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 — 检索"疾病-药物-基因-化学品-突变"在生物医学文献中的标注与关系。当用户问"哪些研究讨论了 BTK 抑制剂与肺曲霉病"、"基因 X 与疾病 Y 的关联"、"药物-基因相互作用"、"找含某突变的文献"、"PubTator / 实体标注 / NER / annotation / biomedical entity / 疾病基因关联 / 药物-基因 / 化学品-疾病 / 突变检索"时使用。无需 API key。**实体级 · 关系挖掘**定位 — 不做文献综合检索(用 pubmed-eutils / europepmc-search)、不做全文(用 BioC)、不做试验(用 ct-v2)。.

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What the file says

# PubTator3 Entity & Relation Search

封装 NLM PubTator3 RESTful API,用于在 PubMed 文献中做**实体级标注 + 关系挖掘**。
聚焦"疾病 - 药物 - 基因 - 化学品 - 突变 - 物种"的联动检索,适合"实体 X 与实体 Y 在文献中怎样被讨论"这类问题。

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## 1. 何时使用本技能

**适合**:
- "哪些文献提到了 BTK 抑制剂用于侵袭性肺曲霉病" — 实体 + 关系
- "基因 EGFR 在非小细胞肺癌中的相关研究" — 共现 / 关联
- "找出讨论 voriconazole 与 CYP2C19 相互作用的文献" — 药物-基因
- "把这一组 PMID 里的疾病/药物/基因都标出来" — 标注提取
- "ibrutinib 在文献中映射到哪个 MeSH/DrugBank ID" — 实体规范化

**不适合(用其他技能)**:
- 用 MeSH 树/出版类型/PubDate 做文献检索 → `pubmed-eutils` + Clinical Queries
- 拿全文 XML/段落 → `BioC` (BioC PubMed/PMC)
- 临床试验注册信息 → `ct-v2` (ClinicalTrials.gov)
- 综合性自然语言检索 → `europepmc-search`

---

## 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,**不需要 API key**,但请遵守速率限制(建议 ≤ 3 req/s,失败时退避)。

核心端点:

| 端点 | 用途 |
|------|------|
| `GET /search/?text=<query>` | 自由文本/实体检索文献 |
| `GET /publications/export/biocjson?pmids=<csv>` | 拉取 PMID 的实体标注 BioC-JSON |
| `GET /entity/autocomplete/?query=<text>&concept=<type>` | 实体规范化(text → ID) |
| `GET /relations?e1=<id>&e2=<id>` | 关系/共现挖掘 |

文档: https://www.ncbi.nlm.nih.gov/research/pubtator3-api/

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## 3. 核心能力(5 个函数)
…

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How to install

mdr add ethanyoq/skill-hub/pubtator-entity-search@git:20260919.e8b19bf

mdr add ethanyoq/skill-hub/pubtator-entity-search@sha256:1a2ca89eab1a707f

[![mdr](https://markdownregistry.com/badge/art_saeiuqf72iagfu66.svg)](https://markdownregistry.com/a/art_saeiuqf72iagfu66)

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Source

API

GET https://markdownregistry.com/api/v1/artifacts/art_saeiuqf72iagfu66
GET https://markdownregistry.com/api/v1/resolve?ref=ethanyoq/skill-hub/pubtator-entity-search
GET https://markdownregistry.com/api/v1/blob/1a2ca89eab1a707fa20964b5dc201ef964dac0ffa66fc7f2a1602dbf0fa54631

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