Standardizing PDF → Markdown Conversion for Obsidian
Hi everyone,
I know - many of you have seen the countless threads and GitHub repos detailing ways to convert PDFs to Markdown. Yet, as Obsidian (and similar tools like Notion) continue to dominate our productivity workflows—and considering Markdown’s central role in prompt engineering—we really need to nail down a standard conversion process that meets our community’s unique requirements. Further, I think we need not just snippets, but really a workflow where we can together contribute to standardize the best pieces of all ideas.
This post is not about another solution … but for a call to standardize the solitons for us as Obsidian community.
The fragmentation of PDF… was always ridiculous. The fact that we are spaming the web now with fragmented 90% solutions… is even more ridiculous.
The Challenge
- Fragmented Solutions: There are tons of approaches out there, but none of them fully address the nuances we need for Obsidian.
- Preservation of Details: We need a method that maintains critical formatting (think math formulas, colorized equations, etc.) exactly the way Obsidian renders them.
- Model Agnostic: The solution should work with various models and be accessible either via a script with API integration or through manual copy-paste methods.
Proposal
Let’s put our heads together to create a community-driven repository that outlines:
- LangChain-style chains & prompt orchestration: Define clear chains and agents that handle the various steps—from parsing the PDF to applying the final Markdown formatting.
- Prompt Engineering Guidelines: Establish a set of guidelines (like the math formatting standard below) that ensure each conversion step produces Obsidian-ready Markdown.
Early Requirements
- Model Agnosticism: Our chains should work regardless of the underlying language model.
- Dual Access Modes: Provide a solution that’s usable both via an API-driven script and manually (through guided copy-pasting).
- Stepwise Formatting: At each stage (e.g., identifying formulas, formatting text blocks, handling images), we’ll need precise prompt guidelines.
Examples
There are many examples of that workflow. Usually, re-formatting the “initial” first version of formulas is for me the last step in that chain. This has two sub-steps: first identifying all formulas in the new markdown file; secondly, reformatting them. Below is one example of how we could assetize the prompt engineering guides to re-format identified math formulas. This is an example for what I want us to standardize:
- The chains / process / workflow
- The best-practice template at each step
Example: Math Formatting as a Final Cleanup Step
Note: The guideline below is just one example—specifically, the math formatting step that I run as one of the last two steps in my conversion chain. After the PDF content has been parsed and most formatting applied, this step ensures that any math expressions are cleaned up for optimal rendering in Obsidian.
# Document – Formatting Math in Obsidian
## Summary
Use **single dollar signs** (`$...$`) for **inline math** and **double dollar signs** (`$$...$$`) for **display math**, making sure **no extra spaces** sneak inside the `$` delimiters. Keep punctuation and spaces **outside** the math fences. If math fails to render, check for hidden spaces, plugin conflicts, or restricted environments. For **color** in math, use `\textcolor{color}{...}`—but note it may require Obsidian’s MathJax color support or additional plugins. Display equations typically handle color more reliably than inline math.
By following these tips, you ensure consistent, error-free (and optionally colorful) math rendering in Obsidian.
---
## Exhaustive Document – Formatting Math in Obsidian
### 1. Inline Math (No Color)
1. **Use Single Dollar Signs**:
```markdown
$f(x)$
```
This renders as *inline* math, e.g., \(f(x)\).
4. **No Extra Spaces Inside** the `$` Delimiters:
- **Correct**: `$f(x)$`
- **Incorrect**: `$ f(x) $`
5. **Punctuation**: Keep commas, periods, etc. **outside** the math fences:
- **Correct**: `the flux is $f(x)$, so we proceed...`
- **Incorrect**: `the flux is $f(x),$ so we proceed...`
6. **Avoid `\( ... \)`** unless you have verified your Obsidian installation or a plugin supports that syntax. The default inline syntax is `$...$`.
7. **Underscores and Carets**: In LaTeX math mode (i.e., inside `$...$`), you do not need to escape `_` or `^`. If you use them **outside** math mode, you may need escaping to avoid Markdown formatting issues, e.g., `\_`.
---
### 2. Display Math (No Color)
8. **Use Double Dollar Signs** for Block Equations:
```markdown
$$
\mathcal{F}: a(\mathbf{x}) \mapsto u(\mathbf{x})
$$
```
This renders a *centered* equation in Obsidian.
9. **Spacing**: Display math is more tolerant about spacing, but it is still best practice to avoid placing content on the same line as the `$$` delimiters:
- **Correct**:
```
$$
x^2 + y^2 = 1
$$
```
- **Incorrect**:
```
$$ x^2 + y^2 = 1 $$
```
10. **Punctuation** still belongs **outside** the `$...$` block.
---
### 3. Inline Math With Color
11. **Color Macros**: Obsidian often supports basic MathJax `\textcolor{color}{...}` commands (e.g., `red`, `blue`, `green`). Some setups also allow `[rgb]{r,g,b}` or named HTML colors, but this may require a plugin or extra configuration.
12. **Syntax Example** (inline, no extra spaces):
```markdown
- $p(\textcolor{blue}{\psi})$
- $\textcolor{red}{\psi}$
- $\textcolor[rgb]{0,1,0}{\psi}$
```
Each should display *\(\psi\)* in the specified color, inline.
13. **Common Limitations**:
- Some Obsidian installations only recognize a handful of named colors.
- Plugin conflicts or incomplete MathJax support can prevent inline color from rendering.
- If inline color fails, confirm no leading/trailing spaces in the `$...$` fences, disable conflicting plugins, or try display math instead.
---
### 4. Display Math With Color
14. **Most Reliable** for color usage, as spacing quirks are less common and extended macros often work better in block mode:
```markdown
$$
\textcolor{blue}{\psi(r,z)} =
\nabla \times \textcolor{red}{(\psi \,\hat{\theta})}
$$
```
- \(\psi(r,z)\) in **blue**
- \((\psi \,\hat{\theta})\) in **red**
15. **Extra Color Options**:
- You can define custom colors or run `\require{color}` if your system supports more advanced MathJax configurations.
- If color still fails, check your Obsidian MathJax settings or plugin support.
---
### 5. Escaping Special Characters (Recap)
- **Underscores/Carets** (`_`, `^`) within math mode typically do **not** need backslashes.
- **Curly Braces** `{ ... }` are used for grouping in LaTeX math mode (e.g., `x^{10}`), so these also generally do not need extra escaping inside `$...$`.
- **Outside** math mode, underscores can produce italic text in Markdown, so escape them with a backslash if needed.
---
### 6. Spacing & Punctuation
16. **No Leading/Trailing Spaces**:
- **Correct**: `$f(x)$`
- **Incorrect**: `$ f(x) $`
17. **Keep Punctuation Out** of the math fences:
- **Correct**: `the solution is $f(x)$.`
- **Incorrect**: `the solution is $f(x).$`
18. **Hidden Spaces**: If your math doesn’t render, check for stray or invisible characters near the `$` symbols.
---
### 7. Example of Correct Usage (Obsidian Markdown)
```markdown
## Example Document
We look at a neural operator mapping.
This is **inline math**: $f(x) = \sin(\alpha x)$.
Color inline:
- $\textcolor{blue}{\alpha}$ is a parameter.
Below is a **display equation**:
$$
\mathcal{F}: a(\mathbf{x}) \mapsto u(\mathbf{x})
$$
Here is display math with color:
$$
\textcolor{red}{\psi(r,z)} = \nabla \times \textcolor[rgb]{0,0.7,0}{(\psi \,\hat{\theta})}
$$
We also reference PDE solutions: $u(\mathbf{x})$, where $u$ satisfies
the equation $-\Delta u = f(x)$ on a given domain.
Finally, sets with braces: $\{a_i\}_{i=1}^N$.
```
In preview mode, all the equations (and colors, if supported) should appear correctly.
---
### 8. Final Check & Troubleshooting
19. **Preview Your Note**: Switch to Preview (or Live Preview) in Obsidian to confirm the math (and colors) render correctly.
20. **Check for Spaces/Punctuation**:
- Unintended spaces inside `$...$` delimiters can break inline math.
- Punctuation inside the fences can cause parsing errors.
21. **Plugin & MathJax Settings**:
- If color is not working, verify that Obsidian’s MathJax configuration or a relevant community plugin is enabled.
- Some environments might restrict color macros or only allow a few color names (e.g., `red`, `blue`, `green`).
22. **`\( ... \)` vs `$ ... $`**:
- Obsidian’s default is `$...$`. If you use `\( ... \)` and it fails, revert to `$...$` or ensure you have the plugin that enables `\( ... \)` syntax.
---
By adhering to these guidelines, we can ensure that our PDF-to-Markdown conversion pipeline produces notes that are perfectly optimized for Obsidian—math, color, spacing, and all!
## Let’s Collaborate!
I’d love to hear your thoughts:
- **What other requirements or edge cases should we cover?**
- **Do you have any ideas for additional LangChain-style chains that could further improve the conversion process?**
- **Any suggestions for making the process more seamless for both automated and manual workflows?**
If you’re interested in contributing to this effort—be it through coding, prompt engineering, or simply brainstorming—please reply to this thread or reach out directly. Let’s build a repository of best practices that truly meets the needs of the Obsidian community!
Looking forward to your feedback and ideas.
Cheers,
YGMaerz