pubmed-mcp-tools-reference

# PubMed Search MCP 工具完整參考

## 描述
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。

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## 濃縮理解模型

目前對外是 46 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 |
| 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 |

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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). |

## 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. |

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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: 46 tools in 16 categories*
*Auto-generated by `scripts/count_mcp_tools.py --update-docs`*