[Notes to Self] How I Read for My Prelims

In 2021, I wrote a blog post about how I organized journal articles for literature reviews. My system then involved searching for papers, keeping them in Mendeley, and logging what I found in Excel. I still believe in the basic idea behind that post: no one can remember everything, so every researcher needs a second brain. But reading for my preliminary exams has forced me to rethink what that second brain is supposed to do.

This post is another note to myself and a record of how I have grown as a researcher. As I understand it, the prelim is meant to establish that I have read broadly and deeply enough to engage with my own research questions. It is not simply a test of how many books I can finish or how many citations I can collect. My preparation has therefore had three purposes:

• Read broadly enough to learn from other disciplines and identify gaps.

• Read the classics and understand the main arguments in the field.

• Create a trackable system that I can return to when writing my dissertation and future papers.

The last purpose has become increasingly important. I do not want to finish the prelim with a folder of disconnected notes that I never open again. I want the reading to become part of the theoretical foundation for my dissertation.

START EARLY AND START BROAD

Looking back, one thing that helped me was identifying my main keywords early. I knew that my work would involve culture, education, and spatial inequality, although I did not yet know exactly how these ideas would fit together. Starting with broad concepts allowed me to search across education, sociology, economics, history, migration studies, and cultural sociology instead of staying inside one disciplinary box.

I am especially fond of systematic reviews because they make the search process visible. A search can easily become guided by memory, convenience, or whichever article happens to appear first on Scopus. Using a PRISMA-style process forces me to record where I searched, which keywords I used, how many records I found, which duplicates I removed, and why I excluded certain studies.

The PRISMA flow diagram was created as a reporting tool for systematic reviews, but I also find its logic useful for prelim preparation. It gives me a way to double-check whether an important work appearing on my current list was captured in my earlier searches. It also reveals the boundaries of my reading: What databases, languages, publication types, and keywords shaped what I was able to find?

A systematic search does not eliminate judgment. Keywords change as I learn the field, and classic books are not always captured well by database searches. I therefore supplement the formal search by following reference lists, checking who later cited an important work, and asking which texts scholars repeatedly treat as foundational.

I also find bibliometric review useful at the beginning. Tools such as Bibliometrix and Biblioshiny can show frequently cited authors, recurring keywords, clusters of scholarship, co-citation patterns, and how themes change over time. This does not tell me which argument is correct, and citation counts are not the same as intellectual importance. What it gives me is a map. I can see the main conversations in a field, identify scholars I should know, and notice groups of researchers who may be studying similar problems without citing one another.

Together, systematic and bibliometric reviews help me answer two different questions:

“What belongs in this body of literature?”

and

“How is this body of literature organized?”

Neither can replace close reading, but both help me decide where close reading should begin.

CREATE A SECOND BRAIN I CAN ACTUALLY SEARCH

I have discussed the idea of a second brain in several previous posts (here, here, and here). After preparing for my preliminary exams—and learning from several failed attempts—I have finally settled on a system for organizing mine. During my first year, I used Notion to store all my notes. In theory, it seemed like an ideal all-in-one workspace. In practice, however, accessing and syncing my notes across devices was not as seamless as I needed it to be. I also could not integrate the system easily with Zotero. Because moving information between the two platforms required too much manual work, I gradually stopped maintaining the system.

https://www.youtube.com/watch?v=R0CNzr9Q3ME

My second attempt combined Obsidian with Zotero. This was an improvement, but I was still treating Obsidian as a separate destination where every source required another round of manual entry. I was storing information, but the system was not helping me retrieve and reuse it when I needed to write. That experience made me realize that a second brain should not simply contain my notes. It should reduce the distance between reading, thinking, and writing.

My final solution is surprisingly simple: my second brain is now a folder. It is one working directory containing my fleeting notes, literature notes, permanent notes, project drafts, data, figures, code, and templates. I save my notes as Markdown files so they remain portable and easy to search, edit, and reuse. I open the same directory in both Obsidian and Visual Studio Code, while Zotero remains connected to the workflow as my reference manager.

Obsidian allows me to read, connect, and search my notes while visualizing the relationships among them as a network. Visual Studio Code gives me another way to work directly with the files and integrate tools such as Codex and Claude Code when I need help organizing material, identifying connections, or refining my writing. Codex can search across the directory, retrieve relevant material from different notes, and help incorporate it into another file. Because the files are stored in an open and readable format, I am not limited to what a single application allows me to do.

Keeping everything in one vault is crucial because my projects often overlap. A book I read for a preliminary question may later contribute to a dissertation chapter, a methods note, or an entirely different paper. An idea does not have to remain trapped inside the project for which I originally encountered it. By storing everything as searchable Markdown rather than isolating my notes across separate applications, I can recover an old idea by searching for a concept—even when I have forgotten the author, title, or original project.

The key point is not the number of tools I use, but rather that each tool serves a specific role within an interconnected system:

• Zotero manages sources, PDFs, and annotations.

• Obsidian connects ideas and makes my notes searchable.

• Visual Studio Code allows me to work directly with the entire research directory.

• The vault keeps everything portable, searchable, and reusable.

MY ACTUAL READING FLOW

1. Build the initial reading list

I start by asking experts in the field, especially my advisor, what I should read. I also collect syllabi and add works that I recognize from my earlier systematic review. I then put the initial reading list into an Excel file with basic information about each source. At this stage, I am not trying to understand everything. I am building a map of what I need to read and a way to track my progress.

2. Read and annotate in Zotero

My current workflow begins in Zotero, where I read and annotate PDFs using a limited color system:

• Yellow: core argument

• Green: evidence, data, and statistics

• Blue: theories, concepts, and definitions

• Red: critiques, limitations, and gaps

While reading or listening, I add comments beside important highlights. This is how I try to stay involved in the reading rather than passively collecting quotations. A highlight preserves what the author said. A comment preserves what I was thinking when I encountered it. Without that comment, I may return months later and have no idea why I saved the passage.

I also recommend using the Zotero Connector to import articles with their bibliographic information and PDFs whenever possible. Zotero can automatically rename attachments using consistent details such as the author, year, and title, making sources much easier to locate later. A paid Zotero plan is useful if you need additional cloud storage and want your attachments synchronized across devices. Zotero also has a Read Aloud feature that could serve as an alternative to a Speechify subscription.

3. Turn annotations into literature notes

After I finish reading, I move the material into the vault using a literature-note template for a book, article, or book chapter. The template asks for more than a summary. I record:

• The core argument

• The theoretical framework

• Evidence and data

• Methods

• Limitations

• Connections to other readings

• Possible uses in my own writing

I also extract quotations I may need, although I try not to let quotations substitute for explaining the argument in my own words. Most importantly, I keep my prelim questions in mind during the write-up.

• Why did I read this?

• Which question does it help me answer?

• Does it support, challenge, or complicate my framework?

If I cannot explain the connection, the source may be interesting, but it may not be central to the prelim.

4. Synthesize, rather than collect

The final step is synthesis. I bring my literature notes into the prelim outline and place the ideas in conversation with one another. This is also where the real writing begins. As I write, gaps in my reading become more visible—an unsupported claim, an unclear mechanism, or a perspective I have overlooked. I then return to the literature, add relevant sources, and revise the draft. The process is a loop rather than a straight line: each iteration sharpens the argument, fills another gap, and brings the prelim closer to the paper I want it to become.

Throughout this process, my notes move through several stages. Fleeting thoughts begin as comments and annotations in Zotero. I then develop them into literature notes saved as Markdown files. Finally, the ideas that become part of my prelim are refined into permanent notes and stored in a dedicated subfolder for future reference. I hope to keep expanding and connecting these notes in the spirit of a Zettelkasten, allowing the system—and my thinking—to grow beyond the prelim itself.

Epilogue 

The biggest lesson is that I cannot simply adopt someone else’s system and expect it to work perfectly for me. Other systems can offer inspiration, but finding what works requires experimentation, change, and constant iteration. After several attempts, I now have a second-brain system that seems to fit the way I read, think, and write. The process has taught me to adapt the original idea of the Zettelkasten to the possibilities and demands of research in the digital age. More importantly, the system helps me generate new ideas, examine their connections, and return to them with greater clarity.

This system is still evolving, just as I am still growing as a researcher. I hope to revisit this post in the future and share another update on what continued to work, what failed, and what I changed along the way.

Until next time!