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u9401066/pubmed-search-mcp · Archived

pubmed-mcp-tools-reference

Complete reference for all 41 PubMed Search MCP tools. Triggers: 工?

First seen Jul 15, 2026

Installation

$ npx skills add u9401066/pubmed-search-mcp --skill pubmed-mcp-tools-reference
View on skills.sh ↗ GitHub repository ↗

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Also in this package

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npx skills add u9401066/pubmed-search-mcp
pubmed-search-mcp-harness 3 pubmed-systematic-search 2 pubmed-quick-search 2 pubmed-paper-exploration 2 pubmed-gene-drug-research 2 memory-updater 2 academic-figure-drawing-harness 1 roadmap-updater 1 pipeline-persistence 1 pdf-asset-extractor 1

Browse all from u9401066/pubmed-search-mcp

More details

Agent compatibility

Declared targets from SKILL.md / docs. Unmarked agents are not listed — the skill may still install via the CLI.

Claude Code Not declared
Cursor Not declared
Codex Not declared
GitHub Copilot Not declared
Windsurf Not declared
Gemini CLI Not declared
Cline Not declared
OpenCode Not declared

Repository health

Stars 27
License LICENSE
Default branch master
Open issues 2
Status Archived

Package contents

Files included with this skill beyond the listing page.

  • skill md SKILL.md 7,650 B
  • docs SUMMARY.md 169 B

History

  1. First seen on skills.sh
  2. First recorded snapshot · 1 installs

SKILL.md

PubMed Search MCP 工具完整參考

描述

所有 41 個 MCP 工具的完整參考，包含參數說明和使用範例。

能力導向使用請先看 docs/TOOLSUSAGEGUIDE.zh-TW.md。

⚠️ 注意：此文件由 scripts/countmcptools.py --update-docs 自動生成。
手動修改會在下次執行時被覆蓋。

濃縮理解模型

目前對外是 41 個工具，但建議先用 8 個能力族來理解。

  • 理論最小下限：6 個 multiplexed meta-tools
  • 實務可理解下限：8 個能力族
  • 建議：先學能力族，再查完整工具表

能力族如下：搜尋、查詢規劃、論文探索、全文與取得、視覺與脈絡、實體與術語、結果與記憶、自動化與保存。

工具分類總覽

類別 工具數 主要用途
搜尋工具 1 Unified multi-source literature search gateway
查詢智能 3 MeSH expansion, agent-provided PICO handoff, and query analysis
文章探索 5 相關文章、引用網路
全文工具 2 全文取得與文本挖掘
NCBI 延伸 7 Gene, PubChem, ClinVar
引用網絡 1 引用樹建構與探索
匯出工具 2 引用格式匯出與本機文獻筆記保存
Session 管理 1 PMID 暫存與歷史
機構訂閱 5 OpenURL Link Resolver
視覺搜索 1 圖片分析與搜索 (實驗性)
ICD 轉換 1 ICD-10 與 MeSH 轉換
引用驗證 1 Reference list verification with PubMed evidence
圖表擷取 1 文章圖表與視覺資料擷取
研究編年史 2 研究演化脈絡：持久化、可版本比對、證據支撐的時序主軸與分支投影
圖片搜尋 1 生物醫學圖片搜尋
Pipeline 管理 7 Pipeline 持久化、載入、排程

搜尋工具

Unified multi-source literature search gateway

工具 說明
unified_search Unified Search - Single entry point for multi-source academic search.

查詢智能

MeSH expansion, agent-provided PICO handoff, and query analysis

工具 說明
validatepicoplan Validate agent-provided P/I/C/O and return a runnable PICO pipeline.
generatesearchqueries Gather search intelligence for a topic - returns RAW MATERIALS for Agent to decide.
analyzesearchquery Analyze a search query without executing the search.

文章探索

相關文章、引用網路

工具 說明
fetcharticledetails Fetch detailed information for one or more PubMed articles.
findrelatedarticles Find articles related to a given PubMed article.
findcitingarticles Find articles that cite a given PubMed article.
getarticlereferences Get the references (bibliography) of a PubMed article.
getcitationmetrics Get citation metrics from NIH iCite for articles.

全文工具

全文取得與文本挖掘

工具 說明
get_fulltext Enhanced multi-source fulltext retrieval.
gettextmined_terms Get text-mined annotations from Europe PMC.

NCBI 延伸

Gene, PubChem, ClinVar

工具 說明
search_gene Search NCBI Gene database for gene information.
getgenedetails Get detailed information about a gene by NCBI Gene ID.
getgeneliterature Get PubMed articles linked to a gene.
search_compound Search PubChem for chemical compounds.
getcompounddetails Get detailed information about a compound by PubChem CID.
getcompoundliterature Get PubMed articles linked to a compound.
search_clinvar Search ClinVar for clinical variants.

引用網絡

引用樹建構與探索

工具 說明
buildcitationtree Build a citation tree (network) from a single article.

匯出工具

引用格式匯出與本機文獻筆記保存

工具 說明
prepare_export Export citations to reference manager formats.
saveliteraturenotes Save searched articles as guided local wiki/Foam/Markdown notes.

Session 管理

PMID 暫存與歷史

工具 說明
read_session Read session data through one schema-exact discriminated request.

機構訂閱

OpenURL Link Resolver

工具 說明
configureinstitutionalaccess Configure your institution's link resolver for full-text access.
getinstitutionallink Generate institutional access link (OpenURL) for an article.
listresolverpresets List available institutional link resolver presets.
testinstitutionalaccess Test your institutional link resolver configuration.
diagnoseinstitutionalaccess Diagnose why institutional fulltext access succeeds or fails for an article.

視覺搜索

圖片分析與搜索 (實驗性)

工具 說明
preparefiguresearch Analyze a scientific figure or image for literature search.

ICD 轉換

ICD-10 與 MeSH 轉換

工具 說明
converticdmesh Query the curated ICD/MeSH crosswalk in one explicit direction.

引用驗證

Reference list verification with PubMed evidence

工具 說明
verifyreferencelist Verify a plain-text reference list against PubMed evidence.

圖表擷取

文章圖表與視覺資料擷取

工具 說明
getarticlefigures Get structured figure metadata (label, caption, image URL) and PDF links from a PMC Open Access arti

研究編年史

研究演化脈絡：持久化、可版本比對、證據支撐的時序主軸與分支投影

工具 說明
buildresearchchronicle Build a persisted, versioned, evidence-backed Research Chronicle.
readresearchchronicle Read stored Research Chronicles: load, list, diff, narrate, analyze, compare.

圖片搜尋

生物醫學圖片搜尋

工具 說明
searchbiomedicalimages Search biomedical images from NLM Open-i.

Pipeline 管理

Pipeline 持久化、載入、排程

工具 說明
save_pipeline Save a pipeline configuration for later reuse.
list_pipelines List all saved pipeline configurations.
load_pipeline Load a pipeline configuration for review or editing.
delete_pipeline Permanently delete a saved pipeline configuration and execution history.
getpipelinehistory Get execution history for a saved pipeline.
schedule_pipeline Schedule a saved pipeline for periodic execution.
unschedule_pipeline Remove the active schedule for a saved pipeline.

常用工作流程

快速搜尋

unified_search → fetch_article_details → prepare_export

系統性搜尋

generate_search_queries → Boolean query → analyze_search_query → unified_search

PICO 搜尋

Agent P/I/C/O -> validate_pico_plan handoff -> unified_search(template:pico) / expanded Boolean

論文探索

fetch_article_details → find_related_articles + find_citing_articles + build_citation_tree

全文取得

get_fulltext → get_article_figures / get_text_mined_terms / get_institutional_link

Total: 41 tools in 16 categories Auto-generated by scripts/countmcptools.py --update-docs