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