u9401066 PubMed Search MCP 工具完整參考
描述
PubMed Search MCP 工具的版本相依參考，包含參數說明和使用範例。工具數量必須以目前安裝版本的 runtime registry/resource 為準，不可沿用本檔的歷史數字。
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 pinned v0.4.4 的自動生成索引是 40 個工具，但建議先用 8 個能力族理解；升級後先查 runtime registry。
- 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 |
| 研究時間軸 | 3 | 研究演化追蹤與里程碑偵測 |
| 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 |
| 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). |
研究時間軸
研究演化追蹤與里程碑偵測
| 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. |
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 |
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: 46 tools in 16 categories
Auto-generated by scripts/count_mcp_tools.py --update-docs