Literature search is a skill that takes TONS of practice

• Figuring out what types of keywords/phrases are useful for your topic is trial and error
• Sifting through long lists of search results is very time-consuming
• Pinpointing which part(s) of a paper are relevant can also be difficult

Activity: Find a paper

• Your hypothetical research topic: “Valid statistical inference using data that is augmented with machine learning predictions”
• There are many papers on this topic, but I’m thinking of a specific paper published in the journal Science

Activity: Find a paper

• Which search tool(s) were successful?
• What did you use as a search prompt?
• What would be a good keyword search to identify this (and related) papers?

Google Scholar features demo

• general keyword search
• advanced search (e.g., by author, journal, date)
• linked institutional libraries
• citation information
• alerts (we’ll talk more about these later)
• “Labs”: natural language search query interface [uses AI]

Citation chaining

• Once you’ve found a key paper, you can use its references and citations to find related work

• This can be especially useful if there are several different terms for the same idea, or if you are still learning the jargon for your topic area

• Demo: starting from a seed paper

  • Backward chaining: find 3 papers it cites
  • Forward chaining: find 3 papers that cite it

Zotero: what and why?

• Software that helps you collect, organize, annotate, and cite research sources
• Free¹, open-source, works across Overleaf/Word/Google Docs
• Habits you build now (or don’t) will follow you through your PhD journey

Getting started

• Go to https://www.zotero.org/download/ and install Zotero on your system

• Optional (but recommended): Also install the browser extension “Zotero Connector” (available for Firefox, Chrome, Safari, and Edge)

Activity: Import

Import the 2023 Science article on PPI, as well as two related (citing or cited by) articles into Zotero using any of the following methods:

• Browser connector
• Drag-and-drop PDF
• Manual entry

Make sure to check the metadata for accuracy and completeness!

Library organization

• Strongly recommend using Collections / subcollections: like folders, but an item can live in multiple without duplicating
• There are also Tags: I don’t personally use these, but they can be useful for filtering and searching your library, and they are linked with each item record if you share records with others
• Demo: create a collection for your PPI papers and add the three articles you imported

Annotation

• Built-in PDF reader with annotation tools:

  • highlighting
  • comments / sticky notes
  • freehand drawing

• Notes: on the side pane, rich text formatting

• If you prefer to read/annotate in a different PDF reader, it’s possible you may be able to export/import the annotations in and out of Zotero, but this may depend on your use case (see Zotero documentation for details)

Organization/Annotation - tips

• I Strongly recommend adding a Note (or tag) with key attributes immediately after adding to the collection, before you read deeply
  • so you don’t have to reread the entire paper later to figure out how it relates to your project
• an initial triage now will force you to think through if/how the paper is really relevant to your project
  • if it is not, then don’t add it to your collection!!
  • will save you time later when you’re writing an intro or literature review

Organization/Annotation - tips

• look to abstract, then end of intro/beginning of methods to classify (e.g. motivates your work, solves a similar problem, uses a similar approach for a different problem, etc)
  • see the linked reading for great prompts on writing this summary
• you may find it helpful to create a ‘to read deeply’ collection for papers you want to read later, but don’t add to your main collection until you’ve skimmed and classified them

Activity: Cite-while-you-write in Overleaf

Add .bib file from Zotero to Overleaf to cite¹:

1. Export .bib file from newly created Zotero collection
2. Create a blank Overleaf project; upload the .bib file
3. Link the bib file: \usepackage{biblatex}, \bibliography{}
4. Cite with \cite{} or \textcite{}, add \printbibliography, and compile

The problem

• Searching finds what already exists
• Research doesn’t stop the day you finish your literature review
• It can be useful to use a system that finds new articles without you checking manually
• I’ll share my top 2 recommended tools, but you may find others that work better for you

My favourite tool: Google Scholar Alerts

• Alerts for a specific topic (or researcher)
  • email alerts with lists of relevant new articles
  • very useful if you’ve dialed in a specific keyword search or know of a key researcher in your field
  • can clutter your email inbox

Another useful tool: RSS feeds

• An old technology that still works well for following specific sources (journal or tag from a preprint server)
  • lots of RSS readers available with free tiers (e.g., Inoreader, Feedly, etc.)
  • useful if there are a handful of specific feeds that you want to keep up with, but quickly becomes unmanageable if you have a large number of feeds¹
  • not all sources have an RSS feed (most do)

On your own: choose one of the following

1. Add a Google Scholar alert for a keyword search or researcher relevant to your topic

OR

2. Choose an RSS reader, and add 1-2 relevant arXiv subject RSS feeds relevant to your topic

Homework: One week later

Check your email for the Google Scholar alerts you received or check the RSS reader you set up. Write 2-3 sentences reflecting on the following:

• What did your alert/feed actually catch?
• Do these articles seem useful for your literature search?
• Do you need to broaden or narrow anything?