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Complete reference for all 46 PubMed Search MCP tools. Triggers: 工具列表, all tools, 完整功能, tool reference, 有哪些工具
Orchestrate pre-commit workflow including Memory Bank sync, README/CHANGELOG/ROADMAP updates, and MCP tool count sync. Triggers: GIT, gc, push, commit, 提交, 準備 commit, 要提交了, git commit, pre-commit, 推送.
Codex harness for PubMed Search MCP. Triggers: pubmed search, literature search, unified_search, pipeline, fulltext, release checklist, Codex.
Pipeline persistence — save, load, and reuse structured search plans. Triggers: pipeline, 管道, search plan, 搜尋計畫, 重複搜尋, saved search, 排程, schedule, workflow, DAG
Agent-guided PICO clinical question search using parse_pico handoff and unified_search. Triggers: PICO, 臨床問題, A比B好嗎, treatment comparison, clinical question, 療效比較
Auto-update CHANGELOG.md following Keep a Changelog format. Triggers: CL, changelog, 變更, 版本, version, 更新日誌, whatsnew.
Proactively detect and execute code refactoring to maintain DDD architecture and code quality. Triggers: RF, refactor, 重構, 拆分, split, 模組化, modularize, 太長, cleanup.
| name | pubmed-mcp-tools-reference |
| description | Complete reference for all 46 PubMed Search MCP tools. Triggers: 工具列表, all tools, 完整功能, tool reference, 有哪些工具 |
所有 46 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。
目前對外是 46 個工具，但建議先用 8 個能力族來理解。
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。
| 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 |
Unified multi-source literature search gateway
| 工具 | 說明 |
|---|---|
unified_search | Unified Search - Single entry point for multi-source academic search. |
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. |
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. |
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. |
引用樹建構與探索
| 工具 | 說明 |
|---|---|
build_citation_tree | Build a citation tree (network) from a single article. |
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. |
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。 |
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. |
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-10 與 MeSH 轉換
| 工具 | 說明 |
|---|---|
convert_icd_mesh | Convert between ICD codes and MeSH terms (bidirectional). |
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. |
Reference list verification with PubMed evidence
| 工具 | 說明 |
|---|---|
verify_reference_list | Verify a plain-text reference list against PubMed evidence. |
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 |
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 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. |
unified_search → fetch_article_details → prepare_export
generate_search_queries → Boolean query → analyze_search_query → unified_search
Agent P/I/C/O -> parse_pico handoff -> unified_search(template:pico) / expanded Boolean
fetch_article_details → find_related_articles + find_citing_articles + build_citation_tree
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