research-paper

Research Paper Processing

Processes an academic paper into the knowledge repository following the sources → extract → analysis → studies → synthesis pipeline. Produces confidence-annotated claims traceable to exact source sections.

Apply kb-conventions skill for annotation markers, KB directory layout, frontmatter schema, and synthesis impact rules.

Prerequisites

Add to .claude/settings.json before running:

{
  "permissions": {
    "allow": [
      "Bash(xberg *)",
      "Bash(uvx marker-pdf *)",
      "Bash(curl *)",
      "Bash(mkdir *)",
      "Bash(cp *)"
    ]
  }
}

When to use

• Single paper (PDF or URL) to integrate into a topic KB
• Need structured analysis with traceable claims
• Want synthesis impact assessment against existing KB

For multiple sources requiring multi-axis extraction, use research-extraction instead.

Step 1 — Identify paper and topic

Ask the user (or infer from context):

• Paper source: URL or local PDF path
• Target topic directory within the knowledge base
• Create the topic directory if it does not exist (see kb-conventions for layout)

Step 2 — Acquire the source

URL

mkdir -p "<topic>/sources/<slug>"
curl -L "<url>" -o "<topic>/sources/<slug>/original.pdf"

Skip if file already exists.

Local PDF

Copy to <topic>/sources/<slug>/original.pdf if not already there.

Create source.md

Create <topic>/sources/<slug>/source.md using the template from kb-conventions. Fill title, type, summary, tags, status: draft, last_updated from what is already known (title page, URL, user context). Leave tldr, claims, concepts empty — populated after Step 4.

Step 3 — Extract text

Use the pdf-parse skill to extract text. It selects the right tool automatically (xberg for machine-readable, marker-pdf via uvx for scanned) and handles tool installation.

For academic papers, pass --use_llm --force_ocr to the pdf-parse skill for best quality on scanned sources.