow explanation. An alternative to the keyboard maestro trick that I did was to create a custom popclip extension (really easy) to search pubmed using a tutorial I found here:–mac-50637

  4. multiplebs says:

    I’m curious how you incorporate reading with Skim in your Papers2 and DevonThink workflow. Annotation features in Papers2 & Paper for iOS are not very comfortable, and I’m trying to find an alternative here.

Leave a Reply

%d bloggers like this: