pubmed-mcp-tools-reference

Complete reference for all 44 PubMed Search MCP tools. Triggers: 工具列表, all tools, 完整功能, tool reference, 有哪些工具

Repository: u9401066/research-data-explorer
Last source activity: May 7, 2026 at 12:23
Detected SKILL.md language: Chinese
Stars: 2
Forks: 0

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name	pubmed-mcp-tools-reference
description	Complete reference for all 44 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 44 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。

濃縮理解模型

目前對外是 44 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	文獻搜索入口
查詢智能	3	MeSH 擴展、PICO 解析
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	1	引用格式匯出
Session 管理	5	PMID 暫存與歷史
機構訂閱	4	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
研究時間軸	3	研究演化追蹤與里程碑偵測
引用驗證

工具	說明
`parse_pico`	Parse a clinical question into PICO elements OR accept pre-parsed PICO.
`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.

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.

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

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.

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。

pubmed-mcp-tools-reference

Install options

Review the source files

PubMed Search MCP 工具完整參考

描述

濃縮理解模型

工具分類總覽

PubMed Search MCP 工具完整參考

描述

濃縮理解模型

工具分類總覽

搜尋工具

查詢智能

文章探索

全文工具

NCBI 延伸

引用網絡

匯出工具

Session 管理

機構訂閱

視覺搜索

ICD 轉換

研究時間軸

引用驗證

圖表擷取

圖片搜尋

Pipeline 管理

常用工作流程

快速搜尋

系統性搜尋

PICO 搜尋

論文探索

全文取得

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.

工具	說明
`build_research_timeline`	Build a research timeline for a topic OR specific PMIDs.
`analyze_timeline_milestones`	Analyze milestone distribution for a research topic.
`compare_timelines`	Compare research timelines of multiple topics.

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.

pubmed-mcp-tools-reference

Source facts

Install options

Review the source files

More from this repository

PubMed Search MCP 工具完整參考

描述

濃縮理解模型

工具分類總覽

More from this repository

PubMed Search MCP 工具完整參考

描述

濃縮理解模型

工具分類總覽

搜尋工具

查詢智能

文章探索

全文工具

NCBI 延伸

引用網絡

匯出工具

Session 管理

機構訂閱

視覺搜索

ICD 轉換

研究時間軸

引用驗證

圖表擷取

圖片搜尋

Pipeline 管理

常用工作流程

快速搜尋

系統性搜尋

PICO 搜尋

論文探索

全文取得