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)

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