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.
1---2name: paper-mcp3description: Use the Paper MCP server to fetch paper metadata, sections, figures, citations, and full-text context, then translate that context into structured outputs such as summaries, extraction tables, and implementation-ready notes. Trigger when a task involves paper links/DOIs/arXiv IDs, literature review, citation extraction, or Paper MCP setup and troubleshooting.4---5
6# Paper MCP
7
8Use 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`.
9
10## Paper MCP integration rules
11These rules define how to translate paper inputs into reliable outputs and must be followed for every paper-driven change.
12
13### Required flow (do not skip)
141. Resolve the paper first (URL/DOI/arXiv/PMID) and fetch high-level metadata before requesting full text.
152. If the full response is large or truncated, fetch section-level context and work section-by-section.
163. Fetch a stable citation list before drafting any claims that depend on references.
174. If figures/tables are relevant, fetch those assets and capture captions prior to synthesis.
185. Only after metadata plus content context are collected, generate the user output (summary/table/notes/code-facing plan).
196. Validate all key claims against source excerpts before marking complete.
20
21### Tool mapping rule
22- Paper MCP deployments may expose different tool names.
23- Start by listing available paper MCP tools, then map this workflow to equivalent tools in the current server.
24- 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.
25
26### Implementation rules
27- Treat paper MCP responses as source context, not final prose.
28- Keep outputs traceable: tie each important claim to a section, figure, or citation.
29- Distinguish evidence from inference clearly.
30- Preserve units, metrics, and dataset/task names exactly as written in source context.
31- Prefer concise structured output (tables/checklists) when comparing multiple papers.
32- For code-facing tasks, extract actionable constraints (input shapes, evaluation metrics, baseline numbers, reproducibility requirements).
33
34### Quality rules
35- Do not invent citations, metrics, or section names.
36- Call out uncertainty when context is partial, truncated, or conflicting.
37- If two sources disagree, present both with scope and date/context differences.
38- Keep quoted text short and use paraphrasing for long passages.
39
40## References
41- `references/paper-mcp-config.md` - setup, verification, troubleshooting, and input ID guidance.
42- `references/paper-tools-and-prompts.md` - tool mapping checklist and prompt templates for common paper workflows.
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