「pubmed」の検索結果

PubMedで医学・生命科学の文献を探し、統制語や条件を使った検索式の作成、抄録・書誌情報の取得、再現可能な検索記録の整理を支援するスキル。

• 研究テーマの医学論文を探したいとき
• 主題語と期間で検索式を作りたいとき
• PMIDから抄録・書誌情報を取得

Search academic references for a manuscript and export them to a verified refs CSV, then optionally hand off to cec-sheet. Uses Codex CLI as the search driver, but Codex calls a bundled deterministic PubMed tool (scripts/pubmed_search.py) instead of writing its own E-utilities code — bibliography is fetched live from PubMed so PMIDs are never fabricated. Triggers: "論文検索", "文献検索", "文脈検索", "コンテキスト検索", "原稿の引用を探して", "refs.csv", "codex-refs", "/codex-refs".

Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, integrate into your AI projects.

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Europe PMC RESTful Web Service 多源文献聚合检索原子 skill。一次调用同时召回 PubMed + PMC + AGRICOLA + CABI + 预印本(bioRxiv / medRxiv / ChemRxiv 等)+ 灰色文献,自动按 PMID/PMCID/DOI 三级去重,返回完整元数据(含全文 OA 链接、citations metadata、grants 资助信息)。当任务出现 Europe PMC、多源文献聚合、广召回、RAG 检索、预印本搜索、bioRxiv、medRxiv、全文链接、DOI 检索、跨库去重、灰色文献、资助检索 等触发词时使用。**定位**:广召回 · 多源聚合 · RAG 友好(与 pubmed-eutils 互补——后者做精准官方源、Clinical Queries;本 skill 做"撒网"式广召回)。**不做**:NCBI E-utilities 直检(交给 pubmed-eutils)、临床试验(clinical-trials-v2)、全文 XML 抽取(bioc-fulltext-fetch)、实体识别(pubtator-entity-search)、证据分级(medical-evidence-grading)。

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Europe PMC RESTful Web Service 多源文献聚合检索原子 skill。**使用本 skill 进行医学文献广召回 / RAG 知识库构建 / 跨库聚合 / 预印本扫描 / 全文链接发现**。一次调用同时召回 PubMed (MED) + PMC + AGRICOLA + CABI + 预印本(bioRxiv / medRxiv / ChemRxiv / Research Square)+ NCBI Bookshelf + 专利,自动按 PMID/PMCID/DOI 三级去重,返回完整元数据(全文 OA 链接、citations、grants 资助信息)。**定位:广召回 · 多源 · RAG 友好**(与 pubmed-eutils 互补 — 后者做单源精准官方检索 + Clinical Queries;本 skill 做"撒网"式多源聚合)。触发词:Europe PMC / EuropePMC / 多源文献聚合 / 广召回 / RAG 召回 / RAG 知识库 / 预印本搜索 / preprint search / bioRxiv / medRxiv / ChemRxiv / DOI 检索 / DOI lookup / 全文链接 / full-text links / OA 全文 / PMCID / 灰色文献 / grey literature / 跨库去重 / 资助检索 / grant search / NIH funded / Wellcome funded / citations metadata。**不做**:NCBI E-utilities 直检(→ pubmed-eutils)、临床试验注册(→ clinical-trials-v2)、全文 XML 抽取(→ bioc-fulltext-fetch)、实体识别(→ pubtator-entity-search)、证据分级(→ medical-evidence-grading)、参考文献终态写入(→ evidence-appendix-sync)。

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Search PubMed/PMC medical literature via MCP server. Use for literature search, retrieving abstracts, full-text articles, and citation analysis. Supports MeSH terms, batch fetching, PDF downloads, and RIS export.

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Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

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Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.

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Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.

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Search PubMed biomedical literature database

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Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.

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Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

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Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools. Covers PICO framework for clinical questions, three-tiered search (database-specific, AI-assisted, content extraction), PubMed field tags and MeSH, boolean query construction, and full-text extraction. Use when planning a literature search or choosing a search tier.

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Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.

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Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth. For PubMed use pubmed-database; preprints use biorxiv-database.

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Use when analyzing a researcher's publication record from PubMed. Fetches an author's papers, classifies study types and author position, charts the patterns and writes a strategy report, with an optional trajectory-archetype classification. Works from PubMed metadata only.

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Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.

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Find academic papers across up to 8 sources (OpenAlex / Semantic Scholar / CrossRef / PubMed / arXiv for English, OpenReview for AI venues, plus native-Chinese retrieval via NSSD 国家哲社文献中心 + yiigle 中华医学期刊) with adjustable depth — Quick scan (5 min) to Audit prep (3 hr). Use when the user wants to find papers, run a literature search, gather references, scope a research topic, search Chinese-language / 中文原生 literature (中文文献/中文核心/CSSCI/C刊/国内研究/国内文献/中华××期刊/心理学报/经济研究), or filter results by journal tier (中科院分区/一区/几区, Q1, JCR/SJR quartile, 影响因子/impact factor, 期刊分区, 顶刊/top journal, '按分区筛'), or export paste-ready professional search strategies / 检索式 for external databases (PubMed / WOS / Scopus / Embase / 知网 CNKI / 万方 / SinoMed — '写检索式', '导出检索式', 'WOS 检索式', '知网专业检索', 'search strategy', 'boolean search strategy'). Triggers on search verbs ('find papers', 'literature search', 'papers about X'), review types ('scoping review', 'systematic review', 'SR prep', 'literature review', 'lit review', 'help me write a lit review'), Chinese ('找文献', '找论文', '论文搜索', '学术检索', '文献检索', '文献综述', '综述前期', '求文献', '中文文献', '中文核心', 'CSSCI', 'C刊', '国内研究', '找中文的'). Outputs Shadcn HTML report + BibTeX/RIS/CSV + PRISMA-S log. Do NOT use for: concept explanations ('what is X' / 'X 是什么', e.g. '影响因子怎么算'), writing ('帮我写' / 'help me write a paragraph'), single-paper interpretation or PDF download with metadata (use paper-downloader-portable), or when the user already has a literature set (use literature-set-review).

日本語の概要は準備中です。原文の説明を表示しています。

Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.

日本語の概要は準備中です。原文の説明を表示しています。

Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.

日本語の概要は準備中です。原文の説明を表示しています。

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

日本語の概要は準備中です。原文の説明を表示しています。

Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.

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NLM PubTator3 实体级关系挖掘原子 skill — 在 PubMed 文献里检索"疾病-药物-基因-化学品-突变-物种-细胞系"的标注与关系三元组。当用户问"BTK 与肺曲霉病的关联文献"、"BTK 抑制剂(MeSH D000077180)在哪些研究被讨论"、"标注这些 PMID 中提到的所有疾病/药物/基因实体"、"ibrutinib 的 MeSH/DrugBank ID"、"voriconazole 与 CYP2C19 药物-基因相互作用"、"BRAF V600E 突变 / rs113488022 检索"、"实体共现 / co-mention / 关系挖掘 / 实体规范化 / NER / annotation / entity normalization / disease-gene association / drug-gene interaction / chemical-disease relation" 时使用。无需 API key,跨平台稳定。**实体级 + 关系级**定位 — 不做综合文献检索(走 pubmed-eutils / europepmc-search)、不做全文段落抽取(走 bioc-fulltext-fetch)、不做证据等级排序(走 medical-evidence-grading)。

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当用户询问 ClinicalTrials.gov / 临床试验 / NCT / 试验注册 / 招募状态 / phase 1/2/3 / RCT lookup / sponsor 检索 / interventional trial / observational study / 主次要终点 / trial outcomes / 试验招募中 / recruiting status 时,通过 ClinicalTrials.gov API v2 实时检索官方注册数据。专注实时单次查询(≤1000 条/请求),典型场景: "某 NCT 试验最新状态"、"BTK 抑制剂 Phase 3 在招募试验"、"某试验已发布的主次要终点结果"。明确边界: 批量 >10k 试验 / 全库 SQL 历史分析 → aact-bulk-trials; 关联 PubMed 文献 → pubmed-eutils; RCT 自动 GRADE 评级 → medical-evidence-grading; 引用入报告附录 → evidence-appendix-sync。跨平台无锁(Claude Code / Codex / Cursor 通用)。

日本語の概要は準備中です。原文の説明を表示しています。