pubtator-entity-search SKILL.md skillA
pubtator-entity-search from ethanyoq/skill-hub is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ethanyoq/skill-hub/pubtator-entity-search@git:20260919.e8b19bfPins git:20260919.e8b19bf in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ethanyoq/skill-hub
- Path
archives/user-installed-skills/pubtator-entity-search/36ed1a3ea059827e/pubtator-entity-search/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260919.e8b19bf, committed Sep 19, 2026
- Size
- 9,384 bytes
- Repository stars
- 11
- License
- MIT
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)。.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
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。 --- ## 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/ --- ## 3. 核心能力(5 个函数) …
Read the whole file at its exact version.
How to install
mdr add ethanyoq/skill-hub/pubtator-entity-search@sha256:1a2ca89eab1a707fThe line at the top of this page pins the label git:20260919.e8b19bf, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_saeiuqf72iagfu66)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Sep 19, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (9384 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
ethanyoq/skill-hub · 11 stars · license MIT · pushed 2026-11-07 · branch mine
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
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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