bio-biomart-queries
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 hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).
npx skills add BioTender-max/awesome-bio-agent-skills --skill biomart-queries --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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. - Python: `pybiomart` (https://github.com/jrderuiter/pybiomart) is the lightest client - R: `
- Version Compatibility
- Installation
- BioMart hierarchy
- Decision matrix: BioMart vs Ensembl REST
- Common attribute selectors
- Common filter selectors
- Code patterns
- Bulk ID mapping: Ensembl Gene -> HGNC + RefSeq + UniProt
- Pull gene coordinate table for a chromosome
- Bulk ortholog wide-table (human <-> mouse <-> zebrafish)
- GO term annotation for a gene set
- Version-pinned query (R biomaRt)
- Discover attributes / filters programmatically
- Failure modes
pip install pybiomart pandas
What does the bio-biomart-queries skill do?
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 hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill biomart-queries --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.