pubtator-entity-search skillA
pubtator-entity-search is agent-read markdown (skill) from ethanyoq/skill-hub: 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-sear.
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What the file says
# PubTator3 Entity & Relation Search 封装 NLM PubTator3 RESTful API,做**实体级标注 + 关系挖掘**。聚焦"疾病 — 药物 — 基因 — 化学品 — 突变 — 物种 — 细胞系"的联动检索。 --- ## 1. 何时使用本技能 **适合 (✅ 自动触发)**: | 用户问题 | 路由 | |---|---| | "找 BTK 与肺曲霉病的关联文献" | ✅ 本技能 (`find_co_mentions`) | | "BTK 抑制剂 (MeSH D000077180) 在哪些研究被讨论" | ✅ 本技能 (`search_by_entity`) | | "标注这些 PMID 中提到的所有疾病/药物/基因实体" | ✅ 本技能 (`annotate_pmid`) | | "ibrutinib 在文献中映射到哪个 MeSH/DrugBank" | ✅ 本技能 (`entity_normalize`) | | "voriconazole 与 CYP2C19 相互作用" | ✅ 本技能 (`search_by_relation`) | | "BRAF V600E / rs113488022 突变文献" | ✅ 本技能 (`search_by_entity` concept=variant) | **不适合 (❌ 路由到其他 skill)**: | 用户问题 | 路由 | |---|---| | "查 PubMed 上近 5 年所有 X 的 RCT" | ❌ → `pubmed-eutils` + Clinical Queries | | "MeSH 树 / 出版类型 / PubDate 综合检索" | ❌ → `pubmed-eutils` | | "Europe PMC 综合检索 + 引文" | ❌ → `europepmc-search` | | "全文段落抽取 / BioC 全文" | ❌ → `bioc-fulltext-fetch` | | "证据等级 / GRADE / 推荐级别" | ❌ → `medical-evidence-grading` | | "正在招募的 X 临床试验" | ❌ → `clinical-trials-v2` | --- ## 2. API 概览 (无需 Key) Base URL: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/` PubTator3 是 NLM 开放服务,**无需 API key**,但请遵守速率限制 (≤ 5 req/s,失败时指数退避)。 | 端点 | 用途 | |------|------| …
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How to install
mdr add ethanyoq/skill-hub/pubtator-entity-search@git:20260919.e8b19bfmdr add ethanyoq/skill-hub/pubtator-entity-search@sha256:3b30ff7d363a66b1Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_hr3cpurdwpqtcs5i)
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Source
ethanyoq/skill-hub · 10 stars · license MIT · pushed 2026-09-19 · branch mine
API
GET https://markdownregistry.com/api/v1/artifacts/art_hr3cpurdwpqtcs5i GET https://markdownregistry.com/api/v1/resolve?ref=ethanyoq/skill-hub/pubtator-entity-search GET https://markdownregistry.com/api/v1/blob/3b30ff7d363a66b10524fabfef160bb855d9141e7b080c274d64f8db0f36e9cd
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