bioc-fulltext-fetch SKILL.md skillA
bioc-fulltext-fetch 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/bioc-fulltext-fetch@git:20260912.c74de71Pins git:20260912.c74de71 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/bioc-fulltext-fetch/c1d806facb0db73a/bioc-fulltext-fetch/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260912.c74de71, committed Sep 12, 2026
- Size
- 13,344 bytes
- Repository stars
- 11
- License
- MIT
给定 PMID / PMCID 取结构化全文（BioC XML/JSON）。封装 NLM BioC PubMed API（标题+摘要）和 BioC PMC OA API（开放获取全文），输出按章节切分的段落、表格上下文、RAG 友好 chunk。适合大批量入向量库。触发词：全文抽取 / BioC / RAG 入库 / 文献全文 / PMC 开放获取 / structured fulltext / 段落抽取 / 表格抽取 / fulltext to vector store。.
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
# BioC Fulltext Fetch
封装 NLM BioC API,用于将 PubMed / PMC 文献转换为 RAG 友好的结构化全文 chunk。
## 1. 职责边界（单一职责）
**只做**:给定 PMID / PMCID,取结构化全文(BioC XML/JSON 格式),输出段落、章节、表格上下文、RAG chunk。
**不做**:
- 检索文献(交给 `pubmed-eutils` / `europepmc-search`)
- 实体标注(交给 `pubtator3`)
- 向量化(交给下游的 embedding pipeline / LangChain / LlamaIndex)
- ID 转换(可调用 `pubmed-eutils.elink_pubmed_to_pmc`,但本 skill 不实现 elink)
如果需要这些能力,请使用对应的 skill。
## 2. 何时使用
触发场景:
- "把这批 PMID 的全文取下来,准备入 ChromaDB"
- "我有 PMCID 列表,需要按章节切分做 RAG"
- "提取 Methods 章节段落"
- "找出表格周围的语义文本"
- "Build vector index from PMC open access papers"
不要使用本 skill 当:
- 用户只需要标题/摘要的纯文本 → 用 `pubmed-eutils.efetch`
- 用户需要做语义检索 → 用 `europepmc-search` 或 `pubmed-search`
- 用户需要实体标注(基因/疾病/化合物) → 用 PubTator3 类 skill
## 3. 两个 BioC 端点
| 端点 | 输入 | 覆盖 | 内容 |
|------|------|------|------|
| **BioC PubMed** | PMID | 全 PubMed (~37M) | 标题 + 摘要 + MeSH (结构化) |
| **BioC PMC OA** | PMCID | PMC 开放获取子集 (~10M) | 全文(章节、段落、表格、图注) |
端点示例:
```
# 摘要级
https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_json/{PMID}/unicode
# 全文级
https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/{PMCID}/unicode
```
文档参考:
…Read the whole file at its exact version.
How to install
mdr add ethanyoq/skill-hub/bioc-fulltext-fetch@sha256:5c1973135c04e591The line at the top of this page pins the label git:20260912.c74de71, 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_gygvlomlgnjp4gff)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Sep 12, 2026.
Audit of the latest version
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- 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
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Source
ethanyoq/skill-hub · 11 stars · license MIT · pushed 2026-11-07 · branch mine
API
GET https://markdownregistry.com/api/v1/artifacts/art_gygvlomlgnjp4gff GET https://markdownregistry.com/api/v1/resolve?ref=ethanyoq/skill-hub/bioc-fulltext-fetch GET https://markdownregistry.com/api/v1/blob/5c1973135c04e5910a288dd3eadc41f939303371124ecc4dcc2adb65d1f2199c
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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