# Pubmed MCP Tools Reference

> Version-aware reference for the installed PubMed Search MCP tool surface. Triggers: 工具列表, all tools, 完整功能, tool reference, 有哪些工具

- Skill: `u9401066/pubmed-mcp-tools-reference` (Agent Skill)
- Install (CLI): `npx skillmds@latest add u9401066/pubmed-mcp-tools-reference`
- Raw SKILL.md: https://api.skillmd.com/api/skills/u9401066/pubmed-mcp-tools-reference/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: u9401066 (https://skillmd.com/u/u9401066)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/u9401066/pubmed-mcp-tools-reference

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# 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。

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## 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`_