ncbi-search

Search NCBI databases using E-Utilities API (official, free). Supports multiple databases: PubMed (literature), Gene, Protein, Nucleotide, dbSNP, ClinVar, Taxonomy, etc. Automatically detects search intent and routes to appropriate database. Returns formatted results with key information. Use for biomedical literature, gene information, protein sequences, genetic variants, and more.

NCBI 多数据库智能检索工具，使用官方 E-Utilities API。免费、可靠、无外部依赖。

支持的数据库

数据库	用途	触发关键词
pubmed	文献检索	paper, article, review, 研究, 论文, 文献, 发表
gene	基因信息	gene, 基因, symbol, 编码
protein	蛋白质序列	protein, 蛋白, amino acid, 序列
nucleotide	核酸序列	sequence, DNA, RNA, 序列, 基因组
snp	SNP变异	SNP, variant, 变异, 多态性
clinvar	临床变异	clinvar, clinical variant, 致病突变
taxonomy	物种分类	species, 物种, taxonomy, 分类
biosample	生物样本	biosample, 样本
assembly	基因组组装	genome assembly, 基因组组装
sra	测序数据	SRA, sequencing, 测序数据

智能意图识别

技能会自动判断用户搜索意图：

论文检索（PubMed）

触发条件：查询包含论文相关关键词，或没有明确数据库指向

"Alzheimer disease mechanisms" → PubMed
"recent review on diabetes" → PubMed
"Smith author cancer paper" → PubMed

基因检索

触发条件：基因符号、基因相关关键词

"APOE gene" → Gene
"BRCA1 function" → Gene
"TP53 human" → Gene

蛋白质检索

触发条件：蛋白质相关关键词

"insulin protein sequence" → Protein
"p53 protein" → Protein

变异检索

触发条件：变异相关关键词

"rs12345 SNP" → dbSNP
"BRCA1 pathogenic variant" → ClinVar

使用方式

自动模式（推荐）

# 自动判断搜索意图
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "APOE gene"
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "Alzheimer disease review"
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "insulin protein"

指定数据库

# 明确指定数据库
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "APOE" --db gene
python ~/.agents/skill/ncbi-search/scripts/ncbi_search.py "diabetes" --db pubmed
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "rs429358" --db snp

高级选项

# PubMed 限定年份
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "Alzheimer" --years 5

# 限定文章类型
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "diabetes" --type review

# 限定物种（基因检索）
python ~/.agents/skills/ncbi-search/scripts/ncbi_search.py "APOE" --db gene --organism human

输出示例

PubMed 检索

======================================================================
PubMed Search Results
======================================================================
Query: APOE[Title/Abstract] AND "Alzheimer Disease"[MeSH]
Total: 400 articles | Returned: 10 articles
======================================================================

[1] PMID: 33597265
Title: APOE immunotherapy reduces cerebral amyloid angiopathy...
Authors: Xiong M, Jiang H, Serrano J et al.
Journal: Science translational medicine (2021)
DOI: 10.1126/scitranslmed.abd7522
URL: https://pubmed.ncbi.nlm.nih.gov/33597265/
----------------------------------------------------------------------

Gene 检索

======================================================================
Gene Search Results
======================================================================
Query: APOE[Gene Name] AND human[Organism]
Total: 1 gene | Returned: 1 gene
======================================================================

[1] Gene ID: 348
Symbol: APOE
Name: apolipoprotein E
Organism: Homo sapiens (human)
Chromosome: 19q13.32
Summary: Apolipoprotein E (APOE) is a protein involved in the...
URL: https://www.ncbi.nlm.nih.gov/gene/348
----------------------------------------------------------------------

dbSNP 检索

======================================================================
dbSNP Search Results
======================================================================
Query: rs429358
Total: 1 variant | Returned: 1 variant
======================================================================

[1] rsID: rs429358
Gene: APOE
Alleles: C/T
Clinical: Pathogenic (Alzheimer disease)
Frequency: T=0.14 (EUR)
URL: https://www.ncbi.nlm.nih.gov/snp/rs429358
----------------------------------------------------------------------

API Key 配置

# 设置环境变量
[Environment]::SetEnvironmentVariable("NCBI_API_KEY", "your-api-key", "User")

方式	速率
无 API Key	3 次/秒
有 API Key	10 次/秒

与其他技能配合

任务	技能
基因详细信息	gene-database
蛋白质结构	AlphaFold
文献综述	literature-review
引用管理	citation-verifier

文件结构

ncbi-search/
├── SKILL.md
├── scripts/
│   ├── ncbi_search.py      # 主脚本（多数据库）
│   ├── pubmed_search.py    # PubMed专用
│   └── ncbi_utils.py       # 工具函数
└── references/
    └── query_syntax.md

参考

• E-Utilities 文档: https://www.ncbi.nlm.nih.gov/books/NBK25501/
• 数据库列表: https://www.ncbi.nlm.nih.gov/books/NBK25500/table/chapter.T5/

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技能状态: 就绪 API 要求: NCBI API Key (免费) 费用: 免费