X Openai Ncbi Entrez Skill 08976c4

---
name: x-openai-ncbi-entrez-skill-08976c4
description: Submit compact NCBI Entrez E-Utilities requests for PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows. Use when a user wants concise Entrez search, fetch, summary, or link results; save raw JSON or XML only on request.
---

### 导出副本边界与技能别名

迁移、安装、修复和经验回写只作用于当前加载的目标宿主技能副本。原 Codex 技能/MCP、下载的源码和 `original-skills` 均为来源材料，不因执行本副本而写入；只有用户另行明确要求配置 Codex 产品本身时，才按该产品流程处理指定目标。脚本需要安装目录或状态目录时，显式提供目标路径；不得从 `CODEX_HOME` 隐式推断写入位置。

跨技能名称可能沿用源库别名。先查 [技能别名表](../../skill-aliases.json)，优先选择同来源、同插件的条目，再使用其 `id` 调用或读取对应入口；不得假定旧 `$skill`、`superpowers:skill` 名称在新宿主直接注册。不能确定目标时先核对，不替换真实产品命令或 Shell 环境变量。

## 跨宿主使用约定

本副本供支持 Agent Skills 的客户端使用。先检查当前宿主实际提供的工具、权限和已连接服务，再执行正文工作流。原文中的宿主工具标识是能力参考；只有实际发现该工具时才可调用，其他宿主应使用经核验的等价 MCP、CLI 或 API。没有等价能力的步骤必须报告不可用，不能虚构调用或完成状态。

技能资源以本技能目录为基准；输出写入当前项目中用户指定的位置。通过技能名称或自然语言触发，具体快捷命令由宿主决定。涉及真实产品、模型 API、协议字段和官方网址的名称保持原意。授权、审批、隐私和工具范围限制在迁移后仍然有效；不得为兼容而扩大权限。具体依赖与迁移说明见同目录 `PORTABILITY.md`。

## Operating rules
- Use `scripts/ncbi_entrez.py` for all Entrez calls in this package.
- Use explicit `endpoint` values such as `esearch`, `esummary`, `efetch`, `elink`, or `einfo`.
- Search-style Entrez calls are better with `retmax=10` and `max_items=10`.
- GEO is nested under this skill. Use `db=gds` or `db=geoprofiles` for GEO metadata and load `references/geo.md` only when the user is specifically asking about GEO.
- BLAST workflows belong in `ncbi-blast-skill`. PMC Open Access workflows belong in `ncbi-pmc-skill`. Datasets v2 workflows belong in `ncbi-datasets-skill`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script output by default.
- In final user-facing summaries, never display a bare PMID or DOI. Render every PMID as a Markdown link in the form `[PMID <PMID>](https://pubmed.ncbi.nlm.nih.gov/<PMID>/)` and every DOI as `[<DOI>](https://doi.org/<DOI>)`, including in tables, bullets, parentheticals, and source lists.
- Return raw JSON or XML only if the user explicitly asks for machine-readable output.
- Prefer targeted endpoint calls instead of broad unfiltered dumps.
- If the user needs the full raw response, set `save_raw=true` and report the saved file path.

## Input
- Read one JSON object from stdin.
- Required field: `endpoint`
- Optional fields: `params`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Entrez patterns:
  - `{"endpoint":"esearch","params":{"db":"pubmed","term":"KRAS AND colorectal cancer","retmode":"json","retmax":10},"max_items":10}`
  - `{"endpoint":"esummary","params":{"db":"gene","id":"7157","retmode":"json"},"max_items":10}`
  - `{"endpoint":"efetch","params":{"db":"protein","id":"NP_000537.3","retmode":"xml"},"response_format":"xml","max_items":10}`
  - `{"endpoint":"elink","params":{"dbfrom":"gds","db":"pubmed","id":"200000001","retmode":"json"},"max_items":10}`

## Output
- Success returns `ok`, `source`, endpoint metadata, and either compact `records`, a compact `summary`, or `text_head`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"endpoint":"esearch","params":{"db":"gene","term":"TP53[gene] AND human[orgn]","retmode":"json","retmax":10},"max_items":10}' | python scripts/ncbi_entrez.py
```

## References
- Load `references/geo.md` only when the user specifically needs GEO query patterns.
- Keep the import package limited to this file, `references/geo.md`, and `scripts/ncbi_entrez.py`.