Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
npxskills add davila7/claude-code-templates--skill ensembl-databaseLoading…
Access and query the Ensembl genome database, a comprehensive resource for vertebrate genomic data maintained by EMBL-EBI. The database provides gene annotations, sequences, variants, regulatory information, and comparative genomics data for over 250 species. Current release is 115 (September 2025).
This skill should be used when:
Query gene data by symbol, Ensembl ID, or external database identifiers.
Common operations:
Using the ensembl_rest package:
from ensembl_rest import EnsemblClient
client = EnsemblClient()
# Look up gene by symbol
gene_data = client.symbol_lookup(
species='human',
symbol='BRCA2'
)
# Get detailed gene information
gene_info = client.lookup_id(
id='ENSG00000139618', # BRCA2 Ensembl ID
expand=True
)
Direct REST API (no package):
import requests
server = "https://rest.ensembl.org"
# Symbol lookup
response = requests.get(
f"{server}/lookup/symbol/homo_sapiens/BRCA2",
headers={"Content-Type": "application/json"}
)
gene_data = response.json()
Fetch genomic, transcript, or protein sequences in various formats (JSON, FASTA, plain text).
Operations:
Example:
# Using ensembl_rest package
sequence = client.sequence_id(
id='ENSG00000139618', # Gene ID
content_type='application/json'
)
# Get sequence for a genomic region
region_seq = client.sequence_region(
species='human',
region='7:140424943-140624564' # chromosome:start-end
)
Query genetic variation data and predict variant consequences using the Variant Effect Predictor (VEP).
Capabilities:
VEP example:
# Predict variant consequences
vep_result = client.vep_hgvs(
species='human',
hgvs_notation='ENST00000380152.7:c.803C>T'
)
# Query variant by rsID
variant = client.variation_id(
species='human',
id='rs699'
)
Perform cross-species comparisons to identify orthologs, paralogs, and evolutionary relationships.
Operations:
Example:
# Find orthologs for a human gene
orthologs = client.homology_ensemblgene(
id='ENSG00000139618', # Human BRCA2
target_species='mouse'
)
# Get gene tree
gene_tree = client.genetree_member_symbol(
species='human',
symbol='BRCA2'
)
Find all genomic features (genes, transcripts, regulatory elements) in a specific region.
Use cases:
Example:
# Find all features in a region
features = client.overlap_region(
species='human',
region='7:140424943-140624564',
feature='gene'
)
Convert coordinates between different genome assemblies (e.g., GRCh37 to GRCh38).
Important: Use https://grch37.rest.ensembl.org for GRCh37/hg19 queries and https://rest.ensembl.org for current assemblies.
Example:
from ensembl_rest import AssemblyMapper
# Map coordinates from GRCh37 to GRCh38
mapper = AssemblyMapper(
species='human',
asm_from='GRCh37',
asm_to='GRCh38'
)
mapped = mapper.map(chrom='7', start=140453136, end=140453136)
The Ensembl REST API has rate limits. Follow these practices:
Retry-After header and waitAlways implement proper error handling:
import requests
import time
def query_ensembl(endpoint, params=None, max_retries=3):
server = "https://rest.ensembl.org"
headers = {"Content-Type": "application/json"}
for attempt in range(max_retries):
response = requests.get(
f"{server}{endpoint}",
headers=headers,
params=params
)
if response.status_code == 200:
return response.json()
elif response.status_code == 429:
# Rate limited - wait and retry
retry_after = int(response.headers.get('Retry-After', 1))
time.sleep(retry_after)
else:
response.raise_for_status()
raise Exception(f"Failed after {max_retries} attempts")
uv pip install ensembl_rest
The ensembl_rest package provides a Pythonic interface to all Ensembl REST API endpoints.
No installation needed - use standard HTTP libraries like requests:
uv pip install requests
api_endpoints.md: Comprehensive documentation of all 17 API endpoint categories with examples and parametersensembl_query.py: Reusable Python script for common Ensembl queries with built-in rate limiting and error handlingTo query available species and assemblies:
# List all available species
species_list = client.info_species()
# Get assembly information for a species
assembly_info = client.info_assembly(species='human')
Common species identifiers:
homo_sapiens or humanmus_musculus or mousedanio_rerio or zebrafishdrosophila_melanogaster
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