bio-batch-downloads SKILL.md skillA
bio-batch-downloads from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-batch-downloads@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-batch-downloads/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,770 bytes
- Repository stars
- 662
- License
- MIT
Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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 biopython` then `help(Bio.Entrez.efetch)` to check signatures - CLI: `datasets --version` and `efetch -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')` + chunked `Entrez.efetch()` (BioPython) …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-batch-downloads@sha256:c1e42ade2dbe460bThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_lyyjmaw5fv4yz5m7)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_lyyjmaw5fv4yz5m7 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-batch-downloads GET https://markdownregistry.com/api/v1/blob/c1e42ade2dbe460b4c113c0638df8113adcbdab222f19aee99544f519455d985
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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