Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/thesecondfox/skill/bio-database-access-geo-datanpx skills add thesecondfox/skill --skill bio-database-access-geo-datagit clone --depth 1 https://github.com/thesecondfox/skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-geo-data)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-geo-data"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-geo-data.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00053 | $0.02980 |
| Opus 5 | $0.00026 | $0.01490 |
| Sonnet 5 | $0.00011 | $0.00596 |
| Haiku 4.5 | $0.00005 | $0.00298 |
Grade A, and why
bio-geo-data scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 3d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/ How it starts
The opening of the file, as written. The whole thing — 384 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
GEO Data
Query and access Gene Expression Omnibus datasets using Biopython's Entrez module.
"Find expression datasets in GEO" → Search GEO for microarray/RNA-seq datasets by organism, tissue, or condition, then download expression matrices or link to SRA runs.
- Python:
Entrez.esearch(db='gds', term=...)(BioPython) - CLI:
esearch -db gds -query "term"(Entrez Direct)
Required Setup
from Bio import Entrez
Entrez.email = '[email protected]' # Required by NCBI
Entrez.api_key = 'your_api_key' # Optional
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 |
Searching GEO
Search GEO DataSets (GDS)
from Bio import Entrez
Entrez.email = '[email protected]'
# Search curated datasets
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']}")
Search GEO Series (GSE)
# Search GEO Series via gds database
# 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()
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 3d ago First seen · 384 lines · 53 tokens per session scan A ab169f6f18f2
bio-geo-data is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 53 tokens to every session and 2,980 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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