XzhLoongSkills/skills/research-skills/medical-imaging-review/references/MCP_SETUP.md

MCP Server Configuration for Literature Collection

Set up arxiv-mcp / pubmedmcp / zotero-mcp for use in Phase 2 (Literature Collection + Verification). For each server, this file documents installation, tools available, and the searches that match the workflow.

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ArXiv MCP (Preprints & Latest Research)

Repository: https://github.com/blazickjp/arxiv-mcp-server

Configuration

Add to ~/.claude/mcp.json (or your MCP config file):

{
  "mcpServers": {
    "arxiv": {
      "command": "uvx",
      "args": ["arxiv-mcp-server"],
      "env": {
        "ARXIV_STORAGE_PATH": "~/.arxiv-mcp-server/papers"
      }
    }
  }
}

Available tools

Tool	Purpose
mcp__arxiv-mcp-server__search_papers	Search by keywords with date range and category filters
mcp__arxiv-mcp-server__download_paper	Download paper PDF by arXiv ID
mcp__arxiv-mcp-server__list_papers	List all downloaded papers
mcp__arxiv-mcp-server__read_paper	Read downloaded paper content (Markdown)

Search strategy

Query: "[topic] AND (segmentation OR detection OR classification)"
Categories: cs.CV, eess.IV, cs.LG
Date: Last 3 years for current state of the art
Max results: 50-80 per query (discriminate aggressively — quality over breadth)

Example queries

• "medical image segmentation transformer" (cs.CV, eess.IV)
• "coronary artery deep learning" (cs.CV)
• "CT scan neural network" (eess.IV)
• "foundation model medical segmentation" (cs.CV, cs.LG)

Workflow integration

Per CITATION_INTEGRITY.md Rule 2, when adding an arXiv paper to bibliography:

1. search_papers to find candidates
2. download_paper(paper_id) for promising ones
3. read_paper(paper_id) to read full text (or at least abstract + methods + results)
4. Note actual first author, full author list, exact module names, headline numbers
5. Cross-check: arxiv abstract page = https://arxiv.org/abs/<id> for author list verification

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PubMed MCP (Biomedical Literature)

Repository: https://github.com/grll/pubmedmcp

Access 35+ million biomedical literature citations.

Configuration

{
  "mcpServers": {
    "pubmedmcp": {
      "command": "uvx",
      "args": ["pubmedmcp@latest"],
      "env": {
        "UV_PRERELEASE": "allow",
        "UV_PYTHON": "3.12"
      }
    }
  }
}

Available tools

Tool	Purpose
mcp__pubmed-mcp-server__pubmed_search_articles	Search PubMed with MeSH and free-text queries

Search tips

• Use MeSH terms for precise medical searches
• Combine with publication type filters (Review, Clinical Trial)
• Filter by date for recent literature

Example MeSH queries

• "Deep Learning"[MeSH] AND "Coronary Vessels"[MeSH]
• "Image Processing, Computer-Assisted"[MeSH] AND "Tomography, X-Ray Computed"[MeSH]
• "Cardiac Imaging Techniques"[MeSH] AND "Artificial Intelligence"[MeSH]

Direct WebFetch for verification

pubmed_search_articles returns PMIDs. For metadata verification (CITATION_INTEGRITY.md Rules 1-2):

WebFetch on https://pubmed.ncbi.nlm.nih.gov/<PMID>/
  → Extract: full author list, journal, year, vol, issue, pages, DOI, finding direction

This is the canonical first-source verification step for medical clinical papers.

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Zotero Integration

Access user's local Zotero database via Zotero-MCP.

Direct API Access (fallback)

# List collections
curl -s "http://localhost:23119/api/users/[USER_ID]/collections"

# Get items from a collection
curl -s "http://localhost:23119/api/users/[USER_ID]/collections/[KEY]/items"

Zotero-MCP (recommended)

Repository: https://github.com/54yyyu/zotero-mcp

Provides structured access:

Tool	Purpose
mcp__zotero__zotero_search_collections	Find collections by name / keyword
mcp__zotero__zotero_get_collection_items	List items in a collection
mcp__zotero__zotero_search_items	Search items by keyword
mcp__zotero__zotero_get_item_metadata	Get full metadata for an item
mcp__zotero__zotero_get_item_fulltext	Get full paper text from attached PDF
mcp__zotero__zotero_get_annotations	Get user highlights / notes
mcp__zotero__zotero_semantic_search	Semantic search across library

Workflow integration

For closed-access journals (Med Image Anal, Eur Radiol, JACC family, Lancet family, Nature family), the user often has PDFs in Zotero that aren't accessible via WebFetch. Workflow:

1. mcp__zotero__zotero_search_items(query: "<author> <method>", limit: 5)
2. mcp__zotero__zotero_get_item_metadata(item_key: "<key>")
3. mcp__zotero__zotero_get_item_fulltext(item_key: "<key>") for body content

Extractable fields

• title
• abstractNote
• date
• creators (author list — verify against first-source per Rule 2)
• publicationTitle
• DOI
• tags
• collections

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Source Selection Guide

Source	Best for	Strengths	Workflow phase
ArXiv	Methodological preprints, ML/AI advances	Fast access, CS/AI focus, full text	Phase 2.1
PubMed	Peer-reviewed clinical / validation, MeSH-indexed	Authoritative for medical, free metadata access	Phase 2.2
Zotero	Closed-access journals where user has PDFs	Local, supports fulltext extraction	Phase 2.3
Crossref	DOI verification	API gives canonical metadata	All phases (verification)

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Verification helper commands

For Phase 4 (per-claim verification) and Phase 5 (peer review):

# Crossref by DOI
WebFetch on https://api.crossref.org/works/<DOI>
  → Returns JSON: title, full author list, container-title (journal), volume, issue, page, DOI, published year

# Crossref by topic search
WebFetch on https://api.crossref.org/works?query.bibliographic=<keywords>&rows=5
  → Returns top 5 matching entries

# PubMed by PMID
WebFetch on https://pubmed.ncbi.nlm.nih.gov/<PMID>/
  → Returns parsed page: title, authors, journal info, DOI, abstract

# arXiv abstract page (for author list verification)
WebFetch on https://arxiv.org/abs/<id>
  → Returns abstract + full author list

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When MCP servers fail

If an MCP server is not configured or fails:

• ArXiv fallback: WebFetch on https://arxiv.org/abs/<id> directly
• PubMed fallback: WebFetch on https://pubmed.ncbi.nlm.nih.gov/<PMID>/ directly
• Zotero fallback: ask the user to share PDFs directly, or use direct API access via curl

The skill is designed to work even without MCP — WebFetch on the underlying APIs is always available.