---
name: query-ensembl-ae2df7ebbb94
description: Query Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species comparison. Triggers on "ensembl", "gene coordinates", "genomic location", "exon", "transcript", "variant location", "rsid", "rs number".
---

# Ensembl REST API Query

Query the Ensembl REST API for genomic annotations, sequences, and variants.

## When to Use

- User asks about a gene's genomic location, exons, or transcripts
- User wants to look up an rsID or variant
- User needs genomic/cDNA/protein sequences
- User asks about gene structure or regulatory features
- User wants cross-species gene information

## How to Execute

```python
import requests
import json

BASE_URL = "https://rest.ensembl.org"
HEADERS = {"Content-Type": "application/json", "Accept": "application/json"}

# 1. Gene lookup by symbol
def lookup_gene(symbol, species="homo_sapiens"):
    url = f"{BASE_URL}/lookup/symbol/{species}/{symbol}"
    r = requests.get(url, headers=HEADERS, params={"expand": 1})
    r.raise_for_status()
    return r.json()

# 2. Get sequence
def get_sequence(ensembl_id, seq_type="genomic"):
    url = f"{BASE_URL}/sequence/id/{ensembl_id}"
    r = requests.get(url, headers=HEADERS, params={"type": seq_type})
    r.raise_for_status()
    return r.json()

# 3. Variant lookup by rsID
def lookup_variant(rsid, species="homo_sapiens"):
    url = f"{BASE_URL}/variation/{species}/{rsid}"
    r = requests.get(url, headers=HEADERS)
    r.raise_for_status()
    return r.json()

# 4. Get overlapping features in a region
def overlap_region(species, chrom, start, end, feature="gene"):
    url = f"{BASE_URL}/overlap/region/{species}/{chrom}:{start}-{end}"
    r = requests.get(url, headers=HEADERS, params={"feature": feature})
    r.raise_for_status()
    return r.json()

# 5. Cross-species homologs
def get_homologs(ensembl_id, target_species=None):
    url = f"{BASE_URL}/homology/id/{ensembl_id}"
    params = {}
    if target_species:
        params["target_species"] = target_species
    r = requests.get(url, headers=HEADERS, params=params)
    r.raise_for_status()
    return r.json()

# Example: look up BRCA2
gene = lookup_gene("BRCA2")
print(f"Gene: {gene['display_name']}")
print(f"Ensembl ID: {gene['id']}")
print(f"Location: chr{gene['seq_region_name']}:{gene['start']}-{gene['end']}")
print(f"Strand: {'+' if gene['strand'] == 1 else '-'}")
print(f"Biotype: {gene['biotype']}")
print(f"Description: {gene.get('description', 'N/A')}")
```

## Key Endpoints

| Endpoint | Use |
|----------|-----|
| `/lookup/symbol/{species}/{symbol}` | Gene info by symbol |
| `/lookup/id/{id}` | Info by Ensembl ID |
| `/sequence/id/{id}?type=genomic` | Get sequence |
| `/variation/{species}/{rsid}` | Variant info |
| `/overlap/region/{species}/{chr}:{start}-{end}` | Features in region |
| `/homology/id/{id}` | Orthologs/paralogs |
| `/vep/{species}/hgvs/{hgvs}` | Variant effect prediction |

## Notes

- Region queries max 4,900,000 bp
- Species: `homo_sapiens`, `mus_musculus`, `danio_rerio`, `drosophila_melanogaster`
- Always use `application/json` Accept header

## Follow-up Suggestions

- "Want me to get the protein sequence for this gene?"
- "Should I check for known pathogenic variants?"
- "Want me to find orthologs in mouse?"


---
Source attribution: Runchuan-BU
Original project: https://github.com/Runchuan-BU/BioClaw
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: Runchuan-BU
Original project: https://github.com/Runchuan-BU/BioClaw
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Education & Research
Roles: Business Intelligence Analyst, Data Scientist, Researcher
Specialties: API, Cross Platform
Tools: Ensembl Rest Api
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: ab83b78440d1546c59cb9c8ba8ae46bb5423ce79bc6b1c18b6320edbf90025b6