lit-annotate

Extract structured key points from paper notes or PDFs into vault notes.

Updated May 14, 2026
One-click install
npx skills add https://github.com/jaqg/daimon --skill lit-annotate
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: lit-annotate
Source: https://github.com/jaqg/daimon/tree/main/literature/skills/lit-annotate
Command: npx skills add https://github.com/jaqg/daimon --skill lit-annotate

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pymupdf, and includes scripts (resource) components.

What problem does it solve?

After reading a paper and taking notes, researchers often struggle to convert notes into structured vault content that captures per-paper insights (Methods, Key results, Limitations, and Open questions). lit-annotate automates populating those Key points into an existing vault paper note without overwriting user-written content.

Core Features & Use Cases

  • Works with reading notes, a local PDF, or a URL to derive structured content.
  • Fills the Methods, Key result, Limitations, and Open questions sections while preserving user edits; can optionally expand the Summary and suggest Galaxy links.
  • Reads YAML frontmatter (doi/arxiv, full_text_available, project) and uses project memory to frame open questions; respects vault conventions and per-paper notes.

Quick Start

Provide reading notes or a paper PDF/URL, then run /lit-annotate to populate the Key points in the vault note.

Frequently Asked Questions about lit-annotate

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I extract key points from a PDF into my literature reading notes?

To extract key points from a PDF into literature reading notes, provide the paper PDF or reading notes to the system. It processes the input and populates Methods, Key results, Limitations, and Open questions sections directly into your vault note.

Does lit-annotate overwrite existing content when filling vault paper notes?

No, lit-annotate does not overwrite existing content. It only fills empty sub-bullets under the Key points sections, ensuring your user-written notes and edits remain completely preserved during the annotation process.

Can I use arxiv links and local PDFs to populate structured paper summaries?

Yes, you can use local PDFs and arxiv links to populate structured paper summaries. The system reads existing YAML frontmatter like doi or arxiv identifiers to fetch full text and frame the project context for accurate annotation.

What is the best way to automate organizing methods and limitations from research papers?

The best way to automate organizing methods and limitations from research papers is using a structured annotation skill. It processes text notes or fetched full text to automatically generate categorized sub-bullets for your vault notes.

Do I need pymupdf to process local PDF files for vault annotations?

Yes, you need pymupdf installed to process local PDF files for vault annotations. This dependency enables the system to parse your local PDF documents and extract the structured content needed for your reading notes.

Why are my open questions not generating correctly from the paper text?

Open questions may not generate correctly if the project context is missing. The system uses project memory and existing frontmatter to frame these questions, so ensure your vault paper notes include proper project metadata.