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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-geo-data
Maintainer FreedomIntelligence · Last updated April 1, 2026
Download and parse GEO datasets and series matrices.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-geo-data
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Query and access Gene Expression Omnibus datasets using Biopython's Entrez module.
- handle = Entrez.esearch(db='gds', term='breast cancer AND Homo sapiens[orgn]', retmax=10) record = Entrez.read(handle) handle.close().
- print(f"Found {record['Count']} datasets") print(f"IDs: {record['IdList']}").
Source Doc
Excerpt From SKILL.md
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()
Use cases
- Use bio-geo-data for genomics and bioinformatics workflows.
- Apply bio-geo-data to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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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