skills.rest
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ensembl-api

Query the Ensembl REST API for variant annotation, gene lookup, and sequence retrieval.

1|Updated Oct 25, 2020
Search Tags:#genomics#REST API#ensembl#VEP#variant annotation#hgvs#liftover
One-click install
npx skills add https://github.com/bfairkun/dotfiles --skill ensembl-api-bfairkun
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-api
Source: https://github.com/bfairkun/dotfiles/tree/main/agents/.agents/skills/ensembl-api
Command: npx skills add https://github.com/bfairkun/dotfiles --skill ensembl-api-bfairkun

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Genomics work often requires converting HGVS variant notations, predicting variant effects, lifting coordinates between genome assemblies, and fetching gene or sequence data, which normally means navigating many separate Ensembl endpoints and their quirks. ## Core Features & Use Cases - HGVS Conversion & VEP Annotation: Convert any HGVS, rsID, or SPDI variant to all equivalent representations and predict consequences with SpliceAI, CADD, and gnomAD frequencies. - Lookup, Sequence & Mapping: Retrieve genes and transcripts by ID or symbol, fetch genomic/cDNA/CDS/protein sequences, and lift coordinates between GRCh37 and GRCh38 or map cDNA/CDS/protein positions to genomic coordinates. - Overlap, Phenotype & Xrefs: Find features overlapping a region, pull disease associations from OMIM/ClinVar/GWAS, and resolve cross-references to HGNC, RefSeq, and UniProt. - Use Case: Given a clinical variant like "NM_001042432.2:c.295-23_295-20delCTCA", convert it to genomic HGVS, run VEP for the most severe consequence on the canonical transcript, and retrieve associated phenotypes in one workflow. ## Quick Start Use the ensembl-api skill to convert the HGVS variant NM_001042432.2:c.295-23_295-20delCTCA to genomic coordinates and predict its effect with VEP.

Frequently Asked Questions about ensembl-api

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert HGVS notation to genomic coordinates?▼

Use the Ensembl variant_recoder endpoint with the URL-encoded HGVS string to get all equivalent representations including genomic hgvsg, transcript hgvsc, protein hgvsp, and SPDI forms. Batch conversion of up to 200 variants is supported via POST.

How to predict variant effects with the Ensembl VEP API?▼

Call the vep endpoint by HGVS, region, or rsID with flags like canonical=1, SpliceAI=1, and CADD=1. The response includes most_severe_consequence and per-transcript consequences with splice scores and population frequencies.

Does the Ensembl REST API support GRCh37 (hg19) coordinates?▼

Yes, use https://grch37.rest.ensembl.org as the base URL with the same endpoint paths. You can also lift coordinates between assemblies using the map endpoint, for example /map/homo_sapiens/GRCh37/16:28487761..28487764:1/GRCh38.

Why does variant_recoder return NC_ accessions instead of chromosome names?▼

variant_recoder reports genomic HGVS using RefSeq chromosome accessions such as NC_000016.10 for chr16 on GRCh38. To get the chromosome number, strip the NC_0000 prefix and take the integer part before the dot.

What are the Ensembl REST API rate limits and batch sizes?▼

The API allows 15 requests per second and roughly 55,000 per hour, returning HTTP 429 when exceeded. POST batch limits are about 200 for variant_recoder and vep, 1000 for lookup/id, and 50 for sequence/id.

Can I use biocommons.hgvs with UTA instead of the Ensembl API?▼

biocommons.hgvs with UTA does not work from compute nodes because UTA requires PostgreSQL access on port 5432 rather than HTTP. Use the Ensembl variant_recoder endpoint instead for HGVS normalization over HTTPS.

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