bio-biomart-queries SKILL.md skillA
bio-biomart-queries 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-biomart-queries@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
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- pku-yuangroup/openai4s
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skills/bioskills/bio-database-access-biomart-queries/SKILL.md- Versions recorded
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- git:20260821.2d1b678, committed Aug 21, 2026
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- License
- MIT
Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset…
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: pybiomart 0.9+, R biomaRt 2.58+ (Bioconductor); Ensembl BioMart (release 110+)
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show pybiomart`
- R: `packageVersion('biomaRt')`
The BioMart XML query format is stable across Ensembl releases; the underlying mart names and attribute IDs can change between Ensembl releases. For published work, pin the Ensembl release via `useEnsembl(version=110)`.
# BioMart Queries
**"Bulk-convert IDs / pull coordinate tables / extract ortholog wide tables"** -> BioMart is the right answer for any Ensembl-rooted query producing >5,000 rows. It is a separate service from the Ensembl REST API, with separate rate behavior and a different query model (XML-based, batch-oriented). For one-off lookups (<100 records), Ensembl REST is more convenient; for bulk anything, BioMart wins.
The single most important fact: **BioMart returns a flat table from a single query**. There is no per-record loop, no rate-limit cascade, no async polling. One XML query in; one TSV out.
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How to install
mdr add pku-yuangroup/openai4s/bio-biomart-queries@sha256:49fc30f67f9be277The 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_674xrtomnoho2iys)
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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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_674xrtomnoho2iys GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-biomart-queries GET https://markdownregistry.com/api/v1/blob/49fc30f67f9be2772fcae7f385b459eab8450ff2db420d9aec1b61e8265ea74b
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