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-linkgit 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-link)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-entrez-link"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-entrez-link/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-entrez-link"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-entrez-link.svg" alt="Reviewed on agentmods" width="80" 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 | $0.00044 | $0.02780 |
| Opus 5.5 | $0.00018 | $0.01112 |
| Sonnet 5.5 | $0.00009 | $0.00556 |
| Haiku 4.5 | $0.00004 | $0.00278 |
Grade A, and why
bio-entrez-link 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 1mo 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 — 328 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 Link
Navigate between NCBI databases using Biopython's Entrez module (ELink utility).
"Find related records across NCBI databases" → Use ELink to discover cross-references (e.g., gene to protein, sequence to publication).
- Python:
Entrez.elink(dbfrom=..., db=..., id=...)(BioPython) - CLI:
elink -db protein -target gene(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
Core Function
Entrez.elink() - Cross-Database Links
Find related records in the same or different databases.
# Find proteins linked to a gene
handle = Entrez.elink(dbfrom='gene', db='protein', id='672')
record = Entrez.read(handle)
handle.close()
# Extract linked IDs
linkset = record[0]
if linkset['LinkSetDb']:
links = linkset['LinkSetDb'][0]['Link']
protein_ids = [link['Id'] for link in links]
print(f"Found {len(protein_ids)} linked proteins")
Key Parameters:
| Parameter | Description | Example |
|---|---|---|
dbfrom |
Source database | 'gene' |
db |
Target database | 'protein' |
id |
Source record ID(s) | '672' or '672,675' |
linkname |
Specific link type | 'gene_protein_refseq' |
cmd |
Link command | 'neighbor', 'neighbor_score' |
ELink Result Structure
record[0] # First linkset
record[0]['DbFrom'] # Source database
record[0]['IdList'] # Input IDs
record[0]['LinkSetDb'] # List of link results
record[0]['LinkSetDb'][0]['DbTo'] # Target database
record[0]['LinkSetDb'][0]['LinkName'] # Link name
record[0]['LinkSetDb'][0]['Link'] # List of linked records
record[0]['LinkSetDb'][0]['Link'][0]['Id'] # Linked ID
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.
- 1mo ago First seen · 328 lines · 44 tokens per session scan A 7c0144b5d24a
bio-entrez-link is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 6mo ago), licensed MIT. It adds 44 tokens to every session and 2,780 once invoked, about $0.0002 per session on Opus 5.5. 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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