bio-entrez-fetch SKILL.md skillA
bio-entrez-fetch 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-entrez-fetch@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-entrez-fetch/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 14,939 bytes
- Repository stars
- 662
- License
- MIT
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.
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+, 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: `efetch -version` then `efetch -help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Entrez Fetch **"Download a record by accession from NCBI"** -> EFetch returns the full record content in a chosen format (FASTA, GenBank, XML, MEDLINE, etc.). ESummary returns a lightweight "docsum" object — much faster when only metadata is needed. The agent's first decision is always: does this workflow need the full record, or just metadata? ESummary is 5-10x cheaper than EFetch for the equivalent record set. For "tell me the organism, length, and definition line for 10,000 accessions", ESummary wins by an order of magnitude. - Python: `Entrez.efetch(db=..., id=..., rettype=..., retmode=...)` (BioPython) - CLI: `efetch -db nucleotide -id NM_007294 -format gb` (Entrez Direct, NBK179288) …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-entrez-fetch@sha256:75d9aa9ba53273d5The 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_upkjysgn3gs23szp)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14939 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_upkjysgn3gs23szp GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-entrez-fetch GET https://markdownregistry.com/api/v1/blob/75d9aa9ba53273d56993542c06a1e77ca6b46ec59a7fcffdbaf2be4e995bb6c7
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
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.