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 skills add thesecondfox/skill --skill bio-database-access-entrez-searchgit 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-entrez-search)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-entrez-search"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-entrez-search.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 5.1 | $0.00043 | $0.02569 |
| Opus 5 | $0.00022 | $0.01285 |
| Sonnet 5 | $0.00009 | $0.00514 |
| Haiku 4.5 | $0.00004 | $0.00257 |
Grade A, and why
bio-entrez-search scanned grade A with 0 findings 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 6d 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 314 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
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Entrez Search
Search NCBI databases using Biopython's Entrez module (ESearch, EInfo, EGQuery utilities).
"Search NCBI for records" → Query any NCBI database by keyword, organism, or field-qualified terms and retrieve matching record IDs.
- Python:
Entrez.esearch(db=..., term=...)(BioPython) - CLI:
esearch -db nucleotide -query "term"(Entrez Direct)
Required Setup
from Bio import Entrez
Entrez.email = '[email protected]' # Required by NCBI
Entrez.api_key = 'your_api_key' # Optional, raises rate limit 3->10 req/sec
Core Functions
Entrez.esearch() - Search a Database
Search any NCBI database and get matching record IDs.
handle = Entrez.esearch(db='nucleotide', term='human[orgn] AND BRCA1[gene]')
record = Entrez.read(handle)
handle.close()
print(f"Found {record['Count']} records")
print(f"IDs: {record['IdList']}") # First 20 IDs by default
Key Parameters:
| Parameter | Description | Default |
|---|---|---|
db |
Database to search | Required |
term |
Search query | Required |
retmax |
Max IDs to return | 20 |
retstart |
Starting index (pagination) | 0 |
usehistory |
Store results on server | 'n' |
sort |
Sort order | database-specific |
datetype |
Date field to search | 'pdat' |
reldate |
Records from last N days | None |
mindate |
Start date (YYYY/MM/DD) | None |
maxdate |
End date (YYYY/MM/DD) | None |
ESearch Result Fields:
record['Count'] # Total matching records (string)
record['IdList'] # List of record IDs
record['RetMax'] # Number of IDs returned
record['RetStart'] # Starting index
record['QueryKey'] # For history server (if usehistory='y')
record['WebEnv'] # For history server (if usehistory='y')
record['TranslationSet'] # Query translations applied
record['QueryTranslation'] # Final translated query
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.
- 6d ago First seen · 314 lines · 43 tokens per session scan A 0ad3f8d8369f
bio-entrez-search is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 43 tokens to every session and 2,569 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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