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