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BI

bio-batch-downloads

Maintainer FreedomIntelligence · Last updated April 1, 2026

Batch download bioinformatics data from NCBI, EBI, Ensembl.

OpenClawNanoClawAnalysisReproductionbio-batch-downloads🧠 bioos extended suitebioos extended bioinformatics suitebatch

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-downloads

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Download large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting.
  • handle = Entrez.esearch(db='nucleotide', term='human[orgn] AND mRNA[fkey]', usehistory='y') search = Entrez.read(handle) handle.close().
  • webenv = search['WebEnv'] query_key = search['QueryKey'] total = int(search['Count']).
  • print(f"Found {total} records, stored in history").

Source Doc

Excerpt From SKILL.md

Rate Limits

AuthenticationRequests/SecondDelay Between
Email only30.34 seconds
Email + API key100.1 seconds

Get an API key at: https://www.ncbi.nlm.nih.gov/account/settings/

History Server

The history server stores search results on NCBI servers, enabling efficient batch retrieval without re-sending large ID lists.

How It Works

  1. Search with usehistory='y'
  2. Get WebEnv (session ID) and query_key (result set ID)
  3. Fetch results in batches using these identifiers
  4. Results stay available for ~15 minutes

Use cases

  • Use bio-batch-downloads for genomics and bioinformatics workflows.
  • Apply bio-batch-downloads to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • entrez-search - Build search queries for batch downloads
  • entrez-fetch - Single record fetching
  • sra-data - For raw sequencing data (use SRA toolkit instead)

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