pubmed-mcp-tools-reference

Complete reference for all 35+ PubMed Search MCP tools. Triggers: 工具列表, all tools, 完整功能, tool reference, 有哪些工具

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name	pubmed-mcp-tools-reference
description	Complete reference for all 35+ 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 35+ 個 MCP 工具的完整參考，包含參數說明和使用範例。

工具分類總覽

類別	工具數	主要用途
🔍 PubMed 搜尋	6	核心文獻搜尋
🏥 PICO 臨床搜尋	2	臨床問題分析
🔬 論文探索	3	引用網絡探索
🧬 NCBI Extended	7	基因/化合物/變異
🌍 Europe PMC	4	歐洲文獻+全文
📚 CORE	5	開放取用全文
🤖 Semantic Scholar	2	AI 分析+引用
📊 OpenAlex	4	學術知識圖譜
📤 匯出工具	3	引用格式匯出

🔍 PubMed 搜尋工具

`search_literature`

基本 PubMed 搜尋

search_literature(
    query="remimazolam sedation",     # 搜尋詞
    limit=20,                          # 結果數量（預設 5）
    min_year=2020,                     # 最早年份
    max_year=2024,                     # 最晚年份
    date_from="2024/01/01",           # 精確起始日（YYYY/MM/DD）
    date_to="2024/06/30",             # 精確結束日
    date_type="edat",                  # edat/pdat/mdat
    article_type="Review",             # Clinical Trial, Review, Meta-Analysis
    strategy="relevance"               # relevance, recent, most_cited, impact
)

`generate_search_queries`

產生 MeSH 擴展搜尋策略

generate_search_queries(
    topic="remimazolam ICU sedation",  # 主題
    strategy="comprehensive",           # comprehensive/focused/exploratory
    check_spelling=True,               # 拼字檢查
    include_suggestions=True           # 包含建議查詢
)

`merge_search_results`

合併多個搜尋結果並去重

merge_search_results(
    results_json='[["12345","67890"],["67890","11111"]]'
)
# 或帶 query_id：
# '[{"query_id":"q1","pmids":["12345"]},{"query_id":"q2","pmids":["67890"]}]'

`expand_search_queries`

結果不足時擴展搜尋

expand_search_queries(
    topic="remimazolam",
    existing_query_ids="q1_title,q2_tiab",  # 已執行的查詢
    expansion_type="mesh"                    # mesh/broader/narrower
)

`fetch_article_details`

取得論文詳細資訊

fetch_article_details(pmids="30217674,28523456")

🏥 PICO 臨床搜尋工具

`parse_pico`

解析臨床問題為 PICO 元素

# 自然語言解析
parse_pico(description="remimazolam 在 ICU 比 propofol 好嗎？")

# 或直接提供結構化 PICO
parse_pico(
    description="",
    p="ICU patients",
    i="remimazolam",
    c="propofol",
    o="delirium"
)

🔬 論文探索工具

`find_related_articles`

找相似文章（PubMed Similar Articles）

find_related_articles(pmid="30217674", limit=10)

`find_citing_articles`

找引用這篇的論文

find_citing_articles(pmid="30217674", limit=20)

🧬 NCBI Extended 工具

`search_ncbi_gene`

搜尋 NCBI Gene 資料庫

search_ncbi_gene(query="BRCA1 breast cancer", limit=10)

`get_ncbi_gene_info`

取得基因詳細資訊

get_ncbi_gene_info(gene_id="672")  # BRCA1

`search_pubchem_compound`

搜尋 PubChem 化合物

search_pubchem_compound(query="remimazolam", limit=10)

`get_pubchem_compound_info`

取得化合物詳細資訊

get_pubchem_compound_info(cid="11526795")

`search_clinvar`

搜尋 ClinVar 變異資料庫

search_clinvar(query="BRCA1 pathogenic", limit=20)

`get_clinvar_variation`

取得變異詳細資訊

get_clinvar_variation(variation_id="17661")

`get_ncbi_cross_references`

取得跨資料庫連結

get_ncbi_cross_references(
    source_db="gene",
    target_db="pubmed",
    ids="672"
)

🌍 Europe PMC 工具

`search_europe_pmc`

搜尋 Europe PMC

search_europe_pmc(
    query="remimazolam",
    limit=30,
    has_fulltext=True,   # 只找有全文的
    source="preprint"    # 或 "medline", "pmc"
)

`get_europe_pmc_fulltext`

取得 Europe PMC 全文

get_europe_pmc_fulltext(pmcid="PMC6939411")

`get_europe_pmc_citations`

取得引用資料

get_europe_pmc_citations(pmid="30217674")

`get_europe_pmc_references`

取得參考文獻

get_europe_pmc_references(pmid="30217674")

📚 CORE 工具

`search_core`

搜尋 CORE 開放取用庫

search_core(query="machine learning radiology", limit=30)

`search_core_fulltext`

搜尋全文內容

search_core_fulltext(query="adverse events remimazolam", limit=20)

`get_core_paper`

取得論文詳情

get_core_paper(core_id="12345678")

`get_core_fulltext`

取得全文內容

get_core_fulltext(core_id="12345678")

`find_in_core`

用標題找論文

find_in_core(title="Remimazolam versus midazolam for procedural sedation")

🤖 Semantic Scholar 工具

`search_semantic_scholar`

搜尋 Semantic Scholar

search_semantic_scholar(
    query="deep learning medical imaging",
    limit=30,
    year="2020-2024",          # 年份範圍
    fields_of_study="Medicine"  # 領域篩選
)

`get_semantic_scholar_paper`

取得論文詳情（含影響力指標）

get_semantic_scholar_paper(paper_id="649def34f8be52c8b66281af98ae884c09aef38b")

回傳包含：

citationCount: 總引用數
influentialCitationCount: 有影響力的引用數
tldr: AI 生成摘要

📊 OpenAlex 工具

`search_openalex`

搜尋 OpenAlex

search_openalex(
    query="CRISPR gene editing",
    limit=30,
    from_date="2020-01-01",
    filter="is_oa:true"  # OpenAlex filter syntax
)

`get_openalex_work`

取得作品詳情

get_openalex_work(work_id="W2741809807")

`search_openalex_authors`

搜尋作者

search_openalex_authors(query="Jennifer Doudna")

`get_openalex_author`

取得作者詳情

get_openalex_author(author_id="A5023888391")

📤 匯出工具

`prepare_export`

匯出引用格式

prepare_export(
    pmids="30217674,28523456",  # 或 "last" 使用上次搜尋
    format="ris",               # ris/bibtex/csv/medline/json
    include_abstract=True
)

`get_article_fulltext_links`

取得全文連結

get_article_fulltext_links(pmid="30217674")

`analyze_fulltext_access`

批次分析全文可用性

analyze_fulltext_access(pmids="30217674,28523456")
# 或 "last" 使用上次搜尋結果

常用工作流程

快速搜尋

search_literature → fetch_article_details → prepare_export

系統性搜尋

generate_search_queries → search_literature × N → merge_search_results

PICO 搜尋

parse_pico → generate_search_queries × 4 → search_literature → merge_search_results

論文探索

fetch_article_details → find_related_articles + find_citing_articles

全文取得

analyze_fulltext_access → get_europe_pmc_fulltext 或 get_core_fulltext

參數快速參考

常用篩選參數

參數	說明	範例值
`limit`	結果數量	10, 20, 50, 100
`min_year`	最早年份	2020
`max_year`	最晚年份	2024
`article_type`	文章類型	"Review", "Clinical Trial", "Meta-Analysis"
`strategy`	排序策略	"relevance", "recent", "most_cited"

進階篩選參數 (Phase 2.1 新功能)

參數	說明	可用值
`age_group`	年齡群	newborn, infant, preschool, child, adolescent, young_adult, adult, middle_aged, aged, aged_80
`sex`	性別	male, female
`species`	物種	humans, animals
`language`	語言	english, chinese, japanese, german, french, spanish, korean, italian, portuguese, russian
`clinical_query`	臨床查詢	therapy, diagnosis, prognosis, etiology, clinical_prediction

PubMed 欄位標籤

標籤	說明
`[Title]`	標題
`[Title/Abstract]`	標題或摘要
`[tiab]`	同上（縮寫）
`[MeSH]`	MeSH 詞彙
`[Author]`	作者
`[Journal]`	期刊
`[PMID]`	PubMed ID

Clinical Query Filters

Filter	用途
`therapy[filter]`	治療效果研究
`diagnosis[filter]`	診斷研究
`prognosis[filter]`	預後研究
`etiology[filter]`	病因研究

pubmed-mcp-tools-reference

Source facts

Install options

Review the source files

More from this repository

PubMed Search MCP 工具完整參考

描述

工具分類總覽

🔍 PubMed 搜尋工具

search_literature

generate_search_queries

merge_search_results

expand_search_queries

fetch_article_details

🏥 PICO 臨床搜尋工具

parse_pico

🔬 論文探索工具

find_related_articles

find_citing_articles

🧬 NCBI Extended 工具

search_ncbi_gene

get_ncbi_gene_info

search_pubchem_compound

get_pubchem_compound_info

search_clinvar

get_clinvar_variation

get_ncbi_cross_references

🌍 Europe PMC 工具

search_europe_pmc

get_europe_pmc_fulltext

get_europe_pmc_citations

get_europe_pmc_references

📚 CORE 工具

search_core

search_core_fulltext

get_core_paper

get_core_fulltext

find_in_core

🤖 Semantic Scholar 工具

search_semantic_scholar

get_semantic_scholar_paper

📊 OpenAlex 工具

search_openalex

get_openalex_work

search_openalex_authors

get_openalex_author

📤 匯出工具

prepare_export

get_article_fulltext_links

analyze_fulltext_access

常用工作流程

快速搜尋

系統性搜尋

PICO 搜尋

論文探索

全文取得

參數快速參考

常用篩選參數

進階篩選參數 (Phase 2.1 新功能)

PubMed 欄位標籤

Clinical Query Filters

More from this repository

PubMed Search MCP 工具完整參考

描述

工具分類總覽

🔍 PubMed 搜尋工具

search_literature

generate_search_queries

merge_search_results

expand_search_queries

fetch_article_details

🏥 PICO 臨床搜尋工具

parse_pico

🔬 論文探索工具

find_related_articles

find_citing_articles

🧬 NCBI Extended 工具

search_ncbi_gene

get_ncbi_gene_info

search_pubchem_compound

`search_literature`

`generate_search_queries`

`merge_search_results`

`expand_search_queries`

`fetch_article_details`

`parse_pico`

`find_related_articles`

`find_citing_articles`

`search_ncbi_gene`

`get_ncbi_gene_info`

`search_pubchem_compound`

`get_pubchem_compound_info`

`search_clinvar`

`get_clinvar_variation`

`get_ncbi_cross_references`

`search_europe_pmc`

`get_europe_pmc_fulltext`

`get_europe_pmc_citations`

`get_europe_pmc_references`

`search_core`

`search_core_fulltext`

`get_core_paper`

`get_core_fulltext`

`find_in_core`

`search_semantic_scholar`

`get_semantic_scholar_paper`

`search_openalex`

`get_openalex_work`

`search_openalex_authors`

`get_openalex_author`

`prepare_export`

`get_article_fulltext_links`

`analyze_fulltext_access`

`search_literature`

`generate_search_queries`

`merge_search_results`

`expand_search_queries`

`fetch_article_details`

`parse_pico`

`find_related_articles`

`find_citing_articles`

`search_ncbi_gene`

`get_ncbi_gene_info`

`search_pubchem_compound`

`get_pubchem_compound_info`

`search_clinvar`

`get_clinvar_variation`

`get_ncbi_cross_references`

`search_europe_pmc`

`get_europe_pmc_fulltext`

`get_europe_pmc_citations`

`get_europe_pmc_references`

`search_core`

`search_core_fulltext`

`get_core_paper`

`get_core_fulltext`

`find_in_core`

`search_semantic_scholar`

`get_semantic_scholar_paper`

`search_openalex`

`get_openalex_work`

`search_openalex_authors`

`get_openalex_author`

`prepare_export`

`get_article_fulltext_links`

`analyze_fulltext_access`