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数据与复现
BI
bio-geo-data
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Download and parse GEO datasets and series matrices.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-geo-data
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Query 、 access Gene Expression Omnibus 数据集s ，使用 Biopython's Entrez module。
- handle = Entrez.esearch(db='gds'，term='breast cancer 、 Homo sapiens[orgn]'，retmax=10) record = Entrez.read(handle) handle.close()。
- print(f"Found {record['Count']} 数据集s") print(f"IDs：{record['IdList']}")。
原始文档
SKILL.md 摘录
GEO Database Types
| Database | db value | Description |
|---|---|---|
| GEO DataSets | gds | Curated datasets (GDS*) |
| GEO Profiles | geoprofiles | Individual gene profiles |
GEO Record Types:
| Prefix | Type | Description |
|---|---|---|
| GSE | Series | Complete study/experiment |
| GSM | Sample | Individual sample |
| GPL | Platform | Array/sequencing platform |
| GDS | DataSet | Curated, normalized dataset |
Search GEO DataSets (GDS)
from Bio import Entrez
Entrez.email = '[email protected]'
## Use entry_type filter
handle = Entrez.esearch(db='gds', term='RNA-seq[title] AND human[orgn] AND gse[entry_type]', retmax=10)
record = Entrez.read(handle)
handle.close()
适用场景
- Use bio-geo-data ，用于 genomics 、 bioinformatics workflows。
- Apply bio-geo-data to sequencing，variant，或 omics analysis tasks。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- entrez-search - General database searching
- entrez-link - Link GEO to SRA and other databases
- sra-data - Download raw sequencing data from linked SRA
- batch-downloads - Download multiple GEO records
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