research workflow

literature reviews

I am of the opinion that literature reviews are the most slept-on part of academic publication. It's a near certainty that I find good ideas, new ways of framing old ideas, or interesting questions for the 'future research’ list after reading through a stack of papers. In fact, I think the best advice I ever received about research was to 'find all the papers you think you need to read then read twice as many.’ It primes my mind for writing, makes a good academic tone easier to produce, and helps produce a feeling in me of acceptance within the scientific community. I believe all authors should do their own lit reviews, but we will see if that opinion changes when I have students of my own.

For now, I believe I have a well-crafted literature reviewing workflow which uses a few obscure extensions and tricks but makes life straightforward. The goals of this workflow are:

  1. Quick per paper time

  2. Little/no between-paper time

  3. Searchable notes

  4. Exportable bibliographies

  5. Environmentally kind

I believe I have accomplished this with the following.

Pre-recs

You need

  1. Chrome

  2. Zotero

    1. Zotfile extension

    2. Zotero Connector

  3. Some cloud storage (optional)

And this is all designed to produce quick-but thorough- lit reviews and annotations for futre reference. All of which easily port into a manuscript in Overleaf (recommended) or WYSIWYG editors.

Setup

First you really should set up a Google Scholar shortucut in Chrome. In Chrome, settings (the … button), settings, ‘manage search engines’ . Now, under ‘other search engines’ either find google scholar or ‘add’. Your ‘search engine’ field is just a name, for keyword, these are the keys which you type + tab to change search. Mine are sh, so in the chrome bar I can type ‘sh’ then tab, and then my query. Enter pulls up a scholar tab instead of google. Thank you Bryan for showing me this. (Additionally it’s easy to set something like ‘wa’ to search Wolfram Alpha, or ‘ma’ for google maps etc…)

scholar 

Additionaly, you need to install Zotfile. It's like an 'enhancement suite’ for Zotero which I highly recommend for the annotation extraction alone. The website/github has substantial documentation, but here I'm detailing how to really maximize its use.

Process

  1. Open your library's page and log in so the browser session is properly credentialed

  2. Google Scholar search for your topic and open the top 10ish relavent papers in new tabs

  3. For papers with an extensively high citation count, andor are very old, look at the most popular papers which have cited it/

  4. Open these in new tabs

  5. Use the Zotero chrome plugin to add the papers all to a root level “collection” for this project

  6. Do this for all open tabs

  7. Use the Zotfile Zotero extension to send all papers from the root directory to a synced iclouddropboxetc… folder

  8. Open the iCloud version of the papers either on a computer or tablet

manage 

Review Notes

  1. Read, highlight, annotate to your heart’s content. But at the beginning of each article, leave an annotation which (1) summarizes the paper for me to remember in the future (2) summarizes how I think this will fit in what I'm currently writing, and (3) points out any obvious flaws/holes, future directions

  2. Use Zotfile to ‘pull’ the highlights/annotations back to Zotero desktop by right clicking and 'manage attachments’ (this is the best part)

  3. Use zotfile to extract the annotations (should happen automagically but doesn’t…), again in 'manage attachments’

annotations 
  1. “Create Report” from a custom folder search which pulls all annotated documents which are in the collection AND have extracted annotations

extra 

This report is your literature review from start to finish. Each fact is cited, you can organize all of the papers. I eventually regex the included Zotero citations for the appropriate latex citation keys and copy right into overleaf. Exporting a .bib file is just as easy and it gets append to the previous bib in exactly the same way.

It looks hard/tedious, but I’ve yet to find another way to get background clearly, concisely, and thoroughly to a paper while also creating a string of ‘ctrl-f-able’ notes for my brain to follow its previous thoughts.