Paper MCP

Use the Paper MCP server for paper-driven research and implementation tasks. For setup and debugging details (env vars, config, verification), see references/paper-mcp-config.md.

Paper MCP integration rules

These rules define how to translate paper inputs into reliable outputs and must be followed for every paper-driven change.

Required flow (do not skip)

1. Resolve the paper first (URL/DOI/arXiv/PMID) and fetch high-level metadata before requesting full text.
2. If the full response is large or truncated, fetch section-level context and work section-by-section.
3. Fetch a stable citation list before drafting any claims that depend on references.
4. If figures/tables are relevant, fetch those assets and capture captions prior to synthesis.
5. Only after metadata plus content context are collected, generate the user output (summary/table/notes/code-facing plan).
6. Validate all key claims against source excerpts before marking complete.

Tool mapping rule

• Paper MCP deployments may expose different tool names.
• Start by listing available paper MCP tools, then map this workflow to equivalent tools in the current server.
• If a required capability is missing (for example, no section fetch or no citation endpoint), note the limitation and continue with the best available fallback.

Implementation rules

• Treat paper MCP responses as source context, not final prose.
• Keep outputs traceable: tie each important claim to a section, figure, or citation.
• Distinguish evidence from inference clearly.
• Preserve units, metrics, and dataset/task names exactly as written in source context.
• Prefer concise structured output (tables/checklists) when comparing multiple papers.
• For code-facing tasks, extract actionable constraints (input shapes, evaluation metrics, baseline numbers, reproducibility requirements).

Quality rules

• Do not invent citations, metrics, or section names.
• Call out uncertainty when context is partial, truncated, or conflicting.
• If two sources disagree, present both with scope and date/context differences.
• Keep quoted text short and use paraphrasing for long passages.

References

• references/paper-mcp-config.md - setup, verification, troubleshooting, and input ID guidance.
• references/paper-tools-and-prompts.md - tool mapping checklist and prompt templates for common paper workflows.