Reference Workflow

22 01 2023

This past May I graduated with my PhD. I initially typed that sentence as “I finished…”. But, truly, like a wedding is the formal start of a marriage, the conferment of the PhD degree is just the formal start of a writing career. In the months since I walked across the stage I’ve been trekking through the bog of drafts, revised drafts, and revisions of revised drafts in the pursuit of the research Holy Grail… the peer reviewed paper in an impactful journal.

For me, the most challenging aspect of completing my dissertation, and revising it into publications, has been keeping track of my source material. Over the past five years I’ve tried, discarded, and modified countless ways of tracking the dozens then hundreds, maybe thousands, of references that inform my writing. It turns out, the reading is the easy part. Finding that idea kernel a month later in mounds of paper can take a frustrating amount of time. Enough time that a tracking system became essential. I needed a system that was flexible yet powerful – that would get me to the key ideas easily. I tried color coding, accordion folders, foot high paper piles… until I burned through reams of paper and boxes of laser toner. But, as the piles grew, and the more I organized, the harder it became to find the ideas I was seeking.

I like reading on paper. I like highlighting. I like making notes in the margin. I adore index cards. But, I was drowning in paper. I had to change.

I’ve long read novels on a Kindle. However, I resisted electronic reading for “serious” work. I couldn’t see how it would work for me. But, I had an iPad mini. And, I saw how my students were using the app GoodNotes for annotating class materials. So, I gave it a try. What a game changer!! Going electronic meant giving up my trusty paper, but pdf scans still look like paper. I thought it would mean giving up my fun highlighters and pens. No – Good Notes has fun highlighters and pens.

Okay, so I was making good progress plugging along with my electronic reading – but as I mentioned above, the reading is the easy part. I still had to figure out how to index the key insights for easy retrieval. I had to let go of my trusty index cards, and move to trust a citation manager. I tried a few and found Zotero had the most reliable sync. It allows notes and tags – but they do require some maintenance to be maximally useful. Initially my Zotero was kind of a mess. The resources were entered by the system through a Google Chrome extension button, but I didn’t maintain it beyond that. It was useful for making reference lists, absolutely, but it didn’t help me track my ideas.

My organizational break through came through an ordinary tool that turned out to have extraordinary usefulness – Google Drive. When I realized that Good Notes and Google Drive can talk, I had found the workflow key. I could let go of trying to keep all the reference plates spinning in my head, and trust the system. And, it also gave me a way to pair my reading habit with my Zotero organization, building a stronger system.

The system:

Workflow diagram
  • First, I download the article. I typically search through Google Scholar, because it’s linked to my school library account. EBSCO and other search engines are also options, depending on what paywalls I need to go through.
    • I name files of downloaded articles very specifically so I can quickly identify duplicates: topic, last name of first author, year of publication, title
  • Next, I load the pdf into Google Drive.
  • When I sit down to read, I pull articles from Google Drive into my iPad GoodNotes app.
  • As I read in GoodNotes, I highlight and annotate the articles electronically – directly on the pdf pages.
    • I also highlight any supporting references cited by the authors that may provide further insight
  • I then upload the annotated pdf back into Google Drive.
  • Next, I use folders to keep order in my Google Drive.
    • I upload each article into the topic folder it matches. I’ve found it’s best to do this soon after reading, or I get bogged down
    • Within the topic folder I have three subfolders.
    • 1. One for the unannotated original article copy
    • 2. One for the annotated copies of articles I’ve read but won’t be citing in my manuscript
    • 3. One for the annotated copies that I am likely to cite in the manuscript
  • For the articles I plan to use, I add their citation into Zotero
    • In Zotero you can go wild with folders and tags, but that’s a topic for another day
    • I add my notes from my reading into the notes tab in Zotero – this is key because it makes them searchable (side note of a benefit to GoodNotes – handwritten annotations in GoodNotes are searchable within that app).
  • Finally, I go through the references of the article and search, typically in Google Scholar, for any I want to read. I download them or request them through Interlibrary Loan right then, before I forget
    • Those pdf downloads then get loaded into Google Drive, and await the process starting again

A workable workflow combines flexibility with enough ease of use that I’ll stick with it. My goal is to read one article a day, at least five days a week. I’ve stuck with this now since October. Searching my notes in Zotero allows me to identify insights quickly, making my writing time much more streamlined.

What works for me is not going to seamlessly work for others. But, I share this to provide insight into elements of a system that may also help others tame their piles of paper.

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In Opposition of Predatory Publisher Pricing Policies in Academics #GoOpen #OER

7 11 2015

When I was in grad school, our department chair gave us a mission.  Every time we walked into the medical library, we were to remove from the shelves an issue of a particular journal (I don’t recall which one now) and lay it on a table.  According to him, the library tracked how many journals were used in order to determine which subscriptions were renewed.  The yearly subscription for this particular journal was tens of thousands of dollars per year.

This week, editors of the Elsevier journal Lingua staged a protest – resigning from the publication due to Elsevier’s refusal to allow it to become open access.  In support of the editors, the Association of Public and Land-Grant Universities had this to say:

“Publishers sell back to the universities the very content they as a group produced, and at steadily higher subscription prices,” the statement said. “The system is fundamentally broken.”

I fully agree.  My graduate degree involved university and grant funded research in physiology.  The research was not published (the initial results were negative and the “great flood of 1997” wiped out the -70 freezer with a year worth of samples and also allowed me extended time off to see what I was missing in my little children’s lives – so I wrote up the initial data, cut my losses, and snatched the chance to take the MS and walk away, closing the door on my PhD).  But, if I had plugged on with the PhD and published, my mentor and department chair’s names in the byline could  have landed us in a decent journal.  A journal where libraries would have to pay a chunk of change to make the work available.

My graduate work was completed at a public, state university.  The research in our lab was funded by grants from the March of Dimes and the American Heart Association.  There were no private, commercial, for-profit funds used in my research – or, in fact, for any research in my department.  So, what is the justification for a library to have to pay exorbitant fees to buy access to read the results of this type of research?  If the university or grant fund is providing the lab space for the research, paying publication fees, and also paying for the finished journals where the research is published – aren’t they triple paying?  By extension, aren’t the taxpayers who support the university the ones triple paying as well?  How is this allowed to continue at such outrageous rates?  According to journal owners, there are costs (not to mention substantial profits – higher, even, than Apple). In actuality, it all comes down to “prestige” – paying for the credentials necessary for tenure in high-stakes “publish or perish” environments.

Libraries can’t afford this anymore.  For example, a browse through the “cancelled journalDSCF0826s” list for the University of Illinois library, where I worked for three years as an undergrad, shows a 2007 cancellation for the International Journal of Clothing Science and Technology – a savings of $9,629 a year.  The 2006 cancellation of Lecture Notes in Computer Science saved them $25,000 a year. In 2005, the subscription to the American Institute of Physics Conference Proceedings saved them $21,000 per year.  Together, those three journals could cover the cost of a junior faculty member yearly salary.  What would benefit a student more, access to those three journals – or a smaller English comp class?  At the University of North Dakota (my graduate institution) the university is facing choices between administrative positions and journal subscriptions.  They cannot afford both.

The standard bearers of scientific research are the journals Science and Nature.  I, personally, subscribe to Science.  It’s around $100 a year on the multi-year digital-only plan.  That seems like a reasonable cost to me.  I’ll support that.  Libraries also support Science – you’d be hard-pressed to find a university library that doesn’t stock it on campus.  Maybe the quantity of subscriptions allows a lower cost?  Or maybe the lower cost allows more exposure?  It’s difficult to say for sure, since it takes quite a bit of investigative digging to find the true cost of any particular library journal.  Libraries often negotiate bundled prices which vary from school to school.

Fortunately, the tides are turning.  Last week, the US Department of Education announced a new initiative – #GoOpen.  This proposed policy would require that all research funded by the department be available as an OER (open educational resource).  The policy is supported by the Creative Commons open licensing group.  Although #GoOpen is a P-12 initiative, legislation was also introduced last month to promote OER textbook use in college courses.  Hopefully, the movement will trickle into academic publishing at all levels.

While I support the rights of authors to copyright, and profit from, their original work, I oppose the practice of charging academic authors to publish in journals only to then turn around and CHARGE THEM AGAIN to have their work available in their own school library.  The only party to profit in such a scheme is the publisher.

Last year I wrote an OER Biology textbook, freely available to anyone from my faculty web page.  By the end of 2016, I plan to have four of the six courses I teach using primarily OER resources.  As I’ve stated before, I have no issues with authors profiting from their original work.  I also have no problem with publishers paying their editors and support staff a reasonable wage.  I do however, have an issue with predatory pricing, and I support OER initiatives by making my own work freely available.  US commercial academic publishers have come to see both students and “publish or perish” faculty members as fish in a barrel.  I cannot, in good conscience, support that.








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