Using AppleScript to Automate Notetaking

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Writing setup at London Library[This guest post reprints, with permission, Jason Heppler's post from Saturday. Jason is a Ph.D. candidate in history at the University of Nebraska, Lincoln, where he is also project manager for the William F. Cody Archive. He's also the author of The Rubyist Historian. You can follow him on Twitter at @jaheppler.--JBJ]

On a recent episode of Gabe Weatherhead‘s Generational podcast he spoke with Walton Jones, professor of Behavioral Neurobiology at Korea Advanced Institute of Science and Technology. They talk about Professor Jones’ system for annotating and summarizing academic papers about twenty minutes into the podcast. He’s further detailed his academic workflow on his blog, so be sure to give his explanation a read.

I’ve noted before how I manage my PDFs using the filesystem and Open Meta tagging. I’ve tended to maintain my notes in plain text written directly into DEVONthink, but after listening to Weatherhead’s talk with Jones and reading his post I’ve decided to adopt part of his system.

As a scientist Jones spends much of his time synthesizing the latest research that normally comes to him as a PDF from journals. Where I became interested in his system was 1) his color coded annotations and 2) his method of extracting those annotations to plain text. His system uses colors for different notes, green for references, red for summaries, and so on. Where the system really inspired me was his AppleScript that can process the PDF he has marked up (either in Skim or iAnnotate that scans the PDF and extracts notes based on his categorization using Markdown syntax. He then dumps the notes into VoodooPad. Be sure to read his explanation of his system as my summary doesn’t do it complete justice. [Update: I was remiss in pointing out that the original AppleScript adapted by Walton Jones came from John Sidiropoulos at his blog OrganoGnosi. His blog has lots of advice on using digital tools for academic research.]

The system relies on an AppleScript that looks for annotations in the PDF and extracts the text into Markdown-formatted plain text. I modified the script slightly for my own needs, and made it available here via GitHub’s Gist service. [JBJ: We can't yet embed Gists directly, alas! Apologies for any inconvenience.] For the curious, here’s a partial screenshot of the code:

Screenshot of gist

I take my notes in Skim, which would result in something like:

Skim notes

When the script is run on a PDF, it results in a note formatted in Markdown that looks similar to this:

Screenshot of Markdown output

That’s where the other half of the magic comes in Jones’s system. The note not only includes the text I wanted but also a hyperlink to the page of a particular reference. Transformed into Markdown, the note allows me to click on the reference and be taken back to the source. My notes used to appear similarly, often taking a form such as:

[3] Noting the page number in brackets followed by my notes, thoughts, direct quotes, and so on from a PDF or book.

As I mentioned, my notes were previously entered directly into DEVONthink. But with this new system I’ll be keeping my notes in the same directory as the document I’m taking notes on. From there, DEVONthink will index the directory for easy searching and organizing.

Update on 11/29: Readers have pointed out that the hyperlinking to specific pages isn’t working the way it should. The solution, near as I’ve been able to replicate the problem, points to just how unrobust this system is, unfortunately.

Walton Jones had to work around the problem by writing his own custom URL scheme. You may need to adopt his system to get everything working. But Skim seems to handle page numbers without any problems, at least for me. There are a few things to bear in mind when using the script: 1) The notes must appear in the same directory as the PDF, and 2) the file must match exactly the text in the note (which the script should handle for you). So, for example, example-article.pdf#page=3 must correspond exactly to example-article.pdf and reside in the same directory as the notes, otherwise it doesn’t know where the file is located. Also, be sure that no spaces are included in the filename, otherwise the Markdown linking will not work.

The other area that makes the system tricky to use is the way I’m using it. When I transform the text notes into Markdown, I save the resulting markup as a PDF (either transformed in Marked.app or fed through wkpdf). The PDF file of my notes is opened in Skim, which can handle linking back to the article because all of these actions are happening within the same application. In other words, if you are planning on using the hyperlinking system as I use it, you will need to contain all activity in Skim. Otherwise, you may need to look into Walton Jones’s custom URL scheme. Relatedly, you might check out John Sidiropoulos’s brilliant post on DEVONthink and hyperlinks.

Photo “Writing setup at London Library” by Flickr user TheCreativePenn / Creative Commons licensed BY-2.0

 

Build Your Own Open Access Journal: An Interview with Rob Walsh of Scholastica

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This is the seventh interview in a series, Digital Challenges to Academic Publishing, by Adeline Koh. Each article in this series features an interview with an academic publisher, press or journal editor on how their organization is changing in response to the digital world. The series has featured interviews with Anvil Academic, Stanford Highwire Press, NYU Press, MIT Press and the Penn State University Press. 

Want to start your own open-access journal? Find out more today as I speak with Rob Walsh of Scholastica, a new journal publishing platform. Scholastica aims to make open access feasible for existing and new journals by charging a small $10 fee when an author submits to a journal. This fee can be paid by the author, journal, or an institution that would like to pay on behalf of its authors. The article, if accepted and published, will be made freely available on the web. Scholastica now works with the University of Chicago Law Review, the California Law Review, and smaller journals such as the Strategic Leadership Review.

AK: Thanks Rob for talking to me today. To begin: is Scholastica a “publisher” per se? 

RW: Scholastica is an end-to-end platform for publishing journals, so not a publisher itself but rather a tool to improve scholarly publishing. You can think of Scholastica as a tool for journals like WordPress or Tumblr is a tool for blogs. Our mission is to put control of scholarly publishing back in the hands of scholars, not large corporate publishers.

Want to make your own PeerJ? You can do that through Scholastica. Don’t have the technical know-how to install or update a version of Open Journal Systems? Scholastica is ready for you out of the box. Want to try out a new peer review idea? We love building new models for peer review and publication, so give us a call. We support scholarship by making it easy to run a top-notch peer reviewed journal from submission to review to publication.

Running a journal is complex in terms of communicating with authors and reviewers, managing file versions, gathering reviews, and making published content easily discoverable online. Scholastica provides ready-to-use infrastructure so journal editors can focus on finding the best content and not have to worry about updating software or managing reviewer deadline calendars or keeping track of email attachments – our software does all of that for them.

There are lots of great ideas about how to improve scholarly peer review, and lots of desire to decrease the role large corporate publishers like Elsevier play in scholarly publishing, but scholars need tools to help their ideas actually gain traction.

We’ve spoken with many scholars who love the idea of starting new Open Access journals, but the logistical challenges of setting up the technological infrastructure needed to support a scholarly journal quickly balloon and eclipse the original goal of publishing qualified knowledge to the world. But with a tool like Scholastica, you can start a journal in minutes and have a powerful suite of scholarly journal tools at your fingertips.

AK: What is the history behind Scholastica?

RW: Scholastica was started by a group of friends who met in graduate school at University of Chicago – Brian Cody (Sociology), Rob Walsh (Political Philosophy), and Cory Schires (History). We had individually worked with academic journals, and through our own experiences and our academic colleagues we got a feeling for the problems that journals faces internally.

We all had tech backgrounds, including working in the software startup scene in Chicago, and we felt that giving scholars the infrastructure they need to manage academic publishing themselves was something we could do that would benefit scholarship.

Our team then spent months talking to editors of journals, authors, and reviewers in a variety of fields about problems they had, and got feedback on the software solutions we were building. Fast-forward to two years later and we have a great platform that is helping journals large and small – from the California Law Review to the Strategic Leadership Review.

AK: What is the funding model that Scholastica uses?

RW: Scholastica is a platform for journals, much like WordPress is a platform for blogs. Authors don’t pay to publish “with” us – rather, journals use Scholastica as a tool to manage their journal, so authors and editors use Scholastica to interact with journals.

Journals create accounts on Scholastica, and fees are charged for each article submitted to that journal. The fee can be paid by the author, the journal, or that author’s institution. The latter two options, by the way, result in the journal itself having great software at no charge.Scholastica has a pricing model that scales to fit journals of all shapes and sizes, and this fee supports our team to constantly add new features and improvementsto the software. We have a flat $10 fee per article submission – period. No other fees, no setup costs, no extra costs to publish Open Access articles.

Niche journals that receive only a handful of articles each year get the same powerful features as a journal receiving hundreds of articles a year. Law reviews, which allow authors to submit to multiple journals simultaneously, pay a $5 per submission fee, which they traditionally pass on to authors’ institutions and individual authors.

We’re proud that our $5-$10 per manuscript fee is worlds apart from the thousands of dollar flat fees charged by traditional peer review software providers like Editorial Manager, or the $1350-$2900 in per-manuscript publication fees an author might find with PLOS journals. Our small submission fee allows us to continue creating great software that can be used by journals regardless of discipline.

AK. What is your take on the traditional peer review process, and new forms of peer review? 

RW: In general, our philosophy is to “not the throw out the baby with the bathwater”, meaning that we should preserve the valuable aspects of traditional peer review while also seeking to improve the process through experimenting with new models of review. We believe peer review is a diverse ecosystem of needs and goals that requires a wide range of solutions rather than a one-solution-fits all approach.

With this in mind, Scholastica supports traditional peer review while also giving editors the option to experiment with new, innovative ideas. For example, in Scholastica there is a pool of potential reviewers made up by anyone who has ever signed up for a Scholastica account, so journals are able to invite qualified reviewers from a wide-range of disciplines. Users gain reputation by demonstrating expertise in their fields in the Conversation portion of Scholastica, which helps editors quickly identify the best reviewers. There are gamification elements to writing reviews in Scholastica, which increases incentives and accountability for on-time and high-quality reviews. We are also working with journals to add more alternative peer review process elements, so keep an eye out for more to come!

One thing that we don’t like about many of the new peer review models is that they are either still in the idea phase and so dismissed as pie-in-the-skyhypotheticals, or they require so much technological know-how and time that they are dismissed as being impractical. Scholastica makes it easy for journals to try out these new models in the real world.

AK. How do you look at web metrics as alternate forms of recording scholarly impact? 

RW: We think the altmetrics movement is great, and plan on incorporating various alternative impact measures such as ImpactStory into Scholastica. Not to beat a dead horse, but our opinion is that scholarship is searching for ways to improve the traditional process, and we need both lots of experimentation and to preserve the aspects of traditional impact factors that are valuable. Scholastica as a platform can make it easy for journals and authors to “try out” these alternative impact measures through a one-click interface.

We’re looking to see what new models stick, with stickiness a factor of:

1. impact on the hiring and tenure process;

2. scholars being convinced that the measures correlate with their own sense of which works they think are “hot” or important;

3. widespread adoption within a sub-discipline or across academia;

4. being methodologically respected by the scholarly community

 

AK: Do you think that there is a space for the scholarly monograph in the current and future economy, given that they are expensive to produce and are almost never profitable? What do you think is the future of the monograph?

RW: We work exclusively with journals. That said, from an armchair analyst perspective, monographs are so important for displaying a scholar’s extended or nuanced argument and are so important for hiring/tenure in many fields that it is hard to think of them going away.

It seems like monographs have a potentially bright future via e-publishing, in that e-books can maintain coherence of the monograph (length, structure, etc.) while radically reducing production costs. Promotion might need to fall more on the author and secondary outlets such as book reviews in journals or discussions at professional conferences rather than traditional publisher-led promotion, and we can also imagine new filtering mechanisms, such as more journals dedicated entirely to self-published scholarly monographs or scholarly e-books, cropping up to help increase awareness of e-published monographs.

AK. What do you think is the future of the university press?

RW: We think university presses will continue to play an important role in the future of academic publishing. To continue to be a leading force, however, presses need to be agile and open to new ideas. Some presses are already doing a great job leveraging new technologies and leading innovation, like Stanford and their partnership with Google Book Search. University presses should be the primary force in academic publishing – not corporations like Elsevier.

At Scholastica, we support university presses by offering them a better way to manage their journals. We’re actively working with a few university presses to develop new features that help leverage position of presses as established leaders with the mission to promote good scholarship.