mcpbeat

Query Ensembl

biotender-max/query-ensembl

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".

834 tokens
context cost
the whole folder, loaded on every use
1
files
instructions only
0
copies elsewhere
how many repositories repackaged it
132
stars on the repo
on the repository, not the skill itself

Install

one command, takes just this skill from the repository 
npx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill query-ensembl

The instruction itself

6 sections, as written by the author

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

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?"

How to use it

Copy the folder

Take biotender-max/query-ensembl from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.