My process for bibliography and notes
— June 24, 2020

For those who are starting new in research, you might want to keep running notes and citations for the relavant research papers, journals, books etc. that you come across. This helps maintain clarity of what is important, what has been read already and the notes that help you revisit the material if and when you need to.

After a decade and half worth of haitus, I am starting to delve into research once again. This means reading papers more than I am used to. During my tenure as software engineer in various organizations, most papers I had read were limited and I could afford to read them as many times as I wanted.

Things have changed now and I need tools and new habits to help me navigate through a ton of literature. I cannot afford to spend countless hours on one paragraph in one paper. Above all, I cannot afford to think that all papers and books are created equal and have the same value for my research and eventual PoC that I have to deliver.

Here are a few things I am trying to achieve

1. Forming new habits
   • ability to skim papers
   • jotting down quick notes for the papers
   • peruse references if interesting and get those references
   • revist the papers for deeper read if needed
2. A way to manage a "to-read" list of papers
3. A way to manage "already-read" list of papers
4. Tag papers that need revisiting for deeper read

As you can tell, I do not want a mere list of citations that I have read for my research and projects. I want a traceable way to know what I read, as well as why it was important. Here is an approach I am starting with -

Start with a book on the research, if available. Skim it first.

A book allows easy introduction to the topic without having to figure out which papers to read first on that topic. If a decent book is not available for the field/topic, there might be a way to start with early review papers or first papers.

Note: At the time of writing, I am not aware of anything else to alleviate some starting pains.

Why skim

It is critical that I skim the book to break the habit of deep reading in first pass. If I am spending too much time going deep and trying to retain everything I am losing out on getting a broad idea of the topic at hand. I need to be have broad knowledge as soon as possible so I can then drill down into specifics.

Keep short notes

Skimming does not mean that you avoid taking notes. You aren't reading a novel after all (although I have been known to keep notes on novels). Keeping such notes allows you to come back to them to decide whether something was worthwhile and requires deeper reading. I try to keep notes of the following things:

• Chapter names and general idea
• List of topics each chapter covers
• Mark/tag a chapter important or to revisit
• List of reference from each chapter that you want to fetch

These notes enhance your bibliography.

Next

If you are comfortable at the end, maybe it is worthwhile to revisit the chapters you've marked and fetching the references. I personally fetch all the references at the end of each chapter, if I can. At this time, mark all the papers and chapters yet again if they need revisiting. Tag them further to make sure you can search for them later when you need them.

I find keeping at most three tags just enough to have entropy under control, at the same time not losing my sould in tagging everything.

Remember, the goal is to manage the items and related notes to quickly make a decision on important aspects of the topic at hand.

Another cycle of skimming, taking notes, and moving to next starts!

I hope this will help me build an intuition by helping with new habits of swimming through the giant corpus of any topic that I want to study.

Tools

Save and synchronize papers

I started using Zotero and it has been working fine so far. Some of the key features that I find useful -

• Easy, one-click fetching and saving of papers (browser plugins available)
• Ability to tag them as well as create "collections" to manage files
• Ability to add notes to the papers
• Syncrhonizing your papers list, notes and everything under the Sun
• Works on Linux!
• Works with third-party apps on mobile devices and tablets
• Advanced search that you can save
• Ability to generate ciatations and reports from each item
• You can export your data
• Free for upto 300MB of storage for synchronization

On my iPad, where I do most of the reading, I use PaperShip with Zotero account.

Search and discover papers

A few places I go to, to search papers and to discover new papers.

• arXiv - a preprint to find stuff sooner
• arXiv Sanity - a self hosted private instance for my areas of interest
• Semantic Scholar - Also allows you to create feeds for papers of interest

Notes and tags

I add quick notes in Zotero as well as use local Emacs+Markdown and push the notes to GitHub (or SourceHut if you hate GitHub because of ICE).

I save papers in particular collections in Zotero and tag the papers frequently. For example, I tag "done-reading" when I am done reading and I have a saved search that quickly lets me see all papers I have already read. Another saved search allows me to quickly see all "to read" papers.

I have been using "Cite" feature of Zotero and Semantic Scholar to create the title of each item in the bibliography and underneath that I jot down notes and other relevant details like links.

Feedback

I would love to hear what has worked for you. Is there something I am missing. Reach out to me via email or twitter.

Many thanks to Jonathan Dursi for constantly helping me improve this process.