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 PKU-YuanGroup/OpenAI4S --skill bio-database-access-batch-downloadsgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-database-access-batch-downloads)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-database-access-batch-downloads"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-database-access-batch-downloads/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/pku-yuangroup/openai4s/bio-database-access-batch-downloads"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-database-access-batch-downloads.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 | $0.00104 | $0.03966 |
| Opus 5 | $0.00052 | $0.01983 |
| Sonnet 5 | $0.00021 | $0.00793 |
| Haiku 4.5 | $0.00010 | $0.00397 |
Grade A, and why
bio-batch-downloads 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 9d 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.
from urllib.error import HTTPError This is a copy
97% identical to bio-batch-downloads — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 320 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+, NCBI Datasets CLI 16.0+, Entrez Direct 21.0+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show biopythonthenhelp(Bio.Entrez.efetch)to check signatures - CLI:
datasets --versionandefetch -version
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Batch Downloads
"Download N thousand records from NCBI without getting blocked" -> The right answer is rarely "parallelize requests". For >5000 records the answer is the history server: search once, fetch in chunks server-side. For >100,000 records or whole genomes, the modern answer is NCBI Datasets v2 CLI -- the E-utilities are not optimized for bulk genome/gene data anymore.
This skill encodes (a) when to use each retrieval strategy, (b) the precise rate-limit math, (c) WebEnv lifecycle for long-running jobs, (d) how to design retry/resume, and (e) when to defect to Datasets CLI instead.
- Python:
Entrez.esearch(usehistory='y')+ chunkedEntrez.efetch()(BioPython) - CLI:
datasets download genome accession ...(NCBI Datasets v2 -- preferred for genome/gene bulk) - CLI:
epost | efetch -mode webenv(Entrez Direct)
Required Setup
from Bio import Entrez
import time
Entrez.email = '[email protected]'
Entrez.api_key = 'YOUR_KEY' # 3 -> 10 req/sec; mandatory for bulk
Entrez.tool = 'project-name'
Decision matrix: which retrieval strategy?
| Record count | Source | Strategy | Why |
|---|---|---|---|
| < 200 known IDs | Any db | EFetch with comma-joined id= |
Single round-trip; trivial |
| 200-5,000 known IDs | Any db | EPost (chunked at 200) -> history -> chunked EFetch | URL length limit + chunked retrieval |
| 5,000-100,000 from a query | Any db | ESearch with usehistory='y' -> chunked EFetch |
Push to server once; pull in batches |
| > 100,000 sequences | nucleotide/protein | Consider FTP mirror or Datasets CLI; chunk if E-utils still | NCBI throttles bulk; offline mirror is faster |
| Whole genome assemblies | Assembly/Datasets | datasets download genome accession ... |
Datasets v2 is the modern bulk endpoint |
| All RefSeq for a species | Datasets | datasets download genome taxon ... |
Replaces assembly_summary.txt scraping |
| All gene records for a list | Datasets | datasets download gene gene-id ... |
Cleaner output than EFetch gene XML |
| Raw sequencing reads | SRA | prefetch + fasterq-dump (or ENA mirror) |
See sra-data skill |
What ships with it
4 files 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.
- 9d ago First seen · 320 lines · 104 tokens per session scan A c1e42ade2dbe
bio-batch-downloads is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 104 tokens to every session and 3,966 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 97% identical to bio-batch-downloads, differing in 12 lines, and is treated as a copy.
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