pubmed-mcp-tools-reference

name	pubmed-mcp-tools-reference
description	Complete reference for all 45 PubMed Search MCP tools. Triggers: 工具列表, all tools, 完整功能, tool reference, 有哪些工具

PubMed Search MCP 工具完整參考

描述

所有 45 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/TOOLS_USAGE_GUIDE.zh-TW.md。

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

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濃縮理解模型

目前對外是 45 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。

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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	5	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

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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
parse_pico	Validate agent-provided PICO elements and return a runnable search plan.
generate_search_queries	Gather search intelligence for a topic - returns RAW MATERIALS for Agent to decide.
analyze_search_query	Analyze a search query without executing the search.

文章探索

相關文章、引用網路

工具	說明
fetch_article_details	Fetch detailed information for one or more PubMed articles.
find_related_articles	Find articles related to a given PubMed article.
find_citing_articles	Find articles that cite a given PubMed article.
get_article_references	Get the references (bibliography) of a PubMed article.
get_citation_metrics	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.
get_text_mined_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.
get_gene_details	Get detailed information about a gene by NCBI Gene ID.
get_gene_literature	Get PubMed articles linked to a gene.
search_compound	Search PubChem for chemical compounds.
get_compound_details	Get detailed information about a compound by PubChem CID.
get_compound_literature	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
build_citation_tree	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.
save_literature_notes	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 a single facade.
get_session_pmids	取得 session 中暫存的 PMID 列表。
get_cached_article	從 session 快取取得文章詳情。
get_session_summary	取得當前 session 的摘要資訊。
get_session_log	取得當前 session 的 activity log 與搜尋歷史摘要。

機構訂閱

OpenURL Link Resolver

工具	說明
configure_institutional_access	Configure your institution's link resolver for full-text access.
get_institutional_link	Generate institutional access link (OpenURL) for an article.
list_resolver_presets	List available institutional link resolver presets.
test_institutional_access	Test your institutional link resolver configuration.
diagnose_institutional_access	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
analyze_figure_for_search	Analyze a scientific figure or image for literature search.

ICD 轉換

ICD-10 與 MeSH 轉換

工具	說明
convert_icd_mesh	Convert between ICD codes and MeSH terms (bidirectional).

引用驗證

Reference list verification with PubMed evidence

工具	說明
verify_reference_list	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
get_article_figures	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
build_research_chronicle	Build a persisted, versioned, evidence-backed Research Chronicle.
read_research_chronicle	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
search_biomedical_images	Search biomedical images across Open-i and Europe PMC.

Pipeline 管理

Pipeline 持久化、載入、排程

工具	說明
manage_pipeline	Manage saved pipelines through a single facade.
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	Delete a saved pipeline configuration and its execution history.
get_pipeline_history	Get execution history for a saved pipeline.
schedule_pipeline	Schedule a saved pipeline for periodic execution.

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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 -> parse_pico 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

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Total: 45 tools in 16 categories Auto-generated by scripts/count_mcp_tools.py --update-docs