Ruben Dario Palacio, Ph.D. Profile picture
Dec 10, 2022 19 tweets 8 min read Read on X
Here's how to conduct a literature review using Google Scholar, @zotero, @RsrchRabbit , and @obsdmd .

A step-by-step guide👇 Image
1. In this thread you will learn how to:

• Use Google Scholar to find literature.
• Create a Zotero lit. collection.
• Use Research Rabbit to expand your Zotero lit. collection
• Add highlights and export to PDF notes to obsidian
• Centralize all relevant notes in obsidian
2.

Start by searching in Google Scholar for your research topic:
scholar.google.com

Here, I will use rewilding as an example.

Note that the results show highly-cited papers that are part of the conversation. This is a very useful feature. Image
3.

In Google Scholar clic on each paper of interest to redirect to the publishers website.

Use the Zotero browser connector to extract the reference: zotero.org/download/conne…

If the paper is open access, Zotero will automatically extract the PDF as well. Image
4.

Note that I am saving to a Zotero collection. This is where you hold all the relevant literature for your chosen topic.

I highly encourage you to use collections for all your research projects. Image
5.

Open Research Rabbit and click on "Import Zotero Collection" and then in "Start Sync" Image
6.

Research Rabbit will show you relevant literature to expand your collection.

There are many options and visualizations to explore.

Once you chose a paper, you will have the option to add it to your Zotero collection. Image
7.

The paper will appear in Zotero Collection.

Keep in mind Research Rabbit will not extract the PDF. This is something you need to do with the Zotero Connector (if open access). Image
8.

Once you obtain the PDF, you can open it in Zotero itself (you need Zotero 6) and add highlights. Image
9.

After you have some highlights, close the PDF.

Then click on "Add Note from Annotations" Image
10.

The Annotations will appear as a separate element. Then, right-click and click on "Export Note". Image
11.

You will want to export as Markdown, and make sure to Include Zotero Links.

Zotero links means you can click in a link that will open the PDF within Zotero, and show you exactly the highlighted piece.

(this will make sense in the end, so stick with me) Image
12.

Export to a literature folder in Obsidian.

As a naming convention, use the Citation Key provided by a Zotero plugin called ZotFile (you will need to install it): zotfile.com

Add a @ before each paper name to distinguish these are literature notes. ImageImage
13.

This is how the exported note looks within Obsidian. Image
14.

Finally, in obsidian you can create a new note, and link it to the highlighted notes!

The highlighted notes can take you to the PDF itself, in the exact place where you made the highlight.
15.

And that's it.

You will then keep exporting notes to obsidian, and compiling a literature review document with links to the PDFs in Zotero!

Here is a literature review I did for the third chapter of my PhD thesis. ImageImage
16.

Now, If you've found this thread helpful,

1. Go the top and retweet the first tweet to share it with your colleagues!

2. Follow me @rdpalacio for tips on publishing and academic writing.

3. Consider a small donation for my time and effort
buymeacoffee.com/rdpalacio
17.

[Update 1] Based on the feedback, I've modified the figure to emphasize Google Scholar is not the only database to use! Image
18.

[Update 2] I'm excited to share I'm hosting a 1.5-hour workshop with all the details on this workflow next week!

Register for the event here:
eventbrite.com/e/the-literatu…

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More from @rdpalacio

Oct 5, 2023
🎓 Last year, I got my Ph.D. from @DukeU.

📚 This year, the 3 chapters of my dissertation are published in some of the top journals in my field.

🔍 Wondering how you can do the same?

Here are 10 pieces of advice I have learned!🧵 Image
1. Drop modesty.

Ask yourself, what do I need to publish in high-impact journals?

Do you need more technical skills for your field? Do you need to write or code better?

In my case, I wanted to improve at GIS and stats.

So, determine what you need and go for it! Image
2. Read lots of papers.

How else are you going to identify those research gaps?

How do you know what is relevant if you are not aware of what people are working on?

This is really a non-negotiable thing, but I hear some Ph.D. students say they don't have time to read. Image
Read 12 tweets
Jul 28, 2023
Here's the story of how some senior academics plagiarized my work, led by my former advisor Stuart Pimm.

I reported research misconduct to @DukeU a while ago.

Earlier this year, they had to acknowledge their wrongdoing, though they did so very subtly.

This is what happened👇 Image
I started my Ph.D. under Prof. Stuart Pimm, a leading academic in conservation.

I was just thrilled to be his student. I never checked for red flags.

We published my first chapter together, but things changed when he offered me a topic for the second chapter of my Ph.D.
Image
Image
Stuart asked me to use a GIS workflow he had used for refining bird ranges.

This would help his NGO @SavingNature1 and @ABCbirds do conservation work in Ecuador.

The catch? We were going to report progress to ABC (basically our clients).

Not ideal for Ph.D. research.
Read 19 tweets
Jun 13, 2023
Many people are not aware that the IUCN Range maps are VERY unreliable.

Some are good, some are bad, and most are in-between.

In our 2021 study, we found their overall accuracy was only 62% vs 87% of our data-driven workflow to map ranges (data for 723 forest birds) Image
Most of the IUCN Range maps are expert-drawn and are not updated based on occurrence records.

The map on the left for the Wattled Guan misses most of the occ points (in purple).

On the right, another expert map shows an improved distribution of its portion in Colombia. Image
It's actually quite hard for expert maps to get it right.

In this example with the Hoary puffleg, the IUCN Range Map is just a blob drawn around the wrong place.

It misses some occ points and doesn't correspond to the mountain chain correctly.

I've seen this situation a lot. Image
Read 8 tweets
May 8, 2023
ChatGPT is your personal research assistant, but only if you can use it efficiently.

Here are 12 ways to unlock its potential for many of your academic needs.

I've included real-life screenshots of use cases to help you get started 👇
1. Suggest ideas for the title of a paper. Image
2. Rewriting.

The prompt "rewrite for clarity and style" has worked tremendously well for me. Image
Read 14 tweets
Jan 26, 2023
I'm tired of the hegemony of the IUCN Red List of Threatened Species.

At this point, I think it's actually hampering biodiversity conservation and research.

Yes, it helped tremendously in the past. But not anymore. Here's why:
1/ First, it is flawed.

The categories and criteria are more than 30 years old. They have not aged gracefully. They were conceived before GIS advances, remote sensing. Some simplistic assumptions are used, no use of inference, etc.
2/
The solution? The Red List needs to be updated.

You know, version 2.0. But from the start. No little adjustments. A rethinking of the entire categories and criteria is more than warranted.
Read 11 tweets
Jan 25, 2023
Most folks in academia are overwhelmed with email.

I've been there too. But I finally managed to implement a system that works for me - and I think it will work for you.

So here's a simple method to get your email back in control 👇
1. First, email is a general inbox.

Take the incoming tasks into more dedicated places:

a) Schedule tasks in the calendar
b) Place them into a task-manager
c) Take notes
d) send to the Read-it-later app

Here's a screenshot from @AliAbdaal email system.
2. I use different tools than Ali suggests. My email productivity stack:

email: @gmail
I forward all institutional emails here.

Task-manager:
@todoist

Calendar:
@googlecalendar

Note-Taking:
@obsdmd
I call it my personal Wikipedia.

Read-it-Later:
@raindrop_io
Read 9 tweets

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