PubMed Search MCP

Professional Literature Research Assistant for AI Agents - More than just an API wrapper

A Domain-Driven Design (DDD) based MCP server that serves as an intelligent research assistant for AI agents, providing task-oriented literature search and analysis capabilities.

✨ What's Included:

• 🔧 44 MCP Tools - Streamlined PubMed, Europe PMC, CORE, NCBI database access, and Research Timeline / Context Graph
• 🖼️ OA Figure Extraction - Pull figure captions, direct image URLs, and PDF links from PMC Open Access articles
• 📘 Docs Site - Browse overview, architecture, quick reference, pipeline tutorials, source contracts, troubleshooting, and deployment in one place at docs/index.html
• 📚 24 Claude Skills - Ready-to-use workflow guides for AI agents (Claude Code-specific)
• 📖 Copilot Instructions - VS Code GitHub Copilot integration guide

🌐 Language: English | 繁體中文

📘 Tool Usage Docs: Capability-first guide | Complete index

---

🚀 Quick Install

Prerequisites

• Python 3.10+ — Download

• uv (recommended) — Install uv

  # macOS / Linux
  curl -LsSf https://astral.sh/uv/install.sh | sh
  # Windows
  powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

• NCBI Email — Required by NCBI API policy. Any valid email address.

• NCBI API Key (optional) — Get one here for higher rate limits (10 req/s vs 3 req/s)

• OpenAlex API Key (optional) — set OPENALEX_API_KEY to use authenticated OpenAlex requests instead of mailto-only polite-pool auth

Install & Run

# Option 1: Zero-install with uvx (recommended for trying out)
uvx pubmed-search-mcp

# Option 2: Add as project dependency
uv add pubmed-search-mcp

# Option 3: pip install
pip install pubmed-search-mcp

---

⚙️ Configuration

This MCP server works with any MCP-compatible AI tool. Choose your preferred client:

VS Code / Cursor (.vscode/mcp.json)

{
  "servers": {
    "pubmed-search": {
      "type": "stdio",
      "command": "uvx",
      "args": ["pubmed-search-mcp"],
      "env": {
        "NCBI_EMAIL": "your@email.com"
      }
    }
  }
}

Optional: enable browser-session PDF fallback once and let tools auto-use it:

{
  "servers": {
    "pubmed-search": {
      "type": "stdio",
      "command": "uvx",
      "args": ["pubmed-search-mcp"],
      "env": {
        "NCBI_EMAIL": "your@email.com",
        "BROWSER_FETCH_CONFIG": "{\"enabled\":true,\"auto_enabled\":true,\"broker_url\":\"http://127.0.0.1:8766/fetch\",\"token\":\"local-dev-token\",\"allowed_hosts\":[\"jamanetwork.com\",\"*.jamanetwork.com\",\"nejm.org\",\"*.nejm.org\"]}"
      }
    }
  }
}

With this setting, get_fulltext will automatically try the local broker for institutional or publisher landing pages. Pass allow_browser_session=false only when you want to suppress it for a specific call.

Run the local broker with download interception:

uv sync --extra browser-broker
uv run playwright install chromium
uv run pubmed-browser-fetch-broker --token local-dev-token

The broker launches a persistent browser profile with download interception enabled. Log in once inside that broker-controlled browser window, and subsequent PDF downloads will be captured automatically without a native "Save As" dialog.

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "pubmed-search": {
      "command": "uvx",
      "args": ["pubmed-search-mcp"],
      "env": {
        "NCBI_EMAIL": "your@email.com"
      }
    }
  }
}

Config file location:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

Claude Code

claude mcp add pubmed-search -- uvx pubmed-search-mcp

Or add to .mcp.json in your project root:

{
  "mcpServers": {
    "pubmed-search": {
      "command": "uvx",
      "args": ["pubmed-search-mcp"],
      "env": {
        "NCBI_EMAIL": "your@email.com"
      }
    }
  }
}

Zed AI (settings.json)

Zed editor (z.ai) supports MCP servers natively. Add to your Zed settings.json:

{
  "context_servers": {
    "pubmed-search": {
      "command": "uvx",
      "args": ["pubmed-search-mcp"],
      "env": {
        "NCBI_EMAIL": "your@email.com"
      }
    }
  }
}

Tip: Open Command Palette → zed: open settings to edit, or go to Agent Panel → Settings → "Add Custom Server".

OpenClaw 🦞 (~/.openclaw/openclaw.json)

OpenClaw uses MCP servers via the mcp-adapter plugin. Install the adapter first:

openclaw plugins install mcp-adapter

Then add to ~/.openclaw/openclaw.json:

{
  "plugins": {
    "entries": {
      "mcp-adapter": {
        "enabled": true,
        "config": {
          "servers": [
            {
              "name": "pubmed-search",
              "transport": "stdio",
              "command": "uvx",
              "args": ["pubmed-search-mcp"],
              "env": {
                "NCBI_EMAIL": "your@email.com"
              }
            }
          ]
        }
      }
    }
  }
}

Restart the gateway after configuration:

openclaw gateway restart
openclaw plugins list  # Should show: mcp-adapter | loaded

Cline (cline_mcp_settings.json)

{
  "mcpServers": {
    "pubmed-search": {
      "command": "uvx",
      "args": ["pubmed-search-mcp"],
      "env": {
        "NCBI_EMAIL": "your@email.com"
      },
      "alwaysAllow": [],
      "disabled": false
    }
  }
}

Other MCP Clients

Any MCP-compatible client can use this server via stdio transport:

# Command
uvx pubmed-search-mcp

# With environment variable
NCBI_EMAIL=your@email.com uvx pubmed-search-mcp

Note: NCBI_EMAIL is required by NCBI API policy. Optionally set NCBI_API_KEY for higher rate limits (10 req/s vs 3 req/s). 📖 Detailed Integration Guides: See docs/INTEGRATIONS.md for all environment variables, Copilot Studio setup, Docker deployment, proxy configuration, and troubleshooting.

---

🎯 Design Philosophy

Core Positioning: The intelligent middleware between AI Agents and academic search engines.

Why This Server?

Other tools give you raw API access. We give you vocabulary translation + intelligent routing + research analysis:

Challenge	Our Solution
Agent uses ICD codes, PubMed needs MeSH	✅ Auto ICD→MeSH conversion
Multiple databases, different APIs	✅ Unified Search single entry point
Clinical questions need structured search	✅ PICO toolkit (parse_pico + generate_search_queries for Agent-driven workflow)
Typos in medical terms	✅ ESpell auto-correction
Too many results from one source	✅ Parallel multi-source with dedup
Need to trace research evolution	✅ Research Timeline & Tree with landmark detection, diagnostics, and sub-topic branching
Citation context is unclear	✅ Citation Tree forward/backward/network
Can't access full text	✅ Multi-source fulltext (Europe PMC, CORE, CrossRef)
Gene/drug info scattered across DBs	✅ NCBI Extended (Gene, PubChem, ClinVar)
Need cutting-edge preprints	✅ Preprint search (arXiv, medRxiv, bioRxiv) with peer-review filtering
Export to reference managers	✅ One-click export (RIS, BibTeX, CSV, MEDLINE)

Key Differentiators

1. Vocabulary Translation Layer - Agent speaks naturally, we translate to each database's terminology (MeSH, ICD-10, text-mined entities)
2. Unified Search Gateway - One unified_search() call, auto-dispatch to PubMed/Europe PMC/CORE/OpenAlex
3. PICO Toolkit - parse_pico() decomposes clinical questions into P/I/C/O elements; Agent then calls generate_search_queries() per element and builds Boolean query
4. Research Timeline & Lineage Tree - Detect milestones with policy-driven heuristics, identify landmark papers via multi-signal scoring, surface timeline diagnostics, and visualize research evolution as branching trees by sub-topic
5. Citation Network Analysis - Build multi-level citation trees to map an entire research landscape from a single paper
6. Full Research Lifecycle - From search → discovery → full text → analysis → export, all in one server
7. Agent-First Design - Output optimized for machine decision-making, not human reading

---

📡 External APIs & Data Sources

This MCP server integrates with multiple academic databases and APIs:

Core Data Sources

Source	Coverage	Vocabulary	Auto-Convert	Description
NCBI PubMed	36M+ articles	MeSH	✅ Native	Primary biomedical literature
NCBI Entrez	Multi-DB	MeSH	✅ Native	Gene, PubChem, ClinVar
Europe PMC	33M+	Text-mined	✅ Extraction	Full text XML access
CORE	200M+	None	➡️ Free-text	Open access aggregator
Semantic Scholar	200M+	S2 Fields	➡️ Free-text	AI-powered recommendations
OpenAlex	250M+	Concepts	➡️ Free-text	Open scholarly metadata
NIH iCite	PubMed	N/A	N/A	Citation metrics (RCR)

🔑 Key: ✅ = Full vocabulary support | ➡️ = Query pass-through (no controlled vocabulary)

ICD Codes: Auto-detected and converted to MeSH before PubMed search

Environment Variables

# Required
NCBI_EMAIL=your@email.com          # Required by NCBI policy

# Optional - For higher rate limits
NCBI_API_KEY=your_ncbi_api_key     # Get from: https://www.ncbi.nlm.nih.gov/account/settings/
CORE_API_KEY=your_core_api_key     # Get from: https://core.ac.uk/services/api
S2_API_KEY=your_s2_api_key         # Get from: https://www.semanticscholar.org/product/api

# Optional - Network settings
HTTP_PROXY=http://proxy:8080       # HTTP proxy for API requests
HTTPS_PROXY=https://proxy:8080     # HTTPS proxy for API requests

🔄 How It Works: The Middleware Architecture

┌─────────────────────────────────────────────────────────────────────────────┐
│                              AI AGENT                                        │
│                                                                              │
│   "Find papers about I10 hypertension treatment in diabetic patients"       │
│                                                                              │
└─────────────────────────────────┬───────────────────────────────────────────┘
                                  │
                                  ▼
┌─────────────────────────────────────────────────────────────────────────────┐
│                     🔄 PUBMED SEARCH MCP (MIDDLEWARE)                        │
│  ┌─────────────────────────────────────────────────────────────────────────┐│
│  │  1️⃣ VOCABULARY TRANSLATION                                              ││
│  │     • ICD-10 "I10" → MeSH "Hypertension"                                ││
│  │     • "diabetic" → MeSH "Diabetes Mellitus"                             ││
│  │     • ESpell: "hypertention" → "hypertension"                           ││
│  └─────────────────────────────────────────────────────────────────────────┘│
│  ┌─────────────────────────────────────────────────────────────────────────┐│
│  │  2️⃣ INTELLIGENT ROUTING                                                 ││
│  │     ┌──────────┐  ┌──────────┐  ┌──────────┐  ┌──────────┐             ││
│  │     │ PubMed   │  │Europe PMC│  │   CORE   │  │ OpenAlex │             ││
│  │     │  36M+    │  │   33M+   │  │  200M+   │  │  250M+   │             ││
│  │     │  (MeSH)  │  │(fulltext)│  │  (OA)    │  │(metadata)│             ││
│  │     └────┬─────┘  └────┬─────┘  └────┬─────┘  └────┬─────┘             ││
│  │          └──────────────┴──────────────┴──────────────┘                 ││
│  │                              ▼                                          ││
│  │  3️⃣ RESULT AGGREGATION: Dedupe + Rank + Enrich                         ││
│  └─────────────────────────────────────────────────────────────────────────┘│
└─────────────────────────────────┬───────────────────────────────────────────┘
                                  │
                                  ▼
┌─────────────────────────────────────────────────────────────────────────────┐
│                         UNIFIED RESULTS                                      │
│   • 150 unique papers (deduplicated from 4 sources)                          │
│   • Ranked by relevance + citation impact (RCR)                              │
│   • Full text links enriched from Europe PMC                                 │
└─────────────────────────────────────────────────────────────────────────────┘

---

🛠️ MCP Tools Overview

If you want to understand the tool surface as a usable system, do not start by memorizing 40 tool names.

Start with the Tools Usage Guide: it compresses the current 40 tools into 8 capability families, explains the theoretical lower bound, and gives intent-based routing for both humans and agents.

🔍 Search & Query Intelligence

┌─────────────────────────────────────────────────────────────────┐
│                      SEARCH ENTRY POINT                          │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│   unified_search()          ← 🌟 Single entry for all sources    │
│        │                                                         │
│        ├── Quick search     → Direct multi-source query          │
│        ├── PICO hints       → Detects comparison, shows P/I/C/O  │
│        └── ICD expansion    → Auto ICD→MeSH conversion           │
│                                                                  │
│   Sources: PubMed · Europe PMC · CORE · OpenAlex                 │
│   Auto: Deduplicate → Rank → Enrich full-text links              │
│                                                                  │
├─────────────────────────────────────────────────────────────────┤
│   QUERY INTELLIGENCE                                             │
│                                                                  │
│   generate_search_queries() → MeSH expansion + synonym discovery │
│   parse_pico()              → PICO element decomposition         │
│   analyze_search_query()    → Query analysis without execution   │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘

🔬 Discovery Tools (After Finding Key Papers)

                        Found important paper (PMID)
                                   │
           ┌───────────────────────┼───────────────────────┐
           │                       │                       │
           ▼                       ▼                       ▼
    ┌─────────────┐        ┌─────────────┐        ┌─────────────┐
    │  BACKWARD   │        │  SIMILAR    │        │  FORWARD    │
    │  ◀──────    │        │  ≈≈≈≈≈≈     │        │  ──────▶    │
    │             │        │             │        │             │
    │ get_article │        │find_related │        │find_citing  │
    │ _references │        │ _articles   │        │ _articles   │
    │             │        │             │        │             │
    │ Foundation  │        │  Similar    │        │ Follow-up   │
    │  papers     │        │   topic     │        │  research   │
    └─────────────┘        └─────────────┘        └─────────────┘

    fetch_article_details()   → Detailed article metadata
    get_citation_metrics()    → iCite RCR, citation percentile
    build_citation_tree()     → Full network visualization (6 formats)

📚 Full Text, Figure Extraction & Export

Category	Tools
Full Text	get_fulltext → Multi-source retrieval (Europe PMC, CORE, PubMed, CrossRef)
Figures	get_article_figures → Extract figure labels, captions, image URLs, and PDF links from PMC Open Access articles
Figure-aware Full Text	get_fulltext(include_figures=True) → Embed figure metadata alongside structured fulltext
Text Mining	get_text_mined_terms → Extract genes, diseases, chemicals
Export	prepare_export → RIS, BibTeX, CSV, MEDLINE, JSON

🖼️ OA Figure-First Exploration

Use the PMC Open Access path when an agent needs evidence figures, not just article text:

• get_article_figures(identifier="PMC12086443") → Figure labels, captions, image URLs, and PDF/article links
• get_fulltext(pmcid="PMC7096777", include_figures=True) → Structured fulltext with figures inline
• Figure output preserves article context, so agents can connect each figure back to the sections where it is mentioned

🧬 NCBI Extended Databases

Tool	Description
search_gene	Search NCBI Gene database
get_gene_details	Gene details by NCBI Gene ID
get_gene_literature	PubMed articles linked to a gene
search_compound	Search PubChem compounds
get_compound_details	Compound details by PubChem CID
get_compound_literature	PubMed articles linked to a compound
search_clinvar	Search ClinVar clinical variants

🕰️ Research Timeline & Lineage Tree

Tool	Description
build_research_timeline	Build timeline/tree with landmark detection and formatted diagnostics. Output: text, tree, mermaid, mindmap, json
analyze_timeline_milestones	Analyze milestone distribution with diagnostics payload
compare_timelines	Compare multiple topic timelines with per-topic diagnostics

🏥 Institutional Access & ICD Conversion

Tool	Description
configure_institutional_access	Configure institution's link resolver
get_institutional_link	Generate OpenURL access link
list_resolver_presets	List resolver presets
test_institutional_access	Test resolver configuration
convert_icd_mesh	Convert between ICD codes and MeSH terms (bidirectional)
unified_search	Auto-detect ICD codes in queries and expand them to MeSH

💾 Session Management

Tool	Description
get_session_pmids	Retrieve cached PMID lists
get_cached_article	Get article from session cache (no API cost)
get_session_summary	Session status overview

Dynamic MCP resources are also available for agents that can read resources directly:

• session://context — active session status
• session://last-search — latest search metadata
• session://last-search/pmids — latest PMID list + CSV form
• session://last-search/results — cached article payloads for the latest search

🔁 Pipeline Management

manage_pipeline is the primary facade for pipeline CRUD, history, and scheduling. The more specific pipeline tools remain available as compatibility wrappers.

Tool	Description
manage_pipeline	Primary facade for save, list, load, delete, history, and schedule actions
save_pipeline	Save a pipeline config for later reuse (YAML/JSON, auto-validated)
list_pipelines	List saved pipelines (filter by tag/scope)
load_pipeline	Load pipeline from name or file for review/editing
delete_pipeline	Delete pipeline and its execution history
get_pipeline_history	View execution history with article diff analysis
schedule_pipeline	Create, update, or remove recurring pipeline schedules

Step-by-step tutorials:

• English: docs/PIPELINE_MODE_TUTORIAL.en.md
• 繁體中文: docs/PIPELINE_MODE_TUTORIAL.md

👁️ Vision & Image Search

Tool	Description
analyze_figure_for_search	Analyze scientific figure for search
search_biomedical_images	Search biomedical images across Open-i (X-ray, microscopy, photos, diagrams)

📄 Preprint Search

Search arXiv, medRxiv, and bioRxiv preprint servers via unified_search options flags:

• preprints: Enable dedicated preprint search and show results in a separate section.
• all_types: Keep non-peer-reviewed content in main aggregated results.

Recommended combinations:

• Empty options: Peer-reviewed results only.
• options="preprints": Peer-reviewed main results plus a separate preprint section.
• options="preprints, all_types": Separate preprint section plus non-peer-reviewed content retained in main results.
• options="all_types": No dedicated preprint crawl, but non-peer-reviewed items from searched sources are retained.

Preprint detection — articles are identified as preprints by:

• Article type from source API (OpenAlex, CrossRef, Semantic Scholar)
• arXiv ID present without PubMed ID
• Known preprint server source or journal name
• DOI prefix matching preprint servers (e.g., 10.1101/ → bioRxiv/medRxiv, 10.48550/ → arXiv)

🌳 Research Context Graph

unified_search can append a lightweight research lineage view built from PMID-backed ranked results:

Option Flag	Description
context_graph	Append a Research Context Graph preview to Markdown output and include research_context in JSON output

This is useful when an agent needs quick thematic branching without making a second build_research_timeline call.

📊 Count-First Orientation

unified_search can also front-load the existing source coverage and decision hints for agents that want routing help before reading the ranked list:

Option Flag	Description
counts_first	Add a source-count table, coverage summary, and next-tool recommendations to the response

Example:

unified_search(query="remimazolam ICU sedation", options="counts_first")

This mode is useful when the agent should decide whether to expand a source, inspect the lead PMID, fetch fulltext, extract figures, or pivot into timeline exploration.

⏱️ MCP Progress Reporting

When the MCP client provides a progress token, unified_search, build_research_timeline, analyze_timeline_milestones, compare_timelines, get_fulltext, and get_text_mined_terms emit progress updates for their major phases. This reduces the "black box" wait time for agents during longer searches.

---

📋 Agent Usage Examples

1️⃣ Quick Search (Simplest)

# Agent just asks naturally - middleware handles everything
unified_search(query="remimazolam ICU sedation", limit=20)

# Or with clinical codes - auto-converted to MeSH
unified_search(query="I10 treatment in E11.9 patients")
#                     ↑ ICD-10           ↑ ICD-10
#                     Hypertension       Type 2 Diabetes

2️⃣ PICO Clinical Question

Simple path — unified_search can search directly (no PICO decomposition):

# unified_search searches as-is; detects "A vs B" pattern and shows PICO hints in metadata
unified_search(query="Is remimazolam better than propofol for ICU sedation?")
# → Multi-source keyword search + PICO hint metadata in output
# ⚠️ This does NOT auto-decompose PICO or expand MeSH!
# For structured PICO search, use the Agent workflow below

Agent workflow — PICO decomposition + MeSH expansion (recommended for clinical questions):

┌─────────────────────────────────────────────────────────────────────────┐
│  "Is remimazolam better than propofol for ICU sedation?"                │
└─────────────────────────────────┬───────────────────────────────────────┘
                                  │
                                  ▼
┌─────────────────────────────────────────────────────────────────────────┐
│                         parse_pico()                                     │
│  ┌─────────┐  ┌─────────┐  ┌─────────┐  ┌─────────┐                     │
│  │    P    │  │    I    │  │    C    │  │    O    │                     │
│  │  ICU    │  │remimaz- │  │propofol │  │sedation │                     │
│  │patients │  │  olam   │  │         │  │outcomes │                     │
│  └────┬────┘  └────┬────┘  └────┬────┘  └────┬────┘                     │
└───────┼────────────┼────────────┼────────────┼──────────────────────────┘
        │            │            │            │
        ▼            ▼            ▼            ▼
┌─────────────────────────────────────────────────────────────────────────┐
│              generate_search_queries() × 4 (parallel)                    │
│                                                                          │
│  P → "Intensive Care Units"[MeSH]                                        │
│  I → "remimazolam" [Supplementary Concept], "CNS 7056"                   │
│  C → "Propofol"[MeSH], "Diprivan"                                        │
│  O → "Conscious Sedation"[MeSH], "Deep Sedation"[MeSH]                   │
└─────────────────────────────────┬───────────────────────────────────────┘
                                  │
                                  ▼
┌─────────────────────────────────────────────────────────────────────────┐
│              Agent combines with Boolean logic                           │
│                                                                          │
│  (P) AND (I) AND (C) AND (O)  ← High precision                           │
│  (P) AND (I OR C) AND (O)     ← High recall                              │
└─────────────────────────────────┬───────────────────────────────────────┘
                                  │
                                  ▼
┌─────────────────────────────────────────────────────────────────────────┐
│              unified_search() (auto multi-source + dedup)                │
│                                                                          │
│  PubMed + Europe PMC + CORE + OpenAlex → Auto deduplicate & rank         │
└─────────────────────────────────────────────────────────────────────────┘

# Step 1: Parse clinical question
parse_pico("Is remimazolam better than propofol for ICU sedation?")
# Returns: P=ICU patients, I=remimazolam, C=propofol, O=sedation outcomes

# Step 2: Get MeSH for each element (parallel!)
generate_search_queries(topic="ICU patients")   # P
generate_search_queries(topic="remimazolam")    # I
generate_search_queries(topic="propofol")       # C
generate_search_queries(topic="sedation")       # O

# Step 3: Agent combines with Boolean
query = '("Intensive Care Units"[MeSH]) AND (remimazolam OR "CNS 7056") AND propofol AND sedation'

# Step 4: Search (auto multi-source, dedup, rank)
unified_search(query=query)

3️⃣ Explore from Key Paper

# Found landmark paper PMID: 33475315
find_related_articles(pmid="33475315")   # Similar methodology
find_citing_articles(pmid="33475315")    # Who built on this?
get_article_references(pmid="33475315")  # What's the foundation?

# Build complete research map
build_citation_tree(pmid="33475315", depth=2, output_format="mermaid")

4️⃣ Gene/Drug Research

# Research a gene
search_gene(query="BRCA1", organism="human")
get_gene_literature(gene_id="672", limit=20)

# Research a drug compound
search_compound(query="propofol")
get_compound_literature(cid="4943", limit=20)

5️⃣ Export Results

# Export last search results
prepare_export(pmids="last", format="ris")      # → EndNote/Zotero
prepare_export(pmids="last", format="bibtex")   # → LaTeX

# Retrieve full text for a selected paper from the last search
get_fulltext(pmid="12345678", extended_sources=True)

6️⃣ Preprint Search

# Include preprints alongside peer-reviewed results
unified_search(query="COVID-19 vaccine efficacy", options="preprints")
# → Main results (peer-reviewed) + Separate preprint section (arXiv, medRxiv, bioRxiv)

# Include preprints and retain non-peer-reviewed items in main results
unified_search(query="CRISPR gene therapy", options="preprints, all_types")
# → Separate preprint section + non-peer-reviewed items retained in main results

# Only peer-reviewed (default behavior)
unified_search("diabetes treatment")
# → Preprints from any source automatically filtered out

# Add a research context graph preview to the same search response
unified_search("remimazolam ICU sedation", options="context_graph")

7️⃣ Pipeline (Reusable Search Plans)

# Save a template-based pipeline through the primary facade
manage_pipeline(
  action="save",
    name="icu_sedation_weekly",
    config="template: pico\nparams:\n  P: ICU patients\n  I: remimazolam\n  C: propofol\n  O: delirium",
    tags="anesthesia,sedation",
    description="Weekly ICU sedation monitoring"
)

# Save a custom DAG pipeline
manage_pipeline(
  action="save",
    name="brca1_comprehensive",
    config="""
steps:
  - id: expand
    action: expand
    params: { topic: BRCA1 breast cancer }
  - id: pubmed
    action: search
    params: { query: BRCA1, sources: pubmed, limit: 50 }
  - id: expanded
    action: search
    inputs: [expand]
    params: { strategy: mesh, sources: pubmed,openalex, limit: 50 }
  - id: merged
    action: merge
    inputs: [pubmed, expanded]
    params: { method: rrf }
  - id: enriched
    action: metrics
    inputs: [merged]
output:
  limit: 30
  ranking: quality
"""
)

# Execute a saved pipeline
unified_search(pipeline="saved:icu_sedation_weekly")

# List & manage
manage_pipeline(action="list", tag="anesthesia")
manage_pipeline(action="load", source="brca1_comprehensive")  # Review YAML
manage_pipeline(action="history", name="icu_sedation_weekly")  # View past runs

---

🔍 Search Mode Comparison

┌─────────────────────────────────────────────────────────────────────────┐
│                        SEARCH MODE DECISION TREE                         │
├─────────────────────────────────────────────────────────────────────────┤
│                                                                          │
│   "What kind of search do I need?"                                       │
│         │                                                                │
│         ├── Know exactly what to search?                                 │
│         │   └── unified_search(query="topic keywords")                   │
│         │       → Quick, auto-routing to best sources                    │
│         │                                                                │
│         ├── Have a clinical question (A vs B)?                           │
│         │   └── parse_pico() → generate_search_queries() × N             │
│         │       → Agent builds Boolean → unified_search()                │
│         │                                                                │
│         ├── Need comprehensive systematic coverage?                      │
│         │   └── generate_search_queries() → parallel search              │
│         │       → MeSH expansion, multiple strategies, merge             │
│         │                                                                │
│         └── Exploring from a key paper?                                  │
│             └── find_related/citing/references → build_citation_tree     │
│                 → Citation network, research context                     │
│                                                                          │
└─────────────────────────────────────────────────────────────────────────┘

Mode	Entry Point	Best For	Auto-Features
Quick	unified_search()	Fast topic search	ICD→MeSH, multi-source, dedup
PICO	parse_pico() → Agent	Clinical questions	Agent: decompose → MeSH expand → Boolean
Systematic	generate_search_queries()	Literature reviews	MeSH expansion, synonyms
Exploration	find_*_articles()	From key paper	Citation network, related

---

🤖 Claude Skills (AI Agent Workflows)

Pre-built workflow guides in .claude/skills/, divided into Usage Skills (for using the MCP server) and Development Skills (for maintaining the project):

📚 Usage Skills (10) — For AI Agents Using This MCP Server

Skill	Description
pubmed-quick-search	Basic search with filters
pubmed-systematic-search	MeSH expansion, comprehensive
pubmed-pico-search	Clinical question decomposition
pubmed-paper-exploration	Citation tree, related articles
pubmed-gene-drug-research	Gene/PubChem/ClinVar
pubmed-fulltext-access	Europe PMC, CORE full text
pubmed-export-citations	RIS/BibTeX/CSV export
pubmed-multi-source-search	Cross-database unified search
pubmed-mcp-tools-reference	Complete tool reference guide
pipeline-persistence	Save, load, reuse search plans

🔧 Development Skills (13) — For Project Contributors

Skill	Description
changelog-updater	Auto-update CHANGELOG.md
code-refactor	DDD architecture refactoring
code-reviewer	Code quality & security review
ddd-architect	DDD scaffold for new features
git-doc-updater	Sync docs before commits
git-precommit	Pre-commit workflow orchestration
memory-checkpoint	Save context to Memory Bank
memory-updater	Update Memory Bank files
project-init	Initialize new projects
readme-i18n	Multilingual README sync
readme-updater	Sync README with code changes
roadmap-updater	Update ROADMAP.md status
test-generator	Generate test suites

📁 Location: .claude/skills/*/SKILL.md (Claude Code-specific, and the single source of truth for repo skills) Do not mirror or split repo skills into .github/skills/. These repo skills are project-scoped and should remain version-controlled. Personal cross-project skills belong in a user directory such as ~/.copilot/skills/ or ~/.claude/skills/, not in this repository.

---

🏗️ Architecture (DDD)

This project uses Domain-Driven Design (DDD) architecture, with literature research domain knowledge as the core model.

src/pubmed_search/
├── domain/                     # Core business logic
│   └── entities/article.py     # UnifiedArticle, Author, etc.
├── application/                # Use cases
│   ├── search/                 # QueryAnalyzer, ResultAggregator
│   ├── export/                 # Citation export (RIS, BibTeX...)
│   └── session/                # SessionManager
├── infrastructure/             # External systems
│   ├── ncbi/                   # Entrez, iCite, Citation Exporter
│   ├── sources/                # Europe PMC, CORE, CrossRef...
│   └── http/                   # HTTP clients
├── presentation/               # User interfaces
│   ├── mcp_server/             # MCP tools, prompts, resources
│   │   └── tools/              # discovery, strategy, pico, export...
│   └── api/                    # REST API (Copilot Studio)
└── shared/                     # Cross-cutting concerns
    ├── exceptions.py           # Unified error handling
    └── async_utils.py          # Rate limiter, retry, circuit breaker

Internal Mechanisms (Transparent to Agent)

Mechanism	Description
Session	Auto-create, auto-switch
Cache	Auto-cache search results, avoid duplicate API calls
Rate Limit	Auto-comply with NCBI API limits (0.34s/0.1s)
MeSH Lookup	generate_search_queries() auto-queries NCBI MeSH database
ESpell	Auto spelling correction (remifentanyl → remifentanil)
Query Analysis	Each suggested query shows how PubMed actually interprets it

Vocabulary Translation Layer (Key Feature)

Our Core Value: We are the intelligent middleware between Agent and Search Engines, automatically handling vocabulary standardization so Agent doesn't need to know each database's terminology.

Different data sources use different controlled vocabulary systems. This server provides automatic conversion:

API / Database	Vocabulary System	Auto-Conversion
PubMed / NCBI	MeSH (Medical Subject Headings)	✅ Full support via expand_with_mesh()
ICD Codes	ICD-10-CM / ICD-9-CM	✅ Auto-detect & convert to MeSH
Europe PMC	Text-mined entities (Gene, Disease, Chemical)	✅ get_text_mined_terms() extraction
OpenAlex	OpenAlex Concepts (deprecated)	❌ Free-text only
Semantic Scholar	S2 Field of Study	❌ Free-text only
CORE	None	❌ Free-text only
CrossRef	None	❌ Free-text only

Automatic ICD → MeSH Conversion

When searching with ICD codes (e.g., I10 for Hypertension), unified_search() automatically:

1. Detects ICD-10/ICD-9 patterns via detect_and_expand_icd_codes()
2. Looks up corresponding MeSH terms from internal mapping (ICD10_TO_MESH, ICD9_TO_MESH)
3. Expands query with MeSH synonyms for comprehensive search

# Agent calls unified_search with clinical terminology
unified_search(query="I10 treatment outcomes")

# Server auto-expands to PubMed-compatible query
"(I10 OR Hypertension[MeSH]) treatment outcomes"

📖 Full architecture documentation: ARCHITECTURE.md

MeSH Auto-Expansion + Query Analysis

When calling generate_search_queries("remimazolam sedation"), internally it:

1. ESpell Correction - Fix spelling errors
2. MeSH Query - Entrez.esearch(db="mesh") to get standard vocabulary
3. Synonym Extraction - Get synonyms from MeSH Entry Terms
4. Query Analysis - Analyze how PubMed interprets each query

{
  "mesh_terms": [
    {
      "input": "remimazolam",
      "preferred": "remimazolam [Supplementary Concept]",
      "synonyms": ["CNS 7056", "ONO 2745"]
    }
  ],
  "all_synonyms": ["CNS 7056", "ONO 2745", ...],
  "suggested_queries": [
    {
      "id": "q1_title",
      "query": "(remimazolam sedation)[Title]",
      "purpose": "Exact title match - highest precision",
      "estimated_count": 8,
      "pubmed_translation": "\"remimazolam sedation\"[Title]"
    },
    {
      "id": "q3_and",
      "query": "(remimazolam AND sedation)",
      "purpose": "All keywords required",
      "estimated_count": 561,
      "pubmed_translation": "(\"remimazolam\"[Supplementary Concept] OR \"remimazolam\"[All Fields]) AND (\"sedate\"[All Fields] OR ...)"
    }
  ]
}

Value of Query Analysis: Agent thinks remimazolam AND sedation only searches these two words, but PubMed actually expands to Supplementary Concept + synonyms, results go from 8 to 561. This helps Agent understand the difference between intent and actual search.

---

🔒 HTTPS Deployment

Enable HTTPS secure communication for production environments.

Copilot Studio Quick Start

# Step 1: Generate SSL certificates
./scripts/generate-ssl-certs.sh

# Step 2: Start HTTPS service (Docker)
./scripts/start-https-docker.sh up

# Verify deployment
curl -k https://localhost/

HTTPS Endpoints

Service	URL	Description
MCP SSE	https://localhost/sse	SSE connection (MCP)
Messages	https://localhost/messages	MCP POST
Health	https://localhost/health	Health check

Claude Desktop Configuration

{
  "mcpServers": {
    "pubmed-search": {
      "url": "https://localhost/sse"
    }
  }
}

---

🏢 Microsoft Copilot Studio Integration

Integrate PubMed Search MCP with Microsoft 365 Copilot (Word, Teams, Outlook)!

Quick Start

# Start with Streamable HTTP transport (required by Copilot Studio)
uv run python run_server.py --transport streamable-http --port 8765

# Enable Copilot-compatible HTTP semantics while keeping full tool schemas
uv run python run_server.py --transport streamable-http --copilot-compatible --port 8765

# Or use the dedicated script with ngrok
./scripts/start-copilot-studio.sh --with-ngrok

Copilot Studio Configuration

Field	Value
Server name	PubMed Search
Server URL	https://your-server.com/mcp
Authentication	None (or API Key)

📖 Full documentation: copilot-studio/README.md

Use --copilot-compatible with run_server.py for Copilot HTTP semantics, or run_copilot.py if you also need simplified tool schemas.

⚠️ Note: SSE transport deprecated since Aug 2025. Use streamable-http.

---

📖 More documentation:

• Architecture → ARCHITECTURE.md
• Pipeline tutorial (English) → docs/PIPELINE_MODE_TUTORIAL.en.md
• Pipeline tutorial (zh-TW) → docs/PIPELINE_MODE_TUTORIAL.md
• Deployment guide → DEPLOYMENT.md
• Copilot Studio → copilot-studio/README.md

---

🔐 Security

Security Features

Layer	Feature	Description
HTTPS	TLS 1.2/1.3 encryption	All traffic encrypted via Nginx
Rate Limiting	30 req/s	Nginx level protection
Security Headers	XSS/CSRF protection	X-Frame-Options, X-Content-Type-Options
SSE Optimization	24h timeout	Long-lived connections for real-time
No Database	Stateless	No SQL injection risk
No Secrets	In-memory only	No credentials stored

See DEPLOYMENT.md for detailed deployment instructions.

---

📤 Export Formats

Export your search results in formats compatible with major reference managers:

Format	Compatible With	Use Case
RIS	EndNote, Zotero, Mendeley	Universal import
BibTeX	LaTeX, Overleaf, JabRef	Academic writing
CSV	Excel, Google Sheets	Data analysis
MEDLINE	PubMed native format	Archiving
JSON	Programmatic access	Custom processing

Exported Fields

• Core: PMID, Title, Authors, Journal, Year, Volume, Issue, Pages
• Identifiers: DOI, PMC ID, ISSN
• Content: Abstract (HTML tags cleaned)
• Metadata: Language, Publication Type, Keywords
• Access: DOI URL, PMC URL, Full-text availability

Special Character Handling

• BibTeX exports use pylatexenc for proper LaTeX encoding
• Nordic characters (ø, æ, å), umlauts (ü, ö, ä), and accents are correctly converted
• Example: Søren Hansen → S{\o}ren Hansen

---

📚 Citation

GitHub will show Cite this repository from CITATION.cff. If you use PubMed Search MCP in research, methods sections, or internal technical reports, prefer the GitHub-generated citation or reuse the repository metadata directly.

@software{pubmed_search_mcp,
  title = {PubMed Search MCP},
  author = {u9401066},
  url = {https://github.com/u9401066/pubmed-search-mcp}
}

---

📄 License

Apache License 2.0 - see LICENSE

---

🔗 Links

• GitHub Repository
• PyPI Package
• NCBI Entrez Programming Utilities