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.

Output goes to <topic>/sources/<slug>/extracted.md.

Step 4 — Produce a structured analysis

Read <topic>/sources/<slug>/extracted.md and any existing KB documents in <topic>/synthesis/ and <topic>/analysis/. Write the analysis to <topic>/analysis/<slug>.md using the frontmatter schema from kb-conventions.

Required sections

1. Publication details — title, authors, year, venue, DOI
2. Core thesis — main research question and central claim in 2–3 sentences [DIRECT]
3. Key contributions — bullet list, each with [DIRECT], [INFERRED], or [SPECULATIVE] citation
4. Mathematical foundations — equations, proofs, formal definitions (if present)
5. Algorithms — pseudocode or step-by-step for all algorithms, each with section reference
6. Architecture / system design — component relationships, diagrams described in prose
7. Experimental results — datasets, metrics, key findings with [DIRECT] citations
8. Limitations and open problems — what the paper acknowledges as unsolved
9. Relation to existing KB — cross-reference with <topic>/analysis/ and <topic>/synthesis/; use blockquote markers > ⚠ DIVERGES FROM KB: or > ✦ NEW: where relevant
10. Glossary — domain-specific terms introduced, each with [DIRECT] definition

Step 4b — Apply anti-slop

Apply the anti-slop skill to <topic>/analysis/<slug>.md before proceeding. Do NOT modify citation markers, confidence annotations, blockquotes, or code blocks — prose quality only.

Step 4c — Update source.md

After completing the analysis, update <topic>/sources/<slug>/source.md:

• tldr: one-sentence key takeaway derived from the Core thesis section
• status: active (was draft)
• concepts: slugs of any <topic>/synthesis/ pages this source informs
• sources: slugs of cited papers if this is a survey
• confidence: 0.8–1.0 if claims are verified [DIRECT]; 0.5–0.7 if mostly [INFERRED]; 0.1–0.4 if mostly [SPECULATIVE]
• claims: add 3–7 key claims from the analysis using the claim schema in kb-conventions

Step 5 — Update analysis index

See kb-conventions for index format. Add entry to <topic>/analysis/README.md; create it if absent.

Step 6 — Assess synthesis impact

See kb-conventions for synthesis impact rules and divergence markers.

Output summary

✓ Source:    <topic>/sources/<slug>/original.pdf
✓ Extract:   <topic>/sources/<slug>/extracted.md
✓ Metadata:  <topic>/sources/<slug>/source.md
✓ Analysis:  <topic>/analysis/<slug>.md
✓ Index:     <topic>/analysis/README.md
~ Synthesis: <NEW / DIVERGES / no impact>