Chapter 9: Organizing Your Research¶
“Reading papers is step one. Remembering, comparing, and building on them—that’s where real research begins.”
Why This Chapter Matters¶
It’s one thing to read 30+ papers.
It’s another to remember which one used BERT, which one used SVMs, and which one had that perfect diagram you need—but you forgot the title.
Without a system, you’ll fall into the trap of:
- Re-downloading the same PDFs over and over
- Forgetting key insights
- Citing the wrong paper—or not citing at all
- Wasting weeks during your literature review
This chapter helps you set up a research tracking system that grows with your thesis, supports your writing, and saves your sanity.
Conceptual Breakdown¶
🔹 What Does “Organizing Research” Actually Mean?
It means:
- Tracking what you’ve already read
- Tagging papers by topic, method, dataset, etc.
- Writing structured notes (not just highlighting)
- Having a place where you can search, filter, and retrieve ideas quickly
In short: building your own personal research database.
🔹 Tools You Can Use
You don’t need all of these. Start with one or two.
| Tool | What It’s Good For |
|---|---|
| Zotero | Reference management, citation generation, note-taking |
| Obsidian | Markdown-based, bi-directional notes, research graphs |
| Notion | All-in-one dashboard, tags, tables, databases |
| OneNote | Flexible note-taking, drawings, annotations |
| Google Sheets / Excel | Simple but powerful for building a literature matrix |
✅ Choose the tool that fits your thinking style—not the one with the most features.
🔹 Build a Literature Matrix
One of the most effective tools is a literature matrix—a table summarizing each paper.
| Paper | Problem Addressed | Method | Dataset | Results | Strengths | Limitations | Notes |
|---|---|---|---|---|---|---|---|
This helps you:
- See patterns across papers
- Compare methods side-by-side
- Identify open gaps and research opportunities
You can build it in Google Sheets, Notion, or Obsidian tables.
🔹 Tagging and Theming
As you build your reading library, use tags to track themes:
Examples:
- #NLP, #BERT, #low-resource-languages
- #dataset-philippines, #legal-domain, #transformers
- #baseline, #state-of-the-art, #open-question
These help when you’re writing your Related Work section: you can group by theme or method instantly.
🔹 Syncing With Citation Managers
If you're using Zotero, Mendeley, or EndNote:
- Organize papers into folders by topic
- Attach your notes as child items
- Use tags or colored labels
- Export
.bibfiles for LaTeX/BibTeX citations
💡 Pro Tip: Use the Zotero Connector browser extension to save papers with one click—including full metadata and PDFs.
Self-Check Questions¶
- Do you currently have a system for saving and categorizing the papers you’ve read?
- Can you retrieve a paper you read two weeks ago—in under 10 seconds?
- Are you taking notes outside of the PDF file?
Try This Exercise¶
Set Up Your Research Vault
Pick one tool (Zotero, Notion, Obsidian, etc.) and create your basic structure:
- A folder or tag system (e.g., "NLP", "Evaluation", "Philippines")
- A reading log or table
- One sample entry with full notes using the Paper Review Template from Chapter 8
Keep this system lightweight. The goal is consistency, not complexity.
Researcher’s Compass¶
Your brain is for thinking, not remembering every paper you’ve ever read.
Let your system do the remembering, so you can do the thinking.
Organized research means you’re always ready to write, connect, and contribute—without having to start over.
When you build your literature matrix, you're not just collecting papers.
You're creating a map of the knowledge landscape—and finding exactly where your work belongs.